Title
IPRO+/-: a computational protein design tool allowing not only for amino acid changes but also insertions and deletions
Conference Dates
September 15-19, 2019
Abstract
The need for enzymes with new or improved catalytic properties and specificities underpins many challenges in
both biotechnology and pharmaceutical industry. This is typically carried out by changing the native amino acid
composition through single or multiple mutations or recombination. Many computational strategies have been
developed for suggesting amino acid changes (i.e., mutations) likely to usher an altered substrate or cofactor
specificity, improved thermostability or higher turnover. However, by perusing protein family alignments one can
immediately notice the ubiquitous presence of gaps. These gaps imply that not all active enzyme variants have
the same backbone length with insertions and deletions (indels) contributing significantly to the possibilities of
altering enzyme activity by drastically affecting protein repacking. Currently, no algorithms exist which can
systemically position multiple insertions or deletions during in silico protein redesign. In this contribution we
introduce IPRO+/-, a first of its kind integrated environment for protein redesign with respect to a single or
multiple binding imperatives by not only predicting amino acid changes, but also insertions and deletions (see
Figure 1). IPRO+/- allows the user to run standalone programs for (a) predicting energy minimized structural
models of an enzyme with a desired indels and/or mutations, (b) computing binding free energies between
proteins and small molecules, and (c) performing energy minimization on any protein or protein complex. The
contribution will provide an overview of the tasks involved in IPRO+/-, input language terminology, algorithmic
details, software implementation specifics and application highlights. IPRO+/- will be made freely downloadable
from http://www.maranasgroup.com/software.htm upon publication.
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Recommended Citation
Ratul Chowdhury, Matthew J Grisewood, Costas D Maranas, and John Brezovec, "IPRO+/-: a computational protein design tool allowing not only for amino acid changes but also insertions and deletions" in "Enzyme Engineering XXV", Huimin Zhao, University of Illinois at Urbana-Champaign, USA John Wong, Pfizer, USA Eds, ECI Symposium Series, (2019). https://dc.engconfintl.org/enzyme_xxv/128