title: Modeling functional changes to Escherichia coli thymidylate synthase upon single residue replacements: a structure-based approach.
abstract: Escherichia coli thymidylate synthase (TS) is an enzyme that is indispensable to DNA synthesis and cell division, as it provides the only de novo source of dTMP by catalyzing the reductive methylation of dUMP, thus making it a key target for chemotherapeutic agents. High resolution X-ray crystallographic structures are available for TS and, owing to its relatively small size, successful experimental mutagenesis studies have been conducted on the enzyme. In this study, an in silico mutagenesis technique is used to investigate the effects of single amino acid substitutions in TS on enzymatic activity, one that employs the TS protein structure as well as a knowledge-based, four-body statistical potential. For every single residue TS variant, this approach yields both a global structural perturbation score and a set of local environmental perturbation scores that characterize the mutated position as well as all structurally neighboring residues. Global scores for the TS variants are capable of uniquely characterizing groups of residue positions in the enzyme according to their physicochemical, functional, or structural properties. Additionally, these global scores elucidate a statistically significant structure-function relationship among a collection of 372 single residue TS variants whose activity levels have been experimentally determined. Predictive models of TS variant activity are subsequently trained on this dataset of experimental mutants, whose respective feature vectors encode information regarding the mutated position as well as its six nearest residue neighbors in the TS structure, including their environmental perturbation scores.
authors: Laboratory for Structural Bioinformatics, School of Systems Biology, George Mason University , Manassas, VA , USA.
authors: Majid
authors: M
authors: Masso
keywords: Computational mutagenesis; Knowledge-based potential; Machine learning; Structure–function relationships; Thymidylate synthase; Variant function prediction
references: Antiviral Res. 2014 Jun;106:5-12
references: 24681122
references: Nucleic Acids Res. 2007;35(11):3823-35
references: 17526529
references: Bioinformatics. 2008 Sep 15;24(18):2002-9
references: 18632749
references: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references: 10592235
references: Nucleic Acids Res. 1999 Jan 1;27(1):355-7
references: 9847227
references: BMC Genomics. 2013;14 Suppl 4:S3
references: 24268064
references: Conf Proc IEEE Eng Med Biol Soc. 2011;2011:3221-4
references: 22255025
references: Biochemistry. 1990 Jul 31;29(30):6977-86
references: 2223755
references: Proc Natl Acad Sci U S A. 1990 May;87(10):3957-61
references: 2187197
references: Bioinformatics. 2005 Jul 15;21(14):3176-8
references: 15879453
references: Biochemistry. 1993 Oct 5;32(39):10283-8
references: 8399170
references: J Comput Chem. 2004 Oct;25(13):1605-12
references: 15264254
references: Radiology. 1982 Apr;143(1):29-36
references: 7063747
references: Adv Bioinformatics. 2014;2014:278385
references: 25197272
references: J Biol Chem. 1989 Nov 15;264(32):19132-7
references: 2681209
references: Proteins. 1992 Aug;13(4):352-63
references: 1518803
references: Biochem Biophys Res Commun. 2003 May 30;305(2):322-6
references: 12745077
references: Bioinformatics. 2007 Dec 1;23(23):3155-61
references: 17977887
references: Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9367-72
references: 10944209
references: J Comput Aided Mol Des. 1993 Aug;7(4):473-501
references: 8229096
references: Nucleic Acids Res. 2014 Jan;42(Database issue):D485-9
references: 24319146
references: Bioinformatics. 2003 Aug 12;19(12 ):1589-91
references: 12912846
references: Protein Eng Des Sel. 2009 Nov;22(11):665-71
references: 19690089
references: Science. 1991 Jul 12;253(5016):164-70
references: 1853201
references: Mini Rev Med Chem. 2010 Nov;10(13):1211-22
references: 20854257
references: Annu Rev Biochem. 1995;64:721-62
references: 7574499
references: Proteins. 2006 Jul 1;64(1):234-45
references: 16617425
references: Biochemistry. 2002 Jun 4;41(22):7021-9
references: 12033935
references: Bioinformatics. 2004 Oct 12;20(15):2479-81
references: 15073010
references: J Theor Biol. 2010 Oct 21;266(4):560-8
references: 20655929
references: Curr Opin Struct Biol. 1995 Apr;5(2):229-35
references: 7648326