Structure-based approach to the prediction of disulfide bonds in proteins

Protein Engineering, Design and Selection

Volumn 27, Issue 10, 2014, Pages 365-374

  Salam, Noeris K ^a   Adzhigirey, Matvey ^a   Sherman, Woody ^a   Pearlman, David A ^a   Thirumalai, David ^b  

^a SCHRÖDINGER INC   (United States)

^b NONE

Author keywords

Cysteine mutation; Cysteine scanning; Disulfide prediction; Enzyme design; Protein engineering

Indexed keywords

AMINO ACIDS; BIOCHEMICAL ENGINEERING; COVALENT BONDS; ENZYMES; FORECASTING; GENETIC ALGORITHMS; GENETIC ENGINEERING; KNOWLEDGE BASED SYSTEMS;

CYSTEINE MUTATION; CYSTEINE-SCANNING; DISULFIDE BOND FORMATION; FUNCTIONAL PROTEINS; KNOWLEDGE-BASED APPROACH; PROTEIN ENGINEERING; SITE DIRECTED MUTAGENESIS; WILD-TYPE PROTEINS;

SULFUR COMPOUNDS;

PROTEIN; CYSTEINE; DISULFIDE;

CONFERENCE PAPER; DISULFIDE BOND; GENETIC ALGORITHM; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN STABILITY; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION; PROTEIN ENGINEERING; THERMODYNAMICS;

CYSTEINE; DISULFIDES; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN STABILITY; PROTEINS; THERMODYNAMICS;

EID: 84928235982     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzu017     Document Type: Conference Paper

References (23)

1. Berman, H.M., Westbrook, J., Feng, Z., et al. (2000) Nucleic Acids Res., 28, 235-242.
2. Burton, R.E., Hunt, J.A., Fierke, C.A. and Oas, T.G. (2000) Protein Sci., 9, 776-785.
3. Charbonneau, P. (1995) Astrophys. J. Suppl. Ser., 101, 309.
4. Charbonneau, P. (2002) Release Notes for PIKAIA 1.2, NCAR Technical Note TN-451-STR. National Center for Atmospheric Research, Boulder.
5. Dani, V.S., Ramakrishnan, C. and Varadarajan, R. (2003) Protein Eng. Des. Sel., 16, 187-193.
6. Davis, L. (1991) Handbook of Genetic Algorithms. 1st edn. Van Nostrand Reinhold, New York.
7. Dobson, C.M. (2003) Nature, 426, 884-890.
8. Dombkowski, A.A. (2003) Bioinformatics, 19, 1852-1853.
9. Dombkowski, A.A., Sultana, K.Z. and Craig, D.B. (2014) FEBS Lett., 588, 206-212.
10. Flory, P.J. (1956) J. Am. Chem. Soc., 78, 5222-5235.
11. Jorgensen, W.L., Maxwell, D.S. and Tirado-Rives, J. (1996) J. Am. Chem. Soc., 118, 11225-11235.
12. Kim, D.Y., Kandalaft, H., Ding, W., et al. (2012) Protein Eng. Des. Sel., 25, 581-590.
13. Kuroki, R., Inaka, K., Taniyama, Y., Kidokoro, S., Matsushima, M., Kikuchi, M. and Yutani, K. (1992) Biochemistry, 31, 8323-8328.
14. Le, Q.A.T., Joo, J.C., Yoo, Y.J. and Kim, Y.H. (2011) Biotechnol. Bioeng., 109, 867-876.
15. Li, J., Abel, R., Zhu, K., Cao, Y., Zhao, S. and Friesner, R.A. (2011) Proteins Struct. Funct. Bioinform., 79, 2794-2812.
16. Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R. and Sherman, W. (2013) J. Comput. Aided Mol. Des., 27, 221-234.
17. Mårtensson, L.-G., Karlsson, M. and Carlsson, U. (2002) Biochemistry, 41, 15867-15875.
18. Matsumura, M., Signor, G. and Matthews, B.W. (1989) Nature, 342, 291-293.
19. Pace, C.N., Grimsley, G.R., Thomson, J.A. and Barnett, B.J. (1988) J. Biol. Chem., 263, 11820-11825.
20. Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J. and Sherman, W. (2010) J. Chem. Theory Comput., 6, 1509-1519.
21. Siadat, O.R., Lougarre, A., Lamouroux, L., Ladurantie, C. and Fournier, D. (2006) BMC Biochem., 7, 12.
22. Vaz, D.C., Rodrigues, J.R., Sebald, W., Dobson, C.M. and Brito, R.M. (2006) Protein Sci., 15, 33-44.
23. Wahlberg, E. and Härd, T. (2006) J. Am. Chem. Soc., 128, 7651-7660.