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Literature DB >> 2326281

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

L Chiche¹, L M Gregoret, F E Cohen, P A Kollman.

Abstract

A systematic study of solvation free energy of folding for proteins with known crystallographic structures is presented. There is a linear relationship between the solvation free energy of folding and the protein size. This relationship, which can be rationalized by a simple model of chain folding, allows prediction of the solvation free energy of folding for proteins for which no high resolution structures are available. All misfolded structures analyzed show solvation free energies higher than predicted; however, some of the misfolded structures have values close enough to the predicted values so that one must be very careful when using such a criterion to check the correctness of a protein model.

Mesh：

Substances：
Enzymes
Proteins
Solvents

Year: 1990 PMID： 2326281 PMCID： PMC53871 DOI： 10.1073/pnas.87.8.3240

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

14 in total

1. 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

2. Molecular modeling of the HIV-1 protease and its substrate binding site.

Authors: I T Weber; M Miller; M Jaskólski; J Leis; A M Skalka; A Wlodawer
Journal: Science Date: 1989-02-17 Impact factor: 47.728

3. Rebuilding flavodoxin from C alpha coordinates: a test study.

Authors: L S Reid; J M Thornton
Journal: Proteins Date: 1989

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

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

5. Solvation energy in protein folding and binding.

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

6. Surface and inside volumes in globular proteins.

Authors: J Janin
Journal: Nature Date: 1979-02-08 Impact factor: 49.962

7. Construction of a model for the three-dimensional structure of human renal renin.

Authors: W Carlson; M Karplus; E Haber
Journal: Hypertension Date: 1985 Jan-Feb Impact factor: 10.190

8. Relaxin and its structural relationship to insulin.

Authors: N Isaacs; R James; H Niall; G Bryant-Greenwood; G Dodson; A Evans; A C North
Journal: Nature Date: 1978-01-19 Impact factor: 49.962

9. 7-Iron ferredoxin revisited.

Authors: C D Stout
Journal: J Biol Chem Date: 1988-07-05 Impact factor: 5.157

10. Structure of a 7Fe ferredoxin from Azotobacter vinelandii.

Authors: D Ghosh; W Furey; S O'Donnell; C D Stout
Journal: J Biol Chem Date: 1981-05-10 Impact factor: 5.157

18 in total

1. Statistical potentials for fold assessment.

Authors: Francisco Melo; Roberto Sánchez; Andrej Sali
Journal: Protein Sci Date: 2002-02 Impact factor: 6.725

2. Analysis of protein sequence/structure similarity relationships.

Authors: Hin Hark Gan; Rebecca A Perlow; Sharmili Roy; Joy Ko; Min Wu; Jing Huang; Shixiang Yan; Angelo Nicoletta; Jonathan Vafai; Ding Sun; Lihua Wang; Joyce E Noah; Samuela Pasquali; Tamar Schlick
Journal: Biophys J Date: 2002-11 Impact factor: 4.033

10. Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys.

Authors: Dan M Bolser; Ioannis Filippis; Henning Stehr; Jose Duarte; Michael Lappe
Journal: BMC Struct Biol Date: 2008-12-08

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

1. 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.

2. Molecular modeling of the HIV-1 protease and its substrate binding site.

3. Rebuilding flavodoxin from C alpha coordinates: a test study.

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

5. Solvation energy in protein folding and binding.

6. Surface and inside volumes in globular proteins.

7. Construction of a model for the three-dimensional structure of human renal renin.

8. Relaxin and its structural relationship to insulin.

9. 7-Iron ferredoxin revisited.

10. Structure of a 7Fe ferredoxin from Azotobacter vinelandii.

1. Statistical potentials for fold assessment.

2. Analysis of protein sequence/structure similarity relationships.

3. In search for more accurate alignments in the twilight zone.

4. VADAR: a web server for quantitative evaluation of protein structure quality.

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

6. Correlation functions as a tool for protein modeling and structure analysis.

7. Comparative modeling of the three-dimensional structure of type II antifreeze protein.

Review 8. Knowledge-based model building of proteins: concepts and examples.

9. Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding.

10. Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys.