Computer Simulations of Aggregation of Proteins and Peptides

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.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts

Résumé
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.

Contenu
Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins.- Protocols for Rational Design of Protein Solubility and Aggregation Properties using Aggrescan3D Standalone.- Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites. Application to the Interactions of E-cadherins.- Computational Models for Study of Protein Aggregation.- Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.- Contact-based Analysis of Aggregation of Intrinsically Disordered Proteins.- Molecular Insights into the Effect of Metals on Amyloid Aggregation.- From Quantum Mechanics, Classical Mechanics and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases.- Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.- All-atom Molecular Dynamics Simulation Methods for Aggregation of Protein and Peptides: Replica-exchange/permutationand Nonequilibrium Simulations.- Key Factors Controlling Fibril Formation of Proteins- Determination of the Most Stable Packing Of Peptides From Ribosomal S1 Protein, Protein Bgl2p and A peptide in -layers during Molecular Dynamics Simulations.- Molecular Dynamics Simulations Of Protein Aggregation: Protocols For Simulation Setup and Analysis with Markov State Models And Transition Networks.- Challenges in Experimental Methods.- Aggregates Sealed By Ions.- Modifying Amyloid Motif Aggregation through Local Structure.- Assessing the Stability Of Biological Fibrils By Molecular-Scale Simulations.- Predictive Modeling of Neurotoxic -Synuclein Polymorphs.- Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace.- Exploration of Protein Aggregations in Parkinson's Disease through Computational Approaches and Big Data Analytics.- Computational Studies of Protein Aggregation In Preeclampsia.- Final remarks.