A perturbative view of protein structural variation

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 1, 2010, Pages 173-180

  Echave, Julián ^a,b   Fernández, Francisco M ^a  

^a Instituto Nacional de Investigaciones Fisicoquímicas Teóricas y Aplicadas   (Argentina)

^b INSTITUTO DE INVESTIGACIONES FISICOQUÍMICAS TEÓRICAS Y APLICADAS INIFTA   (Argentina)

Author keywords

Elastic network model; Ligand binding; Model; Mutation, perturbation; Protein evolution; Simulation; Structural divergence

Indexed keywords

GLOBIN; MUTANT PROTEIN; MYOGLOBIN;

ARTICLE; CONFORMATIONAL TRANSITION; EVOLUTION; GENETIC CONSERVATION; LIGAND BINDING; MUTATION; NATURAL SELECTION; PH; PRIORITY JOURNAL; PROTEIN STRUCTURE; STATISTICS; WILD TYPE; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; GENETICS; MOLECULAR EVOLUTION; PROTEIN CONFORMATION; PROTEIN DATABASE; WHALE;

ANIMALS; COMPUTER SIMULATION; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GLOBINS; MODELS, GENETIC; MUTATION; MYOGLOBIN; PROTEIN CONFORMATION; WHALES;

EID: 77949400204     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22553     Document Type: Article

References (29)

1. Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR. An analysis of core deformations in protein superfamilies. Biophys J 2005; 88: 1291-1299. (Pubitemid 40975956)
2. Bahar I, Rader AJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 2005; 15: 586-592. (Pubitemid 41393491)
3. Echave J. Evolutionary divergence of protein structure: the linearly forced elastic network model. Chem Phys Lett 2008; 457: 413-416.
4. Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998; 33: 417-429. (Pubitemid 28516346)
5. Hinsen K, Kneller GR. A simplified force field for describing vibrational protein dynamics over the whole frequency range. J Chem Phys 1999; 111: 10766-10769. (Pubitemid 129585444)
6. Hinsen K, Petrescu AJ, Dellerue S, Bellissent-Funel MC, Kneller GR. Harmonicity in slow protein dynamics. Chem Phys 2000; 261: 25-37.
7. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 2001; 80: 505-515. (Pubitemid 32108200)
8. Micheletti C, Carloni P, Maritan A. Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and gaussian models. Proteins 2004; 55: 635-645. (Pubitemid 38620088)
9. Murzin AG, Brenner SE, Hubbard T, Chothia C. Scop-a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995; 247: 536-540.
10. Menke M, Berger B, Cowen L. Matt: local flexibility aids protein multiple structure alignment. Plos Compu Biol 2008;4:e10. (Pubitemid 351230858)
11. Sinha N, Nussinov R. Point mutations and sequence variability in proteins. Redistributions of preexisting populations. Proc Natl Acad Sci USA 2001; 98: 3139-3144.
12. Reuter N, Hinsen K, Lacapere JJ. Transconformations of the SERCAl Ca-ATPase: a normal mode study. Biophys J 2003; 85: 2186-2197. (Pubitemid 37210770)
13. Xu CY, Tobi D, Bahar I. Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T ↔ R2 transition. J Mol Biol 2003; 333: 153-168. (Pubitemid 37153272)
14. Zheng W, Brooks BR, Thirumalai D, Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J 2007; 93: 2289-2299. (Pubitemid 47511128)
15. Keskin O. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies. BMC Struct Biol 2007; 7: 31.
16. Tobi D, Bahar I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci USA. 2005; 102: 18908-18913. (Pubitemid 43049540)
17. Dobbins SE, Lesk VI, Sternberg MJE. Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci USA 2008; 105: 10390-10395.
18. Delarue M, Sanejouand YH. Simplified normal mode analysis of conformational transitions in DNA-dcpendent polymerases: the elastic network model. J Mol Biol 2002; 320: 1011-1024. (Pubitemid 34808821)
19. Rueda M, Chacon P, Orozco M. Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure 2007; 15: 565-575. (Pubitemid 46722600)
20. Hinsen K. Structural flexibility in proteins: impact of the crystal environment. Bioinformatics 2008; 24: 521-528. (Pubitemid 351256296)
21. Emperador A, Carrillo O, Rueda M, Orozco M. Exploring the suitability of coarse-grained techniques for the representation of protein dynamics. Biophys J 2008; 95: 2127-2138.
22. Ikeguchi M, Ueno J, Sato M, Kidera A. Protein structural change upon Iigand binding: linear response theory. Phys Rev Lett 2005; 94: 078102. (Pubitemid 40620748)
23. Zheng WJ, Brooks BR, Doniach S, Thirumalai D. Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure 2005; 13: 565-577. (Pubitemid 40503320)
24. Zheng WJ, Brooks BR. Normal-modes-based prediction of protein conformational changes guided by distance constraints. Biophys J 2005; 88: 3109-3117.
25. Maguid S, Fernandez-Alberti S, Parisi G, Echave J. Evolutionary conservation of protein backbone flexibility. J Mol Evolut 2006; 63: 448-457. (Pubitemid 44611732)
26. Maguid S, Fernandez-Alberti S, Ferrelli L, Echave J. Exploring the common dynamics of homologous proteins. Application to the globin family. Biophys J 2005; 89: 3-13.
27. Maguid S, Fernandez-Alberti S, Echave J. Evolutionary conservation of protein vibrational dynamics. Gene 2008; 422: 7-13.
28. Keskin O, Jernigan RL, Bahar I. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys J 2000; 78: 2093-2106. (Pubitemid 30183603)
29. Zen A, Carnevaie V, Lesk AM, Micheletti C. Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families. Protein Sci 2008; 17: 918-929. (Pubitemid 351629586)