3dfr › Citations

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.

Bolin JT, Filman DJ, Matthews DA, Hamlin RC, Kraut J
J Biol Chem 257 13650-62 (1982)
Cited: 341 times
EuropePMC logo PMID: 6815178

Abstract

X-ray data have been extended to 1.7 A for a binary complex of Escherichia coli dihydrofolate reductase with methotrexate and a ternary complex of Lactobacillus casei dihydrofolate reductase with methotrexate and NADPH. Models for both structures have been refined to R factors of 0.15 and include parameters for fixed and liquid solvent. The two species of dihydrofolate reductase resemble one another even more closely than was thought to be the case prior to refinement. Several new structural features have also been discovered. Among them are a cis peptide linking Gly-97 and Gly-98 (L. Casei numbering) in both species, an alpha helix involving residues 43 through 50 in the E. coli enzyme, and the existence of what may be a specific hydration site on exposed alpha helices. Refinement has led to a revised description of the details of methotrexate binding. We now see that a fixed water molecule mediates the interaction between methotrexate's 2-amino group and Thr-116 (L. casei numbering) and that the inhibitor's 4-amino group makes two hydrogen bonds with the enzyme (instead of one). Other revisions are also discussed. A hypothetical model for substrate binding is proposed in which the pteridine ring is turned upside down while all protein and solvent atoms remain fixed. Asp-26 in this model is hydrogen bonded to the substrate's 2-amino group and to N3.

Reviews - 3dfr mentioned but not cited (1)

  1. What lessons can be learned from studying the folding of homologous proteins? Nickson AA, Clarke J. Methods 52 38-50 (2010)

Articles - 3dfr mentioned but not cited (35)

  1. Benchmarking sets for molecular docking. Huang N, Shoichet BK, Irwin JJ. J Med Chem 49 6789-6801 (2006)
  2. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Zhou H, Zhou Y. Protein Sci. 11 2714-2726 (2002)
  3. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. Huang B, Schroeder M. BMC Struct Biol 6 19 (2006)
  4. CODA: a combined algorithm for predicting the structurally variable regions of protein models. Deane CM, Blundell TL. Protein Sci 10 599-612 (2001)
  5. Evaluation of DOCK 6 as a pose generation and database enrichment tool. Brozell SR, Mukherjee S, Balius TE, Roe DR, Case DA, Rizzo RC. J Comput Aided Mol Des 26 749-773 (2012)
  6. Molecular docking screens using comparative models of proteins. Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. J Chem Inf Model 49 2512-2527 (2009)
  7. Dehydron: a structurally encoded signal for protein interaction. Fernández A, Scott R. Biophys J 85 1914-1928 (2003)
  8. RPBS: a web resource for structural bioinformatics. Alland C, Moreews F, Boens D, Carpentier M, Chiusa S, Lonquety M, Renault N, Wong Y, Cantalloube H, Chomilier J, Hochez J, Pothier J, Villoutreix BO, Zagury JF, Tufféry P. Nucleic Acids Res 33 W44-9 (2005)
  9. Improved prediction of critical residues for protein function based on network and phylogenetic analyses. Thibert B, Bredesen DE, del Rio G. BMC Bioinformatics 6 213 (2005)
  10. Customizing scoring functions for docking. Pham TA, Jain AN. J. Comput. Aided Mol. Des. 22 269-286 (2008)
  11. Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach. Moore GL, Maranas CD. Proc. Natl. Acad. Sci. U.S.A. 100 5091-5096 (2003)
  12. Anticorrelated motions as a driving force in enzyme catalysis: the dehydrogenase reaction. Luo J, Bruice TC. Proc. Natl. Acad. Sci. U.S.A. 101 13152-13156 (2004)
  13. Binding-site assessment by virtual fragment screening. Huang N, Jacobson MP. PLoS One 5 e10109 (2010)
  14. Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening. Du H, Brender JR, Zhang J, Zhang Y. Methods 71 77-84 (2015)
  15. Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison. Chen L, Wu LY, Wang Y, Zhang S, Zhang XS. BMC Struct Biol 6 18 (2006)
  16. The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks. Fernández A, Scott R, Berry RS. Proc Natl Acad Sci U S A 101 2823-2827 (2004)
  17. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. Durrant JD, Lindert S, McCammon JA. J. Mol. Graph. Model. 44 104-112 (2013)
  18. Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. Yu W, Lakkaraju SK, Raman EP, MacKerell AD. J. Comput. Aided Mol. Des. 28 491-507 (2014)
  19. Efficient identification of critical residues based only on protein structure by network analysis. Cusack MP, Thibert B, Bredesen DE, Del Rio G. PLoS ONE 2 e421 (2007)
  20. In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking. Bolstad ES, Anderson AC. Proteins 75 62-74 (2009)
  21. In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking. Bolstad ES, Anderson AC. Proteins 73 566-580 (2008)
  22. Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field. Cui M, Mezei M, Osman R. Protein Eng Des Sel 21 729-735 (2008)
  23. Improved Chou-Fasman method for protein secondary structure prediction. Chen H, Gu F, Huang Z. BMC Bioinformatics 7 Suppl 4 S14 (2006)
  24. Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints. Lin M, Lu HM, Chen R, Liang J. J Chem Phys 129 094101 (2008)
  25. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. Yu W, Lakkaraju SK, Raman EP, Fang L, MacKerell AD. J Chem Inf Model 55 407-420 (2015)
  26. GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes. Kasahara K, Kinoshita K. BMC Bioinformatics 15 12 (2014)
  27. Identification of novel potential antibiotics against Staphylococcus using structure-based drug screening targeting dihydrofolate reductase. Kobayashi M, Kinjo T, Koseki Y, Bourne CR, Barrow WW, Aoki S. J Chem Inf Model 54 1242-1253 (2014)
  28. LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. Lindert S, Durrant JD, McCammon JA. Chem Biol Drug Des 80 358-365 (2012)
  29. A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening. Jasper JB, Humbeck L, Brinkjost T, Koch O. J Cheminform 10 15 (2018)
  30. A rule-based algorithm for automatic bond type perception. Zhang Q, Zhang W, Li Y, Wang J, Zhang L, Hou T. J Cheminform 4 26 (2012)
  31. Mitochondrial selfish elements and the evolution of biological novelties. Milani L, Ghiselli F, Passamonti M. Curr Zool 62 687-697 (2016)
  32. PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking. Hwang SB, Lee CJ, Lee S, Ma S, Kang YM, Cho KH, Kim SY, Kwon OY, Yoon CN, Kang YK, Yoon JH, Nam KY, Kim SG, In Y, Chai HH, Acree WE, Grant JA, Gibson KD, Jhon MS, Scheraga HA, No KT. J Phys Chem B 124 974-989 (2020)
  33. Self-configuring nnU-Net for automatic delineation of the organs at risk and target in high-dose rate cervical brachytherapy, a low/middle-income country's experience. Duprez D, Trauernicht C, Simonds H, Williams O. J Appl Clin Med Phys 24 e13988 (2023)
  34. Improving structural similarity based virtual screening using background knowledge. Girschick T, Puchbauer L, Kramer S. J Cheminform 5 50 (2013)
  35. bPE toolkit: toolkit for computational protein engineering. Jerath G, Hazam PK, Ramakrishnan V. Syst Synth Biol 8 337-341 (2014)


Reviews citing this publication (26)

  1. Hydrogen bonding in globular proteins. Baker EN, Hubbard RE. Prog. Biophys. Mol. Biol. 44 97-179 (1984)
  2. Structure, dynamics, and catalytic function of dihydrofolate reductase. Schnell JR, Dyson HJ, Wright PE. Annu Rev Biophys Biomol Struct 33 119-140 (2004)
  3. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. Böhm HJ. J. Comput. Aided Mol. Des. 12 309-323 (1998)
  4. Roles of electrostatic interaction in proteins. Nakamura H. Q. Rev. Biophys. 29 1-90 (1996)
  5. Enzymatic transition states and transition state analog design. Schramm VL. Annu. Rev. Biochem. 67 693-720 (1998)
  6. The methotrexate story: a paradigm for development of cancer chemotherapeutic agents. Huennekens FM. Adv. Enzyme Regul. 34 397-419 (1994)
  7. The dihydrofolate reductase-thymidylate synthetase gene in the drug resistance of malaria parasites. Hyde JE. Pharmacol. Ther. 48 45-59 (1990)
  8. Glycosidase inhibition: assessing mimicry of the transition state. Gloster TM, Davies GJ. Org. Biomol. Chem. 8 305-320 (2010)
  9. Coupled motions in enzyme catalysis. Nashine VC, Hammes-Schiffer S, Benkovic SJ. Curr Opin Chem Biol 14 644-651 (2010)
  10. Tetrahydrobiopterin and nitric oxide: mechanistic and pharmacological aspects. Werner ER, Gorren AC, Heller R, Werner-Felmayer G, Mayer B. Exp. Biol. Med. (Maywood) 228 1291-1302 (2003)
  11. The mode of action and the mechanism of resistance to antimalarial drugs. Foote SJ, Cowman AF. Acta Trop. 56 157-171 (1994)
  12. Genetic algorithms in molecular recognition and design. Willett P. Trends Biotechnol. 13 516-521 (1995)
  13. The gut-joint axis in rheumatoid arthritis. Zaiss MM, Joyce Wu HJ, Mauro D, Schett G, Ciccia F. Nat Rev Rheumatol 17 224-237 (2021)
  14. Potent inhibitors of de novo pyrimidine and purine biosynthesis as chemotherapeutic agents. Christopherson RI, Lyons SD. Med Res Rev 10 505-548 (1990)
  15. Quantum mechanical effects in enzyme-catalysed hydrogen transfer reactions. Klinman JP. Trends Biochem. Sci. 14 368-373 (1989)
  16. The thymidylate synthesis cycle and anticancer drugs. Douglas KT. Med Res Rev 7 441-475 (1987)
  17. Antivitamins for Medicinal Applications. Zelder F, Sonnay M, Prieto L. Chembiochem 16 1264-1278 (2015)
  18. Conformational analysis of environmental agents: use of X-ray crystallographic data to determine molecular reactivity. Cody V. Environ. Health Perspect. 61 163-183 (1985)
  19. Conformational analysis and computer graphics in drug research. Tollenaere JP, Janssen PA. Med Res Rev 8 1-25 (1988)
  20. Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases. Bertacine Dias MV, Santos JC, Libreros-Zúñiga GA, Ribeiro JA, Chavez-Pacheco SM. Future Med Chem 10 935-959 (2018)
  21. Molecular recognition in applied enzyme chemistry. Suckling CJ. Experientia 47 1139-1148 (1991)
  22. Rational drug design: a multidisciplinary approach. Hunter WN. Mol Med Today 1 31, 34 (1995)
  23. [The key and the lock. I. The basis of drug action] Kubinyi H. Pharm Unserer Zeit 23 158-168 (1994)
  24. Advances in the implications of the gut microbiota on the treatment efficacy of disease-modifying anti-rheumatic drugs in rheumatoid arthritis. Fan J, Jiang T, He D. Front Immunol 14 1189036 (2023)
  25. DMARDs-Gut Microbiota Feedback: Implications in the Response to Therapy. Zaragoza-García O, Castro-Alarcón N, Pérez-Rubio G, Guzmán-Guzmán IP. Biomolecules 10 (2020)
  26. Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions. Goldstein M, Goodey NM. Methods Mol Biol 2253 185-219 (2021)

Articles citing this publication (279)

  1. Development and validation of a genetic algorithm for flexible docking. Jones G, Willett P, Glen RC, Leach AR, Taylor R. J. Mol. Biol. 267 727-748 (1997)
  2. The relation between the divergence of sequence and structure in proteins. Chothia C, Lesk AM. EMBO J. 5 823-826 (1986)
  3. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. Jones G, Willett P, Glen RC. J. Mol. Biol. 245 43-53 (1995)
  4. Helix geometry in proteins. Barlow DJ, Thornton JM. J. Mol. Biol. 201 601-619 (1988)
  5. Interior and surface of monomeric proteins. Miller S, Janin J, Lesk AM, Chothia C. J. Mol. Biol. 196 641-656 (1987)
  6. Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, Wolff J, Genest M, Hagler AT. Proteins 4 31-47 (1988)
  7. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. Ewing TJ, Makino S, Skillman AG, Kuntz ID. J. Comput. Aided Mol. Des. 15 411-428 (2001)
  8. Improvements in protein secondary structure prediction by an enhanced neural network. Kneller DG, Cohen FE, Langridge R. J. Mol. Biol. 214 171-182 (1990)
  9. Very fast prediction and rationalization of pKa values for protein-ligand complexes. Bas DC, Rogers DM, Jensen JH. Proteins 73 765-783 (2008)
  10. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. Böhm HJ. J. Comput. Aided Mol. Des. 8 243-256 (1994)
  11. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. J. Mol. Biol. 285 1711-1733 (1999)
  12. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. Sibanda BL, Blundell TL, Thornton JM. J. Mol. Biol. 206 759-777 (1989)
  13. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, Fogel LJ, Freer ST. Chem. Biol. 2 317-324 (1995)
  14. The computer program LUDI: a new method for the de novo design of enzyme inhibitors. Böhm HJ. J. Comput. Aided Mol. Des. 6 61-78 (1992)
  15. QXP: powerful, rapid computer algorithms for structure-based drug design. McMartin C, Bohacek RS. J. Comput. Aided Mol. Des. 11 333-344 (1997)
  16. Insights into antifolate resistance from malarial DHFR-TS structures. Yuvaniyama J, Chitnumsub P, Kamchonwongpaisan S, Vanichtanankul J, Sirawaraporn W, Taylor P, Walkinshaw MD, Yuthavong Y. Nat. Struct. Biol. 10 357-365 (2003)
  17. Crystallographic refinement of human serum retinol binding protein at 2A resolution. Cowan SW, Newcomer ME, Jones TA. Proteins 8 44-61 (1990)
  18. Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble. Pan H, Lee JC, Hilser VJ. Proc. Natl. Acad. Sci. U.S.A. 97 12020-12025 (2000)
  19. Changing the identity of a transfer RNA. Normanly J, Ogden RC, Horvath SJ, Abelson J. Nature 321 213-219 (1986)
  20. Hydrogen bond stereochemistry in protein structure and function. Ippolito JA, Alexander RS, Christianson DW. J. Mol. Biol. 215 457-471 (1990)
  21. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. Böhm HJ. J. Comput. Aided Mol. Des. 6 593-606 (1992)
  22. LINUS: a hierarchic procedure to predict the fold of a protein. Srinivasan R, Rose GD. Proteins 22 81-99 (1995)
  23. Analysis of the steric strain in the polypeptide backbone of protein molecules. Herzberg O, Moult J. Proteins 11 223-229 (1991)
  24. Flexible ligand docking using conformational ensembles. Lorber DM, Shoichet BK. Protein Sci. 7 938-950 (1998)
  25. Distributions of water around amino acid residues in proteins. Thanki N, Thornton JM, Goodfellow JM. J. Mol. Biol. 202 637-657 (1988)
  26. A mechanism of drug action revealed by structural studies of enoyl reductase. Baldock C, Rafferty JB, Sedelnikova SE, Baker PJ, Stuitje AR, Slabas AR, Hawkes TR, Rice DW. Science 274 2107-2110 (1996)
  27. Ligand solvation in molecular docking. Shoichet BK, Leach AR, Kuntz ID. Proteins 34 4-16 (1999)
  28. Automatic identification and representation of protein binding sites for molecular docking. Ruppert J, Welch W, Jain AN. Protein Sci. 6 524-533 (1997)
  29. Structure of and kinetic channelling in bifunctional dihydrofolate reductase-thymidylate synthase. Knighton DR, Kan CC, Howland E, Janson CA, Hostomska Z, Welsh KM, Matthews DA. Nat. Struct. Biol. 1 186-194 (1994)
  30. Volume changes in protein evolution. Gerstein M, Sonnhammer EL, Chothia C. J. Mol. Biol. 236 1067-1078 (1994)
  31. Structure of ferricytochrome c' from Rhodospirillum molischianum at 1.67 A resolution. Finzel BC, Weber PC, Hardman KD, Salemme FR. J. Mol. Biol. 186 627-643 (1985)
  32. Crystal structure of human dihydrofolate reductase complexed with folate. Oefner C, D'Arcy A, Winkler FK. Eur. J. Biochem. 174 377-385 (1988)
  33. Construction of two Escherichia coli amber suppressor genes: tRNAPheCUA and tRNACysCUA. Normanly J, Masson JM, Kleina LG, Abelson J, Miller JH. Proc. Natl. Acad. Sci. U.S.A. 83 6548-6552 (1986)
  34. Three-dimensional structure in solution of a wheat lipid-transfer protein from multidimensional 1H-NMR data. A new folding for lipid carriers. Gincel E, Simorre JP, Caille A, Marion D, Ptak M, Vovelle F. Eur. J. Biochem. 226 413-422 (1994)
  35. Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs. Li R, Sirawaraporn R, Chitnumsub P, Sirawaraporn W, Wooden J, Athappilly F, Turley S, Hol WG. J. Mol. Biol. 295 307-323 (2000)
  36. NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution. Liepinsh E, Otting G, Wüthrich K. Nucleic Acids Res. 20 6549-6553 (1992)
  37. Trimethoprim resistance transposon Tn4003 from Staphylococcus aureus encodes genes for a dihydrofolate reductase and thymidylate synthetase flanked by three copies of IS257. Rouch DA, Messerotti LJ, Loo LS, Jackson CA, Skurray RA. Mol. Microbiol. 3 161-175 (1989)
  38. Taxonomy and conformational analysis of loops in proteins. Ring CS, Kneller DG, Langridge R, Cohen FE. J. Mol. Biol. 224 685-699 (1992)
  39. Novel method for the rapid evaluation of packing in protein structures. Gregoret LM, Cohen FE. J. Mol. Biol. 211 959-974 (1990)
  40. A structurally conserved water molecule in Rossmann dinucleotide-binding domains. Bottoms CA, Smith PE, Tanner JJ. Protein Sci. 11 2125-2137 (2002)
  41. Crystal structure of Escherichia coli thymidylate synthase containing bound 5-fluoro-2'-deoxyuridylate and 10-propargyl-5,8-dideazafolate. Matthews DA, Appelt K, Oatley SJ, Xuong NH. J. Mol. Biol. 214 923-936 (1990)
  42. A multiple-start Monte Carlo docking method. Hart TN, Read RJ. Proteins 13 206-222 (1992)
  43. Correlation between 15N NMR chemical shifts in proteins and secondary structure. Le H, Oldfield E. J. Biomol. NMR 4 341-348 (1994)
  44. Interaction of pyrimethamine, cycloguanil, WR99210 and their analogues with Plasmodium falciparum dihydrofolate reductase: structural basis of antifolate resistance. Rastelli G, Sirawaraporn W, Sompornpisut P, Vilaivan T, Kamchonwongpaisan S, Quarrell R, Lowe G, Thebtaranonth Y, Yuthavong Y. Bioorg. Med. Chem. 8 1117-1128 (2000)
  45. Manganese superoxide dismutase from Thermus thermophilus. A structural model refined at 1.8 A resolution. Ludwig ML, Metzger AL, Pattridge KA, Stallings WC. J. Mol. Biol. 219 335-358 (1991)
  46. Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions. Poornima CS, Dean PM. J. Comput. Aided Mol. Des. 9 500-512 (1995)
  47. SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups. Singh J, Thornton JM. J. Mol. Biol. 211 595-615 (1990)
  48. Orientational sampling and rigid-body minimization in molecular docking. Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Proteins 17 266-278 (1993)
  49. Sequence variations in the Plasmodium vivax dihydrofolate reductase-thymidylate synthase gene and their relationship with pyrimethamine resistance. de Pécoulas PE, Tahar R, Ouatas T, Mazabraud A, Basco LK. Mol. Biochem. Parasitol. 92 265-273 (1998)
  50. Potential antifolate resistance determinants and genotypic variation in the bifunctional dihydrofolate reductase-thymidylate synthase gene from human and bovine isolates of Cryptosporidium parvum. Vásquez JR, Goozé L, Kim K, Gut J, Petersen C, Nelson RG. Mol. Biochem. Parasitol. 79 153-165 (1996)
  51. Mutations in the dihydrofolate reductase gene of trimethoprim-resistant isolates of Streptococcus pneumoniae. Adrian PV, Klugman KP. Antimicrob. Agents Chemother. 41 2406-2413 (1997)
  52. Stopped-flow NMR spectroscopy: real-time unfolding studies of 6-19F-tryptophan-labeled Escherichia coli dihydrofolate reductase. Hoeltzli SD, Frieden C. Proc. Natl. Acad. Sci. U.S.A. 92 9318-9322 (1995)
  53. The crystal structure of dihydrofolate reductase from Thermotoga maritima: molecular features of thermostability. Dams T, Auerbach G, Bader G, Jacob U, Ploom T, Huber R, Jaenicke R. J. Mol. Biol. 297 659-672 (2000)
  54. A link between protein structure and enzyme catalyzed hydrogen tunneling. Bahnson BJ, Colby TD, Chin JK, Goldstein BM, Klinman JP. Proc. Natl. Acad. Sci. U.S.A. 94 12797-12802 (1997)
  55. 1H-NMR stereospecific assignments by conformational data-base searches. Nilges M, Clore GM, Gronenborn AM. Biopolymers 29 813-822 (1990)
  56. A yeast-based screen reveals that sulfasalazine inhibits tetrahydrobiopterin biosynthesis. Chidley C, Haruki H, Pedersen MG, Muller E, Johnsson K. Nat. Chem. Biol. 7 375-383 (2011)
  57. Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii. Pieper U, Kapadia G, Mevarech M, Herzberg O. Structure 6 75-88 (1998)
  58. Docking by least-squares fitting of molecular surface patterns. Bacon DJ, Moult J. J. Mol. Biol. 225 849-858 (1992)
  59. Protein structure alignment using a genetic algorithm. Szustakowski JD, Weng Z. Proteins 38 428-440 (2000)
  60. The effect of denaturants on protein structure. Dunbar J, Yennawar HP, Banerjee S, Luo J, Farber GK. Protein Sci. 6 1727-1733 (1997)
  61. Early intermediates in the folding of dihydrofolate reductase from Escherichia coli detected by hydrogen exchange and NMR. Jones BE, Matthews CR. Protein Sci. 4 167-177 (1995)
  62. Differences in the amino acid distributions of 3(10)-helices and alpha-helices. Karpen ME, de Haseth PL, Neet KE. Protein Sci. 1 1333-1342 (1992)
  63. Evaluation of library ranking efficacy in virtual screening. Kontoyianni M, Sokol GS, McClellan LM. J Comput Chem 26 11-22 (2005)
  64. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Koretke KK, Luthey-Schulten Z, Wolynes PG. Protein Sci. 5 1043-1059 (1996)
  65. Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase. Tondi D, Slomczynska U, Costi MP, Watterson DM, Ghelli S, Shoichet BK. Chem. Biol. 6 319-331 (1999)
  66. The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 A resolution. Champness JN, Achari A, Ballantine SP, Bryant PK, Delves CJ, Stammers DK. Structure 2 915-924 (1994)
  67. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Wade RC, Mazor MH, McCammon JA, Quiocho FA. Biopolymers 31 919-931 (1991)
  68. Inhibition of beta-lactamase by clavulanate. Trapped intermediates in cryocrystallographic studies. Chen CC, Herzberg O. J. Mol. Biol. 224 1103-1113 (1992)
  69. Recovering the true targets of specific ligands by virtual screening of the protein data bank. Paul N, Kellenberger E, Bret G, Müller P, Rognan D. Proteins 54 671-680 (2004)
  70. Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein. Arai M, Kondrashkina E, Kayatekin C, Matthews CR, Iwakura M, Bilsel O. J. Mol. Biol. 368 219-229 (2007)
  71. A fast and efficient method to generate biologically relevant conformations. Klebe G, Mietzner T. J. Comput. Aided Mol. Des. 8 583-606 (1994)
  72. Structural homologies with ATP- and folate-binding enzymes in the crystal structure of folylpolyglutamate synthetase. Sun X, Bognar AL, Baker EN, Smith CA. Proc. Natl. Acad. Sci. U.S.A. 95 6647-6652 (1998)
  73. The structure of mouse L1210 dihydrofolate reductase-drug complexes and the construction of a model of human enzyme. Stammers DK, Champness JN, Beddell CR, Dann JG, Eliopoulos E, Geddes AJ, Ogg D, North AC. FEBS Lett. 218 178-184 (1987)
  74. Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network. Keil M, Exner TE, Brickmann J. J Comput Chem 25 779-789 (2004)
  75. Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations. Summers NL, Karplus M. J. Mol. Biol. 216 991-1016 (1990)
  76. Refolding of Escherichia coli dihydrofolate reductase: sequential formation of substrate binding sites. Frieden C. Proc. Natl. Acad. Sci. U.S.A. 87 4413-4416 (1990)
  77. Analysis of protein main-chain solvation as a function of secondary structure. Thanki N, Umrania Y, Thornton JM, Goodfellow JM. J. Mol. Biol. 221 669-691 (1991)
  78. Characterization of the gene for the chromosomal dihydrofolate reductase (DHFR) of Staphylococcus epidermidis ATCC 14990: the origin of the trimethoprim-resistant S1 DHFR from Staphylococcus aureus? Dale GE, Broger C, Hartman PG, Langen H, Page MG, Then RL, Stüber D. J. Bacteriol. 177 2965-2970 (1995)
  79. Three-dimensional structure of the bifunctional protein PCD/DCoH, a cytoplasmic enzyme interacting with transcription factor HNF1. Ficner R, Sauer UH, Stier G, Suck D. EMBO J. 14 2034-2042 (1995)
  80. A comparison of heuristic search algorithms for molecular docking. Westhead DR, Clark DE, Murray CW. J. Comput. Aided Mol. Des. 11 209-228 (1997)
  81. A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site. Narayana N, Matthews DA, Howell EE, Nguyen-huu X. Nat. Struct. Biol. 2 1018-1025 (1995)
  82. Hydration in drug design. 2. Influence of local site surface shape on water binding. Poornima CS, Dean PM. J. Comput. Aided Mol. Des. 9 513-520 (1995)
  83. Influence of solvent accessibility and intermolecular contacts on atomic mobilities in hemerythrins. Sheriff S, Hendrickson WA, Stenkamp RE, Sieker LC, Jensen LH. Proc. Natl. Acad. Sci. U.S.A. 82 1104-1107 (1985)
  84. Pharmacophore-based molecular docking to account for ligand flexibility. Joseph-McCarthy D, Thomas BE, Belmarsh M, Moustakas D, Alvarez JC. Proteins 51 172-188 (2003)
  85. Atomic structures of human dihydrofolate reductase complexed with NADPH and two lipophilic antifolates at 1.09 a and 1.05 a resolution. Klon AE, Héroux A, Ross LJ, Pathak V, Johnson CA, Piper JR, Borhani DW. J. Mol. Biol. 320 677-693 (2002)
  86. Flexibases: a way to enhance the use of molecular docking methods. Kearsley SK, Underwood DJ, Sheridan RP, Miller MD. J. Comput. Aided Mol. Des. 8 565-582 (1994)
  87. Highly divergent dihydrofolate reductases conserve complex folding mechanisms. Wallace LA, Robert Matthews C. J. Mol. Biol. 315 193-211 (2002)
  88. Detergent-induced conformational changes of Humicola lanuginosa lipase studied by fluorescence spectroscopy. Jutila A, Zhu K, Patkar SA, Vind J, Svendsen A, Kinnunen PK. Biophys. J. 78 1634-1642 (2000)
  89. Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania. Zuccotto F, Martin AC, Laskowski RA, Thornton JM, Gilbert IH. J. Comput. Aided Mol. Des. 12 241-257 (1998)
  90. Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate. Bennett B, Langan P, Coates L, Mustyakimov M, Schoenborn B, Howell EE, Dealwis C. Proc. Natl. Acad. Sci. U.S.A. 103 18493-18498 (2006)
  91. Cloning and characterization of a novel, plasmid-encoded trimethoprim-resistant dihydrofolate reductase from Staphylococcus haemolyticus MUR313. Dale GE, Langen H, Page MG, Then RL, Stüber D. Antimicrob. Agents Chemother. 39 1920-1924 (1995)
  92. Contributions of left-handed helical residues to the structure and stability of bacteriophage T4 lysozyme. Nicholson H, Söderlind E, Tronrud DE, Matthews BW. J. Mol. Biol. 210 181-193 (1989)
  93. GroEL-mediated folding of structurally homologous dihydrofolate reductases. Clark AC, Frieden C. J. Mol. Biol. 268 512-525 (1997)
  94. A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening. Broughton HB. J. Mol. Graph. Model. 18 247-57, 302-4 (2000)
  95. A new mechanism of methotrexate action revealed by target screening with affinity beads. Uga H, Kuramori C, Ohta A, Tsuboi Y, Tanaka H, Hatakeyama M, Yamaguchi Y, Takahashi T, Kizaki M, Handa H. Mol Pharmacol 70 1832-1839 (2006)
  96. Isolation and characterization of a variant dihydrofolate reductase cDNA from methotrexate-resistant murine L5178Y cells. McIvor RS, Simonsen CC. Nucleic Acids Res. 18 7025-7032 (1990)
  97. Lead discovery of inhibitors of the dihydrofolate reductase domain of Plasmodium falciparum dihydrofolate reductase-thymidylate synthase. Toyoda T, Brobey RK, Sano G, Horii T, Tomioka N, Itai A. Biochem. Biophys. Res. Commun. 235 515-519 (1997)
  98. Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal. Gschwend DA, Kuntz ID. J. Comput. Aided Mol. Des. 10 123-132 (1996)
  99. An essential intermediate in the folding of dihydrofolate reductase. Heidary DK, O'Neill JC, Roy M, Jennings PA. Proc. Natl. Acad. Sci. U.S.A. 97 5866-5870 (2000)
  100. Cloning and characterization of a novel trimethoprim-resistant dihydrofolate reductase from a nosocomial isolate of Staphylococcus aureus CM.S2 (IMCJ1454). Sekiguchi J, Tharavichitkul P, Miyoshi-Akiyama T, Chupia V, Fujino T, Araake M, Irie A, Morita K, Kuratsuji T, Kirikae T. Antimicrob. Agents Chemother. 49 3948-3951 (2005)
  101. Probing the salt bridge in the dihydrofolate reductase-methotrexate complex by using the coordinate-coupled free-energy perturbation method. Singh UC. Proc. Natl. Acad. Sci. U.S.A. 85 4280-4284 (1988)
  102. X-ray crystallographic studies of Candida albicans dihydrofolate reductase. High resolution structures of the holoenzyme and an inhibited ternary complex. Whitlow M, Howard AJ, Stewart D, Hardman KD, Kuyper LF, Baccanari DP, Fling ME, Tansik RL. J. Biol. Chem. 272 30289-30298 (1997)
  103. Appearance of a new trimethoprim resistance gene, dhfrIX, in Escherichia coli from swine. Jansson C, Sköld O. Antimicrob. Agents Chemother. 35 1891-1899 (1991)
  104. Automated site-directed drug design using molecular lattices. Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID. J Mol Graph 10 66-78, 106 (1992)
  105. BUILDER v.2: improving the chemistry of a de novo design strategy. Roe DC, Kuntz ID. J. Comput. Aided Mol. Des. 9 269-282 (1995)
  106. Moritella cold-active dihydrofolate reductase: are there natural limits to optimization of catalytic efficiency at low temperature? Xu Y, Feller G, Gerday C, Glansdorff N. J. Bacteriol. 185 5519-5526 (2003)
  107. ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures. Van Drie JH, Weininger D, Martin YC. J. Comput. Aided Mol. Des. 3 225-251 (1989)
  108. Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility. Kairys V, Gilson MK. J Comput Chem 23 1656-1670 (2002)
  109. Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities. Meng EC, Kuntz ID, Abraham DJ, Kellogg GE. J. Comput. Aided Mol. Des. 8 299-306 (1994)
  110. Protonated state of methotrexate, trimethoprim, and pyrimethamine bound to dihydrofolate reductase. Cocco L, Roth B, Temple C, Montgomery JA, London RE, Blakley RL. Arch. Biochem. Biophys. 226 567-577 (1983)
  111. Structural genomics for drug design against the pathogen Coxiella burnetii. Franklin MC, Cheung J, Rudolph MJ, Burshteyn F, Cassidy M, Gary E, Hillerich B, Yao ZK, Carlier PR, Totrov M, Love JD. Proteins 83 2124-2136 (2015)
  112. A crystallographic comparison between mutated glyceraldehyde-3-phosphate dehydrogenases from Bacillus stearothermophilus complexed with either NAD+ or NADP+. Didierjean C, Rahuel-Clermont S, Vitoux B, Dideberg O, Branlant G, Aubry A. J. Mol. Biol. 268 739-759 (1997)
  113. A hydrophobic cluster forms early in the folding of dihydrofolate reductase. Garvey EP, Swank J, Matthews CR. Proteins 6 259-266 (1989)
  114. Anti-malarial drug development using models of enzyme structure. Li Z, Chen X, Davidson E, Zwang O, Mendis C, Ring CS, Roush WR, Fegley G, Li R, Rosenthal PJ. Chem. Biol. 1 31-37 (1994)
  115. Calibration of effective van der Waals atomic contact radii for proteins and peptides. Iijima H, Dunbar JB, Marshall GR. Proteins 2 330-339 (1987)
  116. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK. Proteins 42 279-293 (2001)
  117. Ligand-receptor docking with the Mining Minima optimizer. David L, Luo R, Gilson MK. J. Comput. Aided Mol. Des. 15 157-171 (2001)
  118. Structure and expression of human dihydropteridine reductase. Lockyer J, Cook RG, Milstien S, Kaufman S, Woo SL, Ledley FD. Proc. Natl. Acad. Sci. U.S.A. 84 3329-3333 (1987)
  119. Synthetic and crystallographic studies of a new inhibitor series targeting Bacillus anthracis dihydrofolate reductase. Beierlein JM, Frey KM, Bolstad DB, Pelphrey PM, Joska TM, Smith AE, Priestley ND, Wright DL, Anderson AC. J. Med. Chem. 51 7532-7540 (2008)
  120. The extremely halophilic archaeon Haloferax volcanii has two very different dihydrofolate reductases. Ortenberg R, Rozenblatt-Rosen O, Mevarech M. Mol. Microbiol. 35 1493-1505 (2000)
  121. A method for biomolecular structural recognition and docking allowing conformational flexibility. Sandak B, Nussinov R, Wolfson HJ. J. Comput. Biol. 5 631-654 (1998)
  122. Crystallographic investigation of the cooperative interaction between trimethoprim, reduced cofactor and dihydrofolate reductase. Champness JN, Stammers DK, Beddell CR. FEBS Lett. 199 61-67 (1986)
  123. Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design. Todorov NP, Dean PM. J. Comput. Aided Mol. Des. 11 175-192 (1997)
  124. Protein function microarrays based on self-immobilizing and self-labeling fusion proteins. Sielaff I, Arnold A, Godin G, Tugulu S, Klok HA, Johnsson K. Chembiochem 7 194-202 (2006)
  125. Structural and functional similarities in the ADP-forming amide bond ligase superfamily: implications for a substrate-induced conformational change in folylpolyglutamate synthetase. Sheng Y, Sun X, Shen Y, Bognar AL, Baker EN, Smith CA. J. Mol. Biol. 302 427-440 (2000)
  126. Both ATPase domains of ClpA are critical for processing of stable protein structures. Kress W, Mutschler H, Weber-Ban E. J. Biol. Chem. 284 31441-31452 (2009)
  127. Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation. Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ. Cell Host Microbe 29 362-377.e11 (2021)
  128. A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch. Trausch JJ, Batey RT. Chem. Biol. 21 205-216 (2014)
  129. Atomic size packing defects in proteins. Connolly ML. Int J Pept Protein Res 28 360-363 (1986)
  130. PRO-LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules. Clark DE, Frenkel D, Levy SA, Li J, Murray CW, Robson B, Waszkowycz B, Westhead DR. J. Comput. Aided Mol. Des. 9 13-32 (1995)
  131. Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory. Exner TE, Keil M, Brickmann J. J Comput Chem 23 1176-1187 (2002)
  132. A free-energy perturbation study of the binding of methotrexate to mutants of dihydrofolate reductase. Singh UC, Benkovic SJ. Proc. Natl. Acad. Sci. U.S.A. 85 9519-9523 (1988)
  133. Chemically induced dimerization of dihydrofolate reductase by a homobifunctional dimer of methotrexate. Kopytek SJ, Standaert RF, Dyer JC, Hu JC. Chem. Biol. 7 313-321 (2000)
  134. Cloning and expression of the dihydrofolate reductase-thymidylate synthase gene from Trypanosoma cruzi. Reche P, Arrebola R, Olmo A, Santi DV, Gonzalez-Pacanowska D, Ruiz-Perez LM. Mol. Biochem. Parasitol. 65 247-258 (1994)
  135. Kinked-helices model of the nicotinic acetylcholine receptor ion channel and its complexes with blockers: simulation by the Monte Carlo minimization method. Tikhonov DB, Zhorov BS. Biophys. J. 74 242-255 (1998)
  136. Probing the interactions between the folding elements early in the folding of Escherichia coli dihydrofolate reductase by systematic sequence perturbation analysis. Arai M, Iwakura M. J. Mol. Biol. 347 337-353 (2005)
  137. 1H, 15N and 13C resonance assignments, secondary structure, and the conformation of substrate in the binary folate complex of Escherichia coli dihydrofolate reductase. Falzone CJ, Cavanagh J, Cowart M, Palmer AG, Matthews CR, Benkovic SJ, Wright PE. J. Biomol. NMR 4 349-366 (1994)
  138. High expression in Escherichia coli of the gene coding for dihydrofolate reductase of the extremely halophilic archaebacterium Haloferax volcanii. Reconstitution of the active enzyme and mutation studies. Blecher O, Goldman S, Mevarech M. Eur. J. Biochem. 216 199-203 (1993)
  139. Lack of dihydrofolate reductase in human tumor and leukemia cells in vivo. Kamen BA, Nylen PA, Whitehead VM, Abelson HT, Dolnick BJ, Peterson DW. Cancer Drug Deliv 2 133-138 (1985)
  140. Native Escherichia coli and murine dihydrofolate reductases contain late-folding non-native structures. Clark AC, Frieden C. J. Mol. Biol. 285 1765-1776 (1999)
  141. Significance of structural changes in proteins: expected errors in refined protein structures. Stroud RM, Fauman EB. Protein Sci. 4 2392-2404 (1995)
  142. Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multiconformation databases. Joseph-McCarthy D, Alvarez JC. Proteins 51 189-202 (2003)
  143. Letter Bio-incorporation of telluromethionine into buried residues of dihydrofolate reductase. Boles JO, Lewinski K, Kunkle M, Odom JD, Dunlap B, Lebioda L, Hatada M. Nat. Struct. Biol. 1 283-284 (1994)
  144. Characterization of the gene for chromosomal trimethoprim-sensitive dihydrofolate reductase of Staphylococcus aureus ATCC 25923. Dale GE, Then RL, Stüber D. Antimicrob. Agents Chemother. 37 1400-1405 (1993)
  145. Dihydrofolate reductase. 1H resonance assignments and coenzyme-induced conformational changes. Hammond SJ, Birdsall B, Searle MS, Roberts GC, Feeney J. J. Mol. Biol. 188 81-97 (1986)
  146. Effect of backbone cyclization on protein folding stability: chain entropies of both the unfolded and the folded states are restricted. Zhou HX. J. Mol. Biol. 332 257-264 (2003)
  147. Long-range structural effects in a second-site revertant of a mutant dihydrofolate reductase. Brown KA, Howell EE, Kraut J. Proc. Natl. Acad. Sci. U.S.A. 90 11753-11756 (1993)
  148. Sequence variation in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) and trypanothione reductase (TR) genes of Trypanosoma cruzi. Machado CA, Ayala FJ. Mol. Biochem. Parasitol. 121 33-47 (2002)
  149. Tolerance for random recombination of domains in prokaryotic and eukaryotic translation systems: Limited interdomain misfolding in a eukaryotic translation system. Hirano N, Sawasaki T, Tozawa Y, Endo Y, Takai K. Proteins 64 343-354 (2006)
  150. Domain motions in dihydrofolate reductase: a molecular dynamics study. Verma CS, Caves LS, Hubbard RE, Roberts GC. J. Mol. Biol. 266 776-796 (1997)
  151. Inhibition of dihydrofolate reductase from bacterial and vertebrate sources by folate, aminopterin, methotrexate and their 5-deaza analogues. Stone SR, Montgomery JA, Morrison JF. Biochem. Pharmacol. 33 175-179 (1984)
  152. Selective coupling of methotrexate to peptide hormone carriers through a gamma-carboxamide linkage of its glutamic acid moiety: benzotriazol-1-yloxytris(dimethylamino)phosphonium hexafluorophosphate activation in salt coupling. Nagy A, Szoke B, Schally AV. Proc. Natl. Acad. Sci. U.S.A. 90 6373-6376 (1993)
  153. pH-dependent conformational changes in Escherichia coli dihydrofolate reductase revealed by Raman difference spectroscopy. Chen YQ, Kraut J, Callender R. Biophys. J. 72 936-941 (1997)
  154. 1H and 15N NMR studies of protonation and hydrogen-bonding in the binding of trimethoprim to dihydrofolate reductase. Bevan AW, Roberts GC, Feeney J, Kuyper L. Eur. Biophys. J. 11 211-218 (1985)
  155. Dynamics of trimethoprim bound to dihydrofolate reductase. Searle MS, Forster MJ, Birdsall B, Roberts GC, Feeney J, Cheung HT, Kompis I, Geddes AJ. Proc. Natl. Acad. Sci. U.S.A. 85 3787-3791 (1988)
  156. Effects of fluorine substitution on the structure and dynamics of complexes of dihydrofolate reductase (Escherichia coli). Lau EY, Gerig JT. Biophys. J. 73 1579-1592 (1997)
  157. Letter NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH. Polshakov VI, Smirnov EG, Birdsall B, Kelly G, Feeney J. J. Biomol. NMR 24 67-70 (2002)
  158. The crystal structure of the Bacillus lentus alkaline protease, subtilisin BL, at 1.4 A resolution. Goddette DW, Paech C, Yang SS, Mielenz JR, Bystroff C, Wilke ME, Fletterick RJ. J. Mol. Biol. 228 580-595 (1992)
  159. The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism. Stenmark P, Moche M, Gurmu D, Nordlund P. J. Mol. Biol. 373 48-64 (2007)
  160. A new approach to the problem of docking two molecules: the ellipsoid algorithm. Billeter M, Havel TF, Kuntz ID. Biopolymers 26 777-793 (1987)
  161. Comparative hydrogen-deuterium exchange for a mesophilic vs thermophilic dihydrofolate reductase at 25 °C: identification of a single active site region with enhanced flexibility in the mesophilic protein. Oyeyemi OA, Sours KM, Lee T, Kohen A, Resing KA, Ahn NG, Klinman JP. Biochemistry 50 8251-8260 (2011)
  162. First report on the systematic sequencing of the small genome of Encephalitozoon cuniculi (Protozoa, Microspora): gene organization of a 4.3 kbp region on chromosome I. Duffieux F, Peyret P, Roe BA, Vivares CP. Microb. Comp. Genomics 3 1-11 (1998)
  163. High resolution fast quantitative docking using Fourier domain correlation techniques. Blom NS, Sygusch J. Proteins 27 493-506 (1997)
  164. Importance of a hydrophobic residue in binding and catalysis by dihydrofolate reductase. Mayer RJ, Chen JT, Taira K, Fierke CA, Benkovic SJ. Proc. Natl. Acad. Sci. U.S.A. 83 7718-7720 (1986)
  165. Molecular structure matching by simulated annealing. I. A comparison between different cooling schedules. Barakat MT, Dean PM. J. Comput. Aided Mol. Des. 4 295-316 (1990)
  166. The solution structure of the complex of Lactobacillus casei dihydrofolate reductase with methotrexate. Gargaro AR, Soteriou A, Frenkiel TA, Bauer CJ, Birdsall B, Polshakov VI, Barsukov IL, Roberts GC, Feeney J. J. Mol. Biol. 277 119-134 (1998)
  167. Tools for building a comprehensive modeling system for virtual screening under real biological conditions: The Computational Titration algorithm. Kellogg GE, Fornabaio M, Chen DL, Abraham DJ, Spyrakis F, Cozzini P, Mozzarelli A. J. Mol. Graph. Model. 24 434-439 (2006)
  168. A molecular docking strategy identifies Eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-dihydrofolate reductase. Atreya CE, Johnson EF, Irwin JJ, Dow A, Massimine KM, Coppens I, Stempliuk V, Beverley S, Joiner KA, Shoichet BK, Anderson KS. J. Biol. Chem. 278 14092-14100 (2003)
  169. Arginyl groups involved in the binding of Anabaena ferredoxin--NADP+ reductase to NADP+ and to ferredoxin. Sancho J, Medina M, Gómez-Moreno C. Eur. J. Biochem. 187 39-48 (1990)
  170. Cell uptake and trafficking behavior of non-covalent, coiled-coil based polymer-drug conjugates. Apostolovic B, Deacon SP, Duncan R, Klok HA. Macromol Rapid Commun 32 11-18 (2011)
  171. Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking. Salaniwal S, Manas ES, Alvarez JC, Unwalla RJ. Proteins 66 422-435 (2007)
  172. Refined structures of oxidized flavodoxin from Anacystis nidulans. Drennan CL, Pattridge KA, Weber CH, Metzger AL, Hoover DM, Ludwig ML. J. Mol. Biol. 294 711-724 (1999)
  173. Structure and dynamics in solution of the complex of Lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate. Polshakov VI, Birdsall B, Frenkiel TA, Gargaro AR, Feeney J. Protein Sci. 8 467-481 (1999)
  174. Target identification by chromatographic co-elution: monitoring of drug-protein interactions without immobilization or chemical derivatization. Chan JN, Vuckovic D, Sleno L, Olsen JB, Pogoutse O, Havugimana P, Hewel JA, Bajaj N, Wang Y, Musteata MF, Nislow C, Emili A. Mol. Cell Proteomics 11 M111.016642 (2012)
  175. Trypanosoma brucei dihydrofolate reductase-thymidylate synthase: gene isolation and expression and characterization of the enzyme. Gamarro F, Yu PL, Zhao J, Edman U, Greene PJ, Santi D. Mol. Biochem. Parasitol. 72 11-22 (1995)
  176. 19F-n.m.r. studies of 3',5'-difluoromethotrexate binding to Lactobacillus casei dihydrofolate reductase. Molecular motion and coenzyme-induced conformational changes. Clore GM, Gronenborn AM, Birdsall B, Feeney J, Roberts GC. Biochem. J. 217 659-666 (1984)
  177. A branch-and-bound method for optimal atom-type assignment in de novo ligand design. Todorov NP, Dean PM. J. Comput. Aided Mol. Des. 12 335-349 (1998)
  178. A hierarchical method for generating low-energy conformers of a protein-ligand complex. Given JA, Gilson MK. Proteins 33 475-495 (1998)
  179. Characterization of dihydrofolate reductase genes from trimethoprim-susceptible and trimethoprim-resistant strains of Enterococcus faecalis. Coque TM, Singh KV, Weinstock GM, Murray BE. Antimicrob. Agents Chemother. 43 141-147 (1999)
  180. Comparative activity of rat liver dihydrofolate reductase with 7,8-dihydrofolate and other 7,8-dihydropteridines. Webber S, Whiteley JM. Arch. Biochem. Biophys. 236 681-690 (1985)
  181. Comparison of protein surfaces using a genetic algorithm. Poirrette AR, Artymiuk PJ, Rice DW, Willett P. J. Comput. Aided Mol. Des. 11 557-569 (1997)
  182. Effect of N-terminal truncation of Plasmodium falciparum dihydrofolate reductase on dihydrofolate reductase and thymidylate synthase activity. Wattanarangsan J, Chusacultanachai S, Yuvaniyama J, Kamchonwongpaisan S, Yuthavong Y. Mol. Biochem. Parasitol. 126 97-102 (2003)
  183. Electron redistribution on binding of a substrate to an enzyme: folate and dihydrofolate reductase. Bajorath J, Kitson DH, Fitzgerald G, Andzelm J, Kraut J, Hagler AT. Proteins 9 217-224 (1991)
  184. Identifying targets for bioreductive agents: using GRID to predict selective binding regions of proteins. Reynolds CA, Wade RC, Goodford PJ. J Mol Graph 7 103-8, 100 (1989)
  185. Improved calculations of compactness and a reevaluation of continuous compact units. Zehfus MH. Proteins 16 293-300 (1993)
  186. Ligand-induced distortion of an active site in thymidylate synthase upon binding anticancer drug 1843U89. Weichsel A, Montfort WR. Nat. Struct. Biol. 2 1095-1101 (1995)
  187. NMR detection of arginine-ligand interactions in complexes of Lactobacillus casei dihydrofolate reductase. Gargaro AR, Frenkiel TA, Nieto PM, Birdsall B, Polshakov VI, Morgan WD, Feeney J. Eur. J. Biochem. 238 435-439 (1996)
  188. New molecular shape descriptors: application in database screening. Good AC, Ewing TJ, Gschwend DA, Kuntz ID. J. Comput. Aided Mol. Des. 9 1-12 (1995)
  189. Protein folding: how the mechanism of GroEL action is defined by kinetics. Frieden C, Clark AC. Proc. Natl. Acad. Sci. U.S.A. 94 5535-5538 (1997)
  190. Pteridine-sulfonamide conjugates as dual inhibitors of carbonic anhydrases and dihydrofolate reductase with potential antitumor activity. Marques SM, Enyedy EA, Supuran CT, Krupenko NI, Krupenko SA, Santos MA. Bioorg. Med. Chem. 18 5081-5089 (2010)
  191. Synergy between combinatorial chemistry and de novo design. Leach AR, Bryce RA, Robinson AJ. J. Mol. Graph. Model. 18 358-67, 526 (2000)
  192. Experimental resolution of the free energies of aqueous solvation contributions to ligand-protein binding: quinone-QA site interactions in the photosynthetic reaction center protein. Warncke K, Dutton PL. Proc. Natl. Acad. Sci. U.S.A. 90 2920-2924 (1993)
  193. Functional concerted motions in the bovine serum retinol-binding protein. Chau PL, van Aalten DM, Bywater RP, Findlay JB. J. Comput. Aided Mol. Des. 13 11-20 (1999)
  194. Location of the active site and proposed catalytic mechanism of pterin-4a-carbinolamine dehydratase. Köster S, Stier G, Ficner R, Hölzer M, Curtius HC, Suck D, Ghisla S. Eur. J. Biochem. 241 858-864 (1996)
  195. Protein fragments as probes in the study of protein folding mechanisms: differential effects of dihydrofolate reductase fragments on the refolding of the intact protein. Hall JG, Frieden C. Proc. Natl. Acad. Sci. U.S.A. 86 3060-3064 (1989)
  196. Selectivity analysis of 5-(arylthio)-2,4-diaminoquinazolines as inhibitors of Candida albicans dihydrofolate reductase by molecular dynamics simulations. Gokhale VM, Kulkarni VM. J. Comput. Aided Mol. Des. 14 495-506 (2000)
  197. Sequence of a putative glutathione synthetase II gene and flanking regions from Anaplasma centrale. Peters JM, Dalrymple BP, Jorgensen WK. Biochem. Biophys. Res. Commun. 182 1040-1046 (1992)
  198. The electrostatic potential of Escherichia coli dihydrofolate reductase. Bajorath J, Kitson DH, Kraut J, Hagler AT. Proteins 11 1-12 (1991)
  199. The structure-based design and synthesis of selective inhibitors of Trypanosoma cruzi dihydrofolate reductase. Zuccotto F, Brun R, Gonzalez Pacanowska D, Ruiz Perez LM, Gilbert IH. Bioorg. Med. Chem. Lett. 9 1463-1468 (1999)
  200. Characterization of a novel bifunctional dihydropteroate synthase/dihydropteroate reductase enzyme from Helicobacter pylori. Levin I, Mevarech M, Palfey BA. J. Bacteriol. 189 4062-4069 (2007)
  201. Consideration of the pH-dependent inhibition of dihydrofolate reductase by methotrexate. Cannon WR, Garrison BJ, Benkovic SJ. J. Mol. Biol. 271 656-668 (1997)
  202. Mutational analysis of Plasmodium falciparum dihydrofolate reductase: the role of aspartate 54 and phenylalanine 223 on catalytic activity and antifolate binding. Sirawaraporn W, Sirawaraporn R, Yongkiettrakul S, Anuwatwora A, Rastelli G, Kamchonwongpaisan S, Yuthavong Y. Mol. Biochem. Parasitol. 121 185-193 (2002)
  203. The coordination of the isomerization of a conserved non-prolyl cis peptide bond with the rate-limiting steps in the folding of dihydrofolate reductase. Svensson AK, O'Neill JC, Matthews CR. J. Mol. Biol. 326 569-583 (2003)
  204. A new tool for the qualitative and quantitative analysis of protein surfaces using B-spline and density of surface neighborhood. Colloc'h N, Mornon JP. J Mol Graph 8 133-40, 146 (1990)
  205. A reexamination of the substrate utilization of 2-thioorotidine-5'-monophosphate by yeast orotidine-5'-monophosphate decarboxylase. Smiley JA, Hay KM, Levison BS. Bioorg. Chem. 29 96-106 (2001)
  206. Automatic superposition of drug molecules based on their common receptor site. Kato Y, Inoue A, Yamada M, Tomioka N, Itai A. J. Comput. Aided Mol. Des. 6 475-486 (1992)
  207. Crystal structures of Klebsiella pneumoniae dihydrofolate reductase bound to propargyl-linked antifolates reveal features for potency and selectivity. Lamb KM, Lombardo MN, Alverson J, Priestley ND, Wright DL, Anderson AC. Antimicrob. Agents Chemother. 58 7484-7491 (2014)
  208. Methotrexate binds in a non-productive orientation to human dihydrofolate reductase in solution, based on NMR spectroscopy. Stockman BJ, Nirmala NR, Wagner G, Delcamp TJ, DeYarman MT, Freisheim JH. FEBS Lett. 283 267-269 (1991)
  209. Pattern recognition strategies for molecular surfaces. II. Surface complementarity. Exner TE, Keil M, Brickmann J. J Comput Chem 23 1188-1197 (2002)
  210. Stabilization of hyperactive dihydrofolate reductase by cyanocysteine-mediated backbone cyclization. Takahashi H, Arai M, Takenawa T, Sota H, Xie QH, Iwakura M. J Biol Chem 282 9420-9429 (2007)
  211. The combined use of selective deuteration and double resonance experiments in assigning the 1H resonances of valine and tyrosine residues of dihydrofolate reductase. Birdsall B, Feeney J, Griffiths DV, Hammond S, Kimber B, King RW, Roberts GC, Searle M. FEBS Lett. 175 364-368 (1984)
  212. 3D 13C/1H NMR-based assignments for side-chain resonances of Lactobacillus casei dihydrofolate reductase. Evidence for similarities between the solution and crystal structures of the enzyme. Soteriou A, Carr MD, Frenkiel TA, McCormick JE, Bauer CJ, Sali D, Birdsall B, Feeney J. J. Biomol. NMR 3 535-546 (1993)
  213. A 1H n.m.r. study of the role of the glutamate moiety in the binding of methotrexate to Lactobacillus casei dihydrofolate reductase. Antonjuk DJ, Birdsall B, Cheung HT, Clore GM, Feeney J, Gronenborn A, Roberts GC, Tran TQ. Br. J. Pharmacol. 81 309-315 (1984)
  214. A new method for predicting binding free energy between receptor and ligand. Takamatsu Y, Itai A. Proteins 33 62-73 (1998)
  215. Binuclear Ni(II)-DpaTyr complex as a high affinity probe for an oligo-aspartate Tag tethered to proteins. Ojida A, Fujishima SH, Honda K, Nonaka H, Uchinomiya SH, Hamachi I. Chem Asian J 5 877-886 (2010)
  216. Conformational studies on beta-bend containing a cis peptide unit. Nagarajaram HA, Paul PK, Ramanarayanan K, Soman KV, Ramakrishnan C. Int J Pept Protein Res 40 383-394 (1992)
  217. FLASHFLOOD: a 3D field-based similarity search and alignment method for flexible molecules. Pitman MC, Huber WK, Horn H, Krämer A, Rice JE, Swope WC. J. Comput. Aided Mol. Des. 15 587-612 (2001)
  218. Factors that cause trimethoprim resistance in Streptococcus pyogenes. Bergmann R, van der Linden M, Chhatwal GS, Nitsche-Schmitz DP. Antimicrob. Agents Chemother. 58 2281-2288 (2014)
  219. Interpretable correlation descriptors for quantitative structure-activity relationships. Spowage BM, Bruce CL, Hirst JD. J Cheminform 1 22 (2009)
  220. Nuclear magnetic resonance detection of bound water molecules in the active site of Lactobacillus casei dihydrofolate reductase in aqueous solution. Gerothanassis IP, Birdsall B, Bauer CJ, Frenkiel TA, Feeney J. J. Mol. Biol. 226 549-554 (1992)
  221. Synthesis, in vitro antitumor activity, dihydrofolate reductase inhibition, DNA intercalation and structure-activity relationship studies of 1,3,5-triazine analogues. Singla P, Luxami V, Paul K. Bioorg. Med. Chem. Lett. 26 518-523 (2016)
  222. The role of local tight packing of hydrophobic groups in beta-structure. Vtyurin N. Proteins 15 62-70 (1993)
  223. Thermal denaturation of bacterial and bovine dihydrofolate reductases and their complexes with NADPH, trimethoprim and methotrexate. Sasso S, Protasevich I, Gilli R, Makarov A, Briand C. J. Biomol. Struct. Dyn. 12 1023-1032 (1995)
  224. Computational studies on pterins and speculations on the mechanism of action of dihydrofolate reductase. Uchimaru T, Tsuzuki S, Tanabe K, Benkovic SJ, Furukawa K, Taira K. Biochem. Biophys. Res. Commun. 161 64-68 (1989)
  225. Fluorescent biphenyl derivatives of phenylalanine suitable for protein modification. Chen S, Fahmi NE, Bhattacharya C, Wang L, Jin Y, Benkovic SJ, Hecht SM. Biochemistry 52 8580-8589 (2013)
  226. Functional role for the conformationally mobile phenylalanine 223 in the reaction of methylenetetrahydrofolate reductase from Escherichia coli. Lee MN, Takawira D, Nikolova AP, Ballou DP, Furtado VC, Phung NL, Still BR, Thorstad MK, Tanner JJ, Trimmer EE. Biochemistry 48 7673-7685 (2009)
  227. Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase. Bliznyuk AA, Gready JE. J. Comput. Aided Mol. Des. 12 325-333 (1998)
  228. Molecular Modeling of Geometries, Charge Distributions, and Binding Energies of Small, Drug-Like Molecules Containing Nitrogen Heterocycles and Exocyclic Amino Groups in the Gas Phase and Aqueous Solution. White BR, Wagner CR, Truhlar DG, Amin EA. J Chem Theory Comput 4 1718-1732 (2008)
  229. Molecular docking studies on DMDP derivatives as human DHFR inhibitors. Srivastava V, Kumar A, Mishra BN, Siddiqi MI. Bioinformation 3 180-188 (2008)
  230. Substrate and inhibitor specificity of Mycobacterium avium dihydrofolate reductase. Böck RA, Soulages JL, Barrow WW. FEBS J. 274 3286-3298 (2007)
  231. 15N NMR studies of the conformation of E. coli dihydrofolate reductase in complex with folate or methotrexate. Huang FY, Yang QX, Huang TH. FEBS Lett. 289 231-234 (1991)
  232. Accuracy of binding mode prediction with a cascadic stochastic tunneling method. Fischer B, Basili S, Merlitz H, Wenzel W. Proteins 68 195-204 (2007)
  233. Changes in the electron density of the cofactor NADPH on binding to E. coli dihydrofolate reductase. Bajorath J, Li ZQ, Fitzgerald G, Kitson DH, Farnum M, Fine RM, Kraut J, Hagler AT. Proteins 11 263-270 (1991)
  234. Distortions in protein helices. Geetha V. Int. J. Biol. Macromol. 19 81-89 (1996)
  235. Hydrogen bonding effects on 31P NMR shielding in the pyrophosphate group of NADPH bound to L. casei dihydrofolate reductase. Gerothanassis IP, Birdsall B, Feeney J. FEBS Lett. 291 21-23 (1991)
  236. PRO_LIGAND: an approach to de novo molecular design. 6. Flexible fitting in the design of peptides. Murray CW, Clark DE, Byrne DG. J. Comput. Aided Mol. Des. 9 381-395 (1995)
  237. Structural mimicry of adenosine by the antitumor agents 4-methoxy- and 4-amino-8-(beta-D-ribofuranosylamino)pyrimido[5,4-d]pyrimidine as viewed by a molecular modeling method. Ghose AK, Viswanadhan VN, Sanghvi YS, Nord LD, Willis RC, Revankar GR, Robins RK. Proc. Natl. Acad. Sci. U.S.A. 86 8242-8246 (1989)
  238. Structural studies on bio-active compounds. Part XV. Structure-activity relationships for pyrimethamine and a series of diaminopyrimidine analogues versus bacterial dihydrofolate reductase. Sansom CE, Schwalbe CH, Lambert PA, Griffin RJ, Stevens MF. Biochim. Biophys. Acta 995 21-27 (1989)
  239. Structure of a partially unfolded form of Escherichia coli dihydrofolate reductase provides insight into its folding pathway. Kasper JR, Liu PF, Park C. Protein Sci. 23 1728-1737 (2014)
  240. TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time. Schellhammer I, Rarey M. J. Comput. Aided Mol. Des. 21 223-238 (2007)
  241. 13C NMR studies of complexes of Escherichia coli dihydrofolate reductase formed with methotrexate and with folic acid. Cheung HT, Birdsall B, Feeney J. FEBS Lett. 312 147-151 (1992)
  242. CGEMA and VGAP: a Colour Graphics Editor for Multiple Alignment using a variable GAP penalty. Application to the muscarinic acetylcholine receptor. Moereels H, De Bie L, Tollenaere JP. J. Comput. Aided Mol. Des. 4 131-145 (1990)
  243. Computer-aided drug design: getting the best results. Dixon JS. Trends Biotechnol. 10 357-363 (1992)
  244. DNA synthesis as a therapeutic target: the first 65 years. Mathews CK. FASEB J. 26 2231-2237 (2012)
  245. Expression and characterization of the Trypanosoma cruzi dihydrofolate reductase domain. Reche P, Arrebola R, Santi DV, Gonzalez-Pacanowska D, Ruiz-Perez LM. Mol. Biochem. Parasitol. 76 175-185 (1996)
  246. Flexible docking of an acetoxyethoxymethyl derivative of thiosemicarbazone into three different species of dihydrofolate reductase. Choi IH, Kim C. Arch. Pharm. Res. 25 807-816 (2002)
  247. Site-specific mutagenesis of dihydrofolate reductase from Escherichia coli. Chen JT, Mayer RJ, Fierke CA, Benkovic SJ. J. Cell. Biochem. 29 73-82 (1985)
  248. The 1H-NMR assignments of the aromatic resonances in complexes of Lactobacillus casei dihydrofolate reductase and the origins of their chemical shifts. Birdsall B, Arnold JR, Jimenez-Barbero J, Frenkiel TA, Bauer CJ, Tendler SJ, Carr MD, Thomas JA, Roberts GC, Feeney J. Eur. J. Biochem. 191 659-668 (1990)
  249. The dihydrofolate reductase-encoding gene dyrA of the hyperthermophilic bacterium Thermotoga maritima. Van de Casteele M, Legrain C, Wilquet V, Glansdorff N. Gene 158 101-105 (1995)
  250. The use of local surface properties for molecular superimposition. Manallack DT. J Mol Model 14 797-805 (2008)
  251. DBMAKER: a set of programs to generate three-dimensional databases based upon user-specified criteria. Ho CM, Marshall GR. J. Comput. Aided Mol. Des. 9 65-86 (1995)
  252. Ligand shape emerges in solvent dipole ordering region at ligand binding site of protein. Murata K, Nagata N, Nakanishi I, Kitaura K. J Comput Chem 31 791-796 (2010)
  253. Peptide fragment studies on the folding elements of dihydrofolate reductase from Escherichia coli. Arai M, Iwakura M. Proteins 62 399-410 (2006)
  254. Segmentation of a protein into structural elements: analysis and classification of segments. Nakashima H, Nishikawa K, Ooi T. J. Protein Chem. 7 509-525 (1988)
  255. 13C-NMR studies of selectively carboxymethylated [methyl-13C]methionine-labeled bacterial dihydrofolate reductase. London RE, Wageman WE, Blakley RL. FEBS Lett. 160 56-60 (1983)
  256. 31P solid-state NMR measurements used to detect interactions between NADPH and water and to determine the ionisation state of NADPH in a protein-ligand complex subjected to low-level hydration. Gerothanassis IP, Barrie PJ, Birdsall B, Feeney J. Eur. J. Biochem. 235 262-266 (1996)
  257. 31P-NMR studies of NADPH, NADP+ and the complex of NADPH and methotrexate with Lactobacillus casei dihydrofolate reductase in the solid state. Gerothanassis IP, Barrie PJ, Birdsall B, Feeney J. Eur. J. Biochem. 226 211-218 (1994)
  258. 3H-n.m.r. studies of multiple conformations and dynamic processes in complexes of folate and methotrexate with Lactobacillus casei dihydrofolate reductase. Curtis N, Moore S, Birdsall B, Bloxsidge J, Gibson CL, Jones JR, Feeney J. Biochem. J. 303 ( Pt 2) 401-405 (1994)
  259. Combinatorial library-based design with Basis Products. Zhou JZ, Shi S, Na J, Peng Z, Thacher T. J. Comput. Aided Mol. Des. 23 725-736 (2009)
  260. Envisioning the loop movements and rotation of the two subdomains of dihydrofolate reductase by elastic normal mode analysis. Luo J, Bruice TC. J. Biomol. Struct. Dyn. 27 245-258 (2009)
  261. Feed-forward neural networks for secondary structure prediction. Barlow TW. J Mol Graph 13 175-183 (1995)
  262. HYDRO: a program for protein hydropathy predictions. Vihinen M, Torkkila E. Comput Methods Programs Biomed 41 121-129 (1993)
  263. Mobility of the spin-labeled side chains of some novel antifolate inhibitors in their complexes with dihydrofolate reductase. Blakley RL, Piper JR, Maharaj G, Appleman JR, Delcamp TJ, Freisheim JH, Kulinski RF, Montgomery JA. Eur. J. Biochem. 196 271-280 (1991)
  264. Molecular structure matching by simulated annealing. II. An exploration of the evolution of configuration landscape problems. Barakat MT, Dean PM. J. Comput. Aided Mol. Des. 4 317-330 (1990)
  265. New antifolate 4,4'-diaminodiphenyl sulfone substituted 2,4-diamino-5-benzylpyrimidines. Proof of their dual mode of action and autosynergism. Wiese M, Schmalz D, Seydel JK. Arch. Pharm. (Weinheim) 329 161-168 (1996)
  266. Novel mechanism-based substrates of dihydrofolate reductase and the thermodynamics of ligand binding: a comparison of theory and experiment for 8-methylpterin and 6,8-dimethylpterin. Cummins PL, Gready JE. Proteins 15 426-435 (1993)
  267. Orientation and structure-building role of the water molecules bound at the contact surface of the dihydrofolate reductase-methotrexate complex. Nagy P. J. Comput. Aided Mol. Des. 2 65-76 (1988)
  268. Photoaffinity analogues of methotrexate as folate antagonist binding probes. Freisheim JH, Ratnam M, Smith PL, Delcamp TJ, Price EM. Adv. Enzyme Regul. 27 15-29 (1988)
  269. Quantitative PET Reporter Gene Imaging with [11C]Trimethoprim. Sellmyer MA, Lee I, Hou C, Lieberman BP, Zeng C, Mankoff DA, Mach RH. Mol. Ther. 25 120-126 (2017)
  270. Reproduction of correct electrostatic field by charges and dipoles on a closed surface. Nakamura H. J Mol Graph 11 30-6, 43 (1993)
  271. Sequence perturbation analysis: addressing amino acid indices to elucidate the C-terminal role of Escherichia coli dihydrofolate reductase. Takahashi H, Yokota A, Takenawa T, Iwakura M. J. Biochem. 145 751-762 (2009)
  272. The folA gene from the Rickettsia endosymbiont of Ixodes pacificus encodes a functional dihydrofolate reductase enzyme. Bodnar JL, Fitch S, Rosati A, Zhong J. Ticks Tick Borne Dis 9 443-449 (2018)
  273. The use of an algorithmic method for small molecule superimpositions in the design of antiviral agents. Diana G, Jaeger EP, Peterson ML, Treasurywala AM. J. Comput. Aided Mol. Des. 7 325-335 (1993)
  274. A Two-Way Interaction between Methotrexate and the Gut Microbiota of Male Sprague-Dawley Rats. Letertre MPM, Munjoma N, Wolfer K, Pechlivanis A, McDonald JAK, Hardwick RN, Cherrington NJ, Coen M, Nicholson JK, Hoyles L, Swann JR, Wilson ID. J Proteome Res 19 3326-3339 (2020)
  275. A conserved SH3-like fold in diverse putative proteins tetramerizes into an oxidoreductase providing an antimicrobial resistance phenotype. Lemay-St-Denis C, Alejaldre L, Jemouai Z, Lafontaine K, St-Aubin M, Hitache K, Valikhani D, Weerasinghe NW, Létourneau M, Thibodeaux CJ, Doucet N, Baron C, Copp JN, Pelletier JN. Philos Trans R Soc Lond B Biol Sci 378 20220040 (2023)
  276. Light activates reduction of methotrexate by NADPH in the ternary complex with Escherichia coli dihydrofolate reductase. Chen YQ, Gulotta M, Cheung HT, Callender R. Photochem. Photobiol. 69 77-85 (1999)
  277. Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex. Narayanan SP, Maeno A, Wada Y, Tate S, Akasaka K. Biomol NMR Assign 10 125-129 (2016)
  278. Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens. Krucinska J, Lombardo MN, Erlandsen H, Estrada A, Si D, Viswanathan K, Wright DL. Commun Biol 5 459 (2022)
  279. Synthesis and efficient isolation procedure for gamma-linked fluorescein methotrexate. Whiteley JM, Webber S, Kerwar SS. Prep. Biochem. 16 143-154 (1986)


Related citations provided by authors (7)

  1. Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. II. Environment of Bound Nadph and Implications for Catalysis. Filman DJ, Bolin JT, Matthews DA, Kraut J J. Biol. Chem. 257 13663- (1982)
  2. Crystal Structure of Avian Dihydrofolate Reductase Containing Phenyltriazine and Nadph. Volz KW, Matthews DA, Alden RA, Freer ST, Hansch C, Kaufman BT, Kraut J J. Biol. Chem. 257 2528- (1982)
  3. Interpretation of Nuclear Magnetic Resonance Spectra for Lactobacillus Casei Dihydrofolate Reductase Based on the X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex. Matthews DA Biochemistry 18 1602- (1979)
  4. Dihydrofolate Reductase from Lactobacillus Casei. Stereochemistry of Nadph Binding. Matthews DA, Alden RA, Freer ST, Xuong N-H, Kraut J J. Biol. Chem. 254 4144- (1979)
  5. Dihydrofolate Reductase from Lactobacillus Casei. X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex. Matthews DA, Alden RA, Bolin JT, Filman DJ, Freer ST, Hamlin R, Hol WGJ, Kisliuk RL, Pastore EJ, Plante LT, Xuong N-H, Kraut J J. Biol. Chem. 253 6946- (1978)
  6. Dihydrofolate Reductase. X-Ray Structure of the Binary Complex with Methotrexate. Matthews DA, Alden RA, Bolin JT, Freer ST, Hamlin R, Xuong N, Kraut J, Poe M, Williams M, Hoogsteen K Science 197 452- (1977)
  7. Properties of Thymidylate Synthetase from Dichloromethotrexate-Resistant Lactobacillus Casei. Crusberg TC, Leary R, Kisliuk RL J. Biol. Chem. 245 5292- (1970)

Quick links