WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations

2017 ◽  
Vol 19 (26) ◽  
pp. 17094-17102 ◽  
Author(s):  
Jiří Černý ◽  
Bohdan Schneider ◽  
Lada Biedermannová
Keyword(s):  
Data Mining ◽  
Protein Structure ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Protein Hydration ◽  
Water Molecules ◽  
Structure Dynamics ◽  
Dynamics And Function ◽  
And Function

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function.

scholarly journals Dynamics and mechanism of ultrafast water–protein interactions

2016 ◽  
Vol 113 (30) ◽  
pp. 8424-8429 ◽  
Author(s):  
Yangzhong Qin ◽  
Lijuan Wang ◽  
Dongping Zhong
Keyword(s):  
Protein Interactions ◽  
Hydration Shell ◽  
Water Dynamics ◽  
Side Chain ◽  
Water Molecules ◽  
Ultrafast Dynamics ◽  
Hydration Water ◽  
Water Side ◽  
Dynamics And Function ◽  
And Function

Protein hydration is essential to its structure, dynamics, and function, but water–protein interactions have not been directly observed in real time at physiological temperature to our awareness. By using a tryptophan scan with femtosecond spectroscopy, we simultaneously measured the hydration water dynamics and protein side-chain motions with temperature dependence. We observed the heterogeneous hydration dynamics around the global protein surface with two types of coupled motions, collective water/side-chain reorientation in a few picoseconds and cooperative water/side-chain restructuring in tens of picoseconds. The ultrafast dynamics in hundreds of femtoseconds is from the outer-layer, bulk-type mobile water molecules in the hydration shell. We also found that the hydration water dynamics are always faster than protein side-chain relaxations but with the same energy barriers, indicating hydration shell fluctuations driving protein side-chain motions on the picosecond time scales and thus elucidating their ultimate relationship.

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