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Literature DB >> 10905826

Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation.

Abstract

The effects of different non-bonded parameters of force fields for NMR structure calculation on the quality of the resulting NMR solution structures were investigated using Interleukin 4 as a model system. NMR structure ensembles were calculated with an ab initio protocol using torsion angle dynamics. The calculations were repeated with five different non-bonded energy functions and parameters. The resulting ensembles were compared with the available X-ray structures, and their quality was assessed with common structure validation programs. In addition, the impact of torsion angle restraints and dihedral energy terms for the sidechains and the backbone was studied. The further improvement of the quality by refinement in explicit solvent was demonstrated. The optimal parameters, including those necessary for water refinement, are available in the new version of the PARALLHDG force field.

Entities: Chemical Gene

Mesh：

Substances：
Interleukin-4

Year: 1999 PMID： 10905826 DOI： 10.1023/a:1008365802830

Source DB: PubMed Journal: J Biomol NMR ISSN： 0925-2738 Impact factor: 2.835

30 in total

1. Loop mobility in a four-helix-bundle protein: 15N NMR relaxation measurements on human interleukin-4.

Authors: C Redfield; J Boyd; L J Smith; R A Smith; C M Dobson
Journal: Biochemistry Date: 1992-11-03 Impact factor: 3.162

2. WHAT IF: a molecular modeling and drug design program.

Authors: G Vriend
Journal: J Mol Graph Date: 1990-03

Review 3. New applications of simulated annealing in X-ray crystallography and solution NMR.

Authors: A T Brünger; P D Adams; L M Rice
Journal: Structure Date: 1997-03-15 Impact factor: 5.006

4. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement.

Authors: P D Adams; N S Pannu; R J Read; A T Brünger
Journal: Proc Natl Acad Sci U S A Date: 1997-05-13 Impact factor: 11.205

5. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

Authors: W L Jorgensen; J Tirado-Rives
Journal: J Am Chem Soc Date: 1988-03-01 Impact factor: 15.419

6. Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure.

Authors: J J Prompers; R H Folmer; M Nilges; P J Folkers; R N Konings; C W Hilbers
Journal: Eur J Biochem Date: 1995-09-01

7. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors: W Kabsch; C Sander
Journal: Biopolymers Date: 1983-12 Impact factor: 2.505

8. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.

Authors: J Kuszewski; A M Gronenborn; G M Clore
Journal: Protein Sci Date: 1996-06 Impact factor: 6.725

9. Human interleukin 4. The solution structure of a four-helix bundle protein.

Authors: L J Smith; C Redfield; J Boyd; G M Lawrence; R G Edwards; R A Smith; C M Dobson
Journal: J Mol Biol Date: 1992-04-20 Impact factor: 5.469

10. Aspects of receptor binding and signalling of interleukin-4 investigated by site-directed mutagenesis and NMR spectroscopy.

Authors: T Müller; T Dieckmann; W Sebald; H Oschkinat
Journal: J Mol Biol Date: 1994-04-08 Impact factor: 5.469

83 in total

10. Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.

Authors: Charalampos G Kalodimos; Alexandre M J J Bonvin; Roberto K Salinas; Rainer Wechselberger; Rolf Boelens; Robert Kaptein
Journal: EMBO J Date: 2002-06-17 Impact factor: 11.598

Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation.

1. Loop mobility in a four-helix-bundle protein: 15N NMR relaxation measurements on human interleukin-4.

2. WHAT IF: a molecular modeling and drug design program.

Review 3. New applications of simulated annealing in X-ray crystallography and solution NMR.

4. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement.

5. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

6. Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure.

7. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

8. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.

9. Human interleukin 4. The solution structure of a four-helix bundle protein.

10. Aspects of receptor binding and signalling of interleukin-4 investigated by site-directed mutagenesis and NMR spectroscopy.

1. Structural characterization of a mutant peptide derived from ubiquitin: implications for protein folding.

2. The hairpin structure of the (6)F1(1)F2(2)F2 fragment from human fibronectin enhances gelatin binding.

3. Unraveling the symmetry ambiguity in a hexamer: calculation of the R6 human insulin structure.

4. Refinement of the protein backbone angle psi in NMR structure calculations.

5. Solution structure of the RNA polymerase subunit RPB5 from Methanobacterium thermoautotrophicum.

6. Improving the quality of protein structures derived by NMR spectroscopy.

7. The structure of Bcl-w reveals a role for the C-terminal residues in modulating biological activity.

8. Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.

9. A refined solution structure of hen lysozyme determined using residual dipolar coupling data.

10. Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.