Variation of the Energy Landscape of a Small Peptide under a Change from the ECEPP/2 Force Field to ECEPP/3

نویسندگان

  • Frank Eisenmenger
  • Ulrich H.E. Hansmann
چکیده

Themulticanonical ansatz is used to study variations in the energy landscape of a small peptide, Met-enkephalin, under a change from the ECEPP/2 force field to ECEPP/3. Local minima with energies up to 5 kcal/mol higher than the global minima are sampled and classified according to H-bridges and backbone angles. The distribution and relative weight for various temperatures of the minima are calculated and compared for the two force fields. We demonstrate that while there are small differences in the energy landscape our results at relevant temperatures are robust under changes between ECEPP/2 to ECEPP/3. New address: Institute for Molecular Science (IMS), Okazaki 444, Japan

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

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Conformational study of Met-enkephalin based on the ECEPP force fields.

We report a computational study of the small peptide Met-enkephalin based on the ECEPP/2 and ECEPP/3 force fields using the basin paving method. We have located a new global minimum when using the ECEPP/3 force field with peptide angles omega fixed at 180 degrees. With this new result, we can conclude that the lowest energy configurations of Met-enkephalin predicted based on all four versions o...

متن کامل

Fast Stochastic Global Optimization Methods and Their Applications to Cluster Crystallization and Protein Folding

Two global optimization methods are proposed in this thesis. They are the multicanonical basin hopping (MUBH) method and the basin paving (BP) method. The MUBH method combines the basin hopping (BH) method, which can be used to efficiently map out an energy landscape associated with local minima, with the multicanonical Monte Carlo (MUCA) method, which encourages the system to move out of energ...

متن کامل

Jooyoung Lee 1,2 Conformational Analysis of the 20-residue Membrane-bound Portion Of

The conformational space of the 20-residue membrane-bound portion of melittin has been investigated extensively with the conformational space annealing (CSA) method and the ECEPP/3 (Empirical Conformational Energy Program for Peptides) algorithm. Starting from random conformations, the CSA method finds that there are at least five different classes of conformations, within 4 kcal/mol, which hav...

متن کامل

Protein Tertiary Structure Prediction Using Evolutionary Algorithms

In this paper, Protein Tertiary Structure Prediction using Evolutionary Algorithms (EAs) such as SelfAdaptive Differential Evolution (SaDE) and Real-coded Genetic Algorithm (RGA) are discussed. RGA is implemented with various crossover and mutation operators. The algorithms are tested on a peptide Metenkephalin. The energy functions used are ECEPP/2 and ECEPP/3 force fields. SaDE and RGA with d...

متن کامل

Conformational Analysis of Benzyloxycarbonyl-Protected Peptides

The benzyloxycarbonyl (Z-) residue, an important protecting group in peptide synthesis, was introduced into the input data set o f the “Empirical Conformational Energy Program for Peptides” (ECEPP) developed by Scheraga and coworkers. With additional modifications ECEPP is now prepared for conformational analysis o f peptides containing this amino end group. Preferred conformations o f the Z-re...

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

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 1997