Ligand binding and circular permutation modify residue interaction network in DHFR

PLoS Computational Biology

Volumn 3, Issue 6, 2007, Pages 1097-1107

  Hu, Zengjian ^a   Bowen, Donnell ^a   Southerland, William M ^a   Del Sol, Antonio ^b   Pan, Yongping ^c   Nussinov, Ruth ^c,d   Ma, Buyong ^c  

^a HOWARD UNIVERSITY COLLEGE OF MEDICINE   (United States)

^b FUJIREBIO INC   (Japan)

^c SAIC FREDERICK INC   (United States)

^d TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME ACTIVITY; GRAPH THEORY; LIGANDS; MOLECULAR DYNAMICS;

ACTIVE SITE; CHAIN CONNECTIVITY; CIRCULAR PERMUTATION; DIHYDROFOLATE REDUCTASE; DYNAMICS SIMULATION; FOLDINGS; INTERACTION NETWORKS; LIGAND BINDING; NETWORK COMMUNICATIONS; SHORT-PATH;

CHAINS;

DIHYDROFOLATE REDUCTASE; ENZYME VARIANT; AMINO ACID; LIGAND;

ARTICLE; BINDING SITE; CONTROLLED STUDY; ENZYME INACTIVATION; LIGAND BINDING; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; RESIDUE ANALYSIS; SIMULATION; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CHEMISTRY; METHODOLOGY; MOLECULAR GENETICS; PROTEIN ANALYSIS; PROTEIN BINDING; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMINO ACIDS; LIGANDS; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP; TETRAHYDROFOLATE DEHYDROGENASE;

EID: 34347326305     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030117     Document Type: Article

References (29)

1. McElheny D, Schnell JR, Lansing JC, Dyson HJ, Wright PE (2005) Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis. Proc Natl Acad Sci U S A 102: 5032-5037.
2. Venkitakrishnan RP, Zaborowski E, McElheny D, Benkovic SJ, Dyson HJ, et al. (2004) Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle. Biochemistry 43: 16046-16055.
3. Sawaya MR, Kraut J (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence. Biochemistry 36: 586-603.
4. Agarwal PK, Billeter SR, Rajagopalan PT, Benkovic SJ, Hammes-Schiffer S (2002) Network of coupled promoting motions in enzyme catalysis. Proc Natl Acad Sci U S A 99: 2794-2799.
5. Iwakura M, Nakamura T, Yamane C, Maki K (2000) Systematic circular permutation of an entire protein reveals essential folding elements. Nat Struct Biol 7: 580-585.
6. Nakamura T, Iwakura M (1999) Circular permutation analysis as a method for distinction of functional elements in the M20 loop of Escherichia coli dihydrofolate reductase. J Biol Chem 274: 19041-19047.
7. Arai M, Iwakura M (2005) Probing the interactions between the folding elements early in the folding of Escherichia coli dihydrofolate reductase by systematic sequence perturbation analysis. J Mol Biol 347: 337-353.
8. Arai M, Iwakura M (2006) Peptide fragment studies on the folding elements of dihydrofolate reductase from Escherichia coli. Proteins 62: 399-410.
9. Svensson AK, Zitzewitz JA, Matthews CR, Smith VF (2006) The relationship between chain connectivity and domain stability in the equilibrium and kinetic folding mechanisms of dihydrofolate reductase from E. coli. Protein Eng Des Sel 19: 175-185.
10. Smith VF, Matthews CR (2001) Testing the role of chain connectivity on the stability and structure of dihydrofolate reductase from E. coli: Fragment complementation and circular permutation reveal stable, alternatively folded forms. Protein Sci 10: 116-128.
11. Pelletier JN, Arndt KM, Pluckthun A, Michnick SW (1999) An in vivo library-versus-library selection of optimized protein-protein interactions. Nat Biotechnol 17: 683-690.
12. Vendruscolo M, Dokholyan NV, Paci E, Karplus M (2002) Small-world view of the amino acids that play a key role in protein folding. Phys Rev E Stat Nonlin Soft Matter Phys 65: 061910.
13. Rao F, Caflisch A (2004) The protein folding network. J Mol Biol 342: 299-306.
14. Dokholyan NV, Li L, Ding F, Shakhnovich EI (2002) Topological determinants of protein folding. Proc Natl Acad Sci U S A 99: 8637-8641.
15. del Sol A, O'Meara P (2005) Small-world network approach to identify key residues in protein-protein interaction. Proteins 58: 672-682.
16. Greene LH, Higman VA (2003) Uncovering network systems within protein structures. J Mol Biol 334: 781-791.
17. Brinda KV, Vishveshwara S (2005) A network representation of protein structures: Implications for protein stability. Biophys J 89: 4159-4170.
18. Atilgan AR, Akan P, Baysal C (2004) Small-world communication of residues and significance for protein dynamics. Biophys J 86: 85-91.
19. Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, et al. (2004) Network analysis of protein structures identifies functional residues. J Mol Biol 344: 1135-1146.
20. Thibert B, Bredesen DE, del Rio G (2005) Improved prediction of critical residues for protein function based on network and phylogenetic analyses. BMC Bioinformatics 6: 213.
21. Ma B, Tsai CJ, Nussinov R (2000) Binding and folding: In search of intramolecular chaperone-like building block fragments. Protein Eng 13: 617-627.
22. Paszkiewicz KH, Sternberg MJ, Lappe M (2006) Prediction of viable circular permutants using a graph theoretic approach. Bioinformatics 22: 1353-1358.
23. Ainavarapu SR, Li L, Badilla CL, Fernandez JM (2005) Ligand binding modulates the mechanical stability of dihydrofolate reductase. Biophys J 89: 3337-3344.
24. Junker JP, Hell K, Schlierf M, Neupert W, Rief M (2005) Influence of substrate binding on the mechanical stability of mouse dihydrofolate reductase. Biophys J 89: L46-L48.
25. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4: 187-217.
26. MacKerell AD Jr, Bashford D, Bellott RL, Dunbrack RL Jr, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
27. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Res 33: W363-W367.
28. Pape U (1980) Algorithm 562 - Shortest-path lengths [H]. ACM TOMS 6: 450-455.
29. Boccaletti S, Pecora LM (2006) Introduction: Stability and pattern formation in networks of dynamical systems. Chaos 16: 15101.