نتایج جستجو برای: folding

تعداد نتایج: 28731  

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2003
Steven S Plotkin Peter G Wolynes

The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological temperatures leads to energy landscapes having a single dominant basin and an overall funnel topography. We show here that, although such a landscape topography is ...

2015
Emily J. Guinn Bharat Jagannathan Susan Marqusee

A fundamental question in protein folding is whether proteins fold through one or multiple trajectories. While most experiments indicate a single pathway, simulations suggest proteins can fold through many parallel pathways. Here, we use a combination of chemical denaturant, mechanical force and site-directed mutations to demonstrate the presence of multiple unfolding pathways in a simple, two-...

Journal: :Biophysical journal 1999
A Kolinski B Ilkowski J Skolnick

Small peptides that might have some features of globular proteins can provide important insights into the protein folding problem. Two simulation methods, Monte Carlo Dynamics (MCD), based on the Metropolis sampling scheme, and Entropy Sampling Monte Carlo (ESMC), were applied in a study of a high-resolution lattice model of the C-terminal fragment of the B1 domain of protein G. The results pro...

Journal: :Cell 2012
Pallav Kosuri Jorge Alegre-Cebollada Jason Feng Anna Kaplan Alvaro Inglés-Prieto Carmen L. Badilla Brent R. Stockwell Jose M. Sanchez-Ruiz Arne Holmgren Julio M. Fernández

PDI catalyzes the oxidative folding of disulfide-containing proteins. However, the sequence of reactions leading to a natively folded and oxidized protein remains unknown. Here we demonstrate a technique that enables independent measurements of disulfide formation and protein folding. We find that non-native disulfides are formed early in the folding pathway and can trigger misfolding. In contr...

Journal: :Physiology 2013
Yalda Javadi Julio M Fernandez Raul Perez-Jimenez

Mechanical forces regulate the function of numerous proteins relevant to physiology. The functions and folding of proteins have been under scrutiny for decades, but it was not until recently that mechanical forces have been considered. Here, we review different techniques for studying protein folding, highlighting their physiological significance.

2007
Tomasz L. Religa Christopher M. Johnson Dung M. Vu Scott H. Brewer Sheena Radford

59 KEY TO ABSTRACT NUMBERING

Journal: :Physical review. E, Statistical, nonlinear, and soft matter physics 2009
Mathieu Gaudreault Jorge Viñals

In order to study solvation effects on protein folding, we analyze the collapse transition of a self-avoiding random walk composed of hydrophobic segments that is embedded in a lattice model of a solvent. As expected, hydrophobic interactions lead to an attractive potential of mean force among chain segments. As a consequence, the random walk in solvent undergoes a collapse transition at a high...

Journal: :Journal of biomolecular structure & dynamics 1997
V A Farutin A A Gorin E M Zdobnov V I Ivanov

Earlier a three-dimensional model for a new unusual DNA conformation referred to as Slipped Loop Structure (SLS) has been suggested by us (1). The same type of folding could occur with RNA as well which means that one must use the A-form of the double helix rather than the B-one. The present paper discusses the creation of an all-atom stereochemically sound model for SLS-RNA. This calculated mo...

2015
Andrew E. Brereton P. Andrew Karplus

During protein folding and as part of some conformational changes that regulate protein function, the polypeptide chain must traverse high-energy barriers that separate the commonly adopted low-energy conformations. How distortions in peptide geometry allow these barrier-crossing transitions is a fundamental open question. One such important transition involves the movement of a non-glycine res...

Journal: :Biophysical journal 2005
S S Plotkin

We determine both barrier heights and prefactors for protein folding by applying constraints determined from experimental rate measurements to a Kramers theory for folding rate. The theoretical values are required to match the experimental values at two conditions of temperature and denaturant that induce the same stability. Several expressions for the prefactor in the Kramers rate equation are...

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