نتایج جستجو برای: folding state

تعداد نتایج: 881953  

Journal: :Methods in molecular biology 2007
Francesco Rao Giovanni Settanni Amedeo Caflisch

Molecular dynamics simulations with an implicit model of the solvent have allowed to investigate the reversible folding of structured peptides. For a 20-residue antiparallel beta-sheet peptide, the simulation results have revealed multiple folding pathways. Moreover, the conformational heterogeneity of the denatured state has been shown to originate from high enthalpy, high entropy basins with ...

Journal: :Journal of molecular biology 2003
Thomas R Weikl Ken A Dill

We develop a simple model for computing the rates and routes of folding of two-state proteins from the contact maps of their native structures. The model is based on the graph-theoretical concept of effective contact order (ECO). The model predicts that proteins fold by "zipping up" in a sequence of small-loop-closure events, depending on the native chain fold. Using a simple equation, with a f...

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2012
Kyle A Beauchamp Robert McGibbon Yu-Shan Lin Vijay S Pande

Markov state models constructed from molecular dynamics simulations have recently shown success at modeling protein folding kinetics. Here we introduce two methods, flux PCCA+ (FPCCA+) and sliding constraint rate estimation (SCRE), that allow accurate rate models from protein folding simulations. We apply these techniques to fourteen massive simulation datasets generated by Anton and Folding@ho...

Journal: :Folding & design 1996
L A Mirny V Abkevich E I Shakhnovich

BACKGROUND The role of intermediates in protein folding has been a matter of great controversy. Although it was widely believed that intermediates play a key role in minimizing the search problem associated with the Levinthal paradox, experimental evidence has been accumulating that small proteins fold fast without any detectable intermediates. RESULTS We study the thermodynamics and kinetics...

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2001
J Rumbley L Hoang L Mayne S W Englander

Direct structural information obtained for many proteins supports the following conclusions. The amino acid sequences of proteins can stabilize not only the final native state but also a small set of discrete partially folded native-like intermediates. Intermediates are formed in steps that use as units the cooperative secondary structural elements of the native protein. Earlier intermediates g...

2015
Liaofu Luo Jun Lv

Starting from the assumption that the protein and RNA folding is an event of quantum transition between molecular conformations,we deduced a folding rate formula and studied the chain length (torsion number) dependence and temperature dependence of the folding rate. The chain length dependence of the folding rate was tested in 65 two-state proteins and 27 RNA molecules. The success of the compa...

2001
Bino John Patrick R. D’Silva Anil K. Lala

Polarity-sensitive fluorescent probes like 8-anilino-1naphthalenesulphonate (ANS) and 1,1′-bis(4-anilino5-naphthalenesulphonic acid (bis-ANS) have been frequently used to detect equilibrium folding intermediates like the molten globule state, as the formation of the latter involves increase in hydrophobic exposure. The ability of these fluorescent probes to bind to the intermediate state thus p...

Journal: :The Journal of chemical physics 2011
Pulak Kumar Ghosh Mai Suan Li Bidhan Chandra Bag

We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding time first increases with driving frequency and then decreases passing through a maximum. With further increase of the driving frequency the mean folding time ...

Journal: :Journal of molecular biology 2002
Bojan Zagrovic Christopher D Snow Michael R Shirts Vijay S Pande

By employing thousands of PCs and new worldwide-distributed computing techniques, we have simulated in atomistic detail the folding of a fast-folding 36-residue alpha-helical protein from the villin headpiece. The total simulated time exceeds 300 micros, orders of magnitude more than previous simulations of a molecule of this size. Starting from an extended state, we obtained an ensemble of fol...

Journal: :Annual review of biophysics and biomolecular structure 2001
L Mirny E Shakhnovich

This review focuses on recent advances in understanding protein folding kinetics in the context of nucleation theory. We present basic concepts such as nucleation, folding nucleus, and transition state ensemble and then discuss recent advances and challenges in theoretical understanding of several key aspects of protein folding kinetics. We cover recent topology-based approaches as well as evol...

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