Literature DB >> 23345762

Structural Characteristics in Protein Hydration Investigated by Cryogenic X-ray Crystal Structure Analyses.

Masayoshi Nakasako1.   

Abstract

Cryogenic X-ray crystallography has heen applied to investigate thehydration structures of proteins. The amount of hydration water moleculesidentified at cryogenic temperature is more than twice those at ambienttemperature, and the structural models of proteins with a lot of hydrationwater molecules have provided much information to elucidate the static anddynamical characteristics of hydration structures of proteins. On proteinsurface, hydration water molecules distribute non-randomly and stillretain the tetrahedral hydrogen-bond geometry as well as in bulk solvent.In addition, water molecules form clathrate-like arrangements to cover thehydrophobic residues exposed to solvent. The standard interaction geometryenables the three-dimensional extension of hydrogen-bond networks aroundprotein molecules and, simultaneously, ensures the concerted reorganizationof hydration structures during the dynamical motion of proteins at work.The hydration structure analyses at cryogenic temperatures may contributeto understanding physical principles governing the dynamics of `molecularmachines' in aqueous environment.

Entities:  

Keywords:  cryogenic X-ray crystallography; hydrogen bond; protein dynamics; protein hydration; water molecule

Year:  2002        PMID: 23345762      PMCID: PMC3456660          DOI: 10.1023/A:1019982220615

Source DB:  PubMed          Journal:  J Biol Phys        ISSN: 0092-0606            Impact factor:   1.365


  15 in total

1.  Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering.

Authors:  M Nakasako; T Fujisawa; S Adachi; T Kudo; S Higuchi
Journal:  Biochemistry       Date:  2001-03-13       Impact factor: 3.162

2.  Tertiary and quaternary structures of photoreactive Fe-type nitrile hydratase from Rhodococcus sp. N-771: roles of hydration water molecules in stabilizing the structures and the structural origin of the substrate specificity of the enzyme.

Authors:  M Nakasako; M Odaka; M Yohda; N Dohmae; K Takio; N Kamiya; I Endo
Journal:  Biochemistry       Date:  1999-08-03       Impact factor: 3.162

3.  Roles of hydration water molecules in molecular packing of the killer toxin from Pichia farinosa in its crystalline state investigated by cryogenic X-ray crystallography.

Authors:  Masayoshi Nakasako; Fumihiko Tsuchiya; Yoji Arata
Journal:  Biophys Chem       Date:  2002-03-28       Impact factor: 2.352

4.  Effect of solvent on collective motions in globular protein.

Authors:  S Hayward; A Kitao; F Hirata; N Go
Journal:  J Mol Biol       Date:  1993-12-20       Impact factor: 5.469

5.  Critical exponents of protonic percolation in hydrated lysozyme powders.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1988-04-01

6.  Protein hydration in solution: experimental observation by x-ray and neutron scattering.

Authors:  D I Svergun; S Richard; M H Koch; Z Sayers; S Kuprin; G Zaccai
Journal:  Proc Natl Acad Sci U S A       Date:  1998-03-03       Impact factor: 11.205

7.  Thermal motions and function of bacteriorhodopsin in purple membranes: effects of temperature and hydration studied by neutron scattering.

Authors:  M Ferrand; A J Dianoux; W Petry; G Zaccaï
Journal:  Proc Natl Acad Sci U S A       Date:  1993-10-15       Impact factor: 11.205

8.  Liquid-like side-chain dynamics in myoglobin.

Authors:  G R Kneller; J C Smith
Journal:  J Mol Biol       Date:  1994-09-23       Impact factor: 5.469

9.  A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment.

Authors:  V Lounnas; B M Pettitt
Journal:  Proteins       Date:  1994-02

10.  The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody.

Authors:  M Nakasako; H Takahashi; N Shimba; I Shimada; Y Arata
Journal:  J Mol Biol       Date:  1999-08-06       Impact factor: 5.469

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  3 in total

1.  A microfabricated fixed path length silicon sample holder improves background subtraction for cryoSAXS.

Authors:  Jesse B Hopkins; Andrea M Katz; Steve P Meisburger; Matthew A Warkentin; Robert E Thorne; Lois Pollack
Journal:  J Appl Crystallogr       Date:  2015-01-30       Impact factor: 3.304

2.  Breaking the radiation damage limit with Cryo-SAXS.

Authors:  Steve P Meisburger; Matthew Warkentin; Huimin Chen; Jesse B Hopkins; Richard E Gillilan; Lois Pollack; Robert E Thorne
Journal:  Biophys J       Date:  2013-01-08       Impact factor: 4.033

3.  Water polygons in high-resolution protein crystal structures.

Authors:  Jonas Lee; Sung-Hou Kim
Journal:  Protein Sci       Date:  2009-07       Impact factor: 6.725

  3 in total

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