A few low-frequency normal modes predominantly contribute to conformational responses of hen egg white lysozyme in the tetragonal crystal to variations of molecular packing controlled by environmental humidity

Biophysical Chemistry

Volumn 159, Issue 2-3, 2011, Pages 237-246

  Takayama, Yuki ^a,b   Nakasako, Masayoshi ^a,b  

^a KEIO UNIVERSITY   (Japan)

^b RIKEN HARIMA INSTITUTE   (Japan)

Author keywords

Conformational change; Humidity control; Normal mode analysis; Protein dynamics; X ray crystallography

Indexed keywords

EGG WHITE; HEN EGG WHITE LYSOZYME; LYSOZYME; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; ENZYME CONFORMATION; HUMIDITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

ANIMALS; CHICKENS; CRYSTALLOGRAPHY, X-RAY; EQUIPMENT DESIGN; HUMIDITY; MODELS, MOLECULAR; MURAMIDASE; PROTEIN CONFORMATION;

EID: 80053381174     PISSN: 03014622     EISSN: 18734200     Source Type: Journal    
DOI: 10.1016/j.bpc.2011.07.001     Document Type: Article

References (53)

1. G.E. Schulz Domain motions in proteins Curr. Opin. Struct. Biol. 1 1991 883 888 (Pubitemid 121002679)
2. L. Vijayalakshmi, R. Krishna, R. Sankaranarayanan, and M. Vijayan An asymmetric dimer of β-lactoglobulin in a low humidity crystal form-structural changes that accompany partial dehydration and protein action Proteins Struct. Funct. Bioinfo. 71 2008 241 249 (Pubitemid 351358607)
3. M. Nakasako Water-protein interactions from high-resolution protein crystallography Phil. Trans. R. Soc. Lond. B359 2004 1191 1206 (Pubitemid 39123211)
4. K.A. Kantardjieff, and B. Rupp Matthews coefficient probabilities: improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals Protein Sci. 12 2003 1865 1871 (Pubitemid 37022809)
5. I. Dobrianov, S. Kriminski, C.L. Caylor, S.G. Lemay, C. Kimmer, A. Kisselev, K.D. Finkelstein, and R.E. Thorne Dynamic response of tetragonal lysozyme crystals to changes in relative humidity: implications for post-growth crystal treatments Acta Cryst. D57 2001 61 68 (Pubitemid 32062676)
6. R. Kodandapani, C.G. Suresh, and M. Vijayan Crystal structure of low humidity tetragonal lysozyme at 2.1-Å resolution. Variability in hydration shell and its structural consequences J. Biol. Chem. 265 1990 16126 16131
7. G.S. Kachalova, V.N. Morozov, T.Ya. Morozova, E.T. Myachin, A.A. Vagin, B.V. Strokopytov, and Yu.V. Nekrasov Comparison of structures of dry and wet hen egg-white lysozyme molecule at 1.8 Å resolution FEBS Lett. 284 1991 91 94
8. K.V.R. Kishan, N.R. Chandra, C. Sudarsanakumar, K. Suguna, and M. Vijayan Water-dependent domain motion and flexibility in ribonuclease A and the invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme Acta Cryst. D51 1995 703 710
9. H.G. Nagendra, C. Sudarsanakumar, and M. Vijayan An X-ray analysis of native monoclinic lysozyme. A case study on the reliability of refined protein structures and a comparison with the low-humidity form in relation to mobility and enzyme action Acta Cryst. D52 1996 1067 1074 (Pubitemid 27093808)
10. B.K. Biswal, and M. Vijayan Structures of human oxy- and deoxyhaemoglobin at different levels of humidity: variability in the T state Acta Cryst. D58 2002 1155 1161 (Pubitemid 34780749)
11. 3 oxidase from Thermus thermophilus Acta Cryst. D61 2005 340 343 (Pubitemid 43965375)
12. R. Kiefersauer, M.E. Than, H. Dobbek, L. Gremer, M. Melero, S. Strobl, J.M. Dias, T. Soulimane, and R. Huber A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidity changes J. Appl. Cryst. 33 2000 1223 1230 (Pubitemid 32120467)
13. T. Sjögren, G. Carlsson, G. Larsson, A. Hajdu, C. Andersson, H. Pettersson, and J. Hajdu Protein crystallography in a vapour stream: data collection, reaction initiation and intermediate trapping in naked hydrated protein crystals J. Appl. Cryst. 35 2002 113 116 (Pubitemid 34538188)
14. J. Sanchez-Weatherby, M.W. Bowler, J. Huet, A. Gobbo, F. Felisaz, B. Lavault, R. Moya, J. Kadlec, R.B.G. Ravelli, and F. Cipriani Improving diffraction by humidity control: a novel device compatible with X-ray beamlines Acta Cryst. D65 2009 1237 1246
15. H. Dobbek, L. Gremer, R. Kiefersauer, R. Huber, and O. Meyer Catalysis at a dinuclear [CuSMo(= O)OH] cluster in a CO dehydrogenase resolved at 1.1-Å resolution Proc. Natl. Acad. Sci. U.S.A. 99 2002 15971 15976 (Pubitemid 35462733)
16. M. Koch, C. Breithaupt, R. Kiefersauer, J. Freigang, R. Huber, and A. Messerschmidt Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis EMBO J. 23 2004 1720 1728 (Pubitemid 38649635)
17. 1-ATPase by controlled dehydration Acta Cryst. D62 2006 991 995 (Pubitemid 44337372)
18. P. Chotiyarnwong, G.B. Stewart-Jones, M. Tarry, W. Dejnirattisai, C. Siebold, M. Koch, D.I. Stuart, K. Harlos, P. Malasit, G. Screaton, J. Mongkolsapaya, and E.Y. Jones Humidity control as a strategy for lattice optimization applied to crystals of HLA-A*1101 complexed with variant peptides from dengue virus Acta Cryst. F63 2007 386 392 (Pubitemid 46722353)
19. G. Feher, and Z. Kam Nucleation and growth of protein crystals: general principles and assays Meth. Enzymol. 114 1985 77 112
20. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Meth. Enzymol. 276 1997 307 326 (Pubitemid 27085611)
21. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Cryst. D53 1997 240 255 (Pubitemid 27235885)
22. Collaborative Computational Project Number 4, The CCP4 suite: programs for protein crystallography Acta Cryst. D50 1994 760 763
23. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Cryst. D60 2004 2126 2132 (Pubitemid 41742764)
24. H.M. Berman, T. Battistuz, T.N. Bhat, W.F. Bluhm, P.E. Bourne, K. Burkhardt, Z. Feng, G.L. Gilliland, S. Iype, S. Jain, P. Fagan, J. Marvin, D. Padilla, V. Ravichandran, B. Schneider, N. Thanki, H. Weissig, D. Westbrook, and C. Zardecki The protein data bank Acta Cryst. D58 2002 899 907 (Pubitemid 34653017)
25. S. Datta, K. Biswal, and M. Vijayan The effect of stabilizing additives on the structure and hydration of proteins: a study involving tetragonal lysozyme Acta Cryst. D57 2001 1614 1620 (Pubitemid 33037725)
26. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Cryst. 26 1993 283 291
27. P.V. Luzzati Traitement statistique des erreurs dans la determination des structures cristallines Acta Cryst. 5 1952 802 810
28. A.A. Vaguine, J. Richelle, and S.J. Wodak SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model Acta Cryst. D55 1999 191 205 (Pubitemid 29053816)
29. J. Painter, and E.A. Merritt TLSMD web server for the generation of multi-group TLS models J. Appl. Cryst. 39 2006 109 111
30. W. Kabsch A solution for the best rotation to relate two sets of vectors Acta Cryst. A32 1976 922 923
31. N.R. Voss, and M. Gerstein 3 V: cavity, channel and cleft volume calculator and extractor Nucl. Acid. Res. 38 2010 W555 W562
32. M.M. Tirion Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys. Rev. Lett. 77 1996 1905 1908 (Pubitemid 126625816)
33. F. Tama, F.X. Gadea, O. Marques, and Y.-H. Sanejouand Building-block approach for determining low-frequency normal modes of macromolecules Protein Struct. Funct. Genet. 41 2000 1 7 (Pubitemid 30666907)
34. M. Gerstein, A. Lesk, and C. Chothia Structural mechanisms for domain movements in proteins Biochemistry 33 1994 6739 6749 (Pubitemid 24190795)
35. M. Ikeguchi, J. Ueno, M. Sato, and A. Kidera Protein structural change upon ligand binding: linear response theory Phys. Rev. Lett. 94 2005 1 4 078102 (Pubitemid 40620748)
36. S. Hayward, and N. Go Investigating protein dynamics in collective coordinate space Annu. Rev. Phys. Chem. 46 1995 223 250
37. F. Tama, and Y.-H. Sanejouand Conformational change of proteins arising from normal mode calculations Protein Eng. 14 2001 1 6 (Pubitemid 32318932)
38. I. Bahar, T.R. Lezon, L.-W. Yang, and E. Eyal Global dynamics of proteins: bridging between structure and function Annu. Rev. Biophys. 9 2010 23 42
39. M. Nakasako, F. Tsuchiya, and Y. Arata Roles of hydration water molecules in molecular packing of the killer toxin from Pichia farinose in its crystalline state investigated by cryogenic X-ray crystallography Biophys. Chem. 95 2002 211 225 (Pubitemid 34327276)
40. D. Matsuoka, and M. Nakasako Probability distributions of hydration water molecules around polar protein atoms obtained by a database analysis J. Phys. Chem. B113 2009 11274 11292
41. M. Nakasako, M. Odaka, M. Yohda, N. Dohmae, K. Takio, N. Kamiya, and I. Endo Tertiary and quaternary structures of photoreactive Fe-type nitrile hydratase from Rhodococcus sp. N-771: roles of hydration water molecules in stabilizing the structures and the structural origin of the substrate specificity of the enzyme Biochemistry 38 1999 9887 9898
42. M. Nakasako, T. Fujisawa, S. Adachi, T. Kudo, and S. Higuchi Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering Biochemistry 40 2001 3069 3079 (Pubitemid 32205350)
43. M. Nakasako Large-scale networks of hydration water molecules around bovine β-trypsin revealed by cryogenic X-ray crystal structure analysis J. Mol. Biol. 289 1999 547 564 (Pubitemid 29295123)
44. V.N. Morozov, G.S. Kachalova, V.U. Evtodienko, N.F. Lanina, and T.Ya. Morozova Permeability of lysozyme tetragonal crystals to water Eur. Biophys. J. 24 1995 93 98
45. A. Zamiri, and S. De Modeling the mechanical response of tetragonal lysozyme crystals Langmuir 26 2010 4251 4257
46. S. Speziale, F. Jiang, C.L. Caylor, S. Kriminski, C.-S. Zha, R.E. Thorne, and T.S. Duffy Sound velocity and elasticity of tetragonal lysozyme crystals by Brillouin spectroscopy Biophys. J. 85 2003 3202 3213 (Pubitemid 37345807)
47. P.S. Kaushal, R. Sankaranarayanan, and M. Vijayan Water-mediated variability in the structure of relaxed-state haemoglobin Acta Cryst. F64 2008 463 469 (Pubitemid 351999130)
48. M. Ueda Rate of evaporation of water by forced convection Appl. Phys. (in Japanese) 29 1969 443 451
49. D.W. Grover, and J.M. Nicol The vapor pressure of glycerine solutions at 20 °C J. Soc. Chem. Ind. 59 1940 175 177
50. B.W. Matthews Solvent content of protein crystals J. Mol. Biol. 33 1968 491 497
51. A.T. Brünger Free R value: a novel statistical quantity for assessing the accuracy of crystal structures Nature 355 1992 472 474
52. W.L. DeLano PyMOL http://www.pymol.org 2002
53. L. Potterton, S. McNicholas, E. Krissinel, J. Gruber, K. Cowtan, P. Emsley, G.N. Murshudov, S. Cohen, A. Perrakis, and M. Noble Developments in the CCP4 molecular-graphics project Acta Cryst. D60 2004 2288 2294 (Pubitemid 41742782)