Discovery of intramolecular signal transduction network based on a new protein dynamics model of energy dissipation

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Ma, Cheng Wei ^a,b   Xiu, Zhi Long ^b   Zeng, An Ping ^a  

^a HAMBURG UNIVERSITY OF TECHNOLOGY   (Germany)

^b DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTATE KINASE; ASPARTOKINASE III; UNCLASSIFIED DRUG; AMINO ACID;

ALGORITHM; ALLOSTERISM; ARTICLE; CONTROLLED STUDY; DESENSITIZATION; ENERGY; ENERGY DISSIPATION; ENZYME REGULATION; ENZYME STRUCTURE; ESCHERICHIA COLI; INTERMOLECULAR SIGNAL TRANSDUCTION NETWORK; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PREDICTION; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; SIGNAL TRANSDUCTION; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; MUTATION; PROTEIN CONFORMATION; PROTEIN MOTIF; THERMODYNAMICS;

ALGORITHMS; AMINO ACID MOTIFS; AMINO ACIDS; ASPARTATE KINASE; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN CONFORMATION; SIGNAL TRANSDUCTION; THERMODYNAMICS;

EID: 84857376645     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031529     Document Type: Article

References (44)

1. Benkovic SJ, Hammes-Schiffer S, (2003) A perspective on enzyme catalysis. Science 301: 1196-1202.
2. Olsson MH, Parson WW, Warshel A, (2006) Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev 106: 1737-1756.
3. Daily MD, Gray JJ, (2009) Allosteric communication occurs via networks of tertiary and quaternary motions in proteins. PLoS Comput Biol 5: e1000293.
4. Smock RG, Gierasch LM, (2009) Sending signals dynamically. Science 324: 198-203.
5. Tsai CJ, Del Sol A, Nussinov R, (2009) Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol Biosyst 5: 207-216.
6. Yang Z, Májek P, Bahar I, (2009) Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PLoS Comput Biol 5: e1000360.
7. Monod J, Wyman J, Changeux JP, (1965) On the nature of allosteric transitions: a plausible model. J Mol Biol 12: 88-118.
8. Koshland DE Jr, Nemethy G, Filmer D, (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5: 365-385.
9. Gunasekaran K, Ma B, Nussinov R, (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57: 433-443.
10. Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R, (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 9: 10-19.
11. Luque I, Leavitt SA, Freire E, (2002) The linkage between protein folding and functional cooperativity: two sides of the same coin? Annu Rev Biophys Biomol Struct 31: 235-256.
12. Kern D, Zuiderweg ER, (2003) The role of dynamics in allosteric regulation. Curr Opin Struct Biol 13: 748-757.
13. Popovych N, Sun S, Ebright RH, Kalodimos CG, (2006) Dynamically driven protein allostery. Nat Struct Mol Biol 13: 831-838.
14. Suel GM, Lockless SW, Wall MA, Ranganathan R, (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10: 59-69.
15. Chen Z, Rappert S, Sun J, Zeng AP, (2011) Integrating molecular dynamics and co-evolutionary analysis for reliable target prediction and deregulation of the allosteric inhibition of aspartokinase for amino acid production. J Biotechnol 154: 248-254.
16. Chen Z, Meyer W, Rappert S, Sun J, Zeng AP, (2011) Co-evolutionary analysis enables rational deregulation of allosteric enzyme inhibition in Corynebacterium glutamicum for lysine production. Appl Environ Microbiol 77: 4352-4360.
17. Ma CW, Xiu ZL, Zeng AP, (2011) A new concept to reveal protein dynamics based on energy dissipation. PLoS ONE 6: e26453.
18. Juanico B, Sanejouand YH, Piazza F, De Los Rios P, (2007) Discrete breathers in nonlinear network models of proteins. Phys Rev Lett 99: 238104.
19. Piazza F, Sanejouand YH, (2008) Discrete breathers in protein structures. Phys Biol 5: 026001.
20. Piazza F, Sanejouand YH, (2009) Long-range energy transfer in proteins. Phys Biol 6: 046014.
21. Antal MA, Böde C, Csermely P, (2009) Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design. Curr Protein Pept Sci 10: 161-172.
22. Farkas IJ, Korcsmáros T, Kovács IA, Mihalik Á, Palotai R, et al. (2011) Network-based tools for the identification of novel drug targets. Sci Signal 4: pt3.
23. Barabasi AL, Albert R, (1999) Emergence of scaling in random networks. Science 286: 509-512.
24. Barabasi AL, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
25. Ma H, Zeng AP, (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19: 270-277.
26. Ma H, Kumar B, Ditges U, Gunzer F, Buer J, et al. (2004) An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res 32: 6643-6649.
27. Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang DU, (2006) Complex networks: structure and dynamics. Phys Rep 424: 175-308.
28. Palla G, Derenyi I, Farkas T, Vicsek T, (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435: 814-818.
29. Ravasz R, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL, (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
30. Watts DJ, Strogatz SH, (1998) Collective dynamics of 'small-world' networks. Nature 393: 440-442.
31. Ramón-Maiques S, Marina A, Gil-Ortiz F, Fita I, Rubio V, (2002) Structure of acetylglutamate kinase, a key enzyme for arginine biosynthesis and a prototype for the amino acid kinase enzyme family, during catalysis. Structure (Camb.) 10: 329-342.
32. Grant GA, (2006) The ACT domain: a small molecule binding domain and its role as a common regulatory element. J Biol Chem 281: 33825-33829.
33. Cassan M, Parsot C, Cohen GN, Patte JC, (1986) Nucleotide sequence of lysC gene encoding the lysine-sensitive aspartokinase III of Escherichia coli K12. Evolutionary pathway leading to three isofunctional enzymes. J Biol Chem 261: 1052-1057.
34. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The protein data bank. Nucleic Acids Res 28: 235-242.
35. Jorgensen WL, (1982) Revised TIPS for simulations of liquid water and aqueous solutions. J Chem Phys 77: 4156-4163.
36. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802.
37. Ryckaert JP, Ciccotti G, Berendsen HJC, (1977) Numerical-integration of Cartesian equations of motion of a system with constraints-molecular dynamics of n-alkanes. J Comput Phys 23: 327-341.
38. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T, (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
39. Lockless SW, Ranganathan R, (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286: 295-299.
40. Schreiber F, Schwöbbermeyer H, (2005) MAVisto: a tool for the exploration of network motifs. Bioinformatics 21: 3572-3574.
41. Miyata YO, Kojima H, Sano K, (2001) Mutation analysis of the feedback inhibition site of aspartokinase III of Esherichia coli K-12 and its use in L-threonine production. Biosci Biotechnol Biochem 65: 1149-1154.
42. Kikuchi Y, Kojima H, Tanaka T, (1999) Mutational analysis of the feedback sites of lysine-sensitive aspartokinase of Escherichia coli. FEMS Microbiol Lett 173: 211-215.
43. Süel GM, Lockless SW, Wall MA, Ranganathan R, (2003) Evolutionarily conserved networks of residues mediate allosteric communication inproteins. Nat Struct Biol 10: 59-69.
44. Estabrook RA, Luo J, Purdy MM, Sharma V, Weakliem P, et al. (2005) Statistical coevolution analysis and molecular dynamics: identification of amino acid pairsessential for catalysis. Proc Natl Acad Sci USA 102: 994-999.