Heme proteins: the role of solvent in the dynamics of gates and portals.
Water plays a pivotal role in the correct functioning of proteins. Hydration is fundamental to their stability and flexibility, to folding process and specific functions, and to protein-protein interactions. In this work, the effects of solvation on proteins dynamics have been investigated by employing molecular dynamics simulations and using myoglobin as a model system. The investigation has been focused on solvent waters residing around/inside the protein, with average times of up to tens of nanoseconds, revealing that these slow waters may have significant effects on biological functioning of the protein. Our study pointed out that water is able to interact with proteins in diverse ways, leading to different kinds of perturbations in their intrinsic dynamic behavior. In particular, for myoglobin it was found that a water molecule can (i) "block" entry/escape of ligands to/from a particular docking site, (ii) act as a "wedge" modulating the dynamics of internal cavities, or (iii) join a "flow" of waters taking a ligand into (or "washing" a ligand away from) the protein interior. The information gathered in this work allowed us to provide a fingerprint of protein solvation state, the hydration sites map, which may represent a novel tool for comparing different forms/species of globular proteins.
Scorciapino
Mariano Andrea
MA
Department of Chemical Sciences, University of Cagliari, Italy.
Robertazzi
Arturo
A
Casu
Mariano
M
Ruggerone
Paolo
P
Ceccarelli
Matteo
M
D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009211:Myoglobin / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry
D008024:Ligands; D009211:Myoglobin; D012997:Solvents