OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold

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 (K d $ 22, 38, and 55 lM) and can selectively bind calcium over magnesium.

Evolution: a guide to perturb protein function and networks

“…Rather redesign means to target, or graft, the amino acids of a functional epitope to modulate function [38,39]. Often the focus of these experiments is on controlling the character of an interaction.…”

Computational strategies for the design of new enzymatic functions

“…31 Obviously, although Rosetta is probably the best-known suite of programs for enzyme design, there exist alternatives. For instance, the matching of the ideal ‘theozyme’ into an existing protein scaffold can be also carried out with OptGraft, 32 Scaffold-Selection, 33 and PRODA_MATCH. 34,35 A different strategy is employed by the SABER program.…”

Computational design of enzyme–ligand binding using a combined energy function and deterministic sequence optimization algorithm

“…residues surrounding the transition state. For catalytic residues, several matching algorithms that anchor these residues onto a set of inert scaffolds have been developed, including Dezymer [6], Orbit [7], RosettaMatch [8], OptGraft [9], ScaffoldSelection [10], ProdaMatch [11], AutoMatch [12], and Saber [13]. RosettaMatch has been shown to facilitate the discovery of de novo enzyme catalysts for targeted reactions including the retro-aldol reaction [14], the Kemp elimination reaction [15], the Diels-Alder reaction [16], and the hydrolysis of esters [17].…”