GROMACS 3.0: a package for molecular simulation and trajectory analysis

TL;DR: The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer, showing good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids.

TL;DR: Analysis of molecular dynamics simulations with atomistic details indicated that ibuprofen molecules prefer to be located in the hydrophobic acyl chain region of DMPC/cholesterol bilayers, which decreases the lateral motion of lipid molecules.

TL;DR: Molecular dynamics simulations of TolC are performed, and two putative gate regions, located at either end of the protein, can be distinguished, which are the extracellular loops and the mouth of the periplasmic domain, respectively.

TL;DR: In the present model, sequence variation and alternative alignments clarify the basis of the species barrier and strain specificity in PrP-based diseases.

TL;DR: In this paper, a simulation program for particle-mesh force calculation is presented, based on a one-dimensional plasma model and a collisionless particle model, which is used to simulate collisionless particle models.

Abstract: The structures of the three major classes of biopolymers-polynucleotides, polypeptides and polysaccharides-are surveyed in the light of the most recent results from X-ray diffraction, electron microscopy and other studies. The review contains an introductory section setting out the basic features of each class of biopolymer: the natures of the 'building blocks', the linkages between them, conformational principles, types of repeating (secondary) structures and so on. The main section on each class is deliberately selective, because of the large amount of structural information now available. The section on polynucleotides concentrates on DNA, reviewing the classical double-helical models and the evidence provided by X-ray fibre diffraction, but also paying special attention to the rapid growth of new information on such features as the variations in helix geometry and in base-stacking, those data being derived primarily from studies of small self-complementary oligonucleotides. Alternative models and the question of right-handed versus left-handed structures are also considered. Among polypeptide structures, both globular and fibrous proteins are described. Globular proteins are treated as a group, with no detailed description of any one of them; this section concentrates on the organisation of globular proteins via folding units and domains, some general features (protein homology, catalysis, flexibility, interaction with water), membrane proteins, immunoglobulins and viruses.

TL;DR: A comparison of a series of extended molecular dynamics simulations of bacteriophage T4 lysozyme in solvent with X‐ray data is presented, revealing that the N‐terminal helix rotates together with either of these two domains.