References

Bauman, J.D., K. Das, W.C. Ho, M. Baweja, D.M. Himmel, A.D. Clark, Jr., D.A. Oren, P.L. Boyer, S.H. Hughes, A.J. Shatkin, and E. Arnold. 2008. Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design. Nucleic Acids Res 36(15): 5083-92.

Benson, D.E., M.S. Wisz, and H.W. Hellinga. 2000. Rational design of nascent metalloen-

zymes. Proc Natl Acad Sci U S A 97(12): 6292-7. Benson, D.E., M.S. Wisz, W. Liu, and H.W. Hellinga. 1998. Construction of a novel redox protein by rational design: Conversion of a disulfide bridge into a mononuclear iron-sulfur center. Biochemistry 37(20): 7070-76. Bolon, D.N., and S.L. Mayo. 2001. Enzyme-like proteins by computational design. Proc Natl Acad Sci U S A 98(25): 14274-9.

Choi, E.J., and S.L. Mayo. 2006. Generation and analysis of proline mutants in protein G. Protein Eng Des Sel 19(6): 285-9.

Choma, C., H. Gratkowski, J.D. Lear, and W.F. DeGrado. 2000. Asparagine-mediated self-association of a model transmembrane helix. Nat Struct Biol 7(2): 161-6.

Clarke, N.D., and S.M. Yuan. 1995. Metal search: A computer program that helps design tet-rahedral metal-binding sites. Proteins 23(2): 256-63.

Cristian, L., P. Piotrowiak, and R.S. Farid. 2003. Mimicking photosynthesis in a computationally designed synthetic metalloprotein. J Am Chem Soc 125(39): 11814-5.

de Lorimier, R.M., J.J. Smith, M.A. Dwyer, L.L. Looger, K.M. Sali, C.D. Paavola, S.S. Rizk, S. Sadigov, D.W. Conrad, L. Loew, and H.W. Hellinga. 2002. Construction of a fluorescent biosensor family. Protein Sci 11(11): 2655-75.

Desjarlais, J.R., and T.M. Handel. 1995. De novo design of the hydrophobic cores of proteins. Protein Sci 4(10): 2006-18.

Desmet, J., M. Demaeyer, B. Hazes, and I. Lasters. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356(6369): 539-42.

Fisinger, S., L. Serrano, and E. Lacroix. 2001. Computational estimation of specific side chain interaction energies in alpha helices. Protein Sci 10(4): 809-18.

Giver, L., A. Gershenson, P.O. Freskgard, and F.H. Arnold. 1998. Directed evolution of a thermostable esterase. Proc Natl Acad Sci U S A 95(22): 12809-13.

Gromiha, M.M., J. An, H. Kono, M. Oobatake, H. Uedaira, and A. Sarai. 1999. ProTherm: Thermodynamic database for proteins and mutants. Nucleic Acids Res 27(1): 286-8.

Guruprasad, K., and S. Rajkumar. 2000. Beta-and gamma-turns in proteins revisited: A new set of amino acid turn-type dependent positional preferences and potentials. J Biosci 25(2): 143-56.

Hellinga, H.W., J.P. Caradonna, and F.M. Richards. 1991. Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. J Mol Biol 222(3): 787-803.

Hellinga, H.W., and F.M. Richards. 1991. Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. J Mol Biol 222(3): 763-85.

Hellinga, H.W., and F.M. Richards. 1994. Optimal sequence selection in proteins of known structure by simulated evolution. Proc Natl Acad Sci U S A 91(13): 5803-07.

Hilvert, D. 2000. Critical analysis of antibody catalysis. Annu Rev Biochem 69: 751-92.

Jain, R.K., and R. Ranganathan. 2004. Local complexity of amino acid interactions in a protein core. Proc Natl Acad Sci U S A 101(1): 111-6.

Jiang, L., E.A. Althoff, F.R. Clemente, L. Doyle, D. Rothlisberger, A. Zanghellini, J.L. Gallaher, J.L. Betker, F. Tanaka, C.F. Barbas, 3rd, D. Hilvert, K.N. Houk, B.L. Stoddard, and D. Baker. 2008. De novo computational design of retro-aldol enzymes. Science 319(5868): 1387-91.

Jiang, L., B. Kuhlman, T. Kortemme, and D. Baker. 2005. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58(4): 893-904.

Jiang, X., H. Farid, E. Pistor, and R.S. Farid. 2000. A new approach to the design of uniquely folded thermally stable proteins. Protein Sci 9(2): 403-16.

Kaplan, J., and W.F. DeGrado. 2004. De novo design of catalytic proteins. Proc Natl Acad Sci U S A 101(32): 11566-70.

Klein-Seetharaman, J., M. Oikawa, S.B. Grimshaw, J. Wirmer, E. Duchardt, T. Ueda, T. Imoto, L.J. Smith, C.M. Dobson, and H. Schwalbe. 2002. Long-range interactions within a nonnative protein. Science 295(5560): 1719-22.

Klemba, M., K.H. Gardner, S. Marino, N.D. Clarke, and L. Regan. 1995. Novel metal-binding proteins by design. Nat Struct Biol 2(5): 368-73.

Korkegian, A., M.E. Black, D. Baker, and B.L. Stoddard. 2005. Computational thermostabili-zation of an enzyme. Science 308(5723): 857-60.

Kumar, S., C.J. Tsai, and R. Nussinov. 2000. Factors enhancing protein thermostability. Protein Eng 13(3): 179-91.

Ladman, Y., J.T. Schwartz, and H.J. Wolfson. 1990. Affine invariant model-based object recognition. IEEE Transactions on Robotics and Automation 6(5): 578-89.

Larson, S.M., J.L. England, J.R. Desjarlais, and V.S. Pande. 2002. Thoroughly sampling sequence space: Large-scale protein design of structural ensembles. Protein Sci 11(12): 2804-13.

Lazar, G.A., J.R. Desjarlais, and T.M. Handel. 1997. De novo design of the hydrophobic core of ubiquitin. Protein Sci 6(6): 1167-78.

Lazaridis, T., and M. Karplus. 1999. Effective energy function for proteins in solution. Proteins 35(2): 133-52.

Lee, C., and M. Levitt. 1991. Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core. Nature 352(6334): 448-51.

Lippow, S.M., K.D. Wittrup, and B. Tidor. 2007. Computational design of antibody-affinity improvement beyond in vivo maturation. Nat Biotechnol 25(10): 1171-6.

Looger, L.L., M.A. Dwyer, J.J. Smith, and H.W. Hellinga. 2003. Computational design of receptor and sensor proteins with novel functions. Nature 423(6936): 185-90.

Looger, L.L., and H.W. Hellinga. 2001. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics. JMol Biol 307(1): 429-45.

Lopez de la Paz, M., E. Lacroix, M. Ramirez-Alvarado, and L. Serrano. 2001. Computer-aided design of beta-sheet peptides. J Mol Biol 312(1): 229-46.

Marshall, S.A., G.A. Lazar, A.J. Chirino, and J.R. Desjarlais. 2003. Rational design and engineering of therapeutic proteins. Drug Discov Today 8(5): 212-21.

Matthews, B.W., H. Nicholson, and W.J. Becktel. 1987. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc Natl Acad Sci U S A 84(19): 6663-7.

Mayo, S.L., B.D. Olafson, and W.A. Goddard. 1990. Dreiding—a generic force-field for molecular simulations. J Phys Chem 94(26): 8897-909.

Mayor, U., N.R. Guydosh, C.M. Johnson, J.G. Grossmann, S. Sato, G.S. Jas, S.M. Freund, D.O. Alonso, V. Daggett, and A.R. Fersht. 2003. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421(6925): 863-7.

Meiler, J., and D. Baker. 2006. ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility. Proteins 65(3): 538-48.

Mena, M.A., T.P. Treynor, S.L. Mayo, and P.S. Daugherty. 2006. Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library. Nat Biotechnol 24(12): 1569-71.

Mitra, K., T.A. Steitz, and D.M. Engelman. 2002. Rational design of "water-soluble" bacteri-orhodopsin variants. Protein Eng 15(6): 485-92.

Mok, K.H., L.T. Kuhn, M. Goez, I.J. Day, J.C. Lin, N.H. Andersen, and P.J. Hore. 2007. A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein. Nature 447(7140): 106-09.

Munoz, V., and L. Serrano. 1995a. Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides. J Mol Biol 245(3): 275-96.

Munoz, V., and L. Serrano. 1995b. Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence. J Mol Biol 245(3): 297-308.

Nemethy, G., S.J. Leach, and H.A. Scheraga. 1966. The influence of amino acid side chains on the free energy of helix-coil transitions. J Phys Chem 70: 998-1004.

Pinto, A.L., H.W. Hellinga, and J.P. Caradonna. 1997. Construction of a catalytically active iron superoxide dismutase by rational protein design. Proc Natl Acad Sci U S A 94(11): 5562-7.

Prajapati, R.S., M. Das, S. Sreeramulu, M. Sirajuddin, S. Srinivasan, V. Krishnamurthy, R. Ranjani, C. Ramakrishnan, and R. Varadarajan. 2007. Thermodynamic effects of proline introduction on protein stability. Proteins 66(2): 480-91.

Rees, D.C., L. DeAntonio, and D. Eisenberg. 1989. Hydrophobic organization of membrane proteins. Science 245(4917): 510-13.

Regan, L., and N.D. Clarke. 1990. A tetrahedral zinc(II)-binding site introduced into a designed protein. Biochemistry 29(49): 10878-83.

Reichmann, D., Y. Phillip, A. Carmi, and G. Schreiber. 2008. On the contribution of water-mediated interactions to protein-complex stability. Biochemistry 47(3): 1051-60.

Reina, J., E. Lacroix, S.D. Hobson, G. Fernandez-Ballester, V. Rybin, M.S. Schwab, L. Serrano, and C. Gonzalez. 2002. Computer-aided design of a PDZ domain to recognize new target sequences. Nat Struct Biol 9(8): 621-7.

Rothlisberger, D., O. Khersonsky, A.M. Wollacott, L. Jiang, J. DeChancie, J. Betker, J.L. Gallaher, E.A. Althoff, A. Zanghellini, O. Dym, S. Albeck, K.N. Houk, D.S. Tawfik, and D. Baker. 2008. Kemp elimination catalysts by computational enzyme design. Nature 453(7192): 190-195.

Saiki, R.K., D.H. Gelfand, S. Stoffel, S.J. Scharf, R. Higuchi, G.T. Horn, K.B. Mullis, and H.A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239(4839): 487-91.

Schweiker, K.L., A. Zarrine-Afsar, A.R. Davidson, and G.I. Makhatadze. 2007. Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions. Protein Sci 16(12): 2694-702.

Scott, K.A., D.O. Alonso, S. Sato, A.R. Fersht, and V. Daggett. 2007. Conformational entropy of alanine versus glycine in protein denatured states. Proc Natl Acad Sci U S A 104(8): 2661-6.

Serov, A.E., E.R. Odintzeva, I.V. Uporov, and V.I. Tishkov. 2005. Use of Ramachandran plot for increasing thermal stability of bacterial formate dehydrogenase. Biochemistry (Mosc) 70(7): 804-08.

Shifman, J.M., and S.L. Mayo. 2002. Modulating calmodulin binding specificity through computational protein design. J Mol Biol 323(3): 417-23.

Shifman, J.M., and S.L. Mayo. 2003. Exploring the origins of binding specificity through the computational redesign of calmodulin. Proc Natl Acad Sci U S A 100(23): 13274-9.

Shimaoka, M., J.M. Shifman, H. Jing, J. Takagi, S.L. Mayo, and T.A. Springer. 2000. Computational design of an integrin I domain stabilized in the open high affinity conformation. Nat Struct Biol 7(8): 674-8.

Slovic, A.M., H. Kono, J.D. Lear, J.G. Saven, and W.F. DeGrado. 2004. Computational design of water-soluble analogues of the potassium channel KcsA. Proc Natl Acad Sci U S A 101(7): 1828-33.

Slovic, A.M., C.M. Summa, J.D. Lear, and W.F. DeGrado. 2003. Computational design of a water-soluble analog of phospholamban. Protein Sci 12(2): 337-48.

Stemmer, W.P. 1994. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370(6488): 389-91.

Su, A., and S.L. Mayo. 1997. Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci 6(8): 1701-07.

Szilagyi, A., and P. Zavodszky. 2000. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: Results of a comprehensive survey. Structure 8(5): 493-504.

Tantillo, D.J., J. Chen, and K.N. Houk. 1998. Theozymes and compuzymes: Theoretical models for biological catalysis. Curr Opin Chem Biol 2: 743-50.

Trevino, S.R., S. Schaefer, J.M. Scholtz, and C.N. Pace. 2007. Increasing protein conformational stability by optimizing beta-turn sequence. J Mol Biol 373(1): 211-8.

Treynor, T.P., C.L. Vizcarra, D. Nedelcu, and S.L. Mayo. 2007. Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. Proc Natl Acad Sci U S A 104(1): 48-53.

van den Burg, B., and V.G. Eijsink. 2002. Selection of mutations for increased protein stability. Curr Opin Biotechnol 13(4): 333-7.

Ventura, S., M.C. Vega, E. Lacroix, I. Angrand, L. Spagnolo, and L. Serrano. 2002. Conformational strain in the hydrophobic core and its implications for protein folding and design. Nat Struct Biol 9(6): 485-93.

Villegas, V.V., A.R. Viguera, F.X. Aviles, and L. Serrano. 1995. Stabilization of proteins by rational design of alpha-helix stability using helix/coil transition theory. Fold Des 1(1): 29-34.

Vogt, G., and P. Argos. 1997. Protein thermal stability: Hydrogen bonds or internal packing? Fold Des 2(4): S40-46.

Walsh, C. 2001. Enabling the chemistry of life. Nature 409(6817): 226-31.

Walsh, S.T., V.I. Sukharev, S.F. Betz, N.L. Vekshin, and W.F. DeGrado. 2001. Hydrophobic core malleability of a de novo designed three-helix bundle protein. J Mol Biol 305(2): 361-73.

Wang, C., P. Bradley, and D. Baker. 2007. Protein-protein docking with backbone flexibility. J Mol Biol 373(2): 503-19.

White, G.W., S. Gianni, J.G. Grossmann, P. Jemth, A.R. Fersht, and V. Daggett. 2005. Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding. J Mol Biol 350(4): 757-75.

Wisz, M.S., C.Z. Garrett, and H.W. Hellinga. 1998. Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design. Biochemistry 37(23): 8269-77.

Zanghellini, A., L. Jiang, A.M. Wollacott, G. Cheng, J. Meiler, E.A. Althoff, D. Rothlisberger, and D. Baker. 2006. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15(12): 2785-94.

17 Modulating Protein Interactions by Rational and Computational Design

0 0

Post a comment