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Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme.

Zhang XJ, Matthews BW
Protein Sci 3 1031-9 (1994)
Related entries: 149l, 150l, 152l

Cited: 64 times
EuropePMC logo PMID: 7920248

Abstract

Solvent-binding sites were compared in 10 different crystal forms of phage T4 lysozyme that were refined using data from 2.6 A to 1.7 A resolution. The sample included 18 crystallographically independent lysozyme molecules. Despite different crystallization conditions, variable crystal contacts, changes due to mutation, and varying attention to solvent during crystallographic refinement, 62% of the 20 most frequently occupied sites were conserved. Allowing for potential steric interference from neighboring molecules in the crystal lattice, this fraction increased to 79% of the sites. There was, however, no solvent-binding site that was occupied in all 18 lysozyme molecules. A buried double site was occupied in 17 instances and 2 other internal sites were occupied 15 times. Apart from these buried sites, the most frequently occupied sites were often at the amino-termini of alpha-helices. Solvent molecules at the most conserved sites tended to have crystallographic thermal factors lower than average, but atoms with low B-factors were not restricted to these sites. Although superficial inspection may suggest that only 50-60% (or less) of solvent-binding sites are conserved in different crystal forms of a protein, it appears that many sites appear to be empty either because of steric interference or because the apparent occupancy of a given site can vary from crystal to crystal. The X-ray method of identifying sites is somewhat subjective and tends to result in specification only of those solvent molecules that are well ordered and bound with high occupancy, even though there is clear evidence for solvent bound at many additional sites.(ABSTRACT TRUNCATED AT 250 WORDS)

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  2. Longitudinal study of circulating protein biomarkers in inflammatory bowel disease. Viennois E, Baker MT, Xiao B, Wang L, Laroui H, Merlin D. J Proteomics 112 166-179 (2015)
  3. Palmitoylation restricts SQSTM1/p62-mediated autophagic degradation of NOD2 to modulate inflammation. Zhou L, He X, Wang L, Wei P, Cai Z, Zhang S, Jin S, Zeng H, Cui J. Cell Death Differ 29 1541-1551 (2022)
  4. New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium. Michalska K, Brown RN, Li H, Jedrzejczak R, Niemann GS, Heffron F, Cort JR, Adkins JN, Babnigg G, Joachimiak A. J Struct Funct Genomics 14 1-10 (2013)
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Reviews citing this publication (6)

  1. Locating and characterizing binding sites on proteins. Mattos C, Ringe D. Nat Biotechnol 14 595-599 (1996)
  2. Protein-water interactions in a dynamic world. Mattos C. Trends Biochem Sci 27 203-208 (2002)
  3. What makes a binding site a binding site? Ringe D. Curr Opin Struct Biol 5 825-829 (1995)
  4. Analysis of the binding surfaces of proteins. Ringe D, Mattos C. Med Res Rev 19 321-331 (1999)
  5. Evidence on close packing and cavities in proteins. Hubbard SJ, Argos P. Curr Opin Biotechnol 6 375-381 (1995)
  6. Biophysical highlights from 54 years of macromolecular crystallography. Richardson JS, Richardson DC. Biophys J 106 510-525 (2014)

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  1. Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Prabu-Jeyabalan M, Nalivaika E, Schiffer CA. Structure 10 369-381 (2002)
  2. Hydrogen bonding stabilizes globular proteins. Myers JK, Pace CN. Biophys J 71 2033-2039 (1996)
  3. Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data. de Groot BL, Hayward S, van Aalten DM, Amadei A, Berendsen HJ. Proteins 31 116-127 (1998)
  4. Solvated docking: introducing water into the modelling of biomolecular complexes. van Dijk AD, Bonvin AM. Bioinformatics 22 2340-2347 (2006)
  5. Hydration and DNA recognition by homeodomains. Billeter M, Güntert P, Luginbühl P, Wüthrich K. Cell 85 1057-1065 (1996)
  6. Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease. Robinson CR, Sligar SG. Proc Natl Acad Sci U S A 95 2186-2191 (1998)
  7. 3dSS: 3D structural superposition. Sumathi K, Ananthalakshmi P, Roshan MN, Sekar K. Nucleic Acids Res 34 W128-32 (2006)
  8. WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes. García-Sosa AT, Mancera RL, Dean PM. J Mol Model 9 172-182 (2003)
  9. Thermal stability determinants of chicken egg-white lysozyme core mutants: hydrophobicity, packing volume, and conserved buried water molecules. Shih P, Holland DR, Kirsch JF. Protein Sci 4 2050-2062 (1995)
  10. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity. Sanschagrin PC, Kuhn LA. Protein Sci 7 2054-2064 (1998)
  11. Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins. Poornima CS, Dean PM. J Comput Aided Mol Des 9 521-531 (1995)
  12. Atomic and residue hydrophilicity in the context of folded protein structures. Kuhn LA, Swanson CA, Pique ME, Tainer JA, Getzoff ED. Proteins 23 536-547 (1995)
  13. Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to generate conformational transition pathway. Harada R, Kitao A. J Chem Phys 139 035103 (2013)
  14. Accounting for water molecules in drug design. Wong SE, Lightstone FC. Expert Opin Drug Discov 6 65-74 (2011)
  15. Conservation of water molecules in an antibody-antigen interaction. Braden BC, Fields BA, Poljak RJ. J Mol Recognit 8 317-325 (1995)
  16. Modeling the hydration layer around proteins: HyPred. Virtanen JJ, Makowski L, Sosnick TR, Freed KF. Biophys J 99 1611-1619 (2010)
  17. Structural and thermodynamic characterization of T4 lysozyme mutants and the contribution of internal cavities to pressure denaturation. Ando N, Barstow B, Baase WA, Fields A, Matthews BW, Gruner SM. Biochemistry 47 11097-11109 (2008)
  18. Conserved water molecules in a large family of microbial ribonucleases. Loris R, Langhorst U, De Vos S, Decanniere K, Bouckaert J, Maes D, Transue TR, Steyaert J. Proteins 36 117-134 (1999)
  19. Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins. Damjanović A, Schlessman JL, Fitch CA, García AE, García-Moreno E B. Biophys J 93 2791-2804 (2007)
  20. Solvent structure at a hydrophobic protein surface. Kovacs H, Mark AE, van Gunsteren WF. Proteins 27 395-404 (1997)
  21. A "structural" water molecule in the family of fatty acid binding proteins. Likić VA, Juranić N, Macura S, Prendergast FG. Protein Sci 9 497-504 (2000)
  22. 'Crystal lattice engineering,' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines. Yamada H, Tamada T, Kosaka M, Miyata K, Fujiki S, Tano M, Moriya M, Yamanishi M, Honjo E, Tada H, Ino T, Yamaguchi H, Futami J, Seno M, Nomoto T, Hirata T, Yoshimura M, Kuroki R. Protein Sci 16 1389-1397 (2007)
  23. Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes. Hummer G, García AE, Soumpasis DM. Biophys J 68 1639-1652 (1995)
  24. DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site. Kearney BM, Johnson CW, Roberts DM, Swartz P, Mattos C. J Mol Biol 426 611-629 (2014)
  25. Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A. Catanzano F, Graziano G, Capasso S, Barone G. Protein Sci 6 1682-1693 (1997)
  26. Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups. Schlessman JL, Abe C, Gittis A, Karp DA, Dolan MA, García-Moreno E B. Biophys J 94 3208-3216 (2008)
  27. Simple, yet powerful methodologies for conformational sampling of proteins. Harada R, Takano Y, Baba T, Shigeta Y. Phys Chem Chem Phys 17 6155-6173 (2015)
  28. Participation of water in Hin recombinase--DNA recognition. Robinson CR, Sligar SG. Protein Sci 5 2119-2124 (1996)
  29. Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study. Schiffer CA, van Gunsteren WF. Proteins 36 501-511 (1999)
  30. HER2-mediated internalization of a targeted prodrug cytotoxic conjugate is dependent on the valency of the targeting ligand. Guillemard V, Nedev HN, Berezov A, Murali R, Saragovi HU. DNA Cell Biol 24 350-358 (2005)
  31. Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data. Durchschlag H, Zipper P. Eur Biophys J 32 487-502 (2003)
  32. Kinetic spectroscopy of heme hydration and ligand binding in myoglobin and isolated hemoglobin chains: an optical window into heme pocket water dynamics. Esquerra RM, López-Peña I, Tipgunlakant P, Birukou I, Nguyen RL, Soman J, Olson JS, Kliger DS, Goldbeck RA. Phys Chem Chem Phys 12 10270-10278 (2010)
  33. Monellin (MNEI) at 1.15 A resolution. Hobbs JR, Munger SD, Conn GL. Acta Crystallogr Sect F Struct Biol Cryst Commun 63 162-167 (2007)
  34. Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins. Harada R, Takano Y, Shigeta Y. J Chem Phys 140 125103 (2014)
  35. Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Dennis S, Camacho CJ, Vajda S. Proteins 38 176-188 (2000)
  36. Mean field analysis of FKBP12 complexes with FK506 and rapamycin: implications for a role of crystallographic water molecules in molecular recognition and specificity. Rejto PA, Verkhivker GM. Proteins 28 313-324 (1997)
  37. Optical detection of disordered water within a protein cavity. Goldbeck RA, Pillsbury ML, Jensen RA, Mendoza JL, Nguyen RL, Olson JS, Soman J, Kliger DS, Esquerra RM. J Am Chem Soc 131 12265-12272 (2009)
  38. Transform and relax sampling for highly anisotropic systems: application to protein domain motion and folding. Kitao A. J Chem Phys 135 045101 (2011)
  39. Characterization of receptors with a new negative image: use in molecular docking and lead optimization. Oshiro CM, Kuntz ID. Proteins 30 321-336 (1998)
  40. Protein-water interactions in ribonuclease A and angiogenin: a molecular dynamics study. Sanjeev BS, Vishveshwara S. Proteins 55 915-923 (2004)
  41. Neutron crystallographic studies of T4 lysozyme at cryogenic temperature. Li L, Shukla S, Meilleur F, Standaert RF, Pierce J, Myles DAA, Cuneo MJ. Protein Sci 26 2098-2104 (2017)
  42. Modification of protein crystal packing by systematic mutations of surface residues: implications on biotemplating and crystal porosity. Wine Y, Cohen-Hadar N, Lamed R, Freeman A, Frolow F. Biotechnol Bioeng 104 444-457 (2009)
  43. Consensus preferred hydration sites in six FKBP12-drug complexes. Faerman CH, Karplus PA. Proteins 23 1-11 (1995)
  44. Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site. Pujadas G, Palau J. Protein Sci 10 1645-1657 (2001)
  45. Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics. Dahanayake JN, Shahryari E, Roberts KM, Heikes ME, Kasireddy C, Mitchell-Koch KR. J Chem Inf Model 59 2407-2422 (2019)
  46. Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution. Harada R, Nakamura T, Shigeta Y. J Comput Chem 37 724-738 (2016)
  47. Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh. Ramirez UD, Freymann DM. Acta Crystallogr D Biol Crystallogr 62 1520-1534 (2006)
  48. LAWS: Local alignment for water sites-Tracking ordered water in simulations. Klyshko E, Kim JS, Rauscher S. Biophys J 122 2871-2883 (2023)
  49. Role of Heme Pocket Water in Allosteric Regulation of Ligand Reactivity in Human Hemoglobin. Esquerra RM, Bibi BM, Tipgunlakant P, Birukou I, Soman J, Olson JS, Kliger DS, Goldbeck RA. Biochemistry 55 4005-4017 (2016)
  50. Solvent interactions and protein dynamics in spin-labeled T4 lysozyme. Stoica I. J Biomol Struct Dyn 21 745-760 (2004)
  51. The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations. Hinge VK, Blinov N, Roy D, Wishart DS, Kovalenko A. J Comput Aided Mol Des 33 913-926 (2019)
  52. OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling. Xu G, Wang Q, Ma J. J Chem Theory Comput 19 1629-1640 (2023)


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