Simulation of peptide folding with explicit water?a mean solvation method

نویسندگان
چکیده

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide.

Solvation effects play a profound role in the energetics of protein folding. While a continuum dielectric model of solvation may provide a sufficiently accurate estimate of the solvation effects, until now this model was too computationally expensive and unstable for folding simulations. Here we proposed a fast yet accurate and robust implementation of the boundary element solution of the Poiss...

متن کامل

Peptide Folding: When Simulation Meets Experiment

The last two decades have seen the horizons of science and engineering being expanded greatly by the use of computer simulation techniques. In particular, computer simulation is the method of choice to study processes that are dangerous, costly, or even impossible to carry out experimentally, or that are of microscopic nature and thereby partially inaccessible to detailed observation. Molecular...

متن کامل

Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface

In this study we investigated the interaction behavior between thirteen different small peptides and a hydrophobic surface using three progressively more complex methods of representing solvation effects: a united-atom implicit solvation method [CHARMM 19 force field (C19) with Analytical Continuum Electrostatics (ACE)], an all-atom implicit solvation method (C22 with GBMV), and an all-atom exp...

متن کامل

Evaluation of configurational entropy methods from peptide folding-unfolding simulation.

A 4-micros molecular dynamics simulation of the second beta-hairpin of the B1 domain of streptococcal protein G is used to characterize the free energy surface and to evaluate different configurational entropy estimators. From the equilibrium folding-unfolding trajectory, 200 000 conformers are clustered according to their root-mean-square deviation (RMSD). The height of the free energy barrier...

متن کامل

Reversible peptide folding in solution by molecular dynamics simulation.

Long-standing questions on how peptides fold are addressed by the simulation at different temperatures of the reversible folding of a peptide in solution in atomic detail. Molecular dynamics simulations correctly predict the structure that is thermodynamically stable at 298 K, irrespective of the initial peptide conformation. The rate of folding and the free energy of folding at different tempe...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

ژورنال

عنوان ژورنال: Proteins: Structure, Function, and Genetics

سال: 1999

ISSN: 0887-3585,1097-0134

DOI: 10.1002/(sici)1097-0134(19990215)34:3<295::aid-prot3>3.0.co;2-t