Addressing the Embeddability Problem in Transition Rate Estimation.

Markov State Models (MSM) and related techniques have gained significant traction as a tool for analyzing and guiding molecular dynamics (MD) simulations due to their ability to extract structural, thermodynamic, and kinetic information on proteins using computationally feasible MD simulations. The MSM analysis often relies on spectral decomposition of empirically generated transition matrices. This work discusses an alternative approach for extracting the thermodynamic and kinetic information from the so-called rate/generator matrix rather than the transition matrix.

Developing a rational approach to designing recombinant proteins for peptide-directed nanoparticle synthesis.

The controlled formation of nanoparticles with optimum characteristics and functional aspects has proven successful peptide-mediated nanoparticle synthesis. However, the effects of the peptide sequence and binding motif on surface features and physicochemical properties of nanoparticles are not well-understood. In this study, we investigate in a comparative manner how a specific peptide known as Pd4 and its two known variants may form nanoparticles both in an isolated state and when attached to a green fluorescent protein (GFPuv).

Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1.

Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV-2 has been significantly more widespread than the 2003 SARS epidemic caused by SARS-CoV-1, despite striking similarities between these two viruses. The SARS-CoV-1 and SARS-CoV-2 spike proteins, both of which bind to host cell angiotensin-converting enzyme 2, have been implied to be a potential source of their differential transmissibility. However, the mechanistic details of prefusion spike protein binding to angiotensin-converting enzyme 2 remain elusive at the molecular level.

Transient local secondary structure in the intrinsically disordered C-term of the Albino3 insertase.

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light-harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma-exposed C-terminus (Alb3-Cterm) that is responsible for binding the LHC-loaded transit complex before LHC membrane insertion. Alb3-Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated.

Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2.

The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to its human receptor remain elusive at the molecular level. Here, we have used an extensive set of unbiased and biased microsecond-level all-atom molecular dynamics (MD) simulations of SARS-CoV-1 and 2 spike proteins to determine the differential dynamic behavior of prefusion spike protein structure in the two viruses.

Structural behavior of fluids from the vapor and liquid region to the supercritical phase.

A metric (χ) is introduced to quantify the relative proportion of particles having a specified number of near neighbors that are characteristic of liquid-phase properties. It can be used as a simple alternative to other methods for the investigation of some aspects of percolation behavior. Values of χ are obtained from molecular-dynamics simulations spanning the heterogeneous vapor and liquid region and the supercritical phase of the Lennard-Jones fluid.

Thermodynamic properties and anomalous behavior of double-Gaussian core model potential fluids.

The structural, thermodynamic, and vapor-liquid equilibria properties of the double-Gaussian core model (DGM) potential are studied via molecular simulation. Results are presented for the pressure (p), potential energy (U), isochoric and isobaric heat capacities (C_{V,p}), isothermal compressibility (β_{T}), isochoric thermal pressure coefficient (γ_{V}), thermal expansion coefficient (α_{p}), speed of sound (ω_{0}), and the Joule-Thomson coefficient (μ_{JT}), which are compared with simulations for the Gaussian core model (GCM) potential. A feature of the simulations is that both the GCM and DGM potentials reproduce many of the anomalous properties of water, such as a maximum density, γ_{V}<0, maximum values for both α_{p} and β_{T}, and minimum values in both C_{p} and ω_{0}.

The Widom Line and the Lennard-Jones Potential.

The phenomenological behavior of the Widom line above the vapor-liquid critical point for the Lennard-Jones (LJ) potential is investigated using four accurate equations of state (EoS) and a comparison with molecular dynamics (MD) simulation data. This involved calculating the supercritical maximum values of the isochoric heat capacity (), isobaric heat capacity (), isothermal compressibility (), and thermal expansion coefficient (). All LJ EoS predict the pressure ()-temperature () Widom line behavior.

Flow of water through carbon nanotubes predicted by different atomistic water models.

Nonequilibrium molecular dynamics simulations are reported to investigate the influence of different atomistic water models on the predicted flow behavior in carbon nanotubes (CNTs) with diameters between 0.81 nm and 1.9 nm.