Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation

Author:

Bárcenas Oriol1ORCID,Kuriata Aleksander2,Zalewski Mateusz2ORCID,Iglesias Valentín13ORCID,Pintado-Grima Carlos1ORCID,Firlik Grzegorz2ORCID,Burdukiewicz Michał13ORCID,Kmiecik Sebastian2ORCID,Ventura Salvador1ORCID

Affiliation:

1. Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona , 08193 Bellaterra, Barcelona, Spain

2. Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland

3. Clinical Research Centre, Medical University of Białystok , Kilińskiego 1, 15-369 Białystok, Poland

Abstract

Abstract Protein aggregation is behind the genesis of incurable diseases and imposes constraints on drug discovery and the industrial production and formulation of proteins. Over the years, we have been advancing the Aggresscan3D (A3D) method, aiming to deepen our comprehension of protein aggregation and assist the engineering of protein solubility. Since its inception, A3D has become one of the most popular structure-based aggregation predictors because of its performance, modular functionalities, RESTful service for extensive screenings, and intuitive user interface. Building on this foundation, we introduce Aggrescan4D (A4D), significantly extending A3D’s functionality. A4D is aimed at predicting the pH-dependent aggregation of protein structures, and features an evolutionary-informed automatic mutation protocol to engineer protein solubility without compromising structure and stability. It also integrates precalculated results for the nearly 500,000 jobs in the A3D Model Organisms Database and structure retrieval from the AlphaFold database. Globally, A4D constitutes a comprehensive tool for understanding, predicting, and designing solutions for specific protein aggregation challenges. The A4D web server and extensive documentation are available at https://biocomp.chem.uw.edu.pl/a4d/. This website is free and open to all users without a login requirement.

Funder

Spanish Ministry of Science and Innovation

Spanish Ministry of Universities

European Union-Next Generation EU

Secretariat of Universities and Research of the Catalan Government

European Social Fund

European Union-NextGenerationEU

ICREA

Publisher

Oxford University Press (OUP)

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