Literature DB >> 6576339

Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data.

W F van Gunsteren, H J Berendsen, J Hermans, W G Hol, J P Postma.   

Abstract

The structure and dynamics of the full unit cell of a protein (bovine pancreatic trypsin inhibitor) containing 4 protein molecules and 560 water molecules have been simulated by using the molecular dynamics method. The obtained structure, atom positional fluctuations, and structure factors are compared with x-ray values. A way of calculating the motional contributions to structure factors is proposed.

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Year:  1983        PMID： 6576339      PMCID： PMC384028          DOI： 10.1073/pnas.80.14.4315

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


  19 in total

1.  Space-filling models of kinase clefts and conformation changes.

Authors:  C M Anderson; F H Zucker; T A Steitz
Journal:  Science       Date:  1979-04-27       Impact factor: 47.728

2.  Dihydrofolate reductase from Lactobacillus casei. X-ray structure of the enzyme methotrexate.NADPH complex.

Authors:  D A Matthews; R A Alden; J T Bolin; D J Filman; S T Freer; R Hamlin; W G Hol; R L Kisliuk; E J Pastore; L T Plante; N Xuong; J Kraut
Journal:  J Biol Chem       Date:  1978-10-10       Impact factor: 5.157

3.  Crystal structure of bovine trypsinogen at 1-8 A resolution. II. Crystallographic refinement, refined crystal structure and comparison with bovine trypsin.

Authors:  H Fehlhammer; W Bode; R Huber
Journal:  J Mol Biol       Date:  1977-04-25       Impact factor: 5.469

4.  Dynamics of folded proteins.

Authors:  J A McCammon; B R Gelin; M Karplus
Journal:  Nature       Date:  1977-06-16       Impact factor: 49.962

5.  Temperature-dependent X-ray diffraction as a probe of protein structural dynamics.

Authors:  H Frauenfelder; G A Petsko; D Tsernoglou
Journal:  Nature       Date:  1979-08-16       Impact factor: 49.962

6.  Crystallographic studies of the dynamic properties of lysozyme.

Authors:  P J Artymiuk; C C Blake; D E Grace; S J Oatley; D C Phillips; M J Sternberg
Journal:  Nature       Date:  1979-08-16       Impact factor: 49.962

Review 7.  Motions in proteins.

Authors:  F R Gurd; T M Rothgeb
Journal:  Adv Protein Chem       Date:  1979

8.  Protein structural fluctuations during a period of 100 ps.

Authors:  M Karplus; J A McCammon
Journal:  Nature       Date:  1979-02-15       Impact factor: 49.962

9.  Computer simulation of the solvent structure around biological macromolecules.

Authors:  A T Hagler; J Moult
Journal:  Nature       Date:  1978-03-16       Impact factor: 49.962

10.  Picosecond dynamics of tyrosine side chains in proteins.

Authors:  J A McCammon; P G Wolynes; M Karplus
Journal:  Biochemistry       Date:  1979-03-20       Impact factor: 3.162
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  30 in total

1.  The hydration shell of myoglobin.

Authors:  F Parak; H Hartmann; M Schmidt; G Corongiu; E Clementi
Journal:  Eur Biophys J       Date:  1992       Impact factor: 1.733

2.  Monte Carlo simulations of a protein molecule with and without hydration energy calculated by the hydration-shell model.

Authors:  H Wako
Journal:  J Protein Chem       Date:  1989-12

3.  A consensus view of protein dynamics.

Authors:  Manuel Rueda; Carles Ferrer-Costa; Tim Meyer; Alberto Pérez; Jordi Camps; Adam Hospital; Josep Lluis Gelpí; Modesto Orozco
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-10       Impact factor: 11.205

4.  Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4.

Authors:  M J Sippl; M Hendlich; P Lackner
Journal:  Protein Sci       Date:  1992-05       Impact factor: 6.725

5.  Atomic-level accuracy in simulations of large protein crystals.

Authors:  D M York; A Wlodawer; L G Pedersen; T A Darden
Journal:  Proc Natl Acad Sci U S A       Date:  1994-08-30       Impact factor: 11.205

6.  Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.

Authors:  Michael E Wall; Gaetano Calabró; Christopher I Bayly; David L Mobley; Gregory L Warren
Journal:  J Am Chem Soc       Date:  2019-03-11       Impact factor: 15.419

Review 7.  Accurate simulation of protein dynamics in solution.

Authors:  M Levitt; R Sharon
Journal:  Proc Natl Acad Sci U S A       Date:  1988-10       Impact factor: 11.205

8.  Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex.

Authors:  David S Cerutti; Isolde Le Trong; Ronald E Stenkamp; Terry P Lybrand
Journal:  Biochemistry       Date:  2008-10-25       Impact factor: 3.162

9.  Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity.

Authors:  P C Sanschagrin; L A Kuhn
Journal:  Protein Sci       Date:  1998-10       Impact factor: 6.725

10.  High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.

Authors:  Jessica L Thomaston; Mercedes Alfonso-Prieto; Rahel A Woldeyes; James S Fraser; Michael L Klein; Giacomo Fiorin; William F DeGrado
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-02       Impact factor: 11.205
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