Journal of Physical Chemistry B
- Print ISSN
- Electronic ISSN
- Impact factor
- Usage rank
- Article count
- Free count
- Free percentage
- PDFs via platforms
- Proquest, CSA, Acm, Acs, and Gale
Conformation and Dynamics at a Flexible Glycosidic Linkage Revealed by NMR Spectroscopy and Molecular Dynamics Simulations: Analysis of β-l-...
The intrinsic flexibility of carbohydrates facilitates different 3D structures in response to altered environments. At glycosidic (1→6)-linkages, three torsion angles are variable, and herein the conformation and dynamics of β-l-Fucp-(1→6)-α-d-Glcp-OMe are investigated using a combination of NMR spe...
Prototropical and Photophysical Properties of Ellipticine inside the Nanocavities of Molecular Containers.
We believe the hydrophobic environment inside the capsule stabilizes the neutral form of the drug in the 2:1 inclusion complex. Deep insight into the molecular picture of these host-guest interactions has been provided by the docking studies followed by quantum chemical calculations....
On the Nature of the Apparent Free Energy of Inserting Amino Acids into Membrane through the Translocon.
We extend and clarify our recent analysis of the insertion problem using well-defined kinetics schemes and a free energy profile. We point out that although the rate constants of some steps are far from being obvious, it is essential to consider explicitly such schemes in order to advance in analyzi...
Rheology of protic ionic liquids and their mixtures.
The rheological properties of five pure protic ionic liquids (ILs), ethylammonium nitrate (EAN), propylammonium nitrate (PAN), ethanolammonium nitrate (EtAN), ethylammonium formate (EAF), and dimethylethylammonium formate (DMEAF), are characterized and interpreted by considering the effects of both...
Computational and experimental characterizations of silver nanoparticle-apolipoprotein biocorona.
We set out to characterize biocorona formation through electron microscopy imaging and circular dichroism spectroscopy that inspired a novel approach for molecular dynamics (MD) simulations of protein-NP interactions. In our present study, we developed a novel GPU-optimized coarse-grained MD simulat...
Interactions affecting the mechanical properties of macromolecular microsphere composite hydrogels.
Macromolecular microsphere composite (MMC) hydrogel is a kind of tough hydrogel fabricated by using peroxidized macromolecular microspheres as polyfunctional initiating and cross-linking centers (PFICC). The contribution of chemical cross-linking (covalent bonding) and physical cross-linking (chain...
Speed-selectivity paradox in the protein search for targets on DNA: is it real or not?
We developed a discrete-state stochastic approach that allowed us to investigate explicitly target search phenomena and to analyze the speed-selectivity paradox. A general dynamic phase diagram for different search regimes is constructed. The effect of the target position on search dynamics is inves...
Single-molecule FRET studies of RNA folding: a Diels-Alderase ribozyme with photolabile nucleotide modifications.
We have incorporated a light-cleavable caging moiety into specific nucleotides of the Diels-Alderase (DAse) ribozyme. In this way, the folding energy landscape was significantly perturbed, and the catalytic activity was essentially suppressed. A careful smFRET efficiency histogram analysis at variou...
Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics.
We model their effect on protein dynamics and DNA binding. We show that the NFAT5 complex without DNA is much more flexible than the complex with DNA. Moreover, DNA binding considerably stabilizes the overall dimeric complex and the NFAT5 dimer is only marginally stable in the absence of DNA. Two se...
Single-particle tracking reveals switching of the HIV fusion peptide between two diffusive modes in membranes.
We describe single-particle tracking (SPT) studies of a 16-amino-acid peptide derived from the HIV fusion protein (FP16), as it interacts with a supported lipid bilayer. FP16 was found to spontaneously insert into and move within the bilayer with two different modes of diffusion, a fast mode with a...