Microsecond kinetics in model single- and double-stranded amylose polymers

Abstract

Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies.

Revision of the GROMOS 56A6CARBO force field: Improving the description of ring‐conformational equilibria in hexopyranose‐based carbohydrates chains

“…A similar flexibilization can actually be deduced from the results of independent simulations concerning α(1→4)‐linked Glc oligosaccharides in water using the GLYCAM06 force field . In this study (see also Supporting Information therein), ΔF i values in the approximate range 5–13 kJ mol −1 were reported for the individual Glc residues within the oligomers, the exact value depending on the chain length (3, 6, or 12 residues) and position along the chain. However, the corresponding value calculated for the unfunctionalized α‐Glc monomer using the same GLYCAM06 force field and the present calculation methodology is 22 kJ mol −1 , i.e., significantly larger.…”

“…The appropriate representation of the hexopyranose ring is a challenging issue in the design of force fields for performing molecular dynamics (MD) simulations of carbohydrates, for two main reasons. First, the interconversion between different ring conformers (puckering) is hindered by large free‐energy barriers, leading to characteristic times on the order of the microsecond . As a result, efficiently probing these transitions in MD requires the application of sampling‐enhancement techniques .…”

“…However, there is substantial indirect evidence suggesting that the high population of inverted chairs is actually an artifact of the 56A6 CARBO force field, namely: In high‐resolution crystallographic structures of protein–carbohydrate complexes involving α‐ d ‐glucose residues, the overwhelming majority of the rings are found in a 4 C 1 conformation (89% according to Ref. based on 174 structures refined at resolutions of 2.0 Å or below). This evidence remains, however, indirect due to the influence of the protein surroundings and crystal environment (see also Ref.…”

“…In AFM experiments involving the pulling of α(1→4)‐linked d ‐galacturonate chains, the presence of specific inflexion points in the force–extension curves suggests a transition from a diaxial to a diequatorial orientation of the linkages relative to the ring. If this interpretation is correct, it implies that the dominant conformation under zero‐force conditions is the 4 C 1 chair. The MD simulations of α(1→4)‐linked oligomers of d ‐hexopyranoses (typically malto‐oligomers, cyclodextrins, and amylose) carried out using other force fields (e.g., GLYCAM, OPLS‐AA, or CHARMM) suggest that the 4 C 1 conformer is the leading one. This evidence also remains indirect, as force fields are affected by uncertainties.…”

Inter‐residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations

“…Oligomers of amylose, namely,m altoheptaose [85] and maltododecaose, have been studied by MD simulations. [86] In the investigation of the conformational preferences of theh eptasaccharide,d ifferentf orce fields were employed for MD simulations on the nanosecond timescale and small-angle X-ray scattering (SAXS) experiments were used to complement the in silico approach; [85] combining SAXS and MD data is an approach that has more recently also been used for ad ecasaccharide containing b-d-Glcp residues. [87] The dodecasaccharide dynamics of the amylose model were analyzed in am ore recent study,e xtendingt he MD simulations to the microsecondt imescale.…”