Description
Book SynopsisThis 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.
Table of Contents1. Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins
Małgorzata 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, Łukasz 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 Aβ peptide in β-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. Gąsior-Głogowska, 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 α-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
