Effect of Single-Point Sequence Alterations on the Aggregation Propensity of a Model Protein

Abstract

Sequences of contemporary proteins are believed to have evolved through process that optimized their overall fitness including their resistance to deleterious aggregation.Biotechnological processing may expose therapeutic proteins to conditions that are much more conducive to aggregation than those encountered in a cellular environment. An important task of protein engineering is to identify alternative sequences that would protect proteins when processed at high concentrations without altering their native structure associated with specific biological function. Our computational studies exploit parallel tempering simulations of coarse-grained model proteins to demonstrate that isolated amino-acid residue substitutions can result in significant changes in the aggregation resistance of the protein in a crowded environment while retaining protein structure in isolation. A thermodynamic analysis of protein clusters subject to competing processes of folding and association shows that moderate mutations can produce effects similar to those caused by changes in system conditions, including temperature, concentration, and solvent composition that affect the aggregation propensity. The range of conditions where a protein can resist aggregation can therefore be tuned by sequence alterations although the protein generally may retain its generic ability for aggregation. *dnb@berkeley.edu 2

Simulations of nucleation and elongation of amyloid fibrils

“…11͑a͒. Equation ͑10͒ also predicts that increasing the peptide length ͑E ϰ L͒ should result in lower C e , in accordance with the experimental finding that the final solubility of ␤ 26-43 is 12-fold lower than that of ␤ [26][27][28][29][30][31][32][33][34][35][36][37][38][39][40] . 71 The equilibrium solubility counted from simulations is between the two theoretical values, as shown in Fig.…”

“…So far, the results we presented only involve the singlefibril case, which tries to mimic heterogeneous nucleation on a specific number of preset heterogeneous seeds ͑e.g., heterogeneous nucleation of A␤ [26][27][28][29][30][31][32][33][34][35][36][37][38][39][40] on A␤ [26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43] , 17 where homogeneous nucleation of A␤ [26][27][28][29][30][31][32][33][34][35][36][37][38][39][40] is unable to occur under the same conditions͒. When homogeneous nucleation occurs and an unspecific number of multiple...…”

“…Based on simulations of a relatively small number of polypeptides and their sequences, a rich phase diagram of possible ordered morphologies was identified. Based on a lattice model 37 for two chains each with 64 residues, the role of sequences on the nature of polymerization was investigated. In an off-lattice model [38][39][40] where the protein structure is of intermediate resolution, molecular dynamics simulations were carried out for tens of 16-mer chains which showed that an amorphous aggregate is a precursor to the fibrillization.…”

The competition between protein folding and aggregation: Off-lattice minimalist model studies

“…Computational costs preclude the determination of the average lifetime of fully folded states at aggregation-prone conditions. Comparisons with relatively faster on-lattice simulations for up to four adjacent 64-mers show a significant increase in aggregation resistance once all the chains have acquired near-native conformations (Bratko et al, 2004).…”

Aggregation in Protein-Based Biotherapeutics: Computational Studies and Tools to Identify Aggregation-Prone Regions

“…14,15,[28][29][30][31][32] In an early study, Gupta et al 28 used multiple chain systems constructed from simple two-dimensional (2D) hydrophobic polar (HP) lattice models. 28 Effects of the changes in denaturant and protein concentration were investigated using Monte Carlo (MC) simulations.…”