Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Bhattacharyya, Moitrayee ^a   Upadhyay, Roopali ^a   Vishveshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

ARTICLE; BINDING SITE; CASE STUDY; CONSENSUS DEVELOPMENT; CONTROLLED STUDY; EXPERIMENTAL STUDY; MATHEMATICAL COMPUTING; MOLECULAR INTERACTION; MOLECULAR STABILITY; NADP BINDING ROSSMANN FOLD DOMAIN; PROTEIN DOMAIN; PROTEIN FOLDING; STRUCTURE ANALYSIS; THEORETICAL STUDY;

BINDING SITES; HYDROGEN BONDING; MODELS, MOLECULAR; MODELS, THEORETICAL; NADP; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 84871305258     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051676     Document Type: Article

References (42)

1. Redfern OC, Dessailly B, Orengo CA, (2008) Exploring the structure and function paradigm. Curr Opin Struct Biol 18: 394-402.
2. Andreeva A, Murzin AG, (2006) Evolution of protein fold in the presence of functional constraints. Curr Opin Struct Biol 16: 399-408.
3. Anfinsen CB, (1973) Principles that Govern the Folding of Protein Chains. Science 181: 223-230.
4. Orengo CA, Jones DT, Thornton JM, (1994) Protein superfamilles and domain superfolds. Nature 372: 631-634.
5. Liu X, Fan K, Wang W, (2004) The number of protein folds and their distribution over families in nature. Proteins: Struct Func Bioinfo 54: 491-499.
6. Wolf YI, Grishin NV, Koonin EV, (2000) Estimating the number of protein folds and families from complete genome data. J Mol Biol 299: 897-905.
7. Zhang Y, Skolnick J, (2005) The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 102: 1029-1034.
8. Orengo CA, Thornton JM, (2005) Protein families and their evolution-A structural perspective. Ann Rev Biochem 74: 867-900.
9. Lee D, de Beer T, Laskowski R, Thornton J, Orengo C, (2011) 1,000 structures and more from the MCSG. BMC Struct Biol 11: 2.
10. William R T, (2007) Evolutionary transitions in protein fold space. Curr Opin Struct Biol 17: 354-361.
11. Rose GD, Fleming PJ, Banavar JR, Maritan A, (2006) A backbone-based theory of protein folding. Proc Natl Acad Sci U S A 103: 16623-16633.
12. Hoang TX, Trovato A, Seno F, Banavar JR, Maritan A, (2004) Geometry and symmetry presculpt the free-energy landscape of proteins. Proc Natl Acad Sci USA 101: 7960-7964.
13. Soundararajan V, Raman R, Raguram S, Sasisekharan V, Sasisekharan R, (2010) Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds. PLoS ONE 5: e9391.
14. Chothia C, Lesk A M, (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823-826.
15. Nagano N, Orengo CA, Thornton JM, (2002) One Fold with Many Functions: The Evolutionary Relationships between TIM Barrel Families Based on their Sequences, Structures and Functions. J Mol Biol 321: 741-765.
16. Choi I-G, Kim S-H, (2006) Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci USA 103: 14056-14061.
17. Dokholyan NV, Shakhnovich B, Shakhnovich EI, (2002) Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci USA 99: 14132-14136.
18. Constance J J, (2003) Moonlighting proteins: old proteins learning new tricks. Trends in Genetics 19: 415-417.
19. Deb D, Vishveshwara S, Vishveshwara S, (2009) Understanding Protein Structure from a Percolation Perspective. Biophys J 97: 1787-1794.
20. Worth CL, Gong S, Blundell TL, (2009) Structural and functional constraints in the evolution of protein families. Nat Rev Mol Cell Biol 10: 709-720.
21. Lockless SW, Ranganathan R, (1999) Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families. Science 286: 295-299.
22. Halabi N, Rivoire O, Leibler S, Ranganathan R, (2009) Protein Sectors: Evolutionary Units of Three-Dimensional Structure. Cell 138: 774-786.
23. Russ WP, Lowery DM, Mishra P, Yaffe MB, Ranganathan R, (2005) Natural-like function in artificial WW domains. Nature 437: 579-583.
24. Keskin O, Jernigan RL, Bahar I, (2000) Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior. Biophys J 78: 2093-2106.
25. Raimondi F, Felline A, Portella G, Orozco M, Fanelli F (2012) Light on the structural communication in Ras GTPases. J Biomol Struct Dyn: 1-16.
26. Capra JA, Singh M, (2007) Predicting functionally important residues from sequence conservation. Bioinformatics 23: 1875-1882.
27. Rossmann MG, Moras D, Olsen KW, (1974) Chemical and biological evolution of a nucleotide-binding protein. Nature 250: 194-199.
28. Arthur M L, (1995) NAD-binding domains of dehydrogenases. Current Opinion in Structural Biology 5: 775-783.
29. Kleiger G, Eisenberg D, (2002) GXXXG and GXXXA Motifs Stabilize FAD and NAD(P)-binding Rossmann Folds Through C(alpha)-H.. O Hydrogen Bonds and van der Waals Interactions. J Mol Biol 323: 69-76.
30. Mirny LA, Shakhnovich EI, (1999) Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 291: 177-196.
31. López-Hernéndez E, Serrano L, (1996) Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Folding and Design 1: 43-55.
32. Sukhwal A, Bhattacharyya M, Vishveshwara S, (2011) Network approach for capturing ligand-induced subtle global changes in protein structures. Acta Cryst Section D 67: 429-439.
33. Smock RG, Rivoire O, Russ WP, Swain JF, Leibler S, et al. (2010) An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol Syst Biol 6.
34. Vijayabaskar MS, Vishveshwara S, (2012) Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks. PLoS Comput Biol 8: e1002505.
35. Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-540.
36. Brenner SE, Koehl P, Levitt M, (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucl Acids Res 28: 254-256.
37. Wang G, Dunbrack RL, (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
38. Bhattacharyya M, Ghosh A, Hansia P, Vishveshwara S, (2010) Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks. Proteins: Struct Func Bioinfo 78: 506-517.
39. Brinda KV, Vishveshwara S, (2005) A network representation of protein structures: implications for protein stability. Biophysical journal 89: 4159-4170.
40. Kannan N, Vishveshwara S, (1999) Identification of side-chain clusters in protein structures by a graph spectral method. J Mol Biol 292: 441-464.
41. Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM, (2006) MUSTANG: A multiple structural alignment algorithm. Proteins: Struct Func Bioinfo 64: 559-574.
42. Palla G, Derenyi I, Farkas I, Vicsek T, (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435: 814-818.