Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility

Abstract

Protein aggregation is a hallmark of a growing number of human disorders and constitutes a major bottleneck in the manufacturing of therapeutic proteins. Therefore, there is a strong need of in-silico methods that can anticipate the aggregative properties of protein variants linked to disease and assist the engineering of soluble protein-based drugs. A few years ago, we developed a method for structure-based prediction of aggregation properties that takes into account the dynamic fluctuations of proteins. The method has been made available as the Aggrescan3D (A3D) web server and applied in numerous studies of protein structure-aggregation relationship. Here, we present a major update of the A3D web server to version 2.0. The new features include: extension of dynamic calculations to significantly larger and multimeric proteins, simultaneous prediction of changes in protein solubility and stability upon mutation, rapid screening for functional protein variants with improved solubility, a REST-ful service to incorporate A3D calculations in automatic pipelines, and a new, enhanced web server interface. A3D 2.0 is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/

pH-Dependent Aggregation in Intrinsically Disordered Proteins Is Determined by Charge and Lipophilicity

“…The concept should be first implemented in a structural predictor, where the intrinsic charge and lipophilic properties of amino acids would be modulated according to the protein conformational properties at any given pH. This step will be analogous to the evolution of AGGRESCAN [14] into our structural A3D aggregation predictor [70][71][72] and thus, perfectly attainable.…”

An in vivo platform to select and evolve aggregation-resistant proteins

“…For example, 10 of the 12 hotspot residues found for scFv WFL are hydrophobic/aromatic in nature and all were substituted with more hydrophilic residues, consistent with the mechanism of aggregation suggested previously for this protein 35 . In accordance with this hypothesis, three different algorithms that predict solubility and aggregation propensity of amino acid sequences within structured 18 and dynamic protein domains 19,45 , identify the same region. These algorithms, however, yield different predictions, confusing the choice of residues to mutate in any rational approach to improve protein behaviour.…”

“…structurally corrected Camsol 18 ), or high aggregation propensity (e.g. Aggregscan3D 45 and SAP 19 ). Comparison of the location of the sequence hotspots identified here for scFv WFL by directed evolution, with those predicted based on these algorithms are shown in Fig.…”

Protocols for fast simulations of protein structure flexibility using CABS-flex and SURPASS

“…Moreover, CABS-flex method is successfully used in Aggrescan3D method [15][16][17][18] to predict the influence of protein flexibility on protein aggregation properties, and in CABS-dock method for simulations of protein flexibility during peptide molecular docking [19][20][21][22]. CABS-flex method is presently available as the CABS-flex 2.0 web server [3] (http://biocomp.chem.uw.edu.pl/CABSflex2) and the standalone package [4].…”