ArticlePloS one2012
A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 42 citations in OpenAlex.
- Enzyme promiscuity in the field of synthetic biology applied to white biotechnology: Opportunities and weaknesses.Biodesign research · 2025Review
- Analytical and functional aspects of protein-ligand interactions: Beyond induced fit and conformational selection.Archives of biochemistry and biophysics · 2021Review
- Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution.Chemical reviews · 2020Review
- Mechanisms of promiscuity among drug metabolizing enzymes and drug transporters.The FEBS journal · 2020Review
- Larger active site in an ancestral hydroxynitrile lyase increases catalytically promiscuous esterase activity.PloS one · 2020Article
- Inconclusive studies on possible CRISPR-Cas off-targets should moderate expectations about enzymes that have evolved to be non-specific.Journal of biosciences · 2018Article
- Editorial: Evolution acting on the same target, but at multiple levels: Proteins as the test case.Journal of biosciences · 2017Article
- Facilitating the Evolution of Esterase Activity from a Promiscuous Enzyme (Mhg) with Catalytic Functions of Amide Hydrolysis and Carboxylic Acid Perhydrolysis by Engineering the Substrate Entrance Tunnel.Applied and environmental microbiology · 2016Article
- Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.PLoS computational biology · 2016Article
- Article
- Computational analysis of perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus.F1000Research · 2016Article
- Biological messiness vs. biological genius: Mechanistic aspects and roles of protein promiscuity.The Journal of steroid biochemistry and molecular biology · 2015Review
- Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution.Angewandte Chemie (International ed. in English) · 2015Review
- Molecular annotation of ketol-acid reductoisomerases from Streptomyces reveals a novel amino acid biosynthesis interlock mediated by enzyme promiscuity.Microbial biotechnology · 2015Article
- Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template.F1000Research · 2014Article
- Modeling catalytic promiscuity in the alkaline phosphatase superfamily.Physical chemistry chemical physics : PCCP · 2013Article
- Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.F1000Research · 2013Article
- Article
- Enumerating pathways of proton abstraction based on a spatial and electrostatic analysis of residues in the catalytic site.PloS one · 2012Article
- Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Promiscuity, the basis for the evolution of new functions through 'tinkering' of residues in the vicinity of the catalytic site, is yet to be quantitatively defined. We present a computational method Promiscuity Indices Estimator (PROMISE)--based on signatures derived from the spatial and electrostatic properties of the catalytic residues, to estimate the promiscuity (PromIndex) of proteins with known active site residues and 3D structure. PromIndex reflects the number of different active site signatures that have congruent matches in close proximity of its native catalytic site, the quality of the matches and difference in the enzymatic activity. Promiscuity in proteins is observed to follow a lognormal distribution (μ = 0.28, σ = 1.1 reduced chi-square = 3.0E-5). The PROMISE predicted promiscuous functions in any protein can serve as the starting point for directed evolution experiments. PROMISE ranks carboxypeptidase A and ribonuclease A amongst the more promiscuous proteins. We have also investigated the properties of the residues in the vicinity of the catalytic site that regulates its promiscuity. Linear regression establishes a weak correlation (R(2)∼0.1) between certain properties of the residues (charge, polar, etc) in the neighborhood of the catalytic residues and PromIndex. A stronger relationship states that most proteins with high promiscuity have high percentages of charged and polar residues within a radius of 3 Å of the catalytic site, which is validated using one-tailed hypothesis tests (P-values∼0.05). Since it is known that these characteristics are key factors in catalysis, their relationship with the promiscuity index cross validates the methodology of PROMISE.
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