Neural network-based prediction of mutation-induced protein stability changes in staphylococcal nuclease at 20 residue positions

Proteins: Structure, Function and Genetics

Volumn 59, Issue 2, 2005, Pages 147-151

  Frenz, Christopher M ^a  

^a NEW YORK MEDICAL COLLEGE   (United States)

Author keywords

Neural networks; Protein stability

Indexed keywords

BACTERIAL ENZYME; MUTANT PROTEIN; NUCLEASE;

ACCURACY; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; CALCULATION; GENE MUTATION; NERVE CELL NETWORK; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN STABILITY; SCORING SYSTEM; STAPHYLOCOCCUS; WILD TYPE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMINO ACIDS; ENZYME STABILITY; MICROCOCCAL NUCLEASE; MUTAGENESIS; MUTAGENESIS, SITE-DIRECTED; NEURAL NETWORKS (COMPUTER); PROTEIN CONFORMATION; RECOMBINANT PROTEINS; STAPHYLOCOCCUS;

EID: 16344386178     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20400     Document Type: Article

References (14)

1. Cleland JL, Jones AJS, Craik CS. Introduction to protein engineering. In: Cleland JL, Craik CS, editors. Protein engineering: principles and practice. New York: Wiley-Liss; 1996. p 1-32.
2. Braxton S. Protein engineering for stability. In: Cleland JL, Craik CS, editors. Protein engineering: principles and practice. New York: Wiley-Liss; 1996. p 299-316.
3. Topham CM, Srinivasan N, Blundell TL. Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables. Protein Eng 1997;10:7-21.
4. Borjesson U, Hunenberger PH. Effect of mutations involving charged residues on the stability of staphylococcal nuclease: a continuum electrostatics study. Protein Eng 2003;16:831-840.
5. Shortle D, Stites WE, Meeker AK. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry 1990;29:8033-8041.
6. Green SM, Meeker AK, Shortle D. Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: evidence for mutational effects on the free energy of the denatured state. Biochemistry 1992;31:5717-5728.
7. Green SM, Shortle D. Patterns of nonadditivity between pairs of stability mutations in staphylococcal nuclease. Biochemistry 1993;32:10131-10139.
8. Meeker AK, Garcia-Moreno EB, Shortle D. Contributions of the ionizable amino acids to the stability of staphylococcal nuclease. Biochemistry 1996;35:6443-6449.
9. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. CABIOS 1992;8:275-282.
10. Levin S, Satir BH. POLINA: detection and evaluation of single amino acid substitutions in protein superfamilies. Bioinformatics 1998;14:374-375.
11. Fausett L. Fundamentals of neural networks. New Jersey: Prentice Hall; 1994.
12. Spencer DS, Stites WE. The M32L substitution of staphylococcal nuclease: diasagreement between theoretical prediction and experimental protein stability. J Mol Biol 1996;257:497-499.
13. Rooman M, Gilis D. Different derivations of knowledge-based potentials and analysis of their robustness and context-dependent predictive power. Eur J Biochem 1998;254:135-143.
14. Fogler HS. Elements of chemical reaction engineering, third ed. New York: Pearson Education; 1998.