Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity.

IF 4.5 3区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Protein Science Pub Date : 2024-10-01 DOI:10.1002/pro.5180

Mateusz Zalewski, Valentin Iglesias, Oriol Bárcenas, Salvador Ventura, Sebastian Kmiecik

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Abstract

Aggrescan4D (A4D) is an advanced computational tool designed for predicting protein aggregation, leveraging structural information and the influence of pH. Building upon its predecessor, Aggrescan3D (A3D), A4D has undergone numerous enhancements aimed at assisting the improvement of protein solubility. This manuscript reviews A4D's updated functionalities and explains the fundamental principles behind its pH-dependent calculations. Additionally, it presents an antibody case study to evaluate its performance in comparison with other structure-based predictors. Notably, A4D integrates advanced protein engineering protocols with pH-dependent calculations, enhancing its utility in advising solubility-enhancing mutations. A4D considers the impact of structural flexibility on aggregation propensities, and includes a large set of precalculated predictions. These capabilities should help to open new avenues for both understanding and managing protein aggregation. A4D is accessible through a dedicated web server at https://biocomp.chem.uw.edu.pl/a4d/.

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Aggrescan4D：根据 pH 值分析和设计蛋白质聚集倾向的综合工具。

Aggrescan4D (A4D) 是一种先进的计算工具，利用结构信息和 pH 值的影响来预测蛋白质的聚集。在其前身 Aggrescan3D (A3D) 的基础上，A4D 进行了大量改进，旨在帮助提高蛋白质的溶解度。本手稿回顾了 A4D 的最新功能，并解释了其与 pH 值相关的计算背后的基本原理。此外，它还介绍了一个抗体案例研究，以评估其与其他基于结构的预测器相比的性能。值得注意的是，A4D 将先进的蛋白质工程协议与 pH 依赖性计算相结合，增强了其在预测溶解度增强突变方面的实用性。A4D 考虑了结构灵活性对聚集倾向的影响，并包含了大量的预计算预测。这些功能将有助于为理解和管理蛋白质聚集开辟新的途径。A4D 可通过 https://biocomp.chem.uw.edu.pl/a4d/ 的专用网络服务器访问。

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来源期刊

Protein Science 生物-生化与分子生物学

CiteScore

12.40

自引率

1.20%

发文量

246

审稿时长

1 months

期刊介绍： Protein Science, the flagship journal of The Protein Society, is a publication that focuses on advancing fundamental knowledge in the field of protein molecules. The journal welcomes original reports and review articles that contribute to our understanding of protein function, structure, folding, design, and evolution. Additionally, Protein Science encourages papers that explore the applications of protein science in various areas such as therapeutics, protein-based biomaterials, bionanotechnology, synthetic biology, and bioelectronics. The journal accepts manuscript submissions in any suitable format for review, with the requirement of converting the manuscript to journal-style format only upon acceptance for publication. Protein Science is indexed and abstracted in numerous databases, including the Agricultural & Environmental Science Database (ProQuest), Biological Science Database (ProQuest), CAS: Chemical Abstracts Service (ACS), Embase (Elsevier), Health & Medical Collection (ProQuest), Health Research Premium Collection (ProQuest), Materials Science & Engineering Database (ProQuest), MEDLINE/PubMed (NLM), Natural Science Collection (ProQuest), and SciTech Premium Collection (ProQuest).