The unfolding effects on the protein hydration shell and partial molar volume: a computational study

2016 ◽  
Vol 18 (40) ◽  
pp. 28175-28182 ◽  
Author(s):  
Sara Del Galdo ◽  
Andrea Amadei
Keyword(s):  
Aqueous Solution ◽  
Computational Analysis ◽  
Computational Study ◽  
Hydration Shell ◽  
Partial Molar Volumes ◽  
Globular Proteins ◽  
Protein Hydration ◽  
Native Protein ◽  
Unfolded State ◽  
Protein Hydration Shell

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes.

Length-scale dependence of protein hydration-shell density

2020 ◽  
Vol 22 (14) ◽  
pp. 7340-7347
Author(s):  
Akash Deep Biswas ◽  
Vincenzo Barone ◽  
Andrea Amadei ◽  
Isabella Daidone
Keyword(s):  
Hydration Shell ◽  
Scale Dependence ◽  
Protein Hydration ◽  
Length Scale ◽  
Protein Size ◽  
Protein Hydration Shell

An increase in protein hydration-shell density relative to that of the bulk is observed (in the range of 4–14%) for all studied proteins and this density-increment, which decreases for decreasing protein size, is caused by the protein size only.

scholarly journals Quantum Behavior of Water Protons in Protein Hydration Shell

2009 ◽  
Vol 96 (5) ◽  
pp. 1939-1943 ◽  
Author(s):  
S.E. Pagnotta ◽  
F. Bruni ◽  
R. Senesi ◽  
A. Pietropaolo
Keyword(s):  
Hydration Shell ◽  
Protein Hydration ◽  
Quantum Behavior ◽  
Protein Hydration Shell

scholarly journals Proton Momentum Distribution in a Protein Hydration Shell

2007 ◽  
Vol 98 (13) ◽  
Author(s):  
R. Senesi ◽  
A. Pietropaolo ◽  
A. Bocedi ◽  
S. E. Pagnotta ◽  
F. Bruni
Keyword(s):  
Momentum Distribution ◽  
Hydration Shell ◽  
Protein Hydration ◽  
Proton Momentum ◽  
Protein Hydration Shell

Protective action of trehalose and glucose on protein hydration shell clarified by using X-ray and neutron scattering

2018 ◽  
Vol 551 ◽  
pp. 249-255 ◽  
Author(s):  
Satoshi Ajito ◽  
Mitsuhiro Hirai ◽  
Hiroki Iwase ◽  
Nobutaka Shimizu ◽  
Noriyuki Igarashi ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Protective Action ◽  
Hydration Shell ◽  
Protein Hydration ◽  
X Ray ◽  
Protein Hydration Shell

Absorption spectra of xanthines in aqueous solution: a computational study

2020 ◽  
Vol 22 (10) ◽  
pp. 5929-5941 ◽  
Author(s):  
Sara Gómez ◽  
Tommaso Giovannini ◽  
Chiara Cappelli
Keyword(s):  
Aqueous Solution ◽  
Absorption Spectra ◽  
Computational Analysis ◽  
Computational Study

We present a detailed computational analysis of the UV/Vis spectra of caffeine, paraxanthine and theophylline in aqueous solution.

2-Deoxyribose Radicals in the Gas Phase and Aqueous Solution. Transient Intermediates of Hydrogen Atom Abstraction from 2-Deoxyribofuranose

2005 ◽  
Vol 70 (11) ◽  
pp. 1769-1786 ◽  
Author(s):  
Luc A. Vannier ◽  
Chunxiang Yao ◽  
František Tureček
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Atom ◽  
Gas Phase ◽  
Computational Study ◽  
Hydrogen Atom Abstraction ◽  
Oh Radical ◽  
Free Energies ◽  
Intramolecular Hydrogen ◽  
Solvation Free Energies ◽  
Transient Intermediates

A computational study at correlated levels of theory is reported to address the structures and energetics of transient radicals produced by hydrogen atom abstraction from C-1, C-2, C-3, C-4, C-5, O-1, O-3, and O-5 positions in 2-deoxyribofuranose in the gas phase and in aqueous solution. In general, the carbon-centered radicals are found to be thermodynamically and kinetically more stable than the oxygen-centered ones. The most stable gas-phase radical, 2-deoxyribofuranos-5-yl (5), is produced by H-atom abstraction from C-5 and stabilized by an intramolecular hydrogen bond between the O-5 hydroxy group and O-1. The order of radical stabilities is altered in aqueous solution due to different solvation free energies. These prefer conformers that lack intramolecular hydrogen bonds and expose O-H bonds to the solvent. Carbon-centered deoxyribose radicals can undergo competitive dissociations by loss of H atoms, OH radical, or by ring cleavages that all require threshold dissociation or transition state energies >100 kJ mol-1. This points to largely non-specific dissociations of 2-deoxyribose radicals when produced by exothermic hydrogen atom abstraction from the saccharide molecule. Oxygen-centered 2-deoxyribose radicals show only marginal thermodynamic and kinetic stability and are expected to readily fragment upon formation.

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