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 (R2∼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.
Highlights
Jensen first proposed that promiscuity shaped the evolution of primitive cells which presumably had minimal gene content [1,2,3]
We first establish that the variation in the computed promiscuity index (PromIndex) for various parameters is within acceptable limits
When we consider a protein from Enzyme Commission (EC) 6, even a single extra match with a protein from EC 3, will add more to the promiscuity index neutralizing the effect of the higher number of EC 3 proteins
Summary
Jensen first proposed that promiscuity shaped the evolution of primitive cells which presumably had minimal gene content [1,2,3]. Promiscuity is distinguished from moonlighting functions which are typically catalyzed using a domain of the protein different from the active site scaffold [9,10]. An attempt at quantifying promiscuity provides a measure of the catalytic efficiencies of an enzyme toward a pre-defined set of substrates, but is limited in its scope and scalability [18]. Since this method assumes a uniform chemical transformation on all substrates, it is more apt for the analysis of multispecific enzymes. ‘Rigorous and quantitative measures of promiscuity’ which will measure the ‘magnitude and degree of promiscuity in a wide range of proteins’ is required [8]
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