ArticleProtein science : a publication of the Protein Society2009
OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold.
Article in Protein science : a publication of the Protein Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- A computational method for design of connected catalytic networks in proteins.Protein science : a publication of the Protein Society · 2019Article
- Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids.ACS catalysis · 2017Article
- Computational approaches forBioscience reports · 2017Review
- Computational tools for the evaluation of laboratory-engineered biocatalysts.Chemical communications (Cambridge, England) · 2016Review
- A fast loop-closure algorithm to accelerate residue matching in computational enzyme design.Journal of molecular modeling · 2016Article
- Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.PloS one · 2016Article
- Computational strategies for the design of new enzymatic functions.Archives of biochemistry and biophysics · 2015Review
- Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm.Journal of molecular modeling · 2015Article
- MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.BMC bioinformatics · 2013Article
- Brønsted-Evans-Polanyi relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory.Journal of molecular modeling · 2012Article
- A matching algorithm for catalytic residue site selection in computational enzyme design.Protein science : a publication of the Protein Society · 2011Article
- Computational design of protein-ligand interfaces: potential in therapeutic development.Trends in biotechnology · 2011Review
- Evolution: a guide to perturb protein function and networks.Current opinion in structural biology · 2010Review
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3 authors.
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Abstract
One of the many challenging tasks of protein design is the introduction of a completely new function into an existing protein scaffold. In this study, we introduce a new computational procedure OptGraft for placing a novel binding pocket onto a protein structure so as its geometry is minimally perturbed. This is accomplished by introducing a two-level procedure where we first identify where are the most appropriate locations to graft the new binding pocket into the protein fold by minimizing the departure from a set of geometric restraints using mixed-integer linear optimization. On identifying the suitable locations that can accommodate the new binding pocket, CHARMM energy calculations are employed to identify what mutations in the neighboring residues, if any, are needed to ensure that the minimum energy conformation of the binding pocket conserves the desired geometry. This computational framework is benchmarked against the results available in the literature for engineering a copper binding site into thioredoxin protein. Subsequently, OptGraft is used to guide the transfer of a calcium-binding pocket from thermitase protein (PDB: 1thm) into the first domain of CD2 protein (PDB:1hng). Experimental characterization of three de novo redesigned proteins with grafted calcium-binding centers demonstrated that they all exhibit high affinities for terbium (Kd) approximately 22, 38, and 55 microM) and can selectively bind calcium over magnesium.
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