Stability and rigidity/flexibility - Two sides of the same coin?

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1834, Issue 5, 2013, Pages 854-866

  Mamonova, Tatyana B ^a   Glyakina, Anna V ^b,c   Galzitskaya, Oxana V ^b   Kurnikova, Maria G ^a,d  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^c INSTITUTE OF MATHEMATICAL PROBLEMS OF BIOLOGY   (Russian Federation)

^d CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

Flexible region; Hydrogen bond; Molecular dynamics simulation; Proteins from thermophilic and mesophilic organisms; Salt bridge

Indexed keywords

SODIUM CHLORIDE;

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; DECOMPOSITION; HYDROGEN BOND; MESOPHILIC BACTERIUM; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STABILITY; PROTEIN STRUCTURE; RIGIDITY; THERMOPHILIC BACTERIUM;

HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION;

EID: 84876293960     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.02.011     Document Type: Article

References (41)

1. I.N. Berezovsky, and E.I. Shakhnovich Physics and evolution of thermophilic adaptation Proc. Natl. Acad. Sci. U. S. A. 102 2005 12742 12747
2. S. Fukuchi, and K. Nishikawa Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J. Mol. Biol. 309 2001 835 843
3. I.N. Berezovsky, W.W. Chen, P.J. Choi, and E.I. Shakhnovich Entropic stabilization of proteins and its proteomic consequences PLoS Comput. Biol. 1 2005 e47
4. K.B. Zeldovich, I.N. Berezovsky, and E.I. Shakhnovich Protein and DNA sequence determinants of thermophilic adaptation PLoS Comput. Biol. 3 1 2007 e5
5. B.-G. Ma, A. Goncearenco, and I.N. Berezovsky Thermophilic adaptation of protein complexes inferred from proteomic homology modeling Structure 18 7 2010 819 828
6. V. Glyakina, S.O. Garbuzynskiy, M.Yu. Lobanov, and O.V. Galzitskaya Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms Bioinformatics 23 17 2007 2231 2238
7. S. Kumar, Ch-J. Tsai, and R. Nussinov Factors enhancing protein thermostability Protein Eng. 13 2000 179 191
8. A. Szilagyi, and P. Zavodszky Structural differences between mesophilic moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey Structure 8 2000 493 504
9. S. Kumar, C.J. Tsai, and R. Nussinov Thermodynamic differences among homologous thermophilic and mesophilic proteins Biochemistry 40 47 2001 14152 14165
10. R.A. Goldstein The evolution and evolutionary consequences of marginal thermostability in proteins Proteins 79 5 2011 1396 1407
11. R.A. Goldstein Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: insights from the quasi-chemical approximation Protein Sci. 16 9 2007 1887 1895
12. A. Paiardini, R. Sali, F. Bossa, and S. Pascarella "Hot cores" in proteins: comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms BMC Struct. Biol. 8 2008 14
13. T. Lazaridis, I. Lee, and M. Karplus Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin Protein Sci. 6 12 1997 2589 2605
14. A.A. Polyansky, P.E. Volynsky, A.S. Arseniev, and R.G. Efremov Adaptation of a membrane-active peptide to heterogeneous environment. I. Structural plasticity of the peptide J. Phys. Chem. B 113 4 2009 1107 1119
15. Z. Guo, L.N. Xu, and L.X. Zhou The mechanism of TC23O's thermostability: a molecular dynamics simulation study J. Biomol. Struct. Dyn. 23 6 2006 603 612
16. M. Karlström, I.H. Steen, G. Tibbelin, T. Lien, N.K. Birkeland, and R. Ladenstein Crystallization and preliminary X-ray structure analysis of isocitrate dehydrogenase from two hyperthermophiles, Aeropyrum pernix and Thermotoga maritima Acta Crystallogr. D Biol. Crystallogr. 58 12 2002 2162 2164
17. J.H. Missimer, M.O. Steinmetz, R. Baron, F.K. Winkler, R.A. Kammerer, X. Daura, and W.F. van Gunsteren Configurational entropy elucidates the role of salt-bridge networks in protein thermostability Protein Sci. 16 7 2007 1349 1359
18. P.I. de Bakker, P.H. Hünenberger, and J.A. McCammon Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability J. Mol. Biol. 285 4 1999 1811 1830
19. A.S. Thomas, and A.H. Elcock Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures J. Am. Chem. Soc. 126 7 2004 2208 2214
20. C. Danciulescu, R. Ladenstein, and L. Nilsson Dynamic arrangement of ion pairs and individual contributions to the thermal stability of the cofactor-binding domain of glutamate dehydrogenase from Thermotoga maritima Biochemistry 46 29 2007 8537 8549
21. R. Ladenstein, and G. Antranikian Proteins from hyperthermophiles: stability and enzymatic catalysis close to the boiling point of water Adv. Biochem. Eng. Biotechnol. 61 1998 37 85
22. M. Tang, and S. Yip Atomistic simulation of thermomechanical properties of beta-SiC Phys. Rev. B: Condens. Matter 52 21 1995 15150 15159
23. J.H. Lebbink, V. Consalvi, R. Chiaraluce, K.D. Berndt, and R. Ladenstein Structural and thermodynamic studies on a salt-bridge triad in the NADP-binding domain of glutamate dehydrogenase from Thermotoga maritima: cooperativity and electrostatic contribution to stability Biochemistry 41 52 2002 15524 15535
24. M. Tiberti, and E. Papaleo Dynamic properties of extremophilic subtilisin-like serine-proteases J. Struct. Biol. 174 1 2011 69 83
25. D. Fraccalvieri, M. Tiberti, A. Pandini, L. Bonati, and E. Papaleo Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics Mol. Biosyst. 8 10 2012 2680 2691
26. O.V. Galzitskaya, S.O. Garbuzynskiy, and M.Yu. Lobanov FoldUnfold: web server for the prediction of disordered regions in protein chain Bioinformatics 22 23 2006 2948 2949
27. O.V. Galzitskaya, S.A. Garbuzynskiy, and M.Yu. Lobanov Prediction of natively unfolded regions in protein chain Mol. Biol. (Moscow) 40 2006 341 348
28. O.V. Galzitskaya, S.O. Garbuzynskiy, and M.Yu. Lobanov Prediction of amyloidogenic and disordered regions in protein chain PLoS 2 2006 1639 1648
29. N.V. Dovidchenko, N.S. Bogatyreva, and O.V. Galzitskaya Prediction of loop regions in protein sequence J. Bioinform. Comput. Biol. 6 2008 1035 1047
30. T.B. Mamonova, A.V. Glyakina, M.G. Kurnikova, and O.V. Galzitskaya Flexibility and mobility in mesophilic and thermophilic homologous proteins from molecular dynamics and FoldUnfold method J. Bioinform. Comput. Biol. 8 3 2010 377 394
31. N.V. Dovidchenko, and O.V. Galzitskaya Prediction of status residue to be protected or not protected from hydrogen exchange using amino acid sequence only Open Biochem. J. 2 2008 77 80
32. T. Mamonova, B. Hespenheide, R. Straub, M.F. Thorpe, and M. Kurnikova Protein flexibility using constraints from molecular dynamics simulations Phys. Biol. 2 4 2005 S137 S147
33. D.J. Jacobs, A.J. Rader, L.A. Kuhn, and M.F. Thorpe Protein flexibility predictions using graph theory Proteins Struct. Funct. Genet. 44 2 2001 150 165
34. M.F. Thorpe, M. Lei, A.J. Rader, D.J. Jacobs, and L.A. Kuhn Protein flexibility and dynamics using constraint theory J. Mol. Graph. Model. 19 1 2001 60 69
35. B.M. Hespenheide, A.J. Rader, M.F. Thorpe, and L.A. Kuhn Identifying protein folding cores from the evolution of flexible regions during unfolding J. Mol. Graph. Model. 21 2002 195 207
36. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 4 1995 536 540
37. D.A. Case Normal mode analysis of protein dynamics Curr. Opin. Struct. Biol. 4 1994 285 290
38. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman A 2nd generation force field for the simulation of proteins, nucleic-acids, and organic-molecules J. Am. Chem. Soc. 117 1995 5179 5197
39. D.F. Stickle, L.G. Presta, K.A. Dill, and G.D. Rose Hydrogen-bonding in globular-proteins J. Mol. Biol. 226 1992 1143 1159
40. D. Xu, C.J. Tsai, and R. Nussinov Hydrogen bonds and salt bridges across protein-protein interfaces Protein Eng. 10 1997 999 1012
41. A.J. Rader, B.M. Hespenheide, L.A. Kuhn, and M.F. Thorpe Protein unfolding: rigidity lost Proc. Natl. Acad. Sci. U. S. A. 99 6 2002 3540 3545