Predicting affinity- and specificity-enhancing mutations at protein-protein interfaces

Biochemical Society Transactions

Volumn 41, Issue 5, 2013, Pages 1166-1169

  Sharabi, Oz ^a   Shirian, Jason ^a   Shifman, Julia M ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Binding affinity; Binding landscape; Protein design; Protein protein interaction; Saturated mutagenesis

Indexed keywords

ACETYLCHOLINESTERASE; FASCICULIN; MATRIX METALLOPROTEINASE 14; SNAKE VENOM; TISSUE INHIBITOR OF METALLOPROTEINASE 2;

ARTICLE; BINDING AFFINITY; CALCULATION; ENZYME ACTIVE SITE; FITNESS; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; STATIC ELECTRICITY; SYNTHETIC BIOLOGY; TORPEDO CALIFORNICA;

COMPUTATIONAL BIOLOGY; HUMANS; MATRIX METALLOPROTEINASE 14; MATRIX METALLOPROTEINASE 9; MUTATION; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPS; SENSITIVITY AND SPECIFICITY; TISSUE INHIBITOR OF METALLOPROTEINASE-2;

EID: 84884653264     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20130121     Document Type: Article

References (29)

1. Ernst, A. and Sidhu, S.S. (2009) Phage display systems for protein engineering. In Protein Engineering and Design (Park, S.J. and Cochran, J.R., eds), pp. 1-22, CRC Press, Boca Raton
2. Moore, S.J., Olsen, M.J., Cochran, J.R. and Cochran, F.V. (2009) Cell surface display systems for protein engineering. In Protein Engineering and Design (Park, S.J. and Cochran, J.R., eds), pp. 24-50, CRC Press, Boca Raton
3. Barendt, P.A. and Sarkar, C.A. (2009) Cell-free display systems for protein engineering. In Protein Engineering and Design (Park, S.J. and Cochran, J.R., eds), pp. 51-82, CRC Press, Boca Raton
4. Skelton, N.J., Koehler, M.F., Zobel, K., Wong, W.L., Yeh, S., Pisabarro, M.T., Yin, J.P., Lasky, L.A. and Sidhu, S.S. (2003) Origins of PDZ domain ligand specificity: structure determination and mutagenesis of the Erbin PDZ domain. J. Biol. Chem. 278, 7645-7654
5. Yang, J., Swiminathan, C.P., Huang, Y., Guan, R., Cho, S., Kieke, M.C., Kranz, D.M., Mariuzza, R.A. and Sundberg, E.J. (2003) Dissecting cooperative and additive binding energetics in the affinity maturation pathway of a protein-protein interface. J. Biol. Chem. 278, 50412-50421
6. Zhang, Z. and Palzkill, T. (2003) Determinants of binding affinity and specificity for the interaction of TEM-1 and SME-1 β-lactamase with β-lactamase inhibitory protein. J. Biol. Chem. 278, 45706-45712
7. Pal, G., Kouadio, J.L., Artis, D.R., Kossiakoff, A.A. and Sidhu, S.S. (2006) Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. J. Biol. Chem. 281, 22378-22385
8. Luginbühl, B., Kanyo, Z., Jones, R.M., Fletterick, R.J., Prusiner, S.B., Cohen, F.E., Williamson, R.A., Burton, D.R. and Plückthun, A. (2006) Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation. J. Mol. Biol. 363, 75-97
9. Steiner, D., Forrer, P. and Plückthun, A. (2008) Efficient selection of DARPins with sub-nanomolar affinities using SRP phage display. J. Mol. Biol. 382, 1211-1227
10. Zahnd, C., Wyler, E., Schwenk, J.M., Steiner, D., Lawrence, M.C., McKern, N.M., Pecorari, F., Ward, C.W., Joos, T.O. and Plückthun, A. (2007) A designed ankyrin repeat protein evolved to picomolar affinity to Her2. J. Mol. Biol. 369, 1015-1028
11. Sharabi, O., Erijman, A. and Shifman, J.M. (2013) Computational methods for controlling binding specificity. Methods Enzymol. 523, 42-59
12. Dahiyat, B.I. and Mayo, S.L. (1997) De novo protein design: fully automated sequence selection. Science 278, 82-87
13. Sharabi, O., Yanover, C., Dekel, A. and Shifman, J.M. (2011) Optimizing energy function for protein-protein interface design. J. Comput. Chem. 32, 23-32
14. Sharabi, O., Dekel, A. and Shifman, J.M. (2011) Triathlon for energy functions: who is the winner for design of protein-protein interactions? Proteins 79, 1487-1498
15. Harel, M., Kleywegt, G.J., Ravelli, R.B., Silman, I. and Sussman, J.L. (1995) Crystal structure of an acetylcholinesterase-fasciculin complex: interaction of a three-fingered toxin from snake venom with its target. Structure 3, 1355-1366
16. Radic, Z., Kirchhoff, P.D., Quinn, D.M., McCammon, J.A. and Taylor, P. (1997) Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase: distinctions between active center ligands and fasciculin. J. Biol. Chem. 272, 23265-23277
17. Bourne, Y., Taylor, P. and Marchot, P. (1995) Acetylcholinesterase inhibition by fasciculin: crystal structure of the complex. Cell 83, 503-512
18. Kryger, G., Harel, M., Giles, K., Toker, L., Velan, B., Lazar, A., Kronman, C., Barak, D., Ariel, N., Shafferman, A., Silman, I. and Sussman, J.L. (2000) Structures of recombinant native and E202Q mutant human acetylcholinesterase complexed with the snake-venom toxin fasciculin-II. Acta Crystallogr., Sect. D: Biol. Crystallogr. 56, 1385-1394
19. Selzer, T., Albeck, S. and Schreiber, G. (2000) Rational design of faster associating and tighter binding protein complexes. Nat. Struct. Biol. 7, 537-541
20. Sammond, D.W., Eletr, Z.M., Purbeck, C., Kimple, R.J., Siderovski, D.P. and Kuhlman, B. (2007) Structure-based protocol for identifying mutations that enhance protein-protein binding affinities. J. Mol. Biol. 371, 1392-1404
21. Haidar, J.N., Pierce, B., Yu, Y., Tong, W., Li, M. and Weng, Z. (2009) Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC. Proteins: Struct., Funct., Bioinf. 74, 948-960
22. Reynolds, K.A., Hanes, M.S., Thomson, J.A., Atczak, A.J., Berger, J.M., Bonomo, R.A., Kirsch, J.F. and Handel, T.M. (2008) Computational redesign of the SHV-1 β-lactamase/β-lactamase inhibitor protein interface. J. Mol. Biol. 382, 1265-1275
23. Hao, J., Serohijos, A.W., Newton, G., Tassone, G., Wang, Z., Sgroi, D.C., Dokholyan, N.V. and Basilion, J.P. (2008) Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers. PLoS Comput. Biol. 4, e1000138
24. Lippow, S.M., Wittrup, K.D. and Tidor, B. (2007) Computational design of antibody-affinity improvement beyond in vivo maturation. Nat. Biotechnol. 25, 1171-1176
25. Brinckerhoff, C.E. and Matrisian, L.M. (2002) Matrix metalloproteinases: a tail of a frog that became a prince. Nat. Rev. Mol. Cell Biol. 3, 207-214
26. Wei, S., Chen, Y., Chung, L., Nagase, H. and Brew, K. (2003) Protein engineering of the tissue inhibitor of metalloproteinase 1 (TIMP-1) inhibitory domain: in search of selective matrix metalloproteinase inhibitors. J. Biol. Chem. 278, 9831-9834
27. Hamze, A.B., Wei, S., Bahudhanapati, H., Kota, S., Acharya, K.R. and Brew, K. (2007) Constraining specificity in the N-domain of tissue inhibitor of metalloproteinases-1: gelatinase-selective inhibitors. Protein Sci. 16, 1905-1913
28. Fromer, M. and Shifman, J.M. (2009) Tradeoff between stability and multispecificity in the design of promiscuous proteins. PLoS Comput. Biol. 5, e1000627
29. Yosef, E., Politi, R., Choi, M.H. and Shifman, J.M. (2009) Computational design of calmodulin mutants with up to 900-fold increase in binding specificity. J. Mol. Biol. 385, 1470-1480