Literature DB >> 26273871

Simulations of Protein Aggregation: Insights from Atomistic and Coarse-Grained Models.

Alex Morriss-Andrews1, Joan-Emma Shea1.   

Abstract

This Perspective highlights recent computational approaches to protein aggregation, from coarse-grained models to atomistic simulations, using the islet amyloid polypeptide (IAPP) as a case study. We review salient open questions where simulations can make an impact, discuss the successes and challenges met by simulations, and explore new directions.

Entities:  

Year:  2014        PMID： 26273871     DOI： 10.1021/jz5006847

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN： 1948-7185            Impact factor:   6.475


  20 in total

1.  Protein Polymerization into Fibrils from the Viewpoint of Nucleation Theory.

Authors:  Dimo Kashchiev
Journal:  Biophys J       Date:  2015-11-17       Impact factor: 4.033

2.  Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers.

Authors:  Viet Hoang Man; Phuong H Nguyen; Philippe Derreumaux
Journal:  J Phys Chem B       Date:  2017-03-10       Impact factor: 2.991

Review 3.  Multiscale simulation of molecular processes in cellular environments.

Authors:  Mara Chiricotto; Fabio Sterpone; Philippe Derreumaux; Simone Melchionna
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2016-11-13       Impact factor: 4.226

4.  Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape.

Authors:  Zhiguang Jia; Jeremy D Schmit; Jianhan Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2020-04-28       Impact factor: 11.205

5.  On the lack of polymorphism in Aβ-peptide aggregates derived from patient brains.

Authors:  Erik J Alred; Malachi Phillips; Workalemahu M Berhanu; Ulrich H E Hansmann
Journal:  Protein Sci       Date:  2015-04-14       Impact factor: 6.725

6.  A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids.

Authors:  Nurit Haspel; Jie Zheng; Carlos Aleman; David Zanuy; Ruth Nussinov
Journal:  Methods Mol Biol       Date:  2017

7.  Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles.

Authors:  Anna Victoria Martinez; Edyta Małolepsza; Eva Rivera; Qing Lu; John E Straub
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

Review 8.  Molecular simulations of peptide amphiphiles.

Authors:  Anjela Manandhar; Myungshim Kang; Kaushik Chakraborty; Phu K Tang; Sharon M Loverde
Journal:  Org Biomol Chem       Date:  2017-10-04       Impact factor: 3.876

Review 9.  Protein aggregation: in silico algorithms and applications.

Authors:  R Prabakaran; Puneet Rawat; A Mary Thangakani; Sandeep Kumar; M Michael Gromiha
Journal:  Biophys Rev       Date:  2021-01-17

Review 10.  Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.

Authors:  Phuong H Nguyen; Ayyalusamy Ramamoorthy; Bikash R Sahoo; Jie Zheng; Peter Faller; John E Straub; Laura Dominguez; Joan-Emma Shea; Nikolay V Dokholyan; Alfonso De Simone; Buyong Ma; Ruth Nussinov; Saeed Najafi; Son Tung Ngo; Antoine Loquet; Mara Chiricotto; Pritam Ganguly; James McCarty; Mai Suan Li; Carol Hall; Yiming Wang; Yifat Miller; Simone Melchionna; Birgit Habenstein; Stepan Timr; Jiaxing Chen; Brianna Hnath; Birgit Strodel; Rakez Kayed; Sylvain Lesné; Guanghong Wei; Fabio Sterpone; Andrew J Doig; Philippe Derreumaux
Journal:  Chem Rev       Date:  2021-02-05       Impact factor: 60.622
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