a measure of the broad substrate specificity of enzymes based on ‘duplicate’ catalytic residues的基于u201c复制u201d的广泛的底物特异性的酶催化残基.pdfVIP

A Measure of the Broad Substrate Specificity of Enzymes Based on ‘Duplicate’ Catalytic Residues 1 ´ 2 3 Sandeep Chakraborty *, Bjarni Asgeirsson , Basuthkar J. Rao 1 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India, 2 Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland, 3 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India Abstract The ability of an enzyme to select and act upon a specific class of compounds with unerring precision and efficiency is an essential feature of life. Simultaneously, these enzymes often catalyze the reaction of a range of similar substrates of the same class, and also have promiscuous activities on unrelated substrates. Previously, we have established a methodology to quantify promiscuous activities in a wide range of proteins. In the current work, we quantitatively characterize the active site for the ability to catalyze distinct, yet related, substrates (BRASS). A protein with known structure and active site residues provides the framework for computing ‘duplicate’ residues, each of which results in slightly modified replicas of the active site scaffold. Such spatial congruence is supplemented by Finite difference Poisson Boltzmann analysis which filters out electrostatically unfavorable configurations. The congruent configurations are used to compute an index (BrassIndex), which reflects the broad substrate profile of the active site. We identify an acetylhydrolase and a methyltransferase as having the lowest and highest BrassIndex, respectively, from a set of non-homologous proteins extracted from the Cataly