Computer simulations of aggregation of proteins and peptides

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書誌事項

Computer simulations of aggregation of proteins and peptides

edited by Mai Suan Li ... [et al.]

（Methods in molecular biology / John M. Walker, series editor, 2340）（Springer protocols）

Humana Press, c2022

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注記

Other editors: Andrzej Kloczkowski, Marek Cieplak, Maksim Kouza

Includes bibliographical references and index

内容説明・目次

内容説明

This volume provides computational methods and reviews various aspects of computational studies of protein aggregation. Chapters discuss the relationship between protein misfolding and protein aggregation, methods of prediction of aggregation propensities of protein, peptides, protein structure, results of computer simulations of aggregation, and computational simulations focused on specific diseases such as Alzheimer's, Parkinson's, and preeclampsia. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computer Simulations of Aggregation of Proteins and Peptides aims to ensure successful results in the further study of this vital field.

目次

1. Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins Malgorzata Kotulska and Jakub W. Wojciechowski 2. Protocols for Rational Design of Protein Solubility and Aggregation Properties using Aggrescan3D Standalone Aleksander Kuriata, Aleksandra E. Badaczewska-Dawid, Jordi Pujols, Salvador Ventura, and Sebastian Kmiecik 3. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites. Application to the Interactions of E-cadherins Robert L. Jernigan, Pranav Khade, Ambuj Kumar, and Andrzej Kloczkowski 4. Computational Models for Study of Protein Aggregation Nguyen Truong Co, Mai Suan Li, and Pawel Krupa 5. Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field Ana V. Rojas, Gia G. Maisuradze, Harold A. Scheraga, and Adam Liwo 6. Contact-based Analysis of Aggregation of Intrinsically Disordered Proteins Marek Cieplak, Lukasz Mioduszewski, and Mateusz Chwastyk 7. Molecular Insights into the Effect of Metals on Amyloid Aggregation Yifat Miller 8. From Quantum Mechanics, Classical Mechanics and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases Orkid Coskuner-Weber, M. Gokhan Habiboglu, David Teplow, and Vladimir N. Uversky 9. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation Phuong H. Nguyen and Philippe Derreumaux 10. All-atom Molecular Dynamics Simulation Methods for Aggregation of Protein and Peptides: Replica-exchange/permutation and Nonequilibrium Simulations Satoru G. Itoh and Hisashi Okumura 11. Key Factors Controlling Fibril Formation of Proteins Tran Thi Minh Thu, Andrzej Kloczkowski, Mai Suan Li, and Maksim Kouza 12. Determination of the Most Stable Packing Of Peptides From Ribosomal S1 Protein, Protein Bgl2p and A peptide in -layers during Molecular Dynamics Simulations Glyakina A.V., Balabaev N.K., and Galzitskaya O.V 13. Molecular Dynamics Simulations Of Protein Aggregation: Protocols For Simulation Setup and Analysis with Markov State Models And Transition Networks Suman Samantray, Wibke Schumann, Alexander-Maurice Illig, Arghadwip Paul, Bogdan Barz, and Birgit Strodel 14. Challenges in Experimental Methods Marlena E. Gasior-Glogowska, Natalia Szulc, and Monika Szefczyk 15. Aggregates Sealed By Ions Giovanni La Penna and Silvia Morante 16. Modifying Amyloid Motif Aggregation through Local Structure Sofia Bali and Lukasz A. Joachimiak 17. Assessing the Stability Of Biological Fibrils By Molecular-Scale Simulations Rodrigo A. Moreira 18. Predictive Modeling of Neurotoxic -Synuclein Polymorphs Liang Xu, Shayon Bhattacharya, and Damien Thompson 19. Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace Shayon Bhattacharya, Liang Xu, and Damien Thompson 20. Exploration of Protein Aggregations in Parkinson's Disease through Computational Approaches and Big Data Analytics Saba Shahzadi, Muhammad Yasir, Bisma Jawad, Sumbal Baber, Mubashir Hassan 21. Computational Studies of Protein Aggregation In Preeclampsia Maksim Kouza, Andrzej Kolinski, Irina Buhimschi, and Andrzej Kloczkowski 22. Final remarks Mai Suan Li, Andrzej Kloczkowski, Marek Cieplak, and Maksim Kouza

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