Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1 : 1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein, together with the solvent, is coarse-grained.

We calculate full 3D pressure fields for inhomogeneous nanoscale systems using molecular dynamics simulation data. The fields represent systems with increasing level of complexity, ranging from semivesicles and vesicles to membranes characterized by coexistence of two phases, including also a protein-membrane complex. We show that the 3D pressure field is distinctly different for curved and planar bilayers, the pressure field depends strongly on the phase of the membrane, and that an integral protein modulates the tension and elastic properties of the membrane.

Effects of steric obstruction on random flight chains are examined. Spatial probability distributions are elaborated to calculate residual dipolar couplings and residual chemical shift anisotropy, parameters that are acquired by NMR spectroscopy from solutes dissolved in dilute liquid crystals. Calculations yield chain length and residue position-dependent values in good agreement with simulations to provide understanding of recently acquired data from denatured proteins.

Mechano-sensitive channels are ubiquitous membrane proteins that activate in response to increasing tension in the lipid membrane. They facilitate a sudden, nonselective release of solutes and water that safeguards the integrity of the cell in hypo-or hyper-osmotic shock conditions. We have simulated the rapid release of content from a pressurized liposome through a particular mechano-sensitive protein channel, MscL, embedded in the liposomal membrane. We show that a single channel is able to relax the liposome, stressed to the point of bursting, in a matter of microseconds. We map the full activation-deactivation cycle of MscL in near-atomic detail and are able to quantify the rapid decrease in liposomal stress as a result of channel activation. This provides a computational tool that opens the way to contribute to the rational design of functional nano-containers.coarse-grained | molecular dynamics simulation | MARTINI force field | protein channel | drug delivery vehicle M echano-sensitive channels react to a sudden increase in membrane tension by forming transmembrane pores that counteract the pressure gradient buildup by balancing the osmotic conditions on either side of the cell membrane.(1-4) They have a crucial role in diverse biological functions from sensory feedback to the prevention of cell death by membrane rupture (5, 6). The mechano-sensitive channel of large conductance (MscL) is a pentameric, prevalently helical membrane protein weighing approximately 95 kDa. The crystal structure of an inactive MscL from Mycobacterium tuberculosis (Tb-MscL) has been resolved (4, 7) by X-ray diffraction. Each of the five subunits consist of a transmembrane and a cytoplasmic domain connected by a flexible linker. The two transmembrane helices TM1 and TM2 and the N-terminal helix S1 are arranged in a criss-cross manner with TM1 and TM2 passing through the membrane and S1 parallel to the membrane surface (Fig. 1). The transmembrane complex forms a ring-like structure with a hydrophobic lock region located slightly toward the cytoplasmic side from the center of the membrane. The cytoplasmic domains form a helical bundle at the mouth of the membrane channel.When activated, e.g., by increased membrane tension, MscL forms a nonselective transmembrane channel capable of quickly transporting large amounts of solvent and solutes. The maximum flux through MscL (∼3 nS) is so high that only a handful of the channels could (in theory) dehydrate an entire living cell within seconds (4). In practise, MscLs are usually active no longer than a few hundreds of milliseconds with characteristic, rapidly flickering activation-deactivation cycles plainly visible in single-channel traces (8-10). The existence of multiple subconducting states has been proposed (8), and they have been hypothesised (11) to be the source of the rapid flickering. By introducing ingenious point-mutations (12) at the channel walls the activation and deactivation of MscL can be controlled by ambient pH and/or light (13). This makes MscL a functional nano-valve...

The mechanosensitive channel of large conductance (MscL) has become a model system in which to understand mechanosensation, a process involved in osmoregulation and many other physiological functions. While a high resolution closed state structure is available, details of the open structure and the gating mechanism remain unknown. In this study we combine coarse grained simulations with restraints from EPR and FRET experiments to study the structural changes involved in gating with much greater level of conformational sampling than has previously been possible. We generated a set of plausible open pore structures that agree well with existing open pore structures and gating models. Most interestingly, we found that membrane thinning induces a kink in the upper part of TM1 that causes an outward motion of the periplasmic loop away from the pore centre. This previously unobserved structural change might present a new mechanism of tension sensing and might be related to a functional role in osmoregulation.

The steric obstruction model, that describes the enhanced alignment of folded proteins by anisotropic medium, is extended to account for the residual dipolar couplings of chain-like polypeptides. The average alignment of each chain segment is calculated from an ensemble of conformations represented by a spatial probability distribution. The segmental alignment depends on chain length, flexibility and segment's position in the chain. Residual dipolar couplings in turn depend on internuclear vector directions within each fragment. The results of calculations and simulations explain salient features of the experimental data. With this insight residual dipolar couplings can be interpreted to assess the degree of denaturation, local structures and spatial organization of weakly structured proteins.

The discovery of dilute liquid crystalline media to align biological macromolecules has opened many new possibilities to study protein and nucleic acid structures by NMR spectroscopy. We inspect the basic alignment phenomenon for an ensemble of protein conformations to deduce relative contributions of each member to the residual dipolar coupling signals. We find that molecular fluctuations can affect the alignment and discover a resulting emphasis of certain conformations. However, the internal fluctuations are largely uncorrelated with those of the alignment, implying that proteins have liquidlike molecular surfaces. Furthermore, we consider the implications of a dynamic bias to structure determination using data from the weak alignment method.

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