Document Detail


Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides.
MedLine Citation:
PMID:  15740349     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A new approach, the hypothetical scanning Monte Carlo (HSMC), for calculating the absolute entropy, S, and free energy, F, has been introduced recently and applied first to fluids (argon and water) and later to peptides. In this paper the method is further developed for peptide chains in vacuum. S is calculated from a given MC sample by reconstructing each sample conformation i step-by-step, i.e., calculating transition probabilities (TPs) for the dihedral and bond angles and fixing the related atoms at their positions. At step k of the process the chain's coordinates that have already been determined are kept fixed (the "frozen past") and TP(k) is obtained from a MC simulation of the "future" part of the chain whose TPs as yet have not been determined; when the process is completed the contribution of conformation i to the entropy is, S(i) approximately -ln Pi(k) TP(k). In a recent paper we studied polyglycine chains, modeled by the AMBER force field with constant bond lengths and bond angles (the rigid model). Decaglycine [(Gly)(10)] was studied in the helical, extended, and hairpin microstates, while (Gly)(16) was treated only in the first two microstates. In this paper the samples are increased and restudied, (Gly)(16) is also investigated in the hairpin microstate, and for (Gly)(10) approximations are tested where only part of the future is considered for calculating the TPs. We calculate upper and lower bounds for F and demonstrate that like for fluids, F can be obtained from multiple reconstructions of a single conformation. We also test a more realistic model of (Gly)(10) where the bond angles are allowed to move (the flexible model). Very accurate results for S and F are obtained which are compared to results obtained by the quasiharmonic approximation and the local states method. Thus, differences in entropy and free energy between the three microstates are obtained within errors of 0.1-0.3 kcal/mol. The HSMC method can be applied to a macromolecule with any degree of flexibility, ranging from local fluctuations to a random coil. The present results demonstrate that the difference in stability, DeltaF(mn)=F(m)-F(n) between significantly different microstates m and n, can be obtained from two simulations only without the need to resort to thermodynamic integration. Our long-term goal is to extend this method to any peptide and apply it to a peptide immersed in a box with explicit water.
Authors:
Srinath Cheluvaraja; Hagai Meirovitch
Related Documents :
22376019 - Population pharmacokinetics of native escherichia coli asparaginase.
21219909 - Modeling of biological doses and mechanical effects on bone transduction.
17328589 - Accelerating the replica exchange method through an efficient all-pairs exchange.
21502169 - Constraining predictions of the carbon cycle using data.
21216439 - An open-terrain line source model coupled with street-canyon effects to forecast carbon...
16170049 - Virtual ligand screening against escherichia coli dihydrofolate reductase: improving do...
23356779 - Disentangling decision models: from independence to competition.
22563369 - Correction: an emperor penguin population estimate: the first global, synoptic survey o...
18194109 - A sparse generative model of v1 simple cells with intrinsic plasticity.
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  The Journal of chemical physics     Volume:  122     ISSN:  0021-9606     ISO Abbreviation:  J Chem Phys     Publication Date:  2005 Feb 
Date Detail:
Created Date:  2005-03-02     Completed Date:  2006-05-17     Revised Date:  2007-11-14    
Medline Journal Info:
Nlm Unique ID:  0375360     Medline TA:  J Chem Phys     Country:  United States    
Other Details:
Languages:  eng     Pagination:  54903     Citation Subset:  IM    
Affiliation:
Center for Computational Biology and Bioinformatics and Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Computer Simulation*
Entropy
Models, Chemical*
Monte Carlo Method*
Peptides / chemistry*
Thermodynamics*
Grant Support
ID/Acronym/Agency:
R01 GM61916/GM/NIGMS NIH HHS; R01 GM66090/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Peptides

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  Heat flow in proteins: computation of thermal transport coefficients.
Next Document:  Intramolecular fluorescence quenching in luminescent copolymers containing fluorenone and fluorene u...