The Martini Model in Materials Science.

The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.

Crystal Field in Rare-Earth Complexes: From Electrostatics to Bonding.

The flexibility of first-principles (ab initio) calculations with the SO-CASSCF (complete active space self-consistent field theory with a treatment of the spin-orbit (SO) coupling by state interaction) method is used to quantify the electrostatic and covalent contributions to crystal field parameters. Two types of systems are chosen for illustration: 1) The ionic and experimentally well-characterized PrCl crystal; this study permits a revisitation of the partition of contributions proposed in the early days of crystal field theory; and 2) a series of sandwich molecules [Ln(η -C H ) ] , with Ln=Dy, Ho, Er, and Tm and n=5, 6, and 8, in which the interaction between Ln and the aromatic ligands is more difficult to describe within an electrostatic approach. It is shown that a model with three layers of charges reproduces the electrostatic field generated by the ligands and that the covalency plays a qualitative role.

Development of Chemically Defined Media to Express Trp-Analog-Labeled Proteins in a Lactococcus lactis Trp Auxotroph.

Chemically defined media for growth of Lactococcus lactis strains contain about 50 components, making them laborious and expensive growth media. However, they are crucial for metabolism studies as well as for expression of heterologous proteins labeled with unnatural amino acids. In particular, the L.

Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing.

We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's capacity for converting anisotropic lattice strain to changes in an electrical current at the nanoscale. Using detailed atomistic molecular dynamics (MD) simulations, we study sensor operation at ambient conditions.

Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex.

Nuclear pore complexes (NPCs) allow selective import and export while forming a barrier for untargeted proteins. Using fluorescence microscopy, we measured in vivo the permeability of the Saccharomyces cerevisiae NPC for multidomain proteins of different sizes and found that soluble proteins of 150 kDa and membrane proteins with an extralumenal domain of 90 kDa were still partly localized in the nucleus on a time scale of hours. The NPCs thus form only a weak barrier for the majority of yeast proteins, given their monomeric size.

Bright ion channels and lipid bilayers.

If we look at a simple organism such as a zebrafish under a microscope, we would see many cells working in harmony. If we zoomed in, we would observe each unit performing its own tasks in a special aqueous environment isolated from the other units by a lipid bilayer approximately 5 nm thick. These confined units are social: they communicate with one another by sensing and responding to the chemical changes in their environment through receptors and ion channels.

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition.

Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this representation an elastic network is used as a structural scaffold to describe and maintain the overall shape of a protein and a physics-based coarse-grained model (MARTINI-2.

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2-3 orders of magnitude larger compared to atomistic simulations, providing a bridge between the atomistic and the mesoscopic scale.

Size and shape of the repetitive domain of high molecular weight wheat gluten proteins. II. Hydrodynamic studies.

This study describes the hydrodynamic properties of the repetitive domain of high molecular weight (HMW) wheat proteins, which complement the small-angle scattering (SANS) experiments performed in the first paper of this series. The sedimentation coefficients, s(0), and diffusion coefficients, D(0), were obtained from the homologous HMW proteins dB1 and dB4 that were cloned from the gluten protein HMW Dx5, and expressed in Escherichia coli. Monodisperse conditions for accurate determination of s(0) and D(0), were obtained by screening a series of buffers using dynamic light scattering.

Detergent organisation in crystals of monomeric outer membrane phospholipase A.

The structure of the detergent in crystals of outer membrane phospholipase A (OMPLA) has been determined using neutron diffraction contrast variation. Large crystals were soaked in stabilising solutions, each containing a different H(2)O/D(2)O contrast. From the neutron diffraction at five contrasts, the 12 A resolution structure of the detergent micelle around the protein molecule was determined.

Escherichia coli translocase: the unravelling of a molecular machine.

Protein translocation across the bacterial cytoplasmic membrane has been studied extensively in Escherichia coli. The identification of the components involved and subsequent reconstitution of the purified translocation reaction have defined the minimal constituents that allowed extensive biochemical characterization of the so-called translocase. This functional enzyme complex consists of the SecYEG integral membrane protein complex and a peripherally bound ATPase, SecA.

Diversity of transport mechanisms: common structural principles.

Traditionally, prokaryotic solute transport systems are classified into major groups based on the energetic requirement of the transport process. These include the secondary transporters that are driven by a proton or sodium motive force, and the ATP-binding cassette (ABC) primary transporters, which use the hydrolysis of ATP to fuel transport. These transporters are specified by entirely different architectures of polypeptides.

A single amino acid substitution in SecY stabilizes the interaction with SecA.

The SecYEG complex constitutes a protein conducting channel across the bacterial cytoplasmic membrane. It binds the peripheral ATPase SecA to form the translocase. When isoleucine 278 in transmembrane segment 7 of the SecY subunit was replaced by a unique cysteine, SecYEG supported an increased preprotein translocation and SecA translocation ATPase activity, and allowed translocation of a preprotein with a defective signal sequence.

Protein targeting to the bacterial cytoplasmic membrane.

Proteins that perform their activity within the cytoplasmic membrane or outside this cell boundary must be targeted to the translocation site prior to their insertion and/or translocation. In bacteria, several targeting routes are known; the SecB- and the signal recognition particle-dependent pathways are the best characterized. Recently, evidence for the existence of a third major route, the twin-Arg pathway, was gathered.

Membrane fusion in vesicles of oligomerizable lipids.

Membrane fusion has been examined in a model system of small unilamellar vesicles of synthetic lipids that can be oligomerized through the lipid headgroups. The oligomerization can be induced either in both bilayer leaflets or in the inner leaflet exclusively. Oligomerization leads to denser lipid headgroup packing, with concomitant reduction of lipid lateral diffusion and membrane permeability.

The lantibiotic nisin induces transmembrane movement of a fluorescent phospholipid.

Nisin is a pore-forming antimicrobial peptide. The capacity of nisin to induce transmembrane movement of a fluorescent phospholipid in lipid vesicles was investigated. Unilamellar phospholipid vesicles that contained a fluorescent phospholipid (1-acyl-2-(6-[(7-nitro-2-1, 3-benzoxadiazol-4-yl)amino]caproyl)-sn-glycero-3-phosphocholine) in the inner leaflet of the bilayer were used.

Structural characterization of the hydrophobin SC3, as a monomer and after self-assembly at hydrophobic/hydrophilic interfaces.

Hydrophobins are small fungal proteins that self-assemble at hydrophilic/hydrophobic interfaces into amphipathic membranes that, in the case of Class I hydrophobins, can be disassembled only by treatment with agents like pure trifluoroacetic acid. Here we characterize, by spectroscopic techniques, the structural changes that occur upon assembly at an air/water interface and upon assembly on a hydrophobic solid surface, and the influence of deglycosylation on these events. We determined that the hydrophobin SC3 from Schizophyllum commune contains 16-22 O-linked mannose residues, probably attached to the N-terminal part of the peptide chain.