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Automated identification of functional dynamic contact networks from X-ray crystallography.

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van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS
OpenAccess logo Nat Methods 10 896-902 (2013)
Related entries: 4kjk, 4kjl

Cited: 83 times
EuropePMC logo PMID: 23913260

Abstract

Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of independently determined X-ray crystal structures, can provide mechanistic insights into conformational dynamics. Here we report a new algorithm, CONTACT, that identifies contact networks of conformationally heterogeneous residues directly from high-resolution X-ray crystallography data. Contact networks determined for Escherichia coli dihydrofolate reductase (ecDHFR) predict the observed long-range pattern of NMR chemical shift perturbations of an allosteric mutation. A comparison of contact networks in wild-type and mutant ecDHFR suggests that mutations that alter optimized contact networks of coordinated motions can impair catalytic function. CONTACT-guided mutagenesis can exploit the structure-dynamics-function relationship in protein engineering and design.

Articles - 4kjj mentioned but not cited (5)

  1. Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR. Fenwick RB, van den Bedem H, Fraser JS, Wright PE. Proc Natl Acad Sci U S A 111 E445-54 (2014)
  2. Automated identification of functional dynamic contact networks from X-ray crystallography. van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS. Nat Methods 10 896-902 (2013)
  3. Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR. Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS. Structure 22 899-910 (2014)
  4. Autonomous aggregation suppression by acidic residues explains why chaperones favour basic residues. Houben B, Michiels E, Ramakers M, Konstantoulea K, Louros N, Verniers J, van der Kant R, De Vleeschouwer M, Chicória N, Vanpoucke T, Gallardo R, Schymkowitz J, Rousseau F. EMBO J 39 e102864 (2020)
  5. A single-domain protein catenane of dihydrofolate reductase. Fang J, Li T, Lee J, Im D, Xu L, Liu Y, Seo J, Zhang WB. Natl Sci Rev 10 nwad304 (2023)


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  1. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. PLoS Comput Biol 12 e1004619 (2016)
  2. Keep on moving: discovering and perturbing the conformational dynamics of enzymes. Bhabha G, Biel JT, Fraser JS. Acc Chem Res 48 423-430 (2015)
  3. X-ray Scattering Studies of Protein Structural Dynamics. Meisburger SP, Thomas WC, Watkins MB, Ando N. Chem Rev 117 7615-7672 (2017)
  4. Biophysical and computational methods to analyze amino acid interaction networks in proteins. O'Rourke KF, Gorman SD, Boehr DD. Comput Struct Biotechnol J 14 245-251 (2016)
  5. E pluribus unum, no more: from one crystal, many conformations. Woldeyes RA, Sivak DA, Fraser JS. Curr Opin Struct Biol 28 56-62 (2014)
  6. From local to global changes in proteins: a network view. Vuillon L, Lesieur C. Curr Opin Struct Biol 31 1-8 (2015)
  7. Engineered control of enzyme structural dynamics and function. Boehr DD, D'Amico RN, O'Rourke KF. Protein Sci 27 825-838 (2018)
  8. Hybrid methods for macromolecular structure determination: experiment with expectations. Schröder GF. Curr Opin Struct Biol 31 20-27 (2015)
  9. Designing disorder: Tales of the unexpected tails. Minde DP, Halff EF, Tans S. Intrinsically Disord Proteins 1 e26790 (2013)
  10. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Chem Rev 122 12046-12109 (2022)
  11. Functional roles of enzyme dynamics in accelerating active site chemistry: Emerging techniques and changing concepts. Gao S, Klinman JP. Curr Opin Struct Biol 75 102434 (2022)
  12. Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light. Wilson MA. Annu Rev Biophys 51 79-98 (2022)
  13. A Minireview on Temperature Dependent Protein Conformational Sampling. Dong M. Protein J 40 545-553 (2021)
  14. Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics. Hekstra DR. Annu Rev Biophys 52 255-274 (2023)

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  1. The role of protein dynamics in the evolution of new enzyme function. Campbell E, Kaltenbach M, Correy GJ, Carr PD, Porebski BT, Livingstone EK, Afriat-Jurnou L, Buckle AM, Weik M, Hollfelder F, Tokuriki N, Jackson CJ. Nat Chem Biol 12 944-950 (2016)
  2. Structural basis for binding of human IgG1 to its high-affinity human receptor FcγRI. Kiyoshi M, Caaveiro JM, Kawai T, Tashiro S, Ide T, Asaoka Y, Hatayama K, Tsumoto K. Nat Commun 6 6866 (2015)
  3. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS. Elife 4 e07574 (2015)
  4. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. Elife 7 e36307 (2018)
  5. Rescue of conformational dynamics in enzyme catalysis by directed evolution. Otten R, Liu L, Kenner LR, Clarkson MW, Mavor D, Tawfik DS, Kern D, Fraser JS. Nat Commun 9 1314 (2018)
  6. De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy. Polizzi NF, Wu Y, Lemmin T, Maxwell AM, Zhang SQ, Rawson J, Beratan DN, Therien MJ, DeGrado WF. Nat Chem 9 1157-1164 (2017)
  7. Entropy redistribution controls allostery in a metalloregulatory protein. Capdevila DA, Braymer JJ, Edmonds KA, Wu H, Giedroc DP. Proc Natl Acad Sci U S A 114 4424-4429 (2017)
  8. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. Keedy DA, Fraser JS, van den Bedem H. PLoS Comput Biol 11 e1004507 (2015)
  9. Protein structural ensembles are revealed by redefining X-ray electron density noise. Lang PT, Holton JM, Fraser JS, Alber T. Proc Natl Acad Sci U S A 111 237-242 (2014)
  10. Correlated motions are a fundamental property of β-sheets. Fenwick RB, Orellana L, Esteban-Martín S, Orozco M, Salvatella X. Nat Commun 5 4070 (2014)
  11. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Fischer M, Shoichet BK, Fraser JS. Chembiochem 16 1560-1564 (2015)
  12. A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. Herzik MA, Fraser JS, Lander GC. Structure 27 344-358.e3 (2019)
  13. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Thompson MC, Barad BA, Wolff AM, Sun Cho H, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS. Nat Chem 11 1058-1066 (2019)
  14. Hidden electrostatic basis of dynamic allostery in a PDZ domain. Kumawat A, Chakrabarty S. Proc Natl Acad Sci U S A 114 E5825-E5834 (2017)
  15. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice. Janowski PA, Liu C, Deckman J, Case DA. Protein Sci 25 87-102 (2016)
  16. An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass. Salamanca Viloria J, Allega MF, Lambrughi M, Papaleo E. Sci Rep 7 2838 (2017)
  17. Networks of Dynamic Allostery Regulate Enzyme Function. Holliday MJ, Camilloni C, Armstrong GS, Vendruscolo M, Eisenmesser EZ. Structure 25 276-286 (2017)
  18. Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins. Sfriso P, Duran-Frigola M, Mosca R, Emperador A, Aloy P, Orozco M. Structure 24 116-126 (2016)
  19. Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase. Ruiz-Pernia JJ, Luk LY, García-Meseguer R, Martí S, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. J Am Chem Soc 135 18689-18696 (2013)
  20. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC. Proc Natl Acad Sci U S A 111 17887-17892 (2014)
  21. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity. Papaleo E. Front Mol Biosci 2 28 (2015)
  22. Protein motions and dynamic effects in enzyme catalysis. Luk LY, Loveridge EJ, Allemann RK. Phys Chem Chem Phys 17 30817-30827 (2015)
  23. Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis. Dasgupta M, Budday D, de Oliveira SHP, Madzelan P, Marchany-Rivera D, Seravalli J, Hayes B, Sierra RG, Boutet S, Hunter MS, Alonso-Mori R, Batyuk A, Wierman J, Lyubimov A, Brewster AS, Sauter NK, Applegate GA, Tiwari VK, Berkowitz DB, Thompson MC, Cohen AE, Fraser JS, Wall ME, van den Bedem H, Wilson MA. Proc Natl Acad Sci U S A 116 25634-25640 (2019)
  24. Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. Deis LN, Pemble CW, Qi Y, Hagarman A, Richardson DC, Richardson JS, Oas TG. Structure 22 1467-1477 (2014)
  25. qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Riley BT, Wankowicz SA, de Oliveira SHP, van Zundert GCP, Hogan DW, Fraser JS, Keedy DA, van den Bedem H. Protein Sci 30 270-285 (2021)
  26. Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10. Rujas E, Gulzar N, Morante K, Tsumoto K, Scott JK, Nieva JL, Caaveiro JM. J Virol 89 11975-11989 (2015)
  27. Temperature artifacts in protein structures bias ligand-binding predictions. Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. Chem Sci 12 11275-11293 (2021)
  28. Characterizing RNA ensembles from NMR data with kinematic models. Fonseca R, Pachov DV, Bernauer J, van den Bedem H. Nucleic Acids Res 42 9562-9572 (2014)
  29. Congress Diffuse X-ray scattering to model protein motions. Wall ME, Adams PD, Fraser JS, Sauter NK. Structure 22 182-184 (2014)
  30. Ligand-Binding-Site Structure Shapes Allosteric Signal Transduction and the Evolution of Allostery in Protein Complexes. Abrusán G, Marsh JA. Mol Biol Evol 36 1711-1727 (2019)
  31. Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin. Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS. Structure 25 739-749.e3 (2017)
  32. A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E2 synthase. Brock JS, Hamberg M, Balagunaseelan N, Goodman M, Morgenstern R, Strandback E, Samuelsson B, Rinaldo-Matthis A, Haeggström JZ. Proc Natl Acad Sci U S A 113 972-977 (2016)
  33. Identifying coupled clusters of allostery participants through chemical shift perturbations. Xu Y, Zhang D, Rogawski R, Nimigean CM, McDermott AE. Proc Natl Acad Sci U S A 116 2078-2085 (2019)
  34. Measuring and modeling diffuse scattering in protein X-ray crystallography. Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME. Proc Natl Acad Sci U S A 113 4069-4074 (2016)
  35. Severing of a hydrogen bond disrupts amino acid networks in the catalytically active state of the alpha subunit of tryptophan synthase. Axe JM, O'Rourke KF, Kerstetter NE, Yezdimer EM, Chan YM, Chasin A, Boehr DD. Protein Sci 24 484-494 (2015)
  36. Mapping the Accessible Conformational Landscape of an Insect Carboxylesterase Using Conformational Ensemble Analysis and Kinetic Crystallography. Correy GJ, Carr PD, Meirelles T, Mabbitt PD, Fraser NJ, Weik M, Jackson CJ. Structure 24 977-987 (2016)
  37. Elucidation of potential sites for antibody engineering by fluctuation editing. Yanaka S, Moriwaki Y, Tsumoto K, Sugase K. Sci Rep 7 9597 (2017)
  38. Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. van den Bedem H, Wilson MA. J Synchrotron Radiat 26 958-966 (2019)
  39. Hydrostatic Pressure Studies Distinguish Global from Local Protein Motions in C-H Activation by Soybean Lipoxygenase-1. Hu S, Cattin-Ortolá J, Munos JW, Klinman JP. Angew Chem Int Ed Engl 55 9361-9364 (2016)
  40. Multi-probe relaxation dispersion measurements increase sensitivity to protein dynamics. Fenwick RB, Oyen D, Wright PE. Phys Chem Chem Phys 18 5789-5798 (2016)
  41. Structural and dynamical description of the enzymatic reaction of a phosphohexomutase. Stiers KM, Graham AC, Zhu JS, Jakeman DL, Nix JC, Beamer LJ. Struct Dyn 6 024703 (2019)
  42. Room-temperature serial synchrotron crystallography of the human phosphatase PTP1B. Sharma S, Ebrahim A, Keedy DA. Acta Crystallogr F Struct Biol Commun 79 23-30 (2023)
  43. Comment Visualizing networks of mobility in proteins. Wilson MA. Nat Methods 10 835-837 (2013)
  44. Enzyme activity and structural features of three single-domain phloem cyclophilins from Brassica napus. Hanhart P, Falke S, Garbe M, Rose V, Thieß M, Betzel C, Kehr J. Sci Rep 9 9368 (2019)
  45. Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase. Zaragoza JPT, Offenbacher AR, Hu S, Gee CL, Firestein ZM, Minnetian N, Deng Z, Fan F, Iavarone AT, Klinman JP. Proc Natl Acad Sci U S A 120 e2211630120 (2023)
  46. Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Shanmuganatham KK, Wallace RS, Ting-I Lee A, Plapp BV. Protein Sci 27 750-768 (2018)
  47. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Thorne RE. Acta Crystallogr D Struct Biol 79 78-94 (2023)
  48. Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion. Fenwick RB, Oyen D, van den Bedem H, Dyson HJ, Wright PE. Biophys J 120 296-305 (2021)
  49. The Sampling of Conformational Dynamics in Ambient-Temperature Crystal Structures of Arginine Kinase. Godsey MH, Davulcu O, Nix JC, Skalicky JJ, Brüschweiler RP, Chapman MS. Structure 24 1658-1667 (2016)
  50. Allosteric regulatory control in dihydrofolate reductase is revealed by dynamic asymmetry. Kazan IC, Mills JH, Ozkan SB. Protein Sci 32 e4700 (2023)
  51. Frustration-guided motion planning reveals conformational transitions in proteins. Budday D, Fonseca R, Leyendecker S, van den Bedem H. Proteins 85 1795-1807 (2017)
  52. Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs. Pachov DV, van den Bedem H. PLoS Comput Biol 11 e1004361 (2015)
  53. Role of Active Site Loop Dynamics in Mediating Ligand Release from E. coli Dihydrofolate Reductase. Singh A, Fenwick RB, Dyson HJ, Wright PE. Biochemistry 60 2663-2671 (2021)
  54. Simple approach for ranking structure determining residues. Luna-Martínez OD, Vidal-Limón A, Villalba-Velázquez MI, Sánchez-Alcalá R, Garduño-Juárez R, Uversky VN, Becerril B. PeerJ 4 e2136 (2016)
  55. Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces. Fonseca R, Budday D, van den Bedem H. J Comput Chem 39 711-720 (2018)
  56. Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A. Konovalov KA, Wu CG, Qiu Y, Balakrishnan VK, Parihar PS, O'Connor MS, Xing Y, Huang X. J Chem Phys 158 215101 (2023)
  57. Hidden electrostatic energy contributions define dynamic allosteric communications within p53 during molecular recognition. Bhattacharjee S, Sengupta J. Biophys J 120 4512-4524 (2021)
  58. High-resolution double vision of the allosteric phosphatase PTP1B. Sharma S, Skaist Mehlman T, Sagabala RS, Boivin B, Keedy DA. Acta Crystallogr F Struct Biol Commun 80 1-12 (2024)
  59. Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins. Soltan Ghoraie L, Burkowski F, Zhu M. Proteins 83 497-516 (2015)
  60. Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin. Pitard I, Monet D, Goossens PL, Blondel A, Malliavin TE. Front Mol Biosci 7 586544 (2020)
  61. Angular Mapping of Protein Structure Using Nonlinear Optical Measurements. Clancy B, Moree B, Salafsky J. Biophys J 117 500-508 (2019)
  62. Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study. Vu QV, Nissley DA, Jiang Y, O'Brien EP, Li MS. J Phys Chem B 127 4761-4774 (2023)
  63. Uncovering the role of the flexible C-terminal tail: A model study with Strep-tagged GFP. Lassalle MW, Kondou S. Biochim Open 2 1-8 (2016)
  64. Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins. Soltan Ghoraie L, Burkowski F, Zhu M. Bioinformatics 31 i124-32 (2015)


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