Protein Engineering Protocols - Mycobacteriology research center

Combinatorial Protein Design Strategies 1915. Walsh, S. T. R., Cheng, H., Bryson, J. W., Roder, H., and DeGrado, W. F. (1999)Solution structure and dynamics of a denovo designed three-helix bundle protein.Proc. Natl. Acad. Sci. USA 96, 5486–5491.16. Voigt, C. A., Gordon, D. B., and Mayo, S. L. (2000) Trading accuracy for speed:a quantitative comparison of search algorithms in protein sequence design. J.Mol. Biol. 299, 789–803.17. Gordon, D. B. and Mayo, S. L. (1998) Radical performance enhancements forcombinatorial optimization algorithms based on the dead-end elimination theorem.J. Comput. Chem. 19, 1505–1514.18. Gordon, D. B. and Mayo, S. L. (1999) Branch-and terminate: a combinatorialoptimization algorithm for protein design. Struct. Fold. Des. 7, 1089–1098.19. Pierce, N. A., Spriet, J. A., Desmet, J., and Mayo, S. L. (2000) Conformationalsplitting: a more powerful criterion for dead-end elimination. J. Comput. Chem.21, 999–1009.20. Looger, L. L. and Hellinga, H. W. (2001) Generalized dead-end eliminationalgorithms make large-scale protein side-chain structure prediction tractable:implications for protein design and structural genomics. J. Mol. Biol. 307,429–445.21. Dahiyat, B. I. and Mayo, S. L. (1997) De novo protein design: fully automatedsequence selection. Science 278, 82–87.22. Marshall, S. A. and Mayo, S. L. (2001) Achieving stability and conformationalspecificity in designed proteins via binary patterning. J. Mol. Biol. 305,619–631.23. Malakauskas, S. M. and Mayo, S. L. (1998) Design, structure, and stability of ahyperthermophilic protein variant. Nat. Struct. Biol. 5, 470–475.24. Strop, P. and Mayo, S. L. (1999) Rubredoxin variant folds without iron. J. Am.Chem. Soc. 121, 2341–2345.25. Shimaoka, M., Shifman, J. M., Jing, H., Takagi, L., Mayo, S. L., and Springer, T. A.(2000) Computational design of an integrin i domain stabilized in the open highaffinity conformation. Nat. Struct. Biol. 7, 674–678.26. Benson, D. E., Wisz, M. S., Liu, W., and Hellinga, H. W. (1998) Construction ofa novel redox protein by rational design: conversion of a disulfide bridge into amononuclear iron-sulfur center. Biochemistry 37, 7070–7076.27. DeGrado, W. F., Summa, C. M., Pavone, V., Nastri, F., and Lombardi, A. (1999)De novo design and structural characterization of proteins and metalloproteins.Annu. Rev. Biochem. 68, 779–819.28. Bolon, D. N. and Mayo, S. L. (2001) Enzyme-like proteins by computationaldesign. Proc. Natl. Acad. Sci. USA 98, 14,274–14,279.29. Street, A. G. and Mayo, S. L. (1999) Computational protein design. Struct. Fold.Des. 7, R105–R109.30. Saven, J. G. (2001) Designing protein energy landscapes. Chem. Rev. 101,3113–3130.31. Gromiha, M. M., Uedaira, H., An, J., Selvaraj, S., Prabakaran, P., and Sarai, A.(2002) Protherm, thermodynamic database for proteins and mutants: developmentsin version 3.0. Nucleic Acids Res. 30, 301, 302.