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. Although the rate matrix itself is built from the empirical transition matrix, it provides an alternative approach for estimating both thermodynamic and kinetic quantities, particularly in diffusive processes. A fundamental issue with this approach is known as the embeddability problem. The key contribution of this work is the introduction of a novel method to address the embeddability problem as well as the collection and utilization of existing algorithms previously used in the literature. The algorithms are tested on data from a one-dimensional toy model to show the workings of these methods and discuss the robustness of each method in dependence of lag time and trajectory length.

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 via 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). More importantly, we introduce a novel computational approach to predict the trend of the size and activity of the peptide-directed nanoparticles by estimating the binding affinity of the peptide to a single ion. We used molecular dynamics (MD) simulations to explore the differential behavior of the isolated and GFP-fused peptides and their mutants. Our computed palladium (Pd) binding free energies match the typical nanoparticle sizes reported from transmission electron microscope pictures. Stille coupling and Suzuki-Miyaura reaction turnover frequencies (TOFs) also correspond with computationally predicted Pd binding affinities. The results show that while using Pd4 and its two known variants (A6 and A11) in isolation produces nanoparticles of varying sizes, fusing these peptides to the GFPuv protein produces nanoparticles of similar sizes and activity. In other words, GFPuv reduces the sensitivity of the nanoparticles to the peptide sequence. This study provides a computational framework for designing free and protein-attached peptides that helps in the synthesis of nanoparticles with well-regulated properties.

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. Here, we performed an extensive set of equilibrium and nonequilibrium microsecond-level all-atom molecular dynamics simulations of SARS-CoV-1 and SARS-CoV-2 prefusion spike proteins to determine their differential dynamic behavior. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. These results suggest that not only the receptor-binding domain but also other domains such as the N-terminal domain could play a crucial role in the differential binding behavior of SARS-CoV-1 and SARS-CoV-2 spike proteins.

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. Using a novel combination of experimental and computational techniques such as single-molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site-directed mutagenesis, trypsin digestion assays, and all-atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3-Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter-residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3-Cterm for the LHC-loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3-Oxa1-YidC family of insertases.

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. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. Our results also suggest that not only the receptor binding domain (RBD) but also other domains such as the N-terminal domain (NTD) could play a role in the differential binding behavior of SARS-CoV-1 and 2 spike proteins.

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. The supercritical phase can be delineated into regions of different structural properties. At different isochoric subcritical conditions, the temperature versus χ behavior shows evidence of inflections, which are associated with the onset of transitions from the vapor and liquid region to the supercritical phase. The analysis suggests a phenomenological requirement for the critical point in terms of a near-equal proportion of near neighbors with gaslike and liquidlike characteristics.

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 (CV), isobaric heat capacity (Cp), isothermal compressibility (ßT), and thermal expansion coefficient (αp). All LJ EoS predict the pressure (p)-temperature (T) Widom line behavior. In contrast, the T-density (ρ) Widom line behavior, observed in MD simulations, is not predicted by any LJ EoS. The calculations highlight the important role of ßT in determining the range of p and T for which Widom line behavior is observed. Analysis of MD data for the supercritical maximum/minimum of CV and Cp suggests the extension of a Clausius-Clapeyron-type relationship from the triple point to the supercritical region. This provides a new description of the Widom line as the near critical part of this larger curve for which other thermodynamic functions also have maximum values.

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 (ß_{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 ß_{T}, and minimum values in both C_{p} and ω_{0}. The presence of attractive interaction enhances the anomalies and also yields some additional features such as a more structured vapor phase and Joule-Thomson inversion.

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. The comparison was made using rigid three-site [simplified point charge (SPC), extended SPC (SCP/E), and transferable intermolecular potential three point (TIP3P)] and four-site (TIP4P and TIP4P/2005) models. In addition, a flexible three-site model (SPC/Fw) was also investigated. The effect of different simulation conditions was determined by generating a flux across the CNT using either a pressure gradient across a membrane separating two water reservoirs or a periodic CNT with a constant force applied to each water molecule. Simulations involving the two water reservoirs indicate that the flux is strongly dependent on the choice of water model, which confirms earlier work. By contrast, this strong model dependency is not a feature of the periodic CNT simulations. Instead, the flux depends mainly on the pore diameter and the molecular density of water inside the CNT. The influence of the water model becomes very small in the periodic CNT simulations, which eliminates distorting entrance/exit effects.