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421 results on '"Polimeno, Antonino"'

131. Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and 13C NMR spin relaxation: conformational preferences of α-l-Rhap-α-(1 → 2)-α-l-Rhap-OMe in water and dimethyl sulfoxide solutions.

Author

Pendrill, Robert, Engström, Olof, Volpato, Andrea, Zerbetto, Mirco, Polimeno, Antonino, and Widmalm, Göran

Abstract

The monosaccharide l-rhamnose is common in bacterial polysaccharides and the disaccharide α-l-Rhap-α-(1 → 2)-α-l-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1′-13C]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR 3JCH and 3JCC coupling constants. Based on these spin–spin couplings the major state and the conformational distribution could be determined with respect to the φ torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The 13C NMR spin relaxation parameters T1, T2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d6 at two magnetic field strengths, with standard deviations ≤1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed 13C relaxation parameters, with an average error of ＜2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of 13C relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less. [ABSTRACT FROM AUTHOR]

Published
2016
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142. Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions

Author

Calligari, Paolo, Gerolin, Marco, Abergel, Daniel, and Polimeno, Antonino

Abstract

In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed.

Published
2017
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