Simulation of High Density Lipoprotein Behavior on a Few Layer Graphene Undergoing Non-Uniform Mechanical Load.

Effect of a nonuniform external mechanical load on high density lipoprotein (HDL) in aqueous medium was investigated using course-grained molecular dynamics simulations. The nonuniform load was achieved by a few layer graphene on one side and closed single-walled carbon nanotube (SWNT) (7, 7) on the opposite side of lipoprotein. The tube had a diameter of 1 nm and was oriented perpendicularly to the graphene.

Donor/acceptor coupling shortcuts in electron transfer within ruthenium-modified derivatives of cytochrome b(562).

Quantitative theoretical studies of long-range electron transfer are still rare, and reliable computational methods to analyze these reactions are still being developed. We re-examined electron transfer reactions in ruthenium-modified cytochrome b562 derivatives focusing on accurate calculation of statistical average of electron transfer rates that are dominated by a small fraction of accessible protein conformations. We performed a series of ab initio calculations of donor/acceptor interactions over protein fragments sampled from long molecular dynamic trajectories and compared computed electron transfer rates to available experimental data.

Control of cytochrome c redox reactivity through off-pathway modifications in the protein hydrogen-bonding network.

Measurements of photoinduced Fe(2+)-to-Ru(3+) electron transfer (ET), supported by theoretical analysis, demonstrate that mutations off the dominant ET pathways can strongly influence the redox reactivity of cytochrome c. The effects arise from the change in the protein dynamics mediated by the intraprotein hydrogen-bonding network.

Modeling DNA-bending in the nucleosome: role of AA periodicity.

This paper uses atomistic molecular mechanics within the framework of the JUMNA model to study the bending properties of DNA segments, with emphasis on understanding the role of the 10 bp periodicity associated with AA repeats that has been found to dominate in nucleosomal DNA. The calculations impose a bending potential on 18 bp segments that is consistent with nucleosome structures (i.e.

Cooperative melting in caged dimers with only two DNA duplexes.

Small molecule-DNA hybrids with only two parallel DNA duplexes (rSMDH2) displayed sharper melting profiles compared to unmodified DNA duplexes, consistent with predictions from neighboring-duplex theory. Using adjusted thermodynamic parameters obtained from a coarse-grain dynamic simulation, the experimental data fit well to an analytical model.

Using DNA to Link Gold Nanoparticles, Polymers and Molecules: a Theoretical Perspective.

This Perspective describes theoretical studies aimed at understanding the structural and thermal properties of materials in which DNA is used to link gold nanoparticles, or polymers or organic molecules. Particularly in the case of gold nanoparticles, the materials derived from this structural motif have proven to be important for biological sensing and other applications, however additional applications may arise as a result of recent advances in the preparation of crystalline materials based on DNA-linked particles. From a theory perspective these are challenging materials to describe due to the large number of atoms, and the polyelectrolyte character of DNA, however there has been important progress recently using all-atom and coarse-grained molecular dynamics, and with analytical theory.

DNA melting in small-molecule-DNA-hybrid dimer structures: experimental characterization and coarse-grained molecular dynamics simulations.

When DNA hybridization is used to link together nanoparticles or molecules, the melting transition of the resulting DNA-linked material often is very sharp. In this paper, we study a particularly simple version of this class of material based on a small-molecule-DNA-hybrid (SMDH) structure that has three DNA strands per 1,3,5-tris(phenylethynyl)benzene core. By varying the concentration of the SMDHs, it is possible to produce either SMDH dimers or bulk aggregates, with the former having highly packed duplex DNA while the latter has an extended network.

Coupling coherence distinguishes structure sensitivity in protein electron transfer.

Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b562 derivatives reveals two distinct protein-mediated coupling limits. A structure-insensitive regime arises for redox partners coupled through dynamically averaged multiple-coupling pathways (in seven of the nine derivatives) where heme-edge coupling leads to the multiple-pathway regime. A structure-dependent limit governs redox partners coupled through a dominant pathway (in two of the nine derivatives) where axial-ligand coupling generates the single-pathway limit and slower rates.

Photoselected electron transfer pathways in DNA photolyase.

Cyclobutane dimer photolyases are proteins that bind to UV-damaged DNA containing cyclobutane pyrimidine dimer lesions. They repair these lesions by photo-induced electron transfer. The electron donor cofactor of a photolyase is a two-electron-reduced flavin adenine dinucleotide (FADH(-)).

Ab initio based calculations of electron-transfer rates in metalloproteins.

A long-standing challenge in electron-transfer theory is to compute accurate rates of long-distance reactions in proteins. We describe an ab initio Hartree-Fock approach to compute electronic-coupling interactions and electron-transfer rates in proteins that allows the favorable comparison with experiment. The method includes the following key features; each is essential for reliable rate computations: (1) summing contributions over multiple tunneling pathways, (2) averaging couplings over thermally accessible protein conformations, (3) describing donor and acceptor electronic structure explicitly, including solvation effects, and averaging coupling over multiple energy-level crossings of the nearly degenerate donor-acceptor ligand-field states, and (4) eliminating basis set artifacts associated with diffuse basis functions.