Alexander J Dear, Georg Meisl, Jing Hu, Tuomas P J Knowles, Sara Linse
{"title":"Kinetics of seeded protein aggregation: Theory and application.","authors":"Alexander J Dear, Georg Meisl, Jing Hu, Tuomas P J Knowles, Sara Linse","doi":"10.1063/5.0273677","DOIUrl":null,"url":null,"abstract":"<p><p>\"Seeding\" is the addition of preformed fibrils to a solution of monomeric protein to accelerate its aggregation into new fibrils. It is a versatile and widely used tool for scientists studying protein aggregation kinetics, as it enables the isolation and separate study of discrete reaction steps contributing to protein aggregation, specifically elongation and secondary nucleation. However, the seeding levels required to achieve dominating effects on each of these steps separately have been established largely by trial-and-error due in part to the lack of availability of integrated rate laws valid for moderate to high seeding levels and generally applicable to all common underlying reaction mechanisms. Here, we improve on a recently developed mathematical method based on Lie symmetries for solving differential equations and with it derive such an integrated rate law. We subsequently develop simple expressions for the amounts of seed required to isolate each step. We rationalize the empirical observation that fibril seeds must often be broken up into small pieces to successfully isolate elongation. We also derive expressions for average fibril lengths at different times in the aggregation reaction and explore different methods to break up fibrils. This paper will provide an invaluable reference for future experimental and theoretical studies in which seeding techniques are employed and should enable more sophisticated analyses than have been performed to date.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 4","pages":""},"PeriodicalIF":3.1000,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Physics","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1063/5.0273677","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0
Abstract
"Seeding" is the addition of preformed fibrils to a solution of monomeric protein to accelerate its aggregation into new fibrils. It is a versatile and widely used tool for scientists studying protein aggregation kinetics, as it enables the isolation and separate study of discrete reaction steps contributing to protein aggregation, specifically elongation and secondary nucleation. However, the seeding levels required to achieve dominating effects on each of these steps separately have been established largely by trial-and-error due in part to the lack of availability of integrated rate laws valid for moderate to high seeding levels and generally applicable to all common underlying reaction mechanisms. Here, we improve on a recently developed mathematical method based on Lie symmetries for solving differential equations and with it derive such an integrated rate law. We subsequently develop simple expressions for the amounts of seed required to isolate each step. We rationalize the empirical observation that fibril seeds must often be broken up into small pieces to successfully isolate elongation. We also derive expressions for average fibril lengths at different times in the aggregation reaction and explore different methods to break up fibrils. This paper will provide an invaluable reference for future experimental and theoretical studies in which seeding techniques are employed and should enable more sophisticated analyses than have been performed to date.
期刊介绍:
The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance.
Topical coverage includes:
Theoretical Methods and Algorithms
Advanced Experimental Techniques
Atoms, Molecules, and Clusters
Liquids, Glasses, and Crystals
Surfaces, Interfaces, and Materials
Polymers and Soft Matter
Biological Molecules and Networks.