Literature DB >> 16959265

Minimalist protein model as a diagnostic tool for misfolding and aggregation.

Silvina Matysiak1, Cecilia Clementi.   

Abstract

We propose a realistic coarse-grained protein model and a technique to "anchor" the model to available experimental data. We apply this procedure to characterize the effect of multiple mutations on the folding mechanism of protein S6. We show that the mutation of a few "gatekeeper" residues triggers significant changes on the folding landscape of S6. These results suggest that gatekeeper residues control the flexibility of critical regions of S6, that in turn regulates the delicate balance between folding and aggregation. Although obtained with a minimalist protein model, these results are fully consistent with experimental evidence and offer a clue to understand the interplay between folding and aggregation in protein S6.

Entities:  

Mesh:

Substances:

Year:  2006        PMID: 16959265     DOI: 10.1016/j.jmb.2006.07.088

Source DB:  PubMed          Journal:  J Mol Biol        ISSN: 0022-2836            Impact factor:   5.469


  15 in total

1.  Chemically accurate coarse graining of double-stranded DNA.

Authors:  Alexey Savelyev; Garegin A Papoian
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-08       Impact factor: 11.205

2.  Protein folding: then and now.

Authors:  Yiwen Chen; Feng Ding; Huifen Nie; Adrian W Serohijos; Shantanu Sharma; Kyle C Wilcox; Shuangye Yin; Nikolay V Dokholyan
Journal:  Arch Biochem Biophys       Date:  2007-06-08       Impact factor: 4.013

3.  Generic coarse-grained model for protein folding and aggregation.

Authors:  Tristan Bereau; Markus Deserno
Journal:  J Chem Phys       Date:  2009-06-21       Impact factor: 3.488

4.  Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides.

Authors:  Hernán Stamati; Cecilia Clementi; Lydia E Kavraki
Journal:  Proteins       Date:  2010-02-01

5.  Universal distribution of protein evolution rates as a consequence of protein folding physics.

Authors:  Alexander E Lobkovsky; Yuri I Wolf; Eugene V Koonin
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-26       Impact factor: 11.205

6.  Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes.

Authors:  Jayvee R Abella; Dinler Antunes; Kyle Jackson; Gregory Lizée; Cecilia Clementi; Lydia E Kavraki
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-12       Impact factor: 11.205

7.  A Discontinuous Potential Model for Protein-Protein Interactions.

Authors:  Qing Shao; Carol K Hall
Journal:  Found Mol Model Simul (2015)       Date:  2016-06-02

8.  High-resolution MAS NMR analysis of PI3-SH3 amyloid fibrils: backbone conformation and implications for protofilament assembly and structure .

Authors:  Marvin J Bayro; Thorsten Maly; Neil R Birkett; Cait E Macphee; Christopher M Dobson; Robert G Griffin
Journal:  Biochemistry       Date:  2010-09-07       Impact factor: 3.162

9.  Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models.

Authors:  Benjamin M Messer; Maite Roca; Zhen T Chu; Spyridon Vicatos; Alexandra Vardi Kilshtain; Arieh Warshel
Journal:  Proteins       Date:  2010-04

10.  Multiscale characterization of protein conformational ensembles.

Authors:  Amarda Shehu; Lydia E Kavraki; Cecilia Clementi
Journal:  Proteins       Date:  2009-09
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.