ENCoM server: Exploring protein conformational space and the effect of mutations on protein function and stability

Nucleic Acids Research

Volumn 43, Issue W1, 2015, Pages W395-W400

  Frappier, Vincent ^a   Chartier, Matthieu ^a   Najmanovich, Rafael J ^a  

^a UNIVERSITY OF SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; CONTROLLED STUDY; ENTROPY; LIMIT OF QUANTITATION; MEASUREMENT ACCURACY; MOLECULAR DYNAMICS; POINT MUTATION; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STABILITY; THERMOSTABILITY; WEB BROWSER; CHEMICAL STRUCTURE; COMPUTER PROGRAM; INTERNET; TEMPERATURE; VIBRATION;

ENTROPY; INTERNET; MODELS, MOLECULAR; POINT MUTATION; PROTEIN CONFORMATION; PROTEIN STABILITY; SOFTWARE; TEMPERATURE; VIBRATION;

EID: 84979862382     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv343     Document Type: Article

References (40)

1. Frappier, V. and Najmanovich, R.J. (2014) A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations. PLoS Comput. Biol., 10, e1003569.
2. Korkut, A. and Hendrickson, W.A. (2009) A force field for virtual atom molecular mechanics of proteins. Proc. Natl. Acad. Sci. U.S.A., 106, 15667-15672.
3. Doruker, P., Atilgan, A.R. and Bahar, I. (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor. Proteins, 40, 512-524.
4. Atilgan, A.R., Durell, S.R., Jernigan, R.L., Demirel, M.C., Keskin, O. and Bahar, I. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J., 80, 505-515.
5. Lin, T.-L. and Song, G. (2010) Generalized spring tensor models for protein fluctuation dynamics and conformation changes. BMC Struct. Biol., 10(Suppl. 1), S3.
6. Amemiya, T., Koike, R., Kidera, A. and Ota, M. (2012) PSCDB: a database for protein structural change upon ligand binding. Nucleic Acids Res., 40, D554-D558.
7. Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F. and Serrano, L. (2005) The FoldX web server: an online force field. Nucleic Acids Res., 33, W382-W388.
8. Leaver-Fay, A., Tyka, M., Lewis, S.M., Lange, O.F., Thompson, J., Jacak, R., Kaufman, K., Renfrew, P.D., Smith, C.A., Sheffler, W. et al. (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol., 487, 545-574.
9. Zhou, H. and Zhou, Y. (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 11, 2714-2726.
10. Dehouck, Y., Grosfils, A., Folch, B., Gilis, D., Bogaerts, P. and Rooman, M. (2009) Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics, 25, 2537-2543.
11. Yin, S., Ding, F. and Dokholyan, N.V. (2007) Eris: an automated estimator of protein stability. Nat. Methods, 4, 466-467.
12. Parthiban, V., Gromiha, M.M. and Schomburg, D. (2006) CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res., 34, W239-W242.
13. Capriotti, E., Fariselli, P. and Casadio, R. (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res., 33, W306-W310.
14. Masso, M. and Vaisman, I.I. (2010) AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements. Protein Eng. Des. Sel., 23, 683-687.
15. Boehr, D.D., Schnell, J.R., McElheny, D., Bae, S.-H., Duggan, B.M., Benkovic, S.J., Dyson, H.J. and Wright, P.E. (2013) A Distal Mutation Perturbs Dynamic Amino Acid Networks in Dihydrofolate Reductase. Biochemistry, 52, 4605-4619.
16. Frappier, V. and Najmanovich, R.J. (2015) Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering. Protein Sci., 24, 474-483.
17. Lindahl, E., Azuara, C., Koehl, P. and Delarue, M. (2006) NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res., 34, W52-W56.
18. Suhre, K. and Sanejouand, Y.-H. (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res., 32, W610-W614.
19. Hollup, S.M., Salensminde, G. and Reuter, N. (2005) WEBnm@: a web application for normal mode analyses of proteins. BMC Bioinformatics, 6, 52.
20. Zheng, W. and Doniach, S. (2003) A comparative study of motor-protein motions by using a simple elastic-network model. Proc. Natl. Acad. Sci. U.S.A., 100, 13253-13258.
21. Wako, H. and Endo, S. (2011) Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis. Biophys. Chem., 159, 257-266.
22. Eyal, E., Lum, G. and Bahar, I. (2015) The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics, doi:10.1093/bioinformatics/btu847.
23. Lopéz-Blanco, J.R., Aliaga, J.I., Quintana-Ortí, E.S. and Chacón, P. (2014) iMODS: internal coordinates normal mode analysis server. Nucleic Acids Res., 42, W271-W276.
24. Webb, B. and Sali, A. (2014) Comparative Protein Structure Modeling Using MODELLER. Curr. Protoc. Bioinform., 47, 5.6.1-5.6.32.
25. Mood, A.M. (1971) Partitioning variance in multiple regression analyses as a tool for developing learning models. Am. Educ. Res. J., 8, 191-202.
26. Guerois, R., Nielsen, J.E. and Serrano, L. (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol., 320, 369-387.
27. Eisenmesser, E.Z., Millet, O., Labeikovsky, W., Korzhnev, D.M., Wolf-Watz, M., Bosco, D.A., Skalicky, J.J., Kay, L.E. and Kern, D. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature, 438, 117-121.
28. Doucet, N. (2011) Can enzyme engineering benefit from the modulation of protein motions? Lessons learned from NMR relaxation dispersion experiments. Protein Pept. Lett., 18, 336-343.
29. Giver, L., Gershenson, A., Freskgard, P.O. and Arnold, F.H. (1998) Directed evolution of a thermostable esterase. Proc. Natl. Acad. Sci. U.S.A., 95, 12809-12813.
30. Shoichet, B.K., Baase, W.A., Kuroki, R. and Matthews, B.W. (1995) A relationship between protein stability and protein function. Proc. Natl. Acad. Sci. U.S.A., 92, 452-456.
31. Bloom, J.D., Meyer, M.M., Meinhold, P., Otey, C.R., MacMillan, D. and Arnold, F.H. (2005) Evolving strategies for enzyme engineering. Curr. Opin. Struct. Biol., 15, 447-452.
32. van den Burg, B. and Eijsink, V.G.H. (2002) Selection of mutations for increased protein stability. Curr. Opin. Biotechnol., 13, 333-337.
33. Fields, P.A. (2001) Review: Protein function at thermal extremes: balancing stability and flexibility. Comp. Biochem. Physiol. A Mol. Integr. Physiol., 129, 417-431.
34. Wolf-Watz, M., Thai, V., Henzler-Wildman, K., Hadjipavlou, G., Eisenmesser, E.Z. and Kern, D. (2004) Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nat. Struct. Mol. Biol., 11, 945-949.
35. Floquet, N., Marechal, J.-D., Badet-Denisot, M.-A., Robert, C.H., Dauchez, M. and Perahia, D. (2006) Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors. FEBS Lett., 580, 5130-5136.
36. Abagyan, R., Rueda, M. and Bottegoni, G. (2009) Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J. Chem. Inf. Model, 49, 716-725.
37. Sperandio, O., Mouawad, L., Pinto, E., Villoutreix, B.O., Perahia, D. and Miteva, M.A. (2010) How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur. Biophys. J., 39, 1365-1372.
38. Dobbins, S.E., Lesk, V.I. and Sternberg, M.J.E. (2008) Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking. Proc. Natl. Acad. Sci. U.S.A., 105, 10390-10395.
39. Torchala, M., Moal, I.H., Chaleil, R.A.G., Fernandez-Recio, J. and Bates, P.A. (2013) SwarmDock: a server for flexible protein-protein docking. Bioinformatics, 29, 807-809.
40. Smith, C.A. and Kortemme, T. (2008) Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J. Mol. Biol., 380, 742-756.