Hydrodynamic interactions in protein folding.
نویسندگان
چکیده
We incorporate hydrodynamic interactions (HIs) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HIs facilitate folding. We also study HIV-1 protease and show that HIs make the flap closing dynamics faster. The HIs are found to affect time correlation functions in the vicinity of the native state even though they have no impact on same time characteristics of the structure fluctuations around the native state.
منابع مشابه
The impact of hydrodynamic interactions on protein folding rates depends on temperature
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collecti...
متن کاملFOLDING OF THE INTERACTION OF HISTONE HI WITH SODIUM N-DODECYL SULPHATE
The effects of sodium n-dodecyl sulphate (SDS) on the structure of histone HI has been studied by a combination of e:quilibrium dialysis, U.V. spectroscopy ; polyacrylamide gel electrophoresis, protein titration and viscometery techniques using, 2.5 mM phosphate buffer, pH 6.4. The interaction of H, and SDS in contrast tomanyothel-protein-SDS interactions is organized between V 40 to 70. A...
متن کاملEnergy Study at Different Temperatures for Active Site of Azurin in Water, Ethanol, Methanol and Gas Phase by Monte Carlo Simulations
The interaction between the solute and the solsent molecules play a crucial role in understanding the various molecular processes involved in chemistry and biochemistry, so in this work the potential energy of active site of azurin have been calculated in solvent by the Monte Carlo simulation. In this paper we present quantitative results of Monte Carlo calculations of potential energies of ...
متن کاملOsmolyte-Induced Folding and Stability of Proteins: Concepts and Characterization
It is well-known that the typical protein’s three-dimensional structure is relatively unstable in harsh conditions. A practical approach to maintain the folded state and thus improve the stability and activity of proteins in unusual circumstances is to directly apply stabilizing substances such as osmolytes to the protein-containing solutions. Osmolytes as natural occurring organic molecules ty...
متن کاملHydrodynamic selection of the kinetic pathway of a polymer coil-globule transition.
Recently, the role of hydrodynamic interactions in the selection of a kinetic pathway for phase transitions has attracted considerable attention. Here we study this problem numerically by taking as an example a coil-globule transition of a single polymer, which is a prototype model of protein folding. When a swollen polymer collapses into a globule state, hydrodynamic interactions accelerate th...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- The Journal of chemical physics
دوره 130 12 شماره
صفحات -
تاریخ انتشار 2009