Computer Simulations of Aggregation of Proteins and Peptides

ISBN-13: 9781071615485 / Angielski / Miękka / 2022 / 478 str.

Mai Suan Li; Andrzej Kloczkowski; Marek Cieplak

Opis

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.

Spis treści

1. 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