Journal article
Prediction of distal residue participation in enzyme catalysis
Protein science, v 24(5), pp 762-778
01 May 2015
PMID: 25627867
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of
Pseudomonas putida
nitrile hydratase (ppNH) and for
E
scherichia
coli
alkaline phosphatase (AP). The multilayer active sites of
P
.
putida
nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log
ZP
scores, as is the single-layer active site of
P
.
putida
ketosteroid isomerase. The
log
ZP
score cutoff utilized here results in over-prediction of distal residue involvement in
E. coli
alkaline phosphatase. While fewer experimental data points are available for
P
.
putida
mandelate racemase and for human carbonic anhydrase II, the POOL
log
ZP
scores properly predict the previously reported participation of distal residues.
Metrics
Details
- Title
- Prediction of distal residue participation in enzyme catalysis
- Creators
- Heather R Brodkin - Brandeis UniversityNicholas A DeLateur - Northeastern UniversitySrinivas Somarowthu - Northeastern UniversityCaitlyn L Mills - Northeastern UniversityWalter R Novak - Brandeis UniversityPenny J Beuning - Northeastern UniversityDagmar Ringe - Brandeis UniversityMary Jo Ondrechen - Northeastern University
- Publication Details
- Protein science, v 24(5), pp 762-778
- Publisher
- BlackWell Publishing Ltd
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biochemistry and Molecular Biology
- Web of Science ID
- WOS:000353524700018
- Scopus ID
- 2-s2.0-84943637672
- Other Identifier
- 991020837744304721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology