Systematic optimization model and algorithm for binding sequence selection in computational enzyme design

Protein Science

Volumn 22, Issue 7, 2013, Pages 929-941

  Huang, Xiaoqiang ^a   Han, Kehang ^a   Zhu, Yushan ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

Active site recapitulation; Binding; Computational enzyme design; Computational protein design; Global optimization; Protein ligand interaction

Indexed keywords

ENZYME; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; CATALYSIS; CONTROLLED STUDY; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; GEOMETRY; MATHEMATICAL MODEL; MATHEMATICAL PHENOMENA; MOLECULAR MODEL; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN MOTIF; SYSTEMATIC OPTIMIZATION MODEL; THEORETICAL MODEL;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; ENZYMES; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; THERMODYNAMICS;

EID: 84881308208     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2275     Document Type: Article

References (50)

1. Dahiyat BI, Mayo SL (1997) De novo protein design: fully automated sequence selection. Science 278:82-87.
2. Pinto AL, Hellinga HW, Caradonna JP (1997) Construction of a catalytically active iron superoxide dismutase by rational protein design. Proc Natl Acad Sci USA 94:5562-5567.
3. Benson DE, Wisz MS, Hellinga HW (2000) Rational design of nascent metalloenzymes. Proc Natl Acad Sci USA 97:6292-6297.
4. Benson DE, Haddy AE, Hellinga HW (2002) Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry 41:3262-3269.
5. Hellinga HW, Richards FM (1991) Construction of new ligand-binding sites in proteins of known structure Computer-aided modeling of sites with predefined geometry. J Mol Biol 222:763-785.
6. Bolon DN, Mayo SL (2001) Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 98:14274-14279.
7. Lassila JK, Privett HK, Allen BD, Mayo SL (2006) Combinatorial methods for small-molecule placement in computational enzyme design. Proc Natl Acad Sci USA 103:16710-16715.
8. Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL, Baker D (2008) De novo computational design of retro-aldol enzymes. Science 319:1387-1391.
9. Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D (2008) Kemp elimination catalysts by computational enzyme design. Nature 453:190-195.
10. Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St.Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular diels-alder reaction. Science 329:309-313.
11. Fersht A (1998) Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding. New York: WH Freeman.
12. Baker D (2010) An exciting but challenging road ahead for computational enzyme design. Protein Sci 19:1817-1819.
13. Lassila JK, Baker D, Herschlag D (2010) Origins of catalysis by computationally designed retroaldolase enzymes. Proc Natl Acad Sci USA 107:4937-4942.
14. Frushicheva MP, Cao J, Chu ZT, Warshel A (2010) Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase. Proc Natl Acad Sci USA 107:16869-16874.
15. Khersonsky O, Rothlisberger D, Wollacott AM, Murphy P, Dym O, Albeck S, Kiss G, Houk KN, Baker D, Tawfik DS (2011) Optimization of the in-silico-designed kemp eliminase ke70 by computational design and directed evolution. J Mol Biol 407:391-412.
16. Privett HK, Kiss G, Lee TM, Blomberg R, Chica RA, Thomas LM, Hilvert D, Houk KN, Mayo SL (2012) Iterative approach to computational enzyme design. Proc Natl Acad Sci USA 109:3790-3795.
17. Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Rothlisberger D, Baker D (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15:2785-2794.
18. Leach AR (2001) Molecular modelling: principles and applications. London: Prentice Hall.
19. Zhu YS (2007) Mixed-integer linear programming algorithm for a computational protein design problem. Ind Eng Chem Res 46:839-845.
20. Xiang Z, Honig B (2001) Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 311:421-430.
21. Desmet J, Demaeyer M, Hazes B, Lasters I (1992) The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356:539-542.
22. Goldstein RF (1994) Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J 66:1335-1340.
23. Kuhlman B, Baker D (2000) Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 97:10383-10388.
24. Jaramillo A, Wernisch L, Hery S, Wodak SJ (2002) Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc Natl Acad Sci USA 99:13554-13559.
25. Chakrabarti R, Klibanov AM, Friesner RA (2005) Computational prediction of native protein ligand-binding and enzyme active site sequences. Proc Natl Acad Sci USA 102:10153-10158.
26. Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJT, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, Forouhar F, Kornhaber GJ, Hunt JF, Montelione GT, Tong L, Houk KN, Hilvert D, Baker D (2012) Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. J Am Chem Soc 134:16197-16206.
27. Fung HK, Floudas CA, Taylor MS, Zhang L, Morikis D (2008) Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2. Biophys J 94:584-599.
28. Fung HK, Welsh WJ, Floudas CA (2008) Computational de novo peptide and protein design: rigid templates versus flexible templates. Ind Eng Chem Res 47:993-1001.
29. Klepeis JL, Floudas CA, Morikis D, Tsokos CG, Lambris JD (2004) Design of peptide analogues with improves activity using a novel de novo protein design approach. Ind Eng Chem Res 43:3817-3826.
30. Fung HK, Rao S, Floudas CA, Prokopyev O, Pardalos PM, Rendl F (2005) Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in de novo protein design. J Combin Optim 10:41-60.
31. Khoury GA, Fazelinia H, Chin JW, Pantazes RJ, Cirino PC, Maranas CD (2009) Computational design of Candida boidinii xylose reductase for altered cofactor specificity. Protein Sci 18:2125-2138.
32. Boas FE, Harbury PB (2008) Design of protein-ligand binding based on the molecular-mechanics energy model. J Mol Biol 380:415-424.
33. Bellows ML, Fung HK, Taylor MS, Floudas CA, Lopez de Victoria A, Morikis D (2010) New compstatin variants through two de novo protein design frameworks. Biophys J 98:2337-2346.
34. Bellows ML, Taylor MS, Cole PA, Shen L, Siliciano RF, Fung HK, Floudas CA (2010) Discovery of entry inhibitors for HIV-1 via a new de novo protein design framework. Biophys J 99:3445-3453.
35. Bellows-Peterson ML, Fung HK, Floudas CA, Kieslich CA, Zhang L, Morikis D, Wareham KJ, Monk PN, Hawksworth OA, Woodruff TM (2012) De novo peptide design with c3a receptor agonist and antagonist activities: theoretical predictions and experimental validation. J Med Chem 55:4159-4168.
36. Klepeis JL, Floudas CA, Morikis D, Tsokos CG, Argyropoulos E, Spruce L, Lambris JD (2003) Integrated computational and experimental approach for lead optimization and design of compstatin variants with improved activity. J Am Chem Soc 125:8422-8423.
37. Looger LL, Dwyer MA, Smith JJ, Hellinga HW (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423:185-190.
38. Luo WJ, Pei JF, Zhu YS (2010) A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity. J Mol Model 16:903-913.
39. Huang XQ, Yang J, Zhu YS (2013) A solvated ligand rotamer approach and its application in computational protein design. J Mol Model 19:1355-1367.
40. Lei YL, Luo WJ, Zhu YS (2011) A matching algorithm for catalytic residue site selection in computational enzyme design. Protein Sci 20:1566-1575.
41. Duggleby HJ, Tolley SP, Hill CP, Dodson EJ, Dodson G, Moody PCE (1995) Penicillin acylase has a singleamino-acid catalytic center. Nature 373:264-268.
42. McVey CE, Walsh MA, Dodson GG, Wilson KS, Brannigan JA (2001) Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism. J Mol Biol 313:139-150.
43. Kim Y, Hol WGJ (2001) Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid and glutarate: insight into the basis of its substrate specificity. Chem Biol 8:1253-1264.
44. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616.
45. Dahiyat BI, Benjamin Gordon D, Mayo SL (1997) Automated design of the surface positions of protein helices. Protein Sci 6:1333-1337.
46. Dominy BN, Brooks CL (1999) Development of a generalized born model parametrization for proteins and nucleic acids. J Phys Chem B 103:3765-3773.
47. Vizcarra CL, Zhang NG, Marshall SA, Wingreen NS, Zeng C, Mayo SL (2008) An improved pairwise decomposable finite-difference poisson-boltzmann method for computational protein design. J Comput Chem 29:1153-1162.
48. Zhang N, Zeng C, Wingreen NS (2004) Fast accurate evaluation of protein solvent exposure. Proteins Struct Funct Bioinf 57:565-576.
49. Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M (1995) The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J Comput Chem 16:273-284.
50. Creamer TP (2000) Side-chain conformational entropy in protein unfolded states. Proteins Struct Funct Bioinf 40:443-450.