Literature DB >> 1304346

Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case.

C A Schiffer1, J W Caldwell, R M Stroud, P A Kollman.   

Abstract

A combined force field of molecular mechanics and solvation free energy is tested by carrying out energy minimization and molecular dynamics on several conformations of the alanyl dipeptide. Our results are qualitatively consistent with previous experimental and computational studies, in that the addition of solvation energy stabilizes the C5 conformation of the alanyl dipeptide relative to the C7.

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Year:  1992        PMID： 1304346      PMCID： PMC2142201          DOI： 10.1002/pro.5560010311

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


  12 in total

1.  Prediction of homologous protein structures based on conformational searches and energetics.

Authors:  C A Schiffer; J W Caldwell; P A Kollman; R M Stroud
Journal:  Proteins       Date:  1990

2.  Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II.

Authors:  L Chiche; C Gaboriaud; A Heitz; J P Mornon; B Castro; P A Kollman
Journal:  Proteins       Date:  1989

3.  Atomic solvation parameters applied to molecular dynamics of proteins in solution.

Authors:  L Wesson; D Eisenberg
Journal:  Protein Sci       Date:  1992-02       Impact factor: 6.725

4.  Protein model structure evaluation using the solvation free energy of folding.

Authors:  L Chiche; L M Gregoret; F E Cohen; P A Kollman
Journal:  Proc Natl Acad Sci U S A       Date:  1990-04       Impact factor: 11.205

5.  Criteria that discriminate between native proteins and incorrectly folded models.

Authors:  J Novotný; A A Rashin; R E Bruccoleri
Journal:  Proteins       Date:  1988

6.  Microfolding: conformational probability map for the alanine dipeptide in water from molecular dynamics simulations.

Authors:  A G Anderson; J Hermans
Journal:  Proteins       Date:  1988

7.  Conformational analysis of dipeptides in aqueous solution. II. Molecular structure of glycine and alanine dipeptides by depolarized Rayleigh scattering and laser Raman spectroscopy.

Authors:  M Avignon; C Garrigou-Lagrange; P Bothorel
Journal:  Biopolymers       Date:  1973       Impact factor: 2.505

8.  Solvation energy in protein folding and binding.

Authors:  D Eisenberg; A D McLachlan
Journal:  Nature       Date:  1986 Jan 16-22       Impact factor: 49.962

9.  Monte Carlo simulation of water behavior around the dipeptide N-acetylalanyl-N-methylamide.

Authors:  A T Hagler; D J Osguthorpe; B Robson
Journal:  Science       Date:  1980-05-09       Impact factor: 47.728

10.  Voiding dysfunction in patients with human T-lymphotropic virus type-1-associated myelopathy (HAM).

Authors:  S Komine; K Yoshida; H Yamashita; Z Masaki
Journal:  Paraplegia       Date:  1989-06
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  7 in total

1.  Computational protein design is a challenge for implicit solvation models.

Authors:  Alfonso Jaramillo; Shoshana J Wodak
Journal:  Biophys J       Date:  2004-09-17       Impact factor: 4.033

2.  Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models.

Authors:  Raphael F Ribeiro; Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Comput Aided Mol Des       Date:  2010-04-01       Impact factor: 3.686

3.  Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides.

Authors:  Hernán Stamati; Cecilia Clementi; Lydia E Kavraki
Journal:  Proteins       Date:  2010-02-01

4.  Conformational analysis of a nitroxide side chain in an α-helix with density functional theory.

Authors:  Dora Toledo Warshaviak; Laura Serbulea; K N Houk; Wayne L Hubbell
Journal:  J Phys Chem B       Date:  2010-12-17       Impact factor: 2.991

5.  A double-deletion method to quantifying incremental binding energies in proteins from experiment: example of a destabilizing hydrogen bonding pair.

Authors:  Luis A Campos; Santiago Cuesta-López; Jon López-Llano; Fernando Falo; Javier Sancho
Journal:  Biophys J       Date:  2004-11-19       Impact factor: 4.033

6.  Characterization and 2D NMR study of the stable [9-21, 15-27] 2 disulfide intermediate in the folding of the 3 disulfide trypsin inhibitor EETI II.

Authors:  D Le-Nguyen; A Heitz; L Chiche; M el Hajji; B Castro
Journal:  Protein Sci       Date:  1993-02       Impact factor: 6.725

7.  On the electrostatic component of protein-protein binding free energy.

Authors:  Kemper Talley; Carmen Ng; Michael Shoppell; Petras Kundrotas; Emil Alexov
Journal:  PMC Biophys       Date:  2008-11-05
  7 in total

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