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The role of water in sequence-independent ligand binding by an oligopeptide transporter protein.

Tame JR, Sleigh SH, Wilkinson AJ, Ladbury JE
Nat Struct Biol 3 998-1001 (1996)
Related entries: 1jet, 1jev

Cited: 76 times
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Articles - 1jeu mentioned but not cited (10)

  1. Assessment of programs for ligand binding affinity prediction. Kim R, Skolnick J. J Comput Chem 29 1316-1331 (2008)
  2. Development of quantitative structure-binding affinity relationship models based on novel geometrical chemical descriptors of the protein-ligand interfaces. Zhang S, Golbraikh A, Tropsha A. J Med Chem 49 2713-2724 (2006)
  3. Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction. Su Y, Zhou A, Xia X, Li W, Sun Z. Protein Sci 18 2550-2558 (2009)
  4. Dowser++, a new method of hydrating protein structures. Morozenko A, Stuchebrukhov AA. Proteins 84 1347-1357 (2016)
  5. Compensating stereochemical changes allow murein tripeptide to be accommodated in a conventional peptide-binding protein. Maqbool A, Levdikov VM, Blagova EV, Hervé M, Horler RS, Wilkinson AJ, Thomas GH. J Biol Chem 286 31512-31521 (2011)
  6. Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin. Sridhar A, Ross GA, Biggin PC. PLoS One 12 e0172743 (2017)
  7. Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations. Ben-Shalom IY, Lin Z, Radak BK, Lin C, Sherman W, Gilson MK. J Chem Theory Comput 16 7883-7894 (2020)
  8. Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations. Fogolari F, Corazza A, Fortuna S, Soler MA, VanSchouwen B, Brancolini G, Corni S, Melacini G, Esposito G. PLoS One 10 e0132356 (2015)
  9. Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method. Sherman DB, Zhang S, Pitner JB, Tropsha A. Proteins 56 828-838 (2004)
  10. Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization. Aronica PGA, Fox SJ, Verma CS. ACS Omega 3 4664-4673 (2018)


Reviews citing this publication (8)

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  3. Thermodynamics of drug-DNA interactions. Haq I. Arch Biochem Biophys 403 1-15 (2002)
  4. Searching for specificity in SH domains. Ladbury JE, Arold S. Chem Biol 7 R3-8 (2000)
  5. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Spyrakis F, Cavasotto CN. Arch Biochem Biophys 583 105-119 (2015)
  6. Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges. Ahmad E, Rabbani G, Zaidi N, Khan MA, Qadeer A, Ishtikhar M, Singh S, Khan RH. J Biomol Struct Dyn 31 630-648 (2013)
  7. Messages from ultrahigh resolution crystal structures. Longhi S, Czjzek M, Cambillau C. Curr Opin Struct Biol 8 730-737 (1998)
  8. Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains. Zafra-Ruano A, Luque I. FEBS Lett 586 2619-2630 (2012)

Articles citing this publication (58)

  1. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Proc Natl Acad Sci U S A 108 E1293-301 (2011)
  2. Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2. Newstead S, Drew D, Cameron AD, Postis VL, Xia X, Fowler PW, Ingram JC, Carpenter EP, Sansom MS, McPherson MJ, Baldwin SA, Iwata S. EMBO J 30 417-426 (2011)
  3. Solvated docking: introducing water into the modelling of biomolecular complexes. van Dijk AD, Bonvin AM. Bioinformatics 22 2340-2347 (2006)
  4. The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement. Tyrrell R, Verschueren KH, Dodson EJ, Murshudov GN, Addy C, Wilkinson AJ. Structure 5 1017-1032 (1997)
  5. Adhesive water networks facilitate binding of protein interfaces. Ahmad M, Gu W, Geyer T, Helms V. Nat Commun 2 261 (2011)
  6. Heat capacity effects of water molecules and ions at a protein-DNA interface. Bergqvist S, Williams MA, O'Brien R, Ladbury JE. J Mol Biol 336 829-842 (2004)
  7. Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes. Schiebel J, Gaspari R, Wulsdorf T, Ngo K, Sohn C, Schrader TE, Cavalli A, Ostermann A, Heine A, Klebe G. Nat Commun 9 3559 (2018)
  8. The structural basis for peptide selection by the transport receptor OppA. Berntsson RP, Doeven MK, Fusetti F, Duurkens RH, Sengupta D, Marrink SJ, Thunnissen AM, Poolman B, Slotboom DJ. EMBO J 28 1332-1340 (2009)
  9. Utilising structural knowledge in drug design strategies: applications using Relibase. Günther J, Bergner A, Hendlich M, Klebe G. J Mol Biol 326 621-636 (2003)
  10. Molecular determinants for substrate specificity of the ligand-binding protein OpuAC from Bacillus subtilis for the compatible solutes glycine betaine and proline betaine. Horn C, Sohn-Bösser L, Breed J, Welte W, Schmitt L, Bremer E. J Mol Biol 357 592-606 (2006)
  11. Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope. Covell DG, Wallqvist A. J Mol Biol 269 281-297 (1997)
  12. Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules. Amadasi A, Spyrakis F, Cozzini P, Abraham DJ, Kellogg GE, Mozzarelli A. J Mol Biol 358 289-309 (2006)
  13. Methyl, ethyl, propyl, butyl: futile but not for water, as the correlation of structure and thermodynamic signature shows in a congeneric series of thermolysin inhibitors. Krimmer SG, Betz M, Heine A, Klebe G. ChemMedChem 9 833-846 (2014)
  14. The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction. Yokota A, Tsumoto K, Shiroishi M, Kondo H, Kumagai I. J Biol Chem 278 5410-5418 (2003)
  15. Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins. Clifton BE, Jackson CJ. Cell Chem Biol 23 236-245 (2016)
  16. Scoring functions: a view from the bench. Tame JR. J Comput Aided Mol Des 13 99-108 (1999)
  17. Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Davies TG, Hubbard RE, Tame JR. Protein Sci 8 1432-1444 (1999)
  18. Mass spectrometric and thermodynamic studies reveal the role of water molecules in complexes formed between SH2 domains and tyrosyl phosphopeptides. Chung E, Henriques D, Renzoni D, Zvelebil M, Bradshaw JM, Waksman G, Robinson CV, Ladbury JE. Structure 6 1141-1151 (1998)
  19. Modeling the hydration layer around proteins: HyPred. Virtanen JJ, Makowski L, Sosnick TR, Freed KF. Biophys J 99 1611-1619 (2010)
  20. Multispecific Substrate Recognition in a Proton-Dependent Oligopeptide Transporter. Martinez Molledo M, Quistgaard EM, Flayhan A, Pieprzyk J, Löw C. Structure 26 467-476.e4 (2018)
  21. On the binding mechanism of the peptide receptor of the oligopeptide transport system of Lactococcus lactis. Lanfermeijer FC, Detmers FJ, Konings WN, Poolman B. EMBO J 19 3649-3656 (2000)
  22. A new functional domain of guanine nucleotide dissociation inhibitor (alpha-GDI) involved in Rab recycling. Luan P, Heine A, Zeng K, Moyer B, Greasely SE, Kuhn P, Balch WE, Wilson IA. Traffic 1 270-281 (2000)
  23. Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8. Sakai H, Wang H, Takemoto-Hori C, Kaminishi T, Yamaguchi H, Kamewari Y, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S. J Struct Biol 149 99-110 (2005)
  24. Specificity and interactions of the protein OppA: partitioning solvent binding effects using mass spectrometry. Rostom AA, Tame JR, Ladbury JE, Robinson CV. J Mol Biol 296 269-279 (2000)
  25. Systematic placement of structural water molecules for improved scoring of protein-ligand interactions. Huggins DJ, Tidor B. Protein Eng Des Sel 24 777-789 (2011)
  26. Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses. Tian F, Yang L, Lv F, Luo X, Pan Y. Amino Acids 40 493-503 (2011)
  27. Specificity mutants of the binding protein of the oligopeptide transport system of Lactococcus lactis. Picon A, Kunji ER, Lanfermeijer FC, Konings WN, Poolman B. J Bacteriol 182 1600-1608 (2000)
  28. Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo. Aldeghi M, Ross GA, Bodkin MJ, Essex JW, Knapp S, Biggin PC. Commun Chem 1 19 (2018)
  29. Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks. Rudling A, Orro A, Carlsson J. J Chem Inf Model 58 350-361 (2018)
  30. A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens. El Sahili A, Li SZ, Lang J, Virus C, Planamente S, Ahmar M, Guimaraes BG, Aumont-Nicaise M, Vigouroux A, Soulère L, Reader J, Queneau Y, Faure D, Moréra S. PLoS Pathog 11 e1005071 (2015)
  31. A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling. Arun Prasad P, Gautham N. J Comput Aided Mol Des 22 815-829 (2008)
  32. Structural basis for recognition of dipeptides by peptide transporters. Payne JW, Grail BM, Gupta S, Ladbury JE, Marshall NJ, O'Brien R, Payne GM. Arch Biochem Biophys 384 9-23 (2000)
  33. Thermodynamics of peptide binding to the transporter associated with antigen processing (TAP). Neumann L, Abele R, Tampé R. J Mol Biol 324 965-973 (2002)
  34. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A. Maurer M, de Beer SB, Oostenbrink C. Molecules 21 499 (2016)
  35. Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex. García-Sosa AT, Mancera RL. Mol Inform 29 589-600 (2010)
  36. Specificity of the second binding protein of the peptide ABC-transporter (Dpp) of Lactococcus lactis IL1403. Sanz Y, Toldrá F, Renault P, Poolman B. FEMS Microbiol Lett 227 33-38 (2003)
  37. Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold. Cuneo MJ, Beese LS, Hellinga HW. J Biol Chem 284 33217-33223 (2009)
  38. Inhibitors to the Src SH2 domain: a lesson in structure--thermodynamic correlation in drug design. Henriques DA, Ladbury JE. Arch Biochem Biophys 390 158-168 (2001)
  39. Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation. Huggins DJ, McKenzie GJ, Robinson DD, Narváez AJ, Hardwick B, Roberts-Thomson M, Venkitaraman AR, Grant GH, Payne MC. PLoS Comput Biol 6 e1000880 (2010)
  40. Discovery and structure of a widespread bacterial ABC transporter specific for ergothioneine. Zhang Y, Gonzalez-Gutierrez G, Legg KA, Walsh BJC, Pis Diez CM, Edmonds KA, Giedroc DP. Nat Commun 13 7586 (2022)
  41. Development of a QSAR model for binding of tripeptides and tripeptidomimetics to the human intestinal di-/tripeptide transporter hPEPT1. Andersen R, Jørgensen FS, Olsen L, Våbenø J, Thorn K, Nielsen CU, Steffansen B. Pharm Res 23 483-492 (2006)
  42. Structural and thermodynamic basis for the interaction of the Src SH2 domain with the activated form of the PDGF beta-receptor. Lubman OY, Waksman G. J Mol Biol 328 655-668 (2003)
  43. Desolvation of the substrate-binding protein TauA dictates ligand specificity for the alkanesulfonate ABC importer TauABC. Qu F, ElOmari K, Wagner A, De Simone A, Beis K. Biochem J 476 3649-3660 (2019)
  44. Hydration effects on the efficacy of the Epidermal growth factor receptor kinase inhibitor afatinib. Kannan S, Pradhan MR, Tiwari G, Tan WC, Chowbay B, Tan EH, Tan DS, Verma C. Sci Rep 7 1540 (2017)
  45. Computational analysis of BACE1-ligand complex crystal structures and linear discriminant analysis for identification of BACE1 inhibitors with anti P-glycoprotein binding property. Manoharan P, Chennoju K, Ghoshal N. J Biomol Struct Dyn 36 262-276 (2018)
  46. Influence of Glu-376 --> Gln mutation on enthalpy and heat capacity changes for the binding of slightly altered ligands to medium chain acyl-CoA dehydrogenase. Peterson KM, Gopalan KV, Nandy A, Srivastava DK. Protein Sci 10 1822-1834 (2001)
  47. Target specific proteochemometric model development for BACE1 - protein flexibility and structural water are critical in virtual screening. Manoharan P, Chennoju K, Ghoshal N. Mol Biosyst 11 1955-1972 (2015)
  48. Charges, hydrogen bonds, and correlated motions in the 1 A resolution refined structure of the mating pheromone Er-1 from Euplotes raikovi. Anderson DH, Weiss MS, Eisenberg D. J Mol Biol 273 479-500 (1997)
  49. Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913. Li CY, Chen XL, Qin QL, Wang P, Zhang WX, Xie BB, Su HN, Zhang XY, Zhou BC, Zhang YZ. J Bacteriol 197 1125-1134 (2015)
  50. Study of intermolecular contacts in the proline-rich homeodomain (PRH)-DNA complex using molecular dynamics simulations. Jalili S, Karami L. Eur Biophys J 41 329-340 (2012)
  51. Bridging solvent molecules mediate RNase A - Ligand binding. Ivanov SM, Dimitrov I, Doytchinova IA. PLoS One 14 e0224271 (2019)
  52. Protonation linked equilibria and apparent affinity constants: the thermodynamic profile of the alpha-chymotrypsin-proflavin interaction. Bruylants G, Wintjens R, Looze Y, Redfield C, Bartik K. Eur Biophys J 37 11-18 (2007)
  53. Crystal Structure of the SH3 Domain of ASAP1 in Complex with the Proline Rich Motif (PRM) of MICAL1 Reveals a Unique SH3/PRM Interaction Mode. Jia X, Lin L, Xu S, Li L, Wei Z, Yu C, Niu F. Int J Mol Sci 24 1414 (2023)
  54. Structural and energetic hot-spots for the interaction between a ladder-like polycyclic ether and the anti-ciguatoxin antibody 10C9Fab. Ui M, Tanaka Y, Tsumuraya T, Fujii I, Inoue M, Hirama M, Tsumoto K. Mol Biosyst 7 793-798 (2011)
  55. Insight of endo-1,4-xylanase II from Trichoderma reesei: conserved water-mediated H-bond and ion pairs interactions. Vijayakumar B, Velmurugan D. Protein J 32 649-656 (2013)
  56. Predominant torsional forms adopted by oligopeptide conformers in solution: parameters for molecular recognition. Marshall NJ, Grail BM, Payne JW. J Pept Sci 7 175-189 (2001)
  57. Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes. Kariyawasam NL, Ploetz EA, Swint-Kruse L, Smith PE. Biophys Chem 304 107126 (2024)
  58. pH- and Temperature-Dependent Peptide Binding to the Lactococcus lactis Oligopeptide-Binding Protein A Measured with a Fluorescence Anisotropy Assay. Norcross S, Sunderraj A, Tantama M. ACS Omega 4 2812-2822 (2019)


Related citations provided by authors (3)

  1. The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands. Tame JR, Dodson EJ, Murshudov G, Higgins CF, Wilkinson AJ Structure 3 1395- (1995)
  2. Structure Determination of Oppa at 2.3 Angstroms Resolution Using Multiple Wavelength Anomalous Methods. Glover ID, Denny R, Nguti ND, Mcsweeney S, Thompson A, Dodson E, Wilkinson AJ, Tame JRH Acta Crystallogr. D Biol. Crystallogr. 51 39- (1995)
  3. The Structural Basis of Sequence-Independent Peptide Binding by Oppa Protein. Tame JR, Murshudov GN, Dodson EJ, Neil TK, Dodson GG, Higgins CF, Wilkinson AJ Science 264 1578- (1994)

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