Correlating hydration shell structure with amino acid hydrophobicity

1993 ◽  
Vol 115 (8) ◽  
pp. 3336-3337 ◽  
Author(s):  
David Hecht ◽  
Lema Tadesse ◽  
Lee Walters
Keyword(s):  
Amino Acid ◽  
Shell Structure ◽  
Hydration Shell

scholarly journals Methane Hydration‐Shell Structure and Fragility

2018 ◽  
Vol 57 (46) ◽  
pp. 15133-15137 ◽  
Author(s):  
Xiangen Wu ◽  
Wanjun Lu ◽  
Louis M. Streacker ◽  
Henry S. Ashbaugh ◽  
Dor Ben‐Amotz
Keyword(s):  
Shell Structure ◽  
Hydration Shell

CO2 Hydration Shell Structure and Transformation

2017 ◽  
Vol 8 (13) ◽  
pp. 2971-2975 ◽  
Author(s):  
Samual R. Zukowski ◽  
Pavlin D. Mitev ◽  
Kersti Hermansson ◽  
Dor Ben-Amotz
Keyword(s):  
Shell Structure ◽  
Hydration Shell

Hydration Shell Structure and Dynamics of Curium(III) in Aqueous Solution: First Principles and Empirical Studies

2011 ◽  
Vol 115 (18) ◽  
pp. 4665-4677 ◽  
Author(s):  
Raymond Atta-Fynn ◽  
Eric J. Bylaska ◽  
Gregory K. Schenter ◽  
Wibe A. de Jong
Keyword(s):  
Aqueous Solution ◽  
First Principles ◽  
Shell Structure ◽  
Empirical Studies ◽  
Hydration Shell ◽  
Structure And Dynamics

The hydration shell structure of Li+ investigated by Born–Oppenheimer ab initio QM/MM dynamics

1998 ◽  
Vol 286 (1-2) ◽  
pp. 56-64 ◽  
Author(s):  
Anan Tongraar ◽  
Klaus R Liedl ◽  
Bernd M Rode
Keyword(s):  
Ab Initio ◽  
Shell Structure ◽  
Hydration Shell

Distribution of internal parameters of the hydration shell structure of proteins

BIOPHYSICS ◽  
2014 ◽  
Vol 59 (6) ◽  
pp. 869-875 ◽  
Author(s):  
E. V. Rubtcova ◽  
A. B. Solovey ◽  
V. I. Lobyshev
Keyword(s):  
Shell Structure ◽  
Hydration Shell ◽  
Internal Parameters ◽  
Structure Of Proteins

scholarly journals Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

2015 ◽  
Vol 71 (11) ◽  
pp. 2192-2202 ◽  
Author(s):  
Lada Biedermannová ◽  
Bohdan Schneider
Keyword(s):  
Amino Acid ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Solvent Accessibility ◽  
Hydration Shell ◽  
Protein Crystal ◽  
Water Molecules ◽  
Amino Acid Residues ◽  
Set Up ◽  
Dynamics Simulations

Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

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