High-throughput identification of protein mutant stability computed from a double mutant fitness landscape

Protein Science

Volumn 25, Issue 2, 2016, Pages 530-539

  Wu, Nicholas C ^a,b,c   Olson, C Anders ^a   Sun, Ren ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

fitness profiling; mutagenesis; mutant stability prediction; protein stability

Indexed keywords

MUTANT PROTEIN; BACTERIAL PROTEIN; IGG FC-BINDING PROTEIN, STREPTOCOCCUS;

ARTICLE; GENE CLUSTER; HIGH THROUGHPUT SCREENING; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; THERMODYNAMICS; AMINO ACID SUBSTITUTION; CHEMISTRY; GENETICS; MOLECULAR MODEL; MUTATION; PROTEIN TERTIARY STRUCTURE; STREPTOCOCCUS;

AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; MODELS, MOLECULAR; MUTATION; PROTEIN STABILITY; PROTEIN STRUCTURE, TERTIARY; STREPTOCOCCUS; THERMODYNAMICS;

EID: 84978107423     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2840     Document Type: Article

References (18)

1. Magliery TJ, Lavinder JJ, Sullivan BJ (2011) Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems. Curr Opin Chem Biol 15:443–451.
2. Giver L, Gershenson A, Freskgard PO, Arnold FH (1998) Directed evolution of a thermostable esterase. Proc Natl Acad Sci U S A 95:12809–12813.
3. Foit L, Morgan GJ, Kern MJ, Steimer LR, von Hacht AA, Titchmarsh J, Warriner SL, Radford SE, Bardwell JC. (2009) Optimizing protein stability in vivo. Mol Cell 36:861–871.
4. Fowler DM, Fields S (2014) Deep mutational scanning: a new style of protein science. Nat Methods 11:801–807.
5. Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH. (2005) Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci USA 102:606–611.
6. Wilke CO, Bloom JD, Drummond DA, Raval A (2005) Predicting the tolerance of proteins to random amino acid substitution. Biophys J 89:3714–3720.
7. Bloom JD, Labthavikul ST, Otey CR, Arnold FH (2006) Protein stability promotes evolvability. Proc Natl Acad Sci USA 103:5869–5874.
8. Bershtein S, Segal M, Bekerman R, Tokuriki N, Tawfik DS (2006) Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444:929–932.
9. Gong LI, Suchard MA, Bloom JD (2013) Stability-mediated epistasis constrains the evolution of an influenza protein. Elife 2:e00631
10. Olson CA, Wu NC, Sun R (2014) A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain. Curr Biol 24:2643–2651.
11. Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS (2007) The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369:1318–1332.
12. Gallagher T, Alexander P, Bryan P, Gilliland GL (1994) Two crystal structures of the b1 immunoglobulin-binding domain of streptococcal protein g and comparison with NMR. Biochemistry 33:4721–4729.
13. Das R, Baker D (2008) Macromolecular modeling with rosetta. Annu Rev Biochem 77:363–382.
14. Kellogg EH, Leaver-Fay A, Baker D (2011) Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins 79:830–838.
15. Hopp TP, Woods KR (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 78:3824–3828.
16. Potapov V, Cohen M, Schreiber G (2009) Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. Protein Eng Des Sel 22:553–560.
17. Stein RR, Marks DS, Sander C (2015) Inferring pairwise interactions from biological data using maximum-entropy probability models. PLoS Comput Biol 11:e1004182
18. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637.