Coarse‐grained lattice model simulations of sequence‐structure fitness of a ribosome‐inactivating protein

Abstract

Many realistic protein‐engineering design problems extend beyond the computational limits of what is considered practical when applying all‐atom molecular‐dynamics simulation methods. Lattice models provide computationally robust alternatives, yet most are regarded as too simplistic to accurately capture the details of complex designs. We revisit a coarse‐grained lattice simulation model and demonstrate that a multiresolution modeling approach of reconstructing all‐atom structures from lattice chains is of sufficient accuracy to resolve the comparability of sequence‐structure modifications of the ricin A‐chain (RTA) protein fold. For a modeled structure, the unfolding–folding transition temperature was calculated from the heat capacity using either the potential energy from the lattice model or the all‐atom CHARMM19 force‐field plus a generalized Born solvent approximation. We found, that despite the low‐resolution modeling of conformational states, the potential energy functions were capable of detecting the relative change in the thermodynamic transition temperature that distinguishes between a protein design and the native RTA fold in excellent accord with reported experimental studies of thermal denaturation. A discussion is provided of different sequences fitted to the RTA fold and a possible unfolding model. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 153–159, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Introduction of a disulfide bond leads to stabilization and crystallization of a ricin immunogen

“…Within these regions, pairwise residue sites (Table I) were selected for placement of the SS‐bonds to hinder thermal unraveling of the molecule. The selection of sites was also guided by a previous simulation study of RTA and the truncated chain using a coarse‐grained lattice model 15. The starting modeled structure of the RTA immunogen was built from the PDB structure 1RTC13 and crystallographic waters were deleted.…”

“…A recent computational study of the thermal unfolding of RTA1‐33/44‐198 using coarse‐grained lattice models with all‐atom reconstruction and molecular‐dynamics (MD) simulations predicted pockets of hypermobility 15. Identification of specific regions of local disorder during unfolding provides a rational basis for the follow‐on strategy of introducing precisely localized disulfide (SS‐) bonds to improve RTA1‐33/44‐198.…”