Selecting sequences that fold into a defined 3D structure: A new approach for protein design based on molecular dynamics and energetics

Biophysical Chemistry

Volumn 146, Issue 2-3, 2010, Pages 76-84

  Morra, Giulia ^a   Baragli, Chiara ^a   Colombo, Giorgio ^a  

^a CNR   (Italy)

Author keywords

Molecular dynamics; Protein design; Protein folding; Self organization

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; DECOMPOSITION; ENERGY TRANSFER; MOLECULAR DYNAMICS; MOLECULAR LIBRARY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; DRUG DESIGN; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEINS; THERMODYNAMICS;

EID: 72749109072     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2009.10.007     Document Type: Article

References (34)

1. Bowie J.U., Luthy R., and Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253 (1991) 164-170
2. Watters A.L., Deka P., Corrent C., Callender D., Varani G., Sosnick T., and Baker D. The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell 128 (2007) 613-624
3. Kuhlman B., Dantas G., Ireton G.C., Varani G., Stoddard B.L., and Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 302 (2003) 1364-1368
4. Lee M.R.T., Jerry B., David K., and Peter A. Molecular dynamics in the endgame of protein structure prediction. J.Mol.Biol. 313 (2001) 417-430
5. Dahiyat B.I., and Mayo S.L. De novo protein design: fully automated sequence selection. Science 278 (1997) 82-87
6. Desjarlais J.R., and Handel T.M. De novo design of the hydrophobic cores of proteins. Protein Sci. 4 (1995) 2006-2018
7. Kortemme T., Joachimiak L.A., Bullock A.N., Schuler A.D., Stoddard B.L., and Baker D. Computational redesign of protein-protein interaction specificity. Nature Struct. Mol. Biol. 11 (2004) 371-379
8. Kraemer-Pecore C.M., Lecomte J.T., and Desjarlais J.R. A de novo redesign of the ww domain. Protein Sci. 12 (2003) 2194-2205
9. Harbury, P.B., J.J. Plecs, B. Tidor, T. Alber, and P.S. Kim, High resolution protein design with backbone freedom, Science 282 (1998) 1998.
10. Lockless S.W., and Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286 (1999) 295-299
11. Socolich M., Lockless S.W., Russ W.P., Lee H., Gardner K.H., and Ranganathan R. Evolutionary information for specifying a protein fold. Nature 437 (2005) 512-518
12. Suel G.M., Lockless S.W., Wall M.A., and Ranganathan R. Evolutionary conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10 (2003) 59-69
13. Shulman A.I., Larson C., Magelsdorf D.J., and Ranganathan R. Structural determinants of allosteric ligand activation in rxr heterodimers. Cell 116 (2004) 417-429
14. Russ, W.P., D.M. Lowery, P. Mishra, M.B. Yaffe, and R. Ranganathan, Natural-like function in artificial ww domains, Nature 437 (2005).
15. Tiana G., Simona S., De Mori G.M.S., Broglia R.A., and Colombo G. Understanding the determinants of stability and folding of small globular proteins from their energetics. Protein Sci. 13 (2004) 113-124
16. Ragona L., Colombo G., Catalano M., and Molinari H. Determinants of protein stability and folding: comparative analysis of beta-lactoglobulins and liver basic fatty acid binding protein, proteins: structure. Function and Bioinformatics 61 (2005) 366-376
17. Colacino S., Tiana G., Broglia R.A., and Colombo G. The determinants of stability in the human prion protein: insights into the folding and misfolding from the analysis of the change in the stabilization energy distribution in different condition, proteins: structure. Function and Bioinformatics 62 (2006) 698-707
18. Colacino, S., G. Tiana, and G. Colombo, Similar folds with different stabilization mechanisms: The cases of prion and doppel proteins, BMC Struct. Biol. 6 (2006).
19. Morra G., and Colombo G. Relationship between energy distribution and fold stability: insights from molecular dynamics simulations of native and mutant proteins. Proteins: Struct. Funct. and Bioinf. 72 (2008) 660-672
20. Tiana G., Simona F., De Mori G.M.S., Broglia R.A., and Colombo G. Understanding the determinants of stability and folding of small globular proteins from their energetics. Protein Sci. 13 (2004) 113-124
21. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., and Higgins D.G. Clustalw and clustalx version 2. Bioinformatics 23 (2007) 2948-2974
22. Bastolla, U., M. Porto, H.E. Roman, and M. Vendruscolo, Principal eigenvector of contact matrices and hydrophobicity profiles in proteins, Proteins: structure, function and bioinformatics 58 (2005) 22-30.
23. Klepeis J.L., Lindorff-Larsen K., Dror R.O., and Shaw D.E. Long-timescale molecular dynamics simulations of protein structure and function. Curr. Op. Struct. Biol. 19 (2009) 120-127
24. Shaw D.E., Deneroff M.M., Dror R.O., Kuskin J.S., Larson R.H., Salmon J.K., Young C., Batson B., Bowers K.J., Chao J.C., Eastwood M.P., Gagliardo J., Grossman J.P., Ho C.R., Ierardi D.J., Kolossvary I., Klepeis J.L., Layman T., McLeavey C., Moraes M.A., Mueller R., Priest E.C., Shan Y.B., Spengler J., Theobald M., Towles B., and Wang S.C. Anton, a special-purpose machine for molecular dynamics simulation. Commun. ACM 51 (2008) 91-97
25. van der Spoel, D., E. Lindahl, B. Hess, A.R. van Buuren, E. Apol, P.J. Meulenhoff, D.P. Tieleman, A.L.T.M. Sijbers, K.A. Feenstra, R. van Drunen, and H.J.C. Berendsen, Gromacs user manual version 3.2. Www.Gromacs.Org (Editor, 2004).
26. Hess B., Kutzner C., van der Spoel D., and Lindahl E. Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory and Computation 4 (2008) 435-447
27. De Mori, G.M.S., G. Colombo, and C. Micheletti, Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics., Proteins: Struct. Funct. and Bioinf. 58 (2005) 459-471.
28. Lindahl E., Hess B., and van der Spoel D. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 7 (2001) 306-317
29. van Gunsteren W.F., Daura X., and Mark A.E. Gromos force field. Encyclopedia of Computational Chemistry 2 (1998) 1211-1216
30. Berendsen H.J.C., Grigera J.R., and Straatsma P.R. The missing term in effective pair potentials. J. Phys. Chem. 91 (1987) 6269-6271
31. Hess B., Bekker H., Fraaije J.G.E.M., and Berendsen H.J.C. A linear constraint solver for molecular simulations. J.Comp.Chem. 18 (1997) 1463-1472
32. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Di Nola A., and Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
33. Onufriev A., Bashford D., and Case D.A. Modification of the generalized born model suitable for macromolecules. J. Phys. Chem. B. 104 (2000) 3712-3720
34. Weiser J., Shenkin P.S., and Still W.C. Approximate atomic surfaces from linear combinations of pairwise overlaps (lcpo). J. Comput. Chem. 20 (1999) 217-230