Dynamics and Environmental Characteristics of Spin Labels in a KvAP Voltage Sensor by Molecular Dynamics Simulations.

The nitroxide spin label is the most widely used probe for electron paramagnetic resonance (EPR) spectroscopy studies of the structure and function of biomolecules. However, the role of surrounding environments in determining the dynamics of nitroxide spin labels in biological complex systems remains to be clarified. This study aims to characterize the dynamics and environmental structure of spin labels in the voltage-sensing domain (VSD) of a KvAP potassium channel by means of molecular dynamics (MD) studies.

Thermally induced structural organization of nanodiscs by coarse-grained molecular dynamics simulations.

Membrane scaffold proteins (MSP) nanodiscs have been extensively used in structural study of membrane proteins. In cryo-EM, an incorporation of target proteins into nanodiscs is conducted under a rapid change from cryogenic to ambient temperatures. We present a coarse-grained molecular dynamics (CGMD) study for investigating an effect of temperature on the structural organization of DPPC-nanodisc and POPC-nanodisc.

Conformation, flexibility and hydration of hyaluronic acid by molecular dynamics simulations.

Hyaluronic acid (HA) is a biopolymer of disaccharide with two alternate glycosidic bonds, β(1,3) and β(1,4). A molecular dynamics study presented here unveiled conformational variability in association with the flexibility of the glycosidic linkers, which depends on the number of disaccharide units. HA chain maintains a rigid rod-like conformation with short chain lengths.

Inferring the three-dimensional structures of the X-chromosome during X-inactivation.

The Hi-C experiment can capture the genome-wide spatial proximities of the DNA, based on which it is possible to computationally reconstruct the three-dimensional (3D) structures of chromosomes. The transcripts of the long non-coding RNA (lncRNA) Xist spread throughout the entire X-chromosome and alter the 3D structure of the X-chromosome, which also inactivates one copy of the two X-chromosomes in a cell. The Hi-C experiments are expensive and time-consuming to conduct, but the Hi-C data of the active and inactive X-chromosomes are available.

Conformational response to solvent interaction and temperature of a protein (Histone h3.1) by a multi-grained monte carlo simulation.

Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.

A hierarchical coarse-grained (all-atom-to-all-residue) computer simulation approach: self-assembly of peptides.

A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 ((1)H (2)S (3)S (4)Y (5)W (6)Y (7)A (8)F (9)N (10)N (11)K (12)T) is considered as an example to illustrate the utility.

Variation in structure of a protein (H2AX) with knowledge-based interactions.

The structure of a protein (H2AX) as a function of temperature is examined by three knowledge-based phenomenological interactions, MJ (Miyazawa and Jernigan), BT (Betancourt and Thirumalai), and BFKV (Bastolla et al.) to identify similarities and differences in results. Data from the BT and BFKV residue-residue interactions verify finding with the MJ interaction, i.

Random coil to globular thermal response of a protein (H3.1) with three knowledge-based coarse-grained potentials.

The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.

Supramolecular assembly of a biomineralizing antimicrobial peptide in coarse-grained Monte Carlo simulations.

Monte Carlo simulations are used to model the self-organizing behavior of the biomineralizing peptide KSL (KKVVFKVKFK) in the presence of phosphate. Originally identified as an antimicrobial peptide, KSL also directs the formation of biosilica through a hypothetical supramolecular template that requires phosphate for assembly. Specificity of each residue and the interactions between the peptide and phosphate are considered in a coarse-grained model.

Bioassembled layered silicate-metal nanoparticle hybrids.

Here we report on the bioenabled assembly of layered nanohybrids using peptides identified with regard to their affinity to the nanoparticle surface. A dodecamer peptide termed M1, determined from a phage peptide display library, was found to bind to the surface of a layered aluminosilicate (montmorillonite, MMT). Fusion of a metal binding domain to the M1 peptide or the M1 peptide by itself was able to direct the growth of metal nanoparticles, such as gold and cobalt-platinum, respectively, on the MMT.

Nature of molecular interactions of peptides with gold, palladium, and Pd-Au bimetal surfaces in aqueous solution.

We investigated molecular interactions involved in the selective binding of several short peptides derived from phage-display techniques (8-12 amino acids, excluding Cys) to surfaces of Au, Pd, and Pd-Au bimetal. The quantitative analysis of changes in energy and conformation upon adsorption on even {111} and {100} surfaces was carried out by molecular dynamics simulation using an efficient computational screening technique, including 1000 explicit water molecules and physically meaningful peptide concentrations at pH = 7. Changes in chain conformation from the solution to the adsorbed state over the course of multiple nanoseconds suggest that the peptides preferably interact with vacant sites of the face-centered cubic lattice above the metal surface.

Monte Carlo simulation of a film growth with reactive hydrophobic, polar, and aqueous components by a covalent bond fluctuating model.

Using a bond fluctuating model (BFM), Monte Carlo simulations are performed to study the film growth in a mixture of reactive hydrophobic (H) and hydrophilic (P) groups in a simultaneous reactive and evaporating aqueous (A) solution on a simple three dimensional lattice. In addition to the excluded volume, short range phenomenological interactions among each constituents and kinetic functionalities are used to capture their major characteristics. The simulation involves thermodynamic equilibration via stochastic movement of each constituent by Metropolis algorithm as well as cross-linking reaction among constituents with evaporating aqueous component.

Film formation from aqueous polyurethane dispersions of reactive hydrophobic and hydrophilic components; spectroscopic studies and Monte Carlo simulations.

Film formation of waterborne two-component polyurethanes is exceedingly complex due to the heterogeneous nature along with simultaneous progression of several parallel physicochemical processes which include water evaporation, cross-linking reactions, phase separation, and droplet coalescence, to name a few. While internal reflection infrared imaging (IRIRI) spectroscopy clearly facilitates analysis of chemical changes resulting from film formation, the complexity of processes leading to formation of specific surface/interfacial entities is a major experimental challenge. For this reason, we combined a spectrum of surface/interfacial analytical approaches including IRIRI, atomic force microscopy, and attenuated total reflectance Fourier transform infrared spectroscopy with Monte Carlo computer simulations to advance the limited knowledge of how temperature, stoichiometry, concentration levels, and reactivities of individual components affect the development of surface morphologies and compositional gradients across the film thickness.

Radical initiated polymerization in a bifunctional mixture via computer simulation.

Computer simulations are performed to study the polymerization behavior in a mixture of bifunctional groups such as olefins (A) and acrylates (B) in an effective solvent (a coarse description for vegetable oil derived macromonomers (VOMMs) in solution) on a cubic lattice. A set of interactions between these units and solvent (S) constituents and their relative concentrations (p(A), p(B), and p(S)) are considered. Samples are equilibrated with Metropolis algorithm to model the perceived behavior of VOMMs.