نتایج جستجو برای: folding state

تعداد نتایج: 881953  

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2016
Wookyung Yu Michael C Baxa Isabelle Gagnon Karl F Freed Tobin R Sosnick

The relationship between folding cooperativity and downhill, or barrier-free, folding of proteins under highly stabilizing conditions remains an unresolved topic, especially for proteins such as λ-repressor that fold on the microsecond timescale. Under aqueous conditions where downhill folding is most likely to occur, we measure the stability of multiple H bonds, using hydrogen exchange (HX) in...

Journal: :Journal of molecular biology 2001
J Shimada E L Kussell E I Shakhnovich

We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding, all side-chain and backbone torsions, and uses a Go potential. In this study, we focus on the 46 residue alpha/beta protein crambin and two of its structural components, the helix and helix hairpin. Fo...

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2007
Xianghong Qi John J Portman

A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce minor structural cooperativity are included in the interaction potential. In general, the cooperative folding routes have sharper interfaces between folded ...

Journal: :RNA 2006
Yan-Fei Jiang Mu Xiao Ping Yin Yi Zhang

Recent efforts have been made to unravel the independent roles of monovalent cations in RNA folding, primarily using the Tetrahymena ribozyme as a model. Here we report how monovalent cations impact the folding of the Candida ribozyme. Interestingly, this ribozyme requires an order of magnitude less monovalent cations (Na+ and Tris+) to commit to a new folding starting state in which the J3/4:P...

2002
Jose M. Borreguero Nikolay V. Dokholyan Sergey V. Buldyrev Eugene I. Shakhnovich H. Eugene Stanley

Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA 02138, USA We perform a detailed analysis of the thermodynamics and folding kinetics of the SH3 domain fold with discrete molecular dynamic simulations. We propose a protein model that reproduces some of the experimentally observed thermodynamic and folding kinetic properties of proteins. Specifically, we use our mod...

Journal: :Journal of molecular biology 2002
Jose M Borreguero Nikolay V Dokholyan Sergey V Buldyrev Eugene I Shakhnovich H Eugene Stanley

We perform a detailed analysis of the thermodynamics and folding kinetics of the SH3 domain fold with discrete molecular dynamic simulations. We propose a protein model that reproduces some of the experimentally observed thermodynamic and folding kinetic properties of proteins. Specifically, we use our model to study the transition state ensemble of the SH3 fold family of proteins, a set of uns...

Journal: :Biochemical and biophysical research communications 2012
Greta Hultqvist Søren W Pedersen Celestine N Chi Kristian Strømgaard Stefano Gianni Per Jemth

Most protein domains fold in an apparently co-operative and two-state manner with only the native and denatured states significantly populated at any experimental condition. However, the protein folding energy landscape is often rugged and different transition states may be rate limiting for the folding reaction under different conditions, as seen for the PDZ protein domain family. We have here...

Journal: :Journal of molecular biology 2002
Eric Alm Alexandre V Morozov Tanja Kortemme David Baker

Our understanding of the principles underlying the protein-folding problem can be tested by developing and characterizing simple models that make predictions which can be compared to experimental data. Here we extend our earlier model of folding free energy landscapes, in which each residue is considered to be either folded as in the native state or completely disordered, by investigating the r...

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2007
Del Lucent V Vishal Vijay S Pande

Although most experimental and theoretical studies of protein folding involve proteins in vitro, the effects of spatial confinement may complicate protein folding in vivo. In this study, we examine the folding dynamics of villin (a small fast folding protein) with explicit solvent confined to an inert nanopore. We have calculated the probability of folding before unfolding (P(fold)) under vario...

Journal: :Journal of the American Chemical Society 2011
Edward P O'Brien John Christodoulou Michele Vendruscolo Christopher M Dobson

Identifying and understanding the differences between protein folding in bulk solution and in the cell is a crucial challenge facing biology. Using Langevin dynamics, we have simulated intact ribosomes containing five different nascent chains arrested at different stages of their synthesis such that each nascent chain can fold and unfold at or near the exit tunnel vestibule. We find that the na...

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