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Literature DB >> 15572444

Water clusters in nonpolar cavities.

Subramanian Vaitheeswaran¹, Hao Yin, Jayendran C Rasaiah, Gerhard Hummer.

Abstract

We explore the structure and thermodynamics of water clusters confined in nonpolar cavities. By calculating the grand-canonical partition function term by term, we show that small nonpolar cavities can be filled at equilibrium with highly structured water clusters. The structural and thermodynamic properties of these encapsulated water clusters are similar to those observed experimentally in the gas phase. Water filling is highly sensitive to the size of the cavity and the strength of the interactions with the cavity wall. Water penetration into pores can thus be modulated by small changes in the polarity and structure of the cavity. Implications on water penetration into proteins are discussed.

Entities: Chemical

Mesh：

Substances：
Proteins
Water

Year: 2004 PMID： 15572444 PMCID： PMC535395 DOI： 10.1073/pnas.0407968101

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

23 in total

1. Formation of cyclic water hexamer in liquid helium: the smallest piece of Ice

Authors:
Journal: Science Date: 2000-01-14 Impact factor: 47.728

2. Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam.

Authors: Srabani Taraphder; Gerhard Hummer
Journal: J Am Chem Soc Date: 2003-04-02 Impact factor: 15.419

Review 3. Proton translocation by bacteriorhodopsin and heme-copper oxidases.

Authors: M Wikström
Journal: Curr Opin Struct Biol Date: 1998-08 Impact factor: 6.809

4. Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities.

Authors: A M Buckle; P Cramer; A R Fersht
Journal: Biochemistry Date: 1996-04-09 Impact factor: 3.162

5. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect.

Authors: A E Eriksson; W A Baase; X J Zhang; D W Heinz; M Blaber; E P Baldwin; B W Matthews
Journal: Science Date: 1992-01-10 Impact factor: 47.728

6. Water penetration and escape in proteins.

Authors: A E García; G Hummer
Journal: Proteins Date: 2000-02-15

7. High apparent dielectric constants in the interior of a protein reflect water penetration.

Authors: J J Dwyer; A G Gittis; D A Karp; E E Lattman; D S Spencer; W E Stites; B García-Moreno E
Journal: Biophys J Date: 2000-09 Impact factor: 4.033

8. The catalytic pathway of cytochrome p450cam at atomic resolution.

Authors: I Schlichting; J Berendzen; K Chu; A M Stock; S A Maves; D E Benson; R M Sweet; D Ringe; G A Petsko; S G Sligar
Journal: Science Date: 2000-03-03 Impact factor: 47.728

9. Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR.

Authors: J A Ernst; R T Clubb; H X Zhou; A M Gronenborn; G M Clore
Journal: Science Date: 1995-03-24 Impact factor: 47.728

10. Hydrophobic collapse in multidomain protein folding.

Authors: Ruhong Zhou; Xuhui Huang; Claudio J Margulis; Bruce J Berne
Journal: Science Date: 2004-09-10 Impact factor: 47.728

40 in total

1. Behavior of water in contact with model hydrophobic cavities and tunnels and carbon nanotubes.

Authors: E P Schulz; L M Alarcón; G A Appignanesi
Journal: Eur Phys J E Soft Matter Date: 2011-10-24 Impact factor: 1.890

2. Molecular dynamics free energy calculations to assess the possibility of water existence in protein nonpolar cavities.

Authors: Masataka Oikawa; Yoshiteru Yonetani
Journal: Biophys J Date: 2010-06-16 Impact factor: 4.033

Water clusters in nonpolar cavities.

1. Formation of cyclic water hexamer in liquid helium: the smallest piece of Ice

2. Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam.

Review 3. Proton translocation by bacteriorhodopsin and heme-copper oxidases.

4. Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities.

5. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect.

6. Water penetration and escape in proteins.

7. High apparent dielectric constants in the interior of a protein reflect water penetration.

8. The catalytic pathway of cytochrome p450cam at atomic resolution.

9. Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR.

10. Hydrophobic collapse in multidomain protein folding.

1. Behavior of water in contact with model hydrophobic cavities and tunnels and carbon nanotubes.

2. Molecular dynamics free energy calculations to assess the possibility of water existence in protein nonpolar cavities.

3. Role of electrostatics in modulating hydrophobic interactions and barriers to hydrophobic assembly.

4. Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation.

5. Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover.

6. Enthalpy-entropy contributions to the potential of mean force of nanoscopic hydrophobic solutes.

7. Role of protein cavities on unfolding volume change and on internal dynamics under pressure.

8. CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations.

9. The dewetting transition and the hydrophobic effect.

10. Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins.