Aggrescan4D : structure-informed analysis of pH-dependent protein aggregation
Bárcenas, Oriol (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Kuriata, Aleksander (University of Warsaw)
Zalewski, Mateusz (University of Warsaw)
Iglesias, Valentin (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Pintado-Grima, Carlos (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Firlik, Grzegorz (University of Warsaw)
Burdukiewicz, Michał (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Kmiecik, Sebastian (University of Warsaw)
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")

Date:	2024
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 . This website is free and open to all users without a login requirement.
Grants:	Ministerio de Ciencia, Innovación y Universidades FPU22/03656 Agència de Gestió d'Ajuts Universitaris i de Recerca 2023/FI_3-00018 Agencia Estatal de Investigación PID2022-137963OB-I00
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	Nucleic acids research, Vol. 52, Issue W1 (July 2024) , p. W170-W175, ISSN 1362-4962

DOI: 10.1093/nar/gkae382
PMID: 38738618

6 p, 877.8 KB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Biotecnologia i de Biomedicina (IBB)
Articles > Research articles
Articles > Published articles