Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation. I. Internal Dynamics of Cyclodextrins: \u3b3-Cyclodextrin as a Case Study

In this work, we address the description of the dynamics of cyclodextrins in relation with nuclear magnetic resonance (NMR) relaxation data collected for hydroxymethyl groups. We define an integrated computational approach based on the definition and parametrization of a stochastic equation able to describe the relevant degrees of freedom affecting the NMR observables. The computational protocol merges molecular dynamics simulations and hydrodynamics approaches for the evaluation of most of the molecular parameters entering the stochastic description of the system. We apply the method to the interpretation of the C-13 NMR relaxation of the -CH2OH group of cyclodextrins. We use gamma-cyclodextrin as a case study. Results are in agreement with quantitative and qualitative analyses performed in the past with simpler models and molecular dynamics simulations. The element of novelty in our approach is in the treatment of the coupling of the relevant internal (glucopyranose ring twisting/tilting and hydroxymethyl group jumps) and global (molecular tumbling) degrees of freedom

Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation. 2. Interpretation of Complex Dynamics in Linear Oligosaccharides

A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters

Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation. 2. Interpretation of Complex Dynamics in Linear Oligosaccharides

A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters