Equilibrium sampling for biomolecules under mechanical tension

Molecular Dynamics Simulation of Polyacrylamide Adsorption on Calcite

In poorly consolidated carbonate rock reservoirs, solids production risk, which can lead to increased environmental waste, can be mitigated by injecting formation-strengthening chemicals. Classical atomistic molecular dynamics (MD) simulation is employed to model the interaction of polyacrylamide-based polymer additives with a calcite structure, which is the main component of carbonate formations. Amongst the possible calcite crystal planes employed as surrogates of reservoir rocks, the (1 0 4) plane is shown to be the most suitable surrogate for assessing the interactions with chemicals due to its stability and more realistic representation of carbonate structure. The molecular conformation and binding energies of pure polyacrylamide (PAM), hydrolysed polyacrylamide in neutral form (HPAM), hydrolysed polyacrylamide with 33% charge density (HPAM 33%) and sulfonated polyacrylamide with 33% charge density (SPAM 33%) are assessed to determine the adsorption characteristics onto calcite surfaces. An adsorption-free energy analysis, using an enhanced umbrella sampling method, is applied to evaluate the chemical adsorption performance. The interaction energy analysis shows that the polyacrylamide-based polymers display favourable interactions with the calcite structure. This is attributed to the electrostatic attraction between the amide and carboxyl functional groups with the calcite. Simulations confirm that HPAM33% has a lower free energy than other polymers, presumably due to the presence of the acrylate monomer in ionised form. The superior chemical adsorption performance of HPAM33% agrees with Atomic Force Microscopy experiments reported herein.

Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM)

Oligosaccharides and polysaccharides exert numerous functional roles in biology through their structural diversity and conformational properties. To investigate their conformational properties using computational methods, Hamiltonian replica exchange (H-REX) combined with two-dimensional grid-based correction maps as biasing potentials (bpCMAP) significantly improves the sampling efficiency about glycosidic linkages. In the current study, we extend the application of H-REX with bpCMAP to complex saccharides and establish systematic procedures for bpCMAP construction, determination of replica distribution, and data analysis. Our main findings are that (1) the bpCMAP for each type of glycosidic linkage can be constructed from the corresponding disaccharide using gas-phase umbrella sampling simulations, (2) the replica distribution can be conveniently determined following the exact definition of the average acceptance ratio based on the assigned distribution of biasing potentials, and (3) the extracted free energy surface (or potential of mean force (PMF)) can be improved using the weighted histogram analysis method (WHAM) allowing for the inclusion of data from the excited state replicas in the calculated probability distribution. The method is applied to a branched N-glycan found on the HIV gp120 protein, and a linear N-glycan. Considering the general importance of N-glycans and the wide appreciation of the sampling problem, the present method represents an efficient procedure for the conformational sampling of complex oligo- and polysaccharides under explicit solvent conditions. More generally, the use of WHAM is anticipated to be of general utility for the calculation of PMFs from H-REX simulations in a wide range of macromolecular systems.

Carbohydrate force fields

Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.

Extension of a three-helix bundle domain of myosin VI and key role of calmodulins

The molecular motor protein myosin VI moves toward the minus-end of actin filaments with a step size of 30-36 nm. Such large step size either drastically limits the degree of complex formation between dimer subunits to leave enough length for the lever arms, or requires an extension of the lever arms' crystallographically observed structure. Recent experimental work proposed that myosin VI dimerization triggers the unfolding of the protein's proximal tail domain which could drive the needed lever-arm extension. Here, we demonstrate through steered molecular dynamics simulation the feasibility of sufficient extension arising from turning a three-helix bundle into a long α-helix. A key role is played by the known calmodulin binding that facilitates the extension by altering the strain path in myosin VI. Sequence analysis of the proximal tail domain suggests that further calmodulin binding sites open up when the domain's three-helix bundle is unfolded and that subsequent calmodulin binding stabilizes the extended lever arms.