Assessing the thermodynamic signatures of hydrophobic hydration for several common water models

2010 ◽  
Vol 132 (12) ◽  
pp. 124504 ◽  
Author(s):  
Henry S. Ashbaugh ◽  
Nicholas J. Collett ◽  
Harold W. Hatch ◽  
Jennifer A. Staton
Keyword(s):  
Hydrophobic Hydration ◽  
Water Models ◽  
Thermodynamic Signatures

Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models

2020 ◽  
Vol 22 (8) ◽  
pp. 4758-4771 ◽  
Author(s):  
Karolina Zieba ◽  
Cezary Czaplewski ◽  
Adam Liwo ◽  
Giuseppe Graziano
Keyword(s):  
Hydrophobic Interaction ◽  
Computational Analysis ◽  
Hydrophobic Hydration ◽  
Structural Features ◽  
Large Temperature ◽  
Temperature Range ◽  
Lennard Jones ◽  
Water Models

The study provides a deep computational analysis of the thermodynamic and structural features associated with xenon hydration and its pairwise hydrophobic interaction, over a large temperature range.

Hydrophobic hydration at the level of primitive models

1999 ◽  
Vol 96 (8) ◽  
pp. 1237-1248 ◽  
Author(s):  
MILAN PREDOTA, IVO NEZBEDA
Keyword(s):  
Hydrophobic Hydration

Comparison of 2D triangular C-grid shallow water models

2018 ◽  
Vol 161 ◽  
pp. 136-154 ◽  
Author(s):  
Hamidreza Shirkhani ◽  
Abdolmajid Mohammadian ◽  
Ousmane Seidou ◽  
Hazim Qiblawey
Keyword(s):  
Shallow Water ◽  
Shallow Water Models ◽  
Water Models

scholarly journals Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
N. M.-Mofiz Uddin Khan ◽  
Tatsuya Arai ◽  
Sakae Tsuda ◽  
Hidemasa Kondo
Keyword(s):  
Crystal Structure ◽  
Basal Plane ◽  
Molecular Mechanisms ◽  
Bound Water ◽  
Hydrophobic Hydration ◽  
Water Network ◽  
Molecular Scaffold ◽  
Intermediate Activity ◽  
Mold Fungus ◽  
Antifreeze Activity

AbstractAntifreeze proteins (AFPs) inhibit ice growth by adsorbing onto specific ice planes. Microbial AFPs show diverse antifreeze activity and ice plane specificity, while sharing a common molecular scaffold. To probe the molecular mechanisms responsible for AFP activity, we here characterized the antifreeze activity and crystal structure of TisAFP7 from the snow mold fungus Typhula ishikariensis. TisAFP7 exhibited intermediate activity, with the ability to bind the basal plane, compared with a hyperactive isoform TisAFP8 and a moderately active isoform TisAFP6. Analysis of the TisAFP7 crystal structure revealed a bound-water network arranged in a zigzag pattern on the surface of the protein’s ice-binding site (IBS). While the three AFP isoforms shared the water network pattern, the network on TisAFP7 IBS was not extensive, which was likely related to its intermediate activity. Analysis of the TisAFP7 crystal structure also revealed the presence of additional water molecules that form a ring-like network surrounding the hydrophobic side chain of a crucial IBS phenylalanine, which might be responsible for the increased adsorption of AFP molecule onto the basal plane. Based on these observations, we propose that the extended water network and hydrophobic hydration at IBS together determine the TisAFP activity.

scholarly journals Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

2021 ◽  
Vol 61 (2) ◽  
pp. 869-880 ◽  
Author(s):  
Arkajyoti Sengupta ◽  
Zhen Li ◽  
Lin Frank Song ◽  
Pengfei Li ◽  
Kenneth M. Merz
Keyword(s):  
Monovalent Ions ◽  
Water Models
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