Literature DB >> 24628212

Folding and self-assembly of a small heterotetramer.

Fatih Yaşar1, Adam K Sieradzan2, Ulrich H E Hansmann3.   

Abstract

Designed miniproteins offer a possibility to study folding and association of protein complexes, both experimentally and in silico. Using replica exchange molecular dynamics and the coarse-grain UNRES force field, we have simulated the folding and self-assembly of the heterotetramer BBAThet1, comparing it with that of the homotetramer BBAT1 which has the same size and ββα-fold. For both proteins, association of the tetramer precedes and facilitates folding of the individual chains.

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Year:  2014        PMID: 24628212      PMCID: PMC3977861          DOI: 10.1063/1.4868140

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  29 in total

1.  Discovery and characterization of a discretely folded homotrimeric betabetaalpha peptide.

Authors:  A R Mezo; J J Ottesen; B Imperiali
Journal:  J Am Chem Soc       Date:  2001-02-07       Impact factor: 15.419

2.  Multiplexed-replica exchange molecular dynamics method for protein folding simulation.

Authors:  Young Min Rhee; Vijay S Pande
Journal:  Biophys J       Date:  2003-02       Impact factor: 4.033

3.  Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure.

Authors:  Mayssam H Ali; Christina M Taylor; Gevorg Grigoryan; Karen N Allen; Barbara Imperiali; Amy E Keating
Journal:  Structure       Date:  2005-02       Impact factor: 5.006

Review 4.  Understanding protein folding: small proteins in silico.

Authors:  Olav Zimmermann; Ulrich H E Hansmann
Journal:  Biochim Biophys Acta       Date:  2007-11-06

Review 5.  Principles of protein-protein interactions: what are the preferred ways for proteins to interact?

Authors:  Ozlem Keskin; Attila Gursoy; Buyong Ma; Ruth Nussinov
Journal:  Chem Rev       Date:  2008-03-21       Impact factor: 60.622

6.  Folding proteins by first-passage-times-optimized replica exchange.

Authors:  Walter Nadler; Jan H Meinke; Ulrich H E Hansmann
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2008-12-03

7.  Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats.

Authors:  Amit Mor; Guy Ziv; Yaakov Levy
Journal:  J Comput Chem       Date:  2008-09       Impact factor: 3.376

8.  Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1996-11

9.  Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

Authors:  Cezary Czaplewski; Sebastian Kalinowski; Adam Liwo; Harold A Scheraga
Journal:  J Chem Theory Comput       Date:  2009-03-10       Impact factor: 6.006

10.  Folding and self-assembly of a small protein complex.

Authors:  Adam K Sieradzan; Adam Liwo; Ulrich H E Hansmann
Journal:  J Chem Theory Comput       Date:  2012-09-11       Impact factor: 6.006

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  1 in total

1.  Computational Models for the Study of Protein Aggregation.

Authors:  Nguyen Truong Co; Mai Suan Li; Pawel Krupa
Journal:  Methods Mol Biol       Date:  2022
  1 in total

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