Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units-Radial Distribution Function Histogramming

Assessing the structural stability and drug encapsulation efficiency of poly(ethylene glycol)-poly(L-lactic acid) nanoparticles loaded with atorvastatin calcium: Based on dissipative particle dynamics

Block polymer micelles have been proven highly biocompatible and effective in improving drug utilization for delivering atorvastatin calcium. Therefore, it is of great significance to measure the stability of drug-loading nano micelles from the perspective of block polymer molecular sequence design, which would provide theoretical guidance for subsequent clinical applications. This study aims to investigate the structural stability of drug-loading micelles formed by two diblock/triblock polymers with various block sequences through coarse-grained dissipative particle dynamics (DPD) simulations. From the perspectives of the binding strength of poly(L-lactic acid) (PLLA) and polyethylene glycol (PEG) in nanoparticles, hydrophilic bead surface coverage, and the morphological alteration of nanoparticles induced by shear force, the ratio of hydrophilic/hydrophobic sequence length has been observed to affect the stability of nanoparticles. We have found that for diblock polymers, PEG3kda-PLLA2kda has the best stability (corresponding hydrophilic coverage ratio is 0.832), while PEG4kda-PLLA5kda has the worst (coverage ratio 0.578). For triblock polymers, PEG4kda-PLLA2kda-PEG4kda has the best stability (0.838), while PEG4kda-PLLA5kda-PEG4kda possesses the worst performance (0.731), and the average performance on stability is better than nanoparticles composed of diblock polymers.

Differential Solvent DEEP-STD NMR and MD Simulations Enable the Determinants of the Molecular Recognition of Heparin Oligosaccharides by Antithrombin to Be Disentangled

The interaction of heparin with antithrombin (AT) involves a specific sequence corresponding to the pentasaccharide GlcNAc/NS6S-GlcA-GlcNS3S6S-IdoA2S-GlcNS6S (AGA*IA). Recent studies have revealed that two AGA*IA-containing hexasaccharides, which differ in the sulfation degree of the iduronic acid unit, exhibit similar binding to AT, albeit with different affinities. However, the lack of experimental data concerning the molecular contacts between these ligands and the amino acids within the protein-binding site prevents a detailed description of the complexes. Differential epitope mapping (DEEP)-STD NMR, in combination with MD simulations, enables the experimental observation and comparison of two heparin pentasaccharides interacting with AT, revealing slightly different bound orientations and distinct affinities of both glycans for AT. We demonstrate the effectiveness of the differential solvent DEEP-STD NMR approach in determining the presence of polar residues in the recognition sites of glycosaminoglycan-binding proteins.

Configurational Sampling of All-Atom Solvated Membranes Using Hybrid Nonequilibrium Molecular Dynamics Monte Carlo Simulations

All-atom simulations are a powerful approach to study the structure and dynamics of biological membranes. However, sampling the atomic configurations of inhomogeneous membranes can be challenging due to the slow lateral diffusion of the various constituents. To address this issue, a hybrid nonequilibrium molecular dynamics Monte Carlo (neMD/MC) simulation method is proposed in which randomly chosen lipid molecules are swapped to generate configurations that are subsequently accepted or rejected according to a Metropolis criterion based on the alchemical work for the attempted swap calculated via a short trajectory. A dual-topology framework constraining the common atoms of the exchanging molecules yields a good acceptance probability using switching trajectories as short as 10 ps. The performance of the hybrid neMD/MC algorithm and its ability to sample the distribution of lipids near a transmembrane helix carrying a net charge are illustrated for a binary mixture of charged and zwitterionic lipids.

Dynamic and relativistic effects on Pt-Pt indirect spin-spin coupling in aqueous solution studied by ab initio molecular dynamics and two- vs four-component density functional NMR calculations

Treating 195Pt nuclear magnetic resonance parameters in solution remains a considerable challenge from a quantum chemistry point of view, requiring a high level of theory that simultaneously takes into account the relativistic effects, the dynamic treatment of the solvent-solute system, and the dynamic electron correlation. A combination of Car-Parrinello molecular dynamics (CPMD) and relativistic calculations based on two-component zeroth order regular approximation spin-orbit Kohn-Sham (2c-ZKS) and four-component Dirac-Kohn-Sham (4c-DKS) Hamiltonians is performed to address the solvent effect (water) on the conformational changes and JPtPt1 coupling. A series of bridged PtIII dinuclear complexes [L1-Pt2(NH3)4(Am)2-L2]n+ (Am = α-pyrrolidonate and pivalamidate; L = H2O, Cl-, and Br-) are studied. The computed Pt-Pt coupling is strongly dependent on the conformational dynamics of the complexes, which, in turn, is correlated with the trans influence among axial ligands and with the angle N-C-O from the bridging ligands. The J-coupling is decomposed in terms of dynamic contributions. The decomposition reveals that the vibrational and explicit solvation contributions reduce JPtPt1 of diaquo complexes (L1 = L2 = H2O) in comparison to the static gas-phase magnitude, whereas the implicit solvation and bulk contributions correspond to an increase in JPtPt1 in dihalo (L1 = L2 = X-) and aquahalo (L1 = H2O; L2 = X-) complexes. Relativistic treatment combined with CPMD shows that the 2c-ZKS Hamiltonian performs as well as 4c-DKS for the JPtPt1 coupling.

Liquid-Liquid Crossover in Water Model: Local Structure vs Kinetics of Hydrogen Bonds

In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase diagram of the water model, the thermodynamic region corresponding to the equilibrium liquid phase is divided by a line of the smooth liquid-liquid crossover. In the case of the water model TIP4P/2005, this crossover is revealed by various local order parameters and corresponds to pressures on the order of 3150 ± 350 atm at ambient temperature. In the vicinity of the crossover, the dynamics of water molecules change significantly, which is reflected, in particular, in the fact that the self-diffusion coefficient reaches its maximum values. In addition, changes in the structure also manifest themselves in changes in the kinetics of hydrogen bonding, which are captured by values of such quantities as the average lifetime of hydrogen bonding, the average lifetimes of different local coordination numbers, and the frequencies of changes in different local coordination numbers. An interpretation of the hydrogen bond kinetics in terms of the free energy landscape concept in the space of possible coordination numbers is proposed.

Computational molecular perspectives on novel carbazole derivative as an anti-cancer molecule against CDK1 of breast and colorectal cancers via gene expression studies, novel two-way docking strategies, molecular mechanics and dynamics

With increase in cancer incidences, alternative strategies for disease management are of utmost importance. Carbazole, is a compound that is being studied extensively as an anti-cancer compound. In this work, we aimed to investigate a carbazole derivative against specific cancer types such as breast and colorectal, based on the off-target analyses of carbazole derivative. The present work shortlisted 6 proteins that have an association in both cancer types, and then employed two different molecular docking strategies to examine the binding stability of carbazole derivative: a blind-docking state, where the pockets were undefined and mutation-docking state, where possible mutations were induced within the proteins. The results showed that CDK1 bound best in both states to carbazole derivative, and performed better than an array of positive controls. Molecular dynamic simulations at 100 ns further proved its stability, with carbazole derivative-CDK1-blind and mutated complex having RMSD values between 3.2 and 3.6 Å, and 2.8-3.2 Å respectively. Molecular-mechanics generalized born and surface area solvation disclosed free energy of binding for the complexes as -28.79 ± 3.97 kcal/mol and -31.86 ± 5.09 kcal/mol respectively, with carbazole derivative bound stably within the binding pocket at every 10 ns of the 100 ns trajectory. Radial distribution functions showed that the bell curve was well within 6 Å, thus showing that carbazole derivative and its atoms do not deviate away from the pocket, suggesting its ability to be used as a good anti-cancer compound against breast and colorectal.

Energy renormalization for temperature transferable coarse-graining of silicone polymer

The bottom-up prediction of thermodynamic and mechanical behaviors of polymeric materials based on molecular dynamics (MD) simulation is of critical importance in polymer physics. Although the atomistically informed coarse-grained (CG) model can access greater spatiotemporal scales and retain essential chemical specificity, the temperature-transferable CG model is still a big challenge and hinders widespread application of this technique. Herein, we use a silicone polymer, i.e., polydimethylsiloxane (PDMS), having an incredibly low chain rigidity as a model system, combined with an energy-renormalization (ER) approach, to systematically develop a temperature-transferable CG model. Specifically, by introducing temperature-dependent ER factors to renormalize the effective distance and cohesive energy parameters, the developed CG model faithfully preserved the dynamics, mechanical and conformational behaviors compared with the target all-atomistic (AA) model from glassy to melt regimes, which was further validated by experimental data. With the developed CG model featuring tremendously improved computational efficiency, we systematically explored the influences of cohesive interaction strength and temperature on the dynamical heterogeneity and mechanical response of polymers, where we observed consistent trends with other linear polymers with varying chain rigidity and monomeric structures. This study serves as an extension of our proposed ER approach of developing temperature transferable CG models with diverse segmental structures, highlighting the critical role of cohesive interaction strength on CG modeling of polymer dynamics and thermomechanical behaviors.

Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy

Machine learning potentials, particularly the deep potential (DP) model, have revolutionized molecular dynamics (MD) simulations, striking a balance between accuracy and computational efficiency. To facilitate the DP model's integration with the popular MD engine OpenMM, we have developed a versatile OpenMM plugin. This plugin supports a range of applications, from conventional MD simulations to alchemical free energy calculations and hybrid DP/MM simulations. Our extensive validation tests encompassed energy conservation in microcanonical ensemble simulations, fidelity in canonical ensemble generation, and the evaluation of the structural, transport, and thermodynamic properties of bulk water. The introduction of this plugin is expected to significantly expand the application scope of DP models within the MD simulation community, representing a major advancement in the field.

Comprehending interaction mechanism of natural actives of Colchicum autumnale L. for rheumatoid arthritis using integrative chemoinformatic approaches

This research delves into the realm of therapeutic potential within natural compounds derived from Colchicum autumnale L., emphasizing a holistic perspective on medications used in human therapy. Rather than confining the study to their primary actions, the research endeavors to unveil molecular targets for these natural compounds, with a specific focus on their potential applicability in the treatment of rheumatoid arthritis (RA). The study focuses on understanding interactions between specific natural actives that target RA. Fifteen RA target proteins were identified from OMIM, GeneScan and PharmaGKB. Their structures were downloaded from RCSB PDB. Two active components of C. autumnale L. were chosen for mass spectrometry investigation. Ligand characteristics were determined using the ADMETlab and SwissADME software tools. Molecular docking was performed, and the top three complexes were simulated for 200 ns, along with identification of free binding energies. The compounds β-sitosterol-IL-10 (-6.50 kcal/mol), colchicine-IL-10 (-6.01 kcal/mol), linoleic acid-IL-10 (-7.22 kcal/mol) and linoleic acid-IL-10 (-7.22 kcal/mol) exhibited best binding energies. β-Sitosterol and colchicine showed the highest stability in simulations, confirmed by molecular mechanics free energy binding calculations. This work provides insights into the molecular interaction of natural compounds against RA targets, offering potential therapeutic anti-RA medications.Communicated by Ramaswamy H. Sarma.

Molecular modeling and phylogenetic analyses highlight the role of amino acid 347 of the N1 subtype neuraminidase in influenza virus host range and interspecies adaptation

The N1 neuraminidases (NAs) of avian and pandemic human influenza viruses contain tyrosine and asparagine, respectively, at position 347 on the rim of the catalytic site; the biological significance of this difference is not clear. Here, we used molecular dynamics simulation to model the effects of amino acid 347 on N1 NA interactions with sialyllacto-N-tetraoses 6'SLN-LC and 3'SLN-LC, which represent NA substrates in humans and birds, respectively. Our analysis predicted that Y347 plays an important role in the NA preference for the avian-type substrates. The Y347N substitution facilitates hydrolysis of human-type substrates by resolving steric conflicts of the Neu5Ac2-6Gal moiety with the bulky side chain of Y347, decreasing the free energy of substrate binding, and increasing the solvation of the Neu5Ac2-6Gal bond. Y347 was conserved in all N1 NA sequences of avian influenza viruses in the GISAID EpiFlu database with two exceptions. First, the Y347F substitution was present in the NA of a specific H6N1 poultry virus lineage and was associated with the substitutions G228S and/or E190V/L in the receptor-binding site (RBS) of the hemagglutinin (HA). Second, the highly pathogenic avian H5N1 viruses of the Gs/Gd lineage contained sporadic variants with the NA substitutions Y347H/D, which were frequently associated with substitutions in the HA RBS. The Y347N substitution occurred following the introductions of avian precursors into humans and pigs with N/D347 conserved during virus circulation in these hosts. Comparative evolutionary analysis of site 347 revealed episodic positive selection across the entire tree and negative selection within most host-specific groups of viruses, suggesting that substitutions at NA position 347 occurred during host switches and remained under pervasive purifying selection thereafter. Our results elucidate the role of amino acid 347 in NA recognition of sialoglycan substrates and emphasize the significance of substitutions at position 347 as a marker of host range and adaptive evolution of influenza viruses.

Investigating the Molecular Interactions of Quinoline Derivatives for Antibacterial Activity Against Bacillus subtilis: Computational Biology and In Vitro Study Interpretations

Bacterial infections are evolving and one of the chief problems is emergence and prevalence of antibacterial resistance. Moreover, certain strains of Bacillus subtilis have become resistant to several antibiotics. To counteract this menace, the present work aimed to comprehend the antibacterial activity of synthesized two quinoline derivatives against Bacillus subtilis. Toxicity predictions via Protox II, SwissADME and T.E.S.T (Toxicity Estimation Software Tool) revealed that these derivatives were non-toxic and had little to no adverse effects. Molecular docking studies carried out in Schrodinger with two quinoline derivatives (referred Q1 and Q2) docked against selected target proteins (PDB IDs: 2VAM and1FSE) of B. subtilis demonstrated ideal binding energies (2VAM-Q1: - 4.63 kcal/mol and 2VAM-Q2: - 4.46 kcal/mol, and 1FSE-Q1: - 3.51 kcal/mol, 1FSE-Q2: - 6.34 kcal/mol). These complexes were simulated at 100 ns and the outcomes revealed their stability with slight conformational changes. Anti-microbial assay via disc diffusion method revealed zones of inhibition showing that B. subtilis was inhibited by both Q1 and Q2, with Q2 performing slightly better than Q1, pointing towards its effectiveness against this organism and necessitating further study on other bacteria in prospective studies. Thus, this study demonstrates that our novel quinoline derivatives exhibit antibacterial properties against Bacillus subtilis and can act as potent anti-bacterials.

Compression-induced hexa-to-tetra phase transition of confined germanene

Via molecular dynamics (MD) simulations we find the existence of the new allotrope of two-dimensional (2D) germanene, i.e. 2D tetra-germanene (tetra-Ge) which contains entirely tetragons. We compress 2D hexa-germanene (hexa-Ge) step by step over a broad density range at constant temperature and hexa-tetra Ge phase transition occurs. We find that the compression of hexa-Ge at 2000 K (not far above the melting point of hexa-Ge) leads to the formation of tetra-Ge with the highest quality. Atomic structure of the obtained tetra-Ge at 300 K is analyzed in details. Although fraction of tetragons in the tetra-Ge is very high (larger than 0.99), some defects are found in addition to the skew tetragons. Due to containing almost entirely tetragons, tetra-Ge may exhibit new behaviors unlike those of the hexa-Ge. Subsequent studies in this direction for 2D tetra-Ge. In addition, first-principles calculations under density functional theory confirm the existence of stable tetra-Ge.

Eliminating finite-size effects on the calculation of x-ray scattering from molecular dynamics simulations

Structural studies using x-ray scattering methods for investigating molecules in solution are shifting focus toward describing the role and effects of the surrounding solvent. However, forward models based on molecular dynamics (MD) simulations to simulate structure factors and x-ray scattering from interatomic distributions such as radial distribution functions (RDFs) face limitations imposed by simulations, particularly at low values of the scattering vector q. In this work, we show how the value of the structure factor at q = 0 calculated from RDFs sampled from finite MD simulations is effectively dependent on the size of the simulation cell. To eliminate this error, we derive a new scheme to renormalize the sampled RDFs based on a model of the excluded volume of the particle-pairs they were sampled from, to emulate sampling from an infinite system. We compare this new correction method to two previous RDF-correction methods, developed for Kirkwood-Buff theory applications. We present a quantitative test to assess the reliability of the simulated low-q scattering signal and show that our RDF-correction successfully recovers the correct q = 0 limit for neat water. We investigate the effect of MD-sampling time on the RDF-corrections, before advancing to a molecular example system, comprised of a transition metal complex solvated in a series of water cells with varying densities. We show that our correction recovers the correct q = 0 behavior for all densities. Furthermore, we employ a simple continuum scattering model to dissect the total scattering signal from the solvent-solvent structural correlations in a solute-solvent model system to find two distinct contributions: a non-local density-contribution from the finite, fixed cell size in NVT simulations, and a local contribution from the solvent shell. We show how the second contribution can be approximated without also including the finite-size contribution. Finally, we provide a "best-practices"-checklist for experimentalists planning to incorporate explicit solvation MD simulations in future work, offering guidance for improving the accuracy and reliability of structural studies using x-ray scattering methods in solution.

Exploring the Synergistic Mechanism of AP2A2 Transcription Factor Inhibition via Molecular Modeling and Simulations as a Novel Computational Approach for Combating Breast Cancer: In Silico Interpretations

Studies have shown that transcription factor AP2A2 (activator protein-2 alpha-2) is involved in the expression of DLEC1, a tumor suppressor gene, which, when mutated, will cause breast cancer and is thus an excellent target for breast cancer studies. Therefore, in the present research, a synergistic approach toward combating breast cancer is proposed by blocking AP2A2 factor, and allowing the cancer cells to be sensitive to anti-cancer drugs. The effect of AP2A2 on breast cancer was first understood via gene analysis from cBioPortal. AP2A2 was then modeled using RaptorX and its structure was validated from Ramachandran plots. Using all ligands from MolPort database, molecular docking was performed against AP2A2, from which the top three best docked ligands were studied for toxicity in humans using Protox-II. Once the ligands passed these tests, the best complexes were simulated at 200ns in Desmond Maestro, to comprehend their stabilities, followed by the computations of free energies of binding via Molecular mechanics- Generalized Born Solvent Accessibility method (MM-GBSA). The results showed that molecules MolPort-005-945-556 (sachharolipids), MolPort-001-741-124 (flavonoids), and MolPort-005-944-667 (lignan glycosides) with AP2A2 passed toxicity evaluation and belonged to toxicity classes 6, 5, and 5, respectively, with good docking energies. 200 ns simulations revealed stable complexes with slight conformational changes. Stability of ligands was confirmed via snapshots at every 20 ns of the trajectory. Radial distribution of these molecules against the protein revealed very slight deviation from binding pocket. Additionally, the free binding energies for these complexes were found to be - 54.93 ± 12.982 kcal/mol, - 44.39 ± 14.393 kcal/mol, and - 66.51 ± 13.522 kcal/mol, respectively. A preliminary computational validation of the inability of AP2A2 to bind to DLEC1 in the presence of ligands offers beneficial insights into the potential of these ligands. Therefore, this study sheds light on the potential natural molecules that could stably block AP2A2 with least deviation and act in synergy to aid anti-cancer drugs work on breast cancer cells.

Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions

Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or "material voxels" and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. X-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.

Atomistic Simulations of Hydrated Sulfonated Polybenzophenone Block Copolymer Membranes

We present a classical molecular dynamics simulations study on the nanostructures of the sulfonated polybenzophenone (SPK) block copolymer membranes at 300 K and 353 K. The results of the radial distribution function (RDF) show that the interactions of the sulfonate groups of the membrane with the hydronium ions are more significant than those of water due to the strong electrostatic attraction over the hydrogen bonding. However, the effect of temperatures on the RDF profile seems insignificant. Furthermore, the spatial distribution function (SDF) portrays that the sulfonate groups of the hydrophilic components are preferential binding sites for hydronium ions against the hydrophobic counterpart of the SPK membrane. The mobility of the H3 O+ ions at 300 K and 353 K is two (or three) times lower than that of Nafion/Aciplex. However, the diffusion coefficients for water molecules closely agree with Nafion/Aciplex. This study suggests that water clusters are more localized around the sulfonate groups in the SPK membranes. Thus, the molecular modeling study of SPK block copolymer membranes is warranted to design better-performing membrane electrolytes.

Roxadustat and its failure: A comparative dynamic study

Roxadustat, a small-molecule inhibitor of hypoxia-inducible factor prolyl hydroxylase domain 2 (HIF-PHD2) has been recently overruled by the American Food and Drug Administration (FDA) in Phase 3 clinical trials. This study provides insights into the dynamics of Roxadustat with PHD2 and proposes two FDA-approved drugs; Pemetrexed and Valrubicin to treat chronic kidney disease (CKD). Role of chemical scaffolds such as synthetic pyrimidine-based antifolate is found critical for PHD2 inhibitory activity, which is concurrent with the experimental findings for stimulating Endogenous erythropoietin (EPO) gene expression. Furthermore, Fe⁺² and Mn⁺² in solution are essential for imparting structural stability to the screened carboxylic and non-carboxylic acid drugs. Comparative analysis of FDA-approved drugs namely, Roxadustat, two-hit carboxylic, and non-carboxylic-acid type compounds (Pemetrexed and Valrubicin), as well as the control ligands (KU1 and 4JR), unveil structural dynamics of Roxadustat and its failure. However, the proposed FDA compounds, Pemetrexed and Valrubicin, used to treat mesothelioma, non-small cell lung cancer, and bladder cancer should be subjected to in vitro analysis for renal anemia.

LABYRINTHOPEPTIN A2 DISRUPTS RAFT DOMAINS

Labyrinthopeptins constitute a class of ribosomal synthesized peptides belonging to the type III family of lantibiotics. They exist in different variants and display broad antiviral activities as well as show antiallodynic activity. Although their mechanism of action is not understood, it has been described that Labyrinthopeptins interact with membrane phospholipids modulating its biophysical properties and point out to membrane destabilization as its main point of action. We have used all-atom molecular dynamics to study the location of labyrinthopeptin A2 in a complex membrane as well as the existence of specific interactions with membrane lipids. Our results indicate that labyrinthopeptin A2, maintaining its globular structure, tends to be placed at the membrane interface, mainly between the phosphate atoms of the phospholipids and the oxygen atom of cholesterol modulating the biophysical properties of the membrane lipids. Outstandingly, we have found that labyrinthopeptin A2 tends to be preferentially surrounded by sphingomyelin while excluding cholesterol. The bioactive properties of labyrinthopeptin A2 could be attributed to the specific disorganization of raft domains in the membrane and the concomitant disruption of the overall membrane organization. These results support the improvement of Labyrinthopeptins as therapeutic molecules, opening up new opportunities for future medical advances.

SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories

The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.

Vibrational spectroscopy simulation of solvation effects on a G-quadruplex

It is commonly believed that solvation effects on the vibrational properties of a solute are easily accounted for by simple rules of thumbs, that is, solvating a polar molecule in a polar medium has the only effect of red shifting all its spectroscopical features and, similarly, solvating a polar molecule in a nonpolar medium has the opposite effect. In this work, we use theoretical vibrational spectroscopy at quasi-classical and quantum approximate semiclassical level to gain atomistic insights about solvent-solute interactions for 2'-deoxyguanosine and the G-quadruplex. We employ the quasi-classical trajectory method to include full anharmonicity into our calculated spectra, and then introduce quantum nuclear effects by means of divide-and-conquer semiclassical spectroscopy calculations. Solvation is treated explicitly leading to a good reproducibility of the available experimental data and reliable predictions when an experimental reference is missing.Communicated by Ramaswamy H. Sarma.

Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles

We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations. The actual update expands some of the existing modules and adds 21 new modules to the update 1 published in 2011. The new adds can be divided into three sets that: 1) analyze atomic fluctuations and structural communication; 2) explore ion-channel conformational dynamics and ionic translocation; and 3) compute geometrical indices of structural deformation. Set 1 serves to compute correlations of motions, find geometrically stable domains, identify a dynamically invariant core, find changes in domain-domain separation and mutual orientation, perform wavelet analysis of large-scale simulations, process the output of principal component analysis of atomic fluctuations, perform functional mode analysis, infer regions of mechanical rigidity, analyze overall fluctuations, and perform the perturbation response scanning. Set 2 includes modules specific for ion channels, which serve to monitor the pore radius as well as water or ion fluxes, and measure functional collective motions like receptor twisting or tilting angles. Finally, set 3 includes tools to monitor structural deformations by computing angles, perimeter, area, volume, β-sheet curvature, radial distribution function, and center of mass. The ring perception module is also included, helpful to monitor supramolecular self-assemblies. This update places Wordom among the most suitable, complete, user-friendly, and efficient software for the analysis of biomolecular simulations. The source code of Wordom and the relative documentation are available under the GNU general public license at http://wordom.sf.net.

A Molecular Dynamic Study of the Effects of Surface Partitioning on the OH Radical Interactions with Solutes in Multicomponent Aqueous Aerosols

The surface-bulk partitioning of small saccharide and amide molecules in aqueous droplets was investigated using molecular dynamics. The air-particle interface was modeled using a 80 Å cubic water box containing a series of organic molecules and surrounded by gaseous OH radicals. The properties of the organic solutes within the interface and the water bulk were examined at a molecular level using density profiles and radial pair distribution functions. Molecules containing only polar functional groups such as urea and glucose are found predominantly in the water bulk, forming an exclusion layer near the water surface. Substitution of a single polar group by an alkyl group in sugars and amides leads to the migration of the molecule toward the interface. Within the first 2 nm from the water surface, surface-active solutes lose their rotational freedom and adopt a preferred orientation with the alkyl group pointing toward the surface. The different packing within the interface leads to different solvation shell structures and enhanced interaction between the organic molecules and absorbed OH radicals. The simulations provide quantitative information about the dimension, composition, and organization of the air-water interface as well as about the nonreactive interaction of the OH radicals with the organic solutes. It suggests that increased concentrations, preferred orientations, and decreased solvation near the air-water surface may lead to differences in reactivities between surface-active and surface-inactive molecules. The results are important to explain how heterogeneous oxidation mechanisms and kinetics within interfaces may differ from those of the bulk.

Deciphering the interaction mechanism of natural actives against larval proteins of Aedes aegypti to identify potential larvicides: a computational biology analysis

Aedes aegypti is the target for repellents to curb incidences of vector-borne diseases. Stopping breeding of this mosquito species at its larval stages helps in controlling spread of insect-borne diseases. Therefore, the present study focused on deciphering the mechanism of interaction of selected natural actives against larval proteins of A. aegypti to identify potential natural alternative larvicides. 65 larval proteins were identified from literature, whose structures were modelled and validated using RaptorX and ProCheck. 11 natural actives were selected for predicting their ligand properties and toxicities via Toxicity Estimation Software Tool and ProTox-II. Molecular docking studies were carried out using POAP followed by 100 ns molecular dynamic simulation studies for top three best docked complexes to better understand the robustness of docking, complex stabilities and molecular mechanisms of interactions. Toxicity predictions revealed that 6 molecules belonged to toxicity class 4, and five to toxicity class 5, implying that they were all safe to use. Complexes goniothalamin-translation elongation factor (-10 kcal/mol), andrographolide-acetyl-CoA C-myristoyltransferase (-9.2 kcal/mol) and capillin-translation elongation factor (-8.4 kcal/mol) showed best binding energies. When simulated, capillin-translation elongation factor showed most stability, while the remaining two also evidenced robust docking. Evolutionary studies for top two larval proteins disclosed 100 other insect species in which these proteins can be targeted using various larvicides. Protein-protein interaction network analysis revealed several protein pathways that might be affected due to aforesaid naturals. Therefore, this study provides computational insights into the molecular interaction of naturals against larval proteins, acting as potential natural larvicides.Communicated by Ramaswamy H. Sarma.

Embedding Dynamics in Intrinsic Physicochemical Profiles of Market-Stage Antibody-Based Biotherapeutics

Adequate stability, manufacturability, and safety are crucial to bringing an antibody-based biotherapeutic to the market. Following the concept of holistic in silico developability, we introduce a physicochemical description of 91 market-stage antibody-based biotherapeutics based on orthogonal molecular properties of variable regions (Fvs) embedded in different simulation environments, mimicking conditions experienced by antibodies during manufacturing, formulation, and in vivo. In this work, the evaluation of molecular properties includes conformational flexibility of the Fvs using molecular dynamics (MD) simulations. The comparison between static homology models and simulations shows that MD significantly affects certain molecular descriptors like surface molecular patches. Moreover, the structural stability of a subset of Fv regions is linked to changes in their specific molecular interactions with ions in different experimental conditions. This is supported by the observation of differences in protein melting temperatures upon addition of NaCl. A DEvelopability Navigator In Silico (DENIS) is proposed to compare mAb candidates for their similarity with market-stage biotherapeutics in terms of physicochemical properties and conformational stability. Expanding on our previous developability guidelines (Ahmed et al. Proc. Natl. Acad. Sci. 2021, 118 (37), e2020577118), the hydrodynamic radius and the protein strand ratio are introduced as two additional descriptors that enable a more comprehensive in silico characterization of biotherapeutic drug candidates. Test cases show how this approach can facilitate identification and optimization of intrinsically developable lead candidates. DENIS represents an advanced computational tool to progress biotherapeutic drug candidates from discovery into early development by predicting drug properties in different aqueous environments.

Toxicity evaluation of microplastics to aquatic organisms through molecular simulations and fractional factorial designs

Molecular docking, molecular dynamics modelling, and fractional factorial design methodologies were used in the current work to examine the harmful effects of ten microplastic (MPs) such as polystyrene (PS), polyvinylchloride (PVC), polyurethane (PU), polymethyl methacrylate (PMMA), polyamide (PA), polyethylene terephthalate (PET), polyethylene (PE), polypropylene (PP), polychloropene (PCP) and polycarbonate (PC) on the aquatic organism (zebrafish). The toxicity was evaluated based on the docking of the MPs on cytochrome P450 (CYP P450) protein crystals. The binding affinities (ΔG) followed the order, PC (-6.9 kcal/mol) > PET (-6.1 kcal/mol) > PP (-5.8 kcal/mol) > PA (-5.6 kcal/mol) > PS (-5.1 kcal/mol) > PU (-4.1 kcal/mol) > PMMA (-3.9 kcal/mol) > PCP (-3.3 kcal/mol) > PVC (-2.4 kcal/mol) > PE (-2.1 kcal/mol). The primary driving factors for the binding of the MPs and the protein were hydrophobic force, and hydrogen bonding based on the molecular dynamics analysis and surrounding amino acid residues. Furthermore, a 2^10-5 fractional factorial design method was estimated to identify the main effect and second-order effects of MPs in a composite contamination system on binding affinity/energy to CYP450 receptor protein of zebrafish, combined with a fixed effects model. The findings showed that different MPs combinations had varying impacts on aquatic toxicity; as a consequence, the best combination of MPs with the lowest aquatic toxicity effect could be excluded. The factorial designs showed that the PU-PS and PP-PA combination and single PCP, has the most significant main effect on CYP450 receptor protein of zebrafish which translates to an optimum toxicity level of -4.61 kcal/mol. The investigation offers a theoretical foundation for identifying the hazardous impacts of MPs on aquatic life.

Analysis of Structural Development and Defects during the Anisotropic Growth of Silicon

High-performance polysilicon (P-Si) is fundamental as a resource for manufacturing semiconductor devices with high photoelectric properties. However, experimentally characterizing the solidification process in detail has been difficult on account of the extremely rapid cooling rate and limited available characterization methods. Therefore, this study used molecular dynamics (MD) to investigate Si crystallization behavior through directional solidification at different cooling rates. The entire system was first analyzed in terms of energy and radial distribution function, after which the microstructural evolution was characterized by visualization. Results indicated that the cooling rate significantly affected the directional solidification of Si, and an excessively high cooling rate resulted in a decrease in the long-range order of the system. At the same cooling rate, the crystallization rates of (1 0 0), (1 1 0), and (1 1 1) crystal faces followed a descending order. The configurations of the S-L interface with different crystal faces were distinct. Specifically, while the atom numbers of defect structures that were formed in systems of (1 0 0) and (1 1 0) crystal faces were few, those formed in the (1 1 1) crystal face were more. It was difficult for the (1 0 0) crystal face to form dislocations regardless of the crystallization degree at different cooling rates, and the (1 1 0) crystal face only formed a few dislocations at high cooling rates. Dislocations formed at all cooling rates during the directional solidification of the (1 1 1) crystal face, and there was a weak correlation between the number of dislocations and cooling rates. Twinning mainly occurred during the solidification process of the (1 1 1) crystal face, and there was no obvious linear relation between its number and the cooling rate. Moreover, when high-energy dislocations occurred more often, the system stability decreased. Overall, this work will be helpful to understand the commonness and difference in directional solidification of Si with different crystal faces at different cooling rates.

Reconstruction and Removal Mechanisms of Gel-like Membrane Fouling for Seawater Desalination: Experiments and Molecular Dynamics Simulations

Anti-gel fouling is a key problem faced by membrane desalination, especially for applications in organic acid-rich seawater. In this paper, a chemical crosslinking-based method was used to reconstruct and characterize the gel pollutants produced under the actual operating conditions of seawater desalination. In addition to the calcium alginate/calcium humate three-dimensional network skeleton, salt ions (K+, Na+, Mg2+, Cl−) in solution were also considered to ensure that the reconstructed gel was similar to pollutant gels on membranes under practical operating conditions. Characterizations showed that the reconstructed gel has high thermal insulation and stability, thus adjusting the temperature has no removal effect. Two detergents (sodium citrate and sodium hydroxide) were investigated, and their gel-removal mechanism was elucidated by molecular dynamics simulation. Numerical analysis showed that the electrostatic attraction interaction had a significant role in the gel cleaning process. Owing to the attraction of the lower electrostatic potential region in the cleaning agent, the ion exchange between Na+ in the cleaning agent and Ca2+ in the gel led to the breaking of the Ca2+-induced intermolecular bridge in the complex. As the adhesion of fouling gels decreased, the gel water solubility was increased, resulting in a decrease in weight and strength of the gel. Therefore, the integrity of the gel fouling layer was weakened and can be effectively removed. This study provides a theoretical basis for the removal of gel-like membrane fouling during actual seawater desalination.

Flap sub-domain dynamics of serine-threonine phosphatase (Stp1) of Staphylococcus aureus: an accelerated molecular dynamics simulation study

Vancomycin and daptomycin are commonly used glycopeptide antibiotics to cure Gram-positive staphylococcal infections. The clinical isolates of mutant Staphylococcus aureus strains, Methicillin-Resistant (MRSA) and Vancomycin-Resistant (VRSA), have developed resistance against these antibiotics. A recently discovered Serine/threonine phosphatase (Stp1) is an Mn⁺² containing protein at the active site with a flap sub-domain that participates in the phospho-signaling system of bacterial cell wall formation. The flap sub-domain probably regulates substrates recruitment and release with an extra Mn⁺², possibly highly flexible as in the other homologous family of proteins. In this study, the flap sub-domain has been sampled with conventional and accelerated molecular dynamics (cMD and aMD) simulations to get other sub-optimal conformational states of the protein that are nearly impossible to observe through experimental methods. Trajectory analysis has shown that protein remained static in cMD while dynamic in aMD with RMSD of ∼2Å and ∼3Å, respectively. Accelerated MD has shown greater flexibility of ∼4 Å in the flap sub-domain, while cMD only captured a deviation of ∼ 2 Å. Later, the dynamic cross-correlation map (DCCM) confirmed that the flap sub-domain is significantly more flexible than the other part of the structure, indicating its role in substrate regulation. Secondary structure transition in the flap sub-domain, i.e. 3-10 helix and turn (PRO159 - ILE163) region of the flap sub-domain shifted into α-helix, which is a more stable structure. Further, the trajectory has been clustered, and conformational states extracted, which may be exploited in structure-based antibiotics discovery.

Effect of Cooling Rate on the Crystal Quality and Crystallization Rate of SiC during Rapid Solidification Based on the Solid–Liquid Model

The silicon carbide (SiC) that can achieve better electron concentration and motion control is more suitable for the production of high temperature, high frequency, radiation resistance, and high-power electronic devices. However, the fabrication of the high purity single crystal is challenging, and it is hard to observe the structural details during crystallization. Here, we demonstrate a study of the crystallization of single-crystal SiC by the molecular dynamic simulations. Based on several structure analysis methods, the transition of the solid–liquid SiC interface from a liquid to a zinc-blende structure is theoretically investigated. The results indicate that most of the atoms in the solid–liquid interface begin to crystallize with rapid solidification at low cooling rates, while crystallization does not occur in the system at high cooling rates. As the quenching progresses, the number of system defects decreases, and the distribution is more concentrated in the solid–liquid interface. A maximum crystallization rate is observed for a cooling rate of 1010 K/s. Moreover, when a stronger crystallization effect is observed, the energy is lower, and the system is more stable.

Effects of structural inhomogeneity on equilibration processes in Langevin dynamics

In recent decades, computer experiments have led to an accurate and fundamental understanding of atomic and molecular mechanisms in fluids, such as different kinds of relaxation processes toward steady physical states. In this paper, we investigate how exactly the configuration of initial states in a molecular-dynamics simulation can affect the rates of decay toward equilibrium for the widely known Langevin canonical ensemble. For this purpose, we derive an original expression relating the system relaxation time τ_{sys} and the radial distribution function g(r) in the near-zero and high-density limit. We found that, for an initial state which is slightly marginally inhomogeneous in the number density of atoms, the system relaxation time τ_{sys} is much longer than that for the homogeneous case and an increasing function of the Langevin coupling constant, γ. We also found, during structural equilibration, g(r) at large distances approaches 1 from above for the inhomogeneous case and from below for the macroscopically homogeneous one.

Discovery of novel Glutaminase allosteric inhibitors through drug repurposing and comparative MMGB/PBSA and molecular dynamics simulation

GLS1 enzymes (Glutaminase C (GAC) and kidney-type Glutaminase (KGA)) are gaining prominence as a target for tumor treatment including lung, breast, kidney, prostate, and colorectal. To date, several medicinal chemistry studies are being conducted to develop new and effective inhibitors against GLS1 enzymes. Telaglenastat, a drug that targets the allosteric site of GLS1, has undergone clinical trials for the first time for the therapy of solid tumors and hematological malignancies. A comprehensive computational investigation is performed to get insights into the inhibition mechanism of the Telaglenastat. Some novel inhibitors are also proposed against GLS1 enzymes using the drug repurposing approach using 2D-fingerprinting virtual screening method against 2.4 million compounds, application of pharmacokinetics, Molecular Docking, and Molecular Dynamic (MD) Simulations. A TIP3P water box of 10 Å was defined to solvate both enzymes to improve MD simulation reliability. The dynamics results were validated further by the MMGB/PBSA binding free energy method, RDF, and AFD analysis. Results of these computational analysis revealed a stable binding affinity of Telaglenastat, as well as an FDA approved drug Astemizole (IC₅₀ ∼ 0.9 nM) and a novel para position oriented methoxy group containing Chembridge compound (Chem-64284604) that provides an effective inhibitory action against GAC and KGA.

Chelator-Based Parameterization of the 12-6-4 Lennard-Jones Molecular Mechanics Potential for More Realistic Metal Ion-Protein Interactions

Metal ions are associated with a variety of proteins and play critical roles in a wide range of biochemical processes. There are multiple ways to study and quantify protein–metal ion interactions, including molecular dynamics simulations. Recently, the AMBER molecular mechanics forcefield was modified to include a 12-6-4 Lennard-Jones potential, which allows for a better description of nonbonded terms through the additional pairwise C_ij coefficients. Here, we demonstrate a method of generating C_ij parameters that allows parametrization of specific metal ion-ligating groups in order to tune binding energies computed by thermodynamic integration. The new C_ij coefficients were tested on a series of chelators: ethylenediaminetetraacetic acid, nitrilotriacetic acid, egtazic acid, and the EF1 loop peptides from the proteins lanmodulin and calmodulin. The new parameters show significant improvements in computed binding energies relative to existing force fields and produce coordination numbers and ion-oxygen distances that are in good agreement with experimental values. This parametrization method should be extensible to a range of other systems and could be readily adapted to tune properties other than binding energies.

Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of Spermidine3+ With DNA Double Helices

Polyamines have important roles in the modulation of the cellular function and are ubiquitous in cells. The polyamines putrescine²⁺, spermidine³⁺, and spermine⁴⁺ represent the most abundant organic counterions of the negatively charged DNA in the cellular nucleus. These polyamines are known to stabilize the DNA structure and, depending on their concentration and additional salt composition, to induce DNA aggregation, which is often referred to as condensation. However, the modes of interactions of these elongated polycations with DNA and how they promote condensation are still not clear. In the present work, atomistic molecular dynamics (MD) computer simulations of two DNA fragments surrounded by spermidine³⁺ (Spd³⁺) cations were performed to study the structuring of Spd³⁺ “caged” between DNA molecules. Microsecond time scale simulations, in which the parallel DNA fragments were constrained at three different separations, but allowed to rotate axially and move naturally, provided information on the conformations and relative orientations of surrounding Spm³⁺ cations as a function of DNA-DNA separation. Novel geometric criteria allowed for the classification of DNA-Spd³⁺ interaction modes, with special attention given to Spd³⁺ conformational changes in the space between the two DNA molecules (caged Spd³⁺). This work shows how changes in the accessible space, or confinement, around DNA affect DNA-Spd³⁺ interactions, information fundamental to understanding the interactions between DNA and its counterions in environments where DNA is compacted, e.g. in the cellular nucleus.

Analysis of grain size and five-fold twins during rapid solidification processes inTi3Al alloy

The wide application of titanium aluminum (Ti–Al) intermetallic compounds for aerospace and automotive fields has accelerated the research and development of Ti₃Al alloy. In this study, simulation is adopted to investigate the crystallization behavior during rapid solidification of Ti₃Al alloys using molecular dynamics at different cooling rates of 10¹⁰ K s⁻¹, 10¹¹ K s⁻¹, 10¹² K s⁻¹, and 10¹³ K s⁻¹. The evolution of microstructures is characterized by taking advantage of the average potential energy, the pair distribution function and visualization. The results show that the system has formed a microstructural configuration with the face-centered cubic structure as the main structure and the hexagonal close-packed structure as the supplement. An increase in the cooling rate will reduce the grain size of the alloy, which in turn will increase the number of grains. At the cooling rate at which the alloy can crystallize, the system forms five-fold twin structures. Meanwhile, we obtain a deeper insight into the properties of five-fold twins in terms of atoms on different sites, and establish a standard model of the same specification for comparison to get the commonality and differences of the five-fold twins between the standard and the solidified. In addition, the evolution of dislocation densities and distribution of dislocation lines in the system under different conditions are analyzed. This study further explores crystallization behavior on the atomic scale and it is hoped that this research will contribute to expanding the understanding of Ti₃Al alloy during the growth process.

A deeper insight into the properties of five-fold twins is obtained by establishing a standard five-fold twin nanocluster with the same size as the one gained by solidification for comparison to obtain the commonalities and differences between them.

Ascorbate-and iron-driven redox activity of Dp44mT and emodin facilitates peroxidation of micelles and bicelles

BACKGROUND

Iron (Fe)-induced oxidative stress leads to reactive oxygen species that damage biomembranes, with this mechanism being involved in the activity of some anti-cancer chemotherapeutics.

METHODS

Herein, we compared the effect of Fe complexes of the ligand, di-2-pyridylketone 4,4-dimethyl-3-thiosemicarbazone (Dp44mT), or the potential ligand, Emodin, on lipid peroxidation in cell membrane models (micelles and bicelles). These studies were performed in the presence of hydrogen peroxide (H₂O₂) and the absence or presence of ascorbate.

RESULTS

In the absence of ascorbate, Fe(II)/Emodin mixtures incubated with H₂O₂ demonstrated slight pro-oxidant properties on micelles versus Fe(II) alone, while the Fe(III)-Dp44mT complex exhibited marked antioxidant properties. Examining more physiologically relevant phospholipid-containing bicelles, the Fe(II)- and Fe(III)-Dp44mT complexes demonstrated antioxidant activity without ascorbate. Upon adding ascorbate, there was a significant increase in the peroxidation of micelles and bicelles in the presence of unchelated Fe(II) and H₂O₂. The addition of ascorbate to Fe(III)-Dp44mT substantially increased the peroxidation of micelles and bicelles, with the Fe(III)-Dp44mT complex being reduced by ascorbate to the Fe(II) state, explaining the increased reactivity. Electron paramagnetic resonance spectroscopy demonstrated ascorbyl radical anion generation after mixing ascorbate and Emodin, with signal intensity being enhanced by H₂O₂. This finding suggested Emodin semiquinone radical formation that could play a role in its reactivity via ascorbate-driven redox cycling. Examining cultured melanoma cells in vitro, ascorbate at pharmacological levels enhanced the anti-proliferative activity of Dp44mT and Emodin.

CONCLUSIONS AND GENERAL SIGNIFICANCE

Ascorbate-driven redox cycling of Dp44mT and Emodin promotes their anti-proliferative activity.

Effect of Organic Solvents on the Structure and Activity of a Minimal Lipase

Lipases are ubiquitously used in chemo-enzymatic synthesis and industrial applications. Nevertheless, the modulation of the activity of lipases by organic solvents still is not fully understood at the molecular level. We systematically investigated the activity and structure of lipase A from Bacillus subtilis in binary water-organic solvent mixtures of dimethyl sulfoxide (DMSO), acetonitrile (ACN), and isopropyl alcohol (IPA) using activity assays, fluorescence spectroscopy, molecular dynamics (MD) simulations, and FRET/MD analysis. The enzymatic activity strongly depended on the type and amount of organic solvent in the reaction media. Whereas IPA and ACN reduced the activity of the enzyme, small concentrations of DMSO led to lipase activation via an uncompetitive mechanism. DMSO molecules did not directly interfere with the binding of the substrate in the active site, contrary to what is known for other solvents and enzymes. We propose that the His156-Asp133 interaction, the binding of organic molecules to the active site, and the water accessibility of the substrate are key factors modulating the catalytic activity. Furthermore, we rationalized the role of solvent descriptors on the regulation of enzymatic activity in mixtures with low concentrations of the organic molecule, with prospective implications for the optimization of biocatalytic processes via solvent tuning.

Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function

In order to evaluate the interactions between a potential drug candidate like inhibitor N3 and the residues in substrate binding site of SARS-CoV-2 main protease (M pro ), we used molecular docking and dynamics simulations. The structural features describing the degrees of folding states ofM pro formed by beta-barrels and alpha-helices were analyzed by means of root mean square deviation, root mean square fluctuation, radius of gyration, residue velocity, H-bonding, dihedral angle distributions and radial distribution function. All of the residues forming ligand binding domain (LBD) ofM pro lie within the allowed region of the dihedral angle distributions as observed from the equilibrating best pose ofM pro -N3 system. Sharp peaks of radial distribution function (RDF) for H-bonding atom pairs (about 2 Å radial distance apart) describe the strong interactions between inhibitor and SARS-CoV-2M pro . During MD simulations, HSE163 has the lowest residue speed offering a sharp RDF peak whereas GLN192 has the highest residue speed resulting a flat RDF peak for the H-bonding atom pairs ofM pro -N3 system. Along with negative values of coulombic and Lenard-Jones energies, MM/PBSA free energy of binding contributed by the non-covalent interactions betweenM pro and N3 has been obtained to be -19.45 ± 3.6 kcal/mol. These physical parameters demonstrate the binding nature of an inhibitor inM pro -LBD. This study will be helpful in evaluating the drug candidates which are expected to inhibit the SARS-CoV-2 structural proteins.

A comprehensive computational and principal component analysis on various choline chloride-based deep eutectic solvents to reveal their structural and spectroscopic properties

In this study, the quantum chemical properties, nonbonding interactions, and spectroscopic insights of a wide variety of choline chloride (ChCl)-based deep eutectic solvents were investigated employing molecular dynamics (MD), density functional theory, and spectroscopic analyses. Nine experimentally reported ChCl-based deep eutectic solvents (DESs) were selected for this study where ChCl was common in all the DESs and the hydrogen bond donors (HBDs) were varied. The most energetically favorable cluster was selected using MD simulation followed by density functional theory calculation. The most stable cluster structures were fully optimized, and their quantum chemical properties and IR spectra were computed at the ωB97XD/6-31G++(d,p) level of theory. Principal component analysis was performed to distinguish their behavioral differences and to find out if any correlation exists among the 1:1 and 1:2 clusters. The atom-atom radial distribution functions based on MD simulations revealed that several hydrogen bonds were formed among the donor and acceptor molecules. However, the most prominent hydrogen bonds were found to be N-H_HBD⋯Cl^- for ChCl:U, ChCl:TU, and ChCl:Ace and O-H_HBD⋯Cl^- for ChCl:Glu, ChCl:Ma, ChCl:Ox, ChCl:Gly, and ChCl:Phe. Both N-H_HBD⋯Cl^- and O-H_HBD⋯Cl^- were major interactions for ChCl:Pro, where Cl^- worked as a bridge between Ch⁺ and the respective donors. In addition, the -OH of Ch⁺ showed strong intermolecular interactions with the acceptor groups of the donor molecules, such as C=O and O-H. This study has tried to extract a pattern of the contributions of HBDs by comparing the structural, spectroscopic, and thermodynamic properties of ChCl-based DESs, which have also been successfully correlated with the intermolecular interactions.

Direct observation of ultrafast hydrogen bond strengthening in liquid water

Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network¹, including unusually efficient vibrational energy redistribution and relaxation². An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and many solution-phase chemical reactions. Most existing knowledge of vibrational relaxation in water is built upon ultrafast spectroscopy experiments^2-7. However, these experiments cannot directly resolve the motion of the atomic positions and require difficult translation of spectral dynamics into hydrogen bond dynamics. Here, we measure the ultrafast structural response to the excitation of the OH stretching vibration in liquid water with femtosecond temporal and atomic spatial resolution using liquid ultrafast electron scattering. We observed a transient hydrogen bond contraction of roughly 0.04 Å on a timescale of 80 femtoseconds, followed by a thermalization on a timescale of approximately 1 picosecond. Molecular dynamics simulations reveal the need to treat the distribution of the shared proton in the hydrogen bond quantum mechanically to capture the structural dynamics on femtosecond timescales. Our experiment and simulations unveil the intermolecular character of the water vibration preceding the relaxation of the OH stretch.

Role of the CarH photoreceptor protein environment in the modulation of cobalamin photochemistry

The photochemistry of cobalamins has recently been found to have biological importance, with the discovery of bacterial photoreceptor proteins, such as CarH and AerR. CarH and AerR, are involved in the light regulation of carotenoid biosynthesis and bacteriochlorophyll biosynthesis, respectively, in bacteria. Experimental transient absorption spectroscopic studies have indicated unusual photochemical behavior of 5'-deoxy-5'-adenosylcobalamin (AdoCbl) in CarH, with excited-state charge separation between cobalt and adenosyl and possible heterolytic cleavage of the Co-adenosyl bond, as opposed to the homolytic cleavage observed in aqueous solution and in many AdoCbl-based enzymes. We employ molecular dynamics and hybrid quantum mechanical/molecular mechanical calculations to obtain a microscopic understanding of the modulation of the excited electronic states of AdoCbl by the CarH protein environment, in contrast to aqueous solution and AdoCbl-based enzymes. Our results indicate a progressive stabilization of the electronic states involving charge transfer (CT) from cobalt/corrin to adenine on changing the environment from gas phase to water to solvated CarH. The solvent exposure of the adenosyl ligand in CarH, the π-stacking interaction between a tryptophan and the adenine moiety, and the hydrogen-bonding interaction between a glutamate and the lower axial ligand of cobalt are found to contribute to the stabilization of the states involving CT to adenine. The combination of these three factors, the latter two of which can be experimentally tested via mutagenesis studies, is absent in an aqueous solvent environment and in AdoCbl-based enzymes. The favored CT from metal and/or corrin to adenine in CarH may promote heterolytic cleavage of the cobalt-adenosyl bond proposed by experimental studies. Overall, this work provides novel, to our knowledge, physical insights into the mechanism of CarH function and directions for future experimental investigations. The fundamental understanding of the mechanism of CarH functioning will serve the development of optogenetic tools based on the new class of B₁₂-dependent photoreceptors.

Role of Host-Guest Interaction in Understanding Polymerisation in Metal-Organic Frameworks

Metal-organic frameworks, MOFs, offer an effective template for polymerisation of polymers with precisely controlled structures within the sub-nanometre scales. However, synthetic difficulties such as monomer infiltration, detailed understanding of polymerisation mechanisms within the MOF nanochannels and the mechanism for removing the MOF template post polymerisation have prevented wide scale implementation of polymerisation in MOFs. This is partly due to the significant lack in understanding of the energetic and atomic-scale intermolecular interactions between the monomers and the MOFs. Consequently in this study, we explore the interaction of varied concentration of styrene, and 3,4-ethylenedioxythiophene (EDOT), at the surface and in the nanochannel of Zn₂(1,4-ndc)₂ (dabco), where 1,4-ndc = 1,4-naphthalenedicarboxylate and dabco = 1,4-diazabicyclo[2.2.2]octane. Our results showed that the interactions between monomers are stronger in the nanochannels than at the surfaces of the MOF. Moreover, the MOF-monomer interactions are strongest in the nanochannels and increase with the number of monomers. However, as the number of monomers increases, the monomers turn to bind more strongly at the surface leading to a potential agglomeration of the monomers at the surface.

On the Structure and Flip-flop of Free Docosahexaenoic Acid in a Model Human Brain Membrane

Among the omega-3 fatty acids, docosahexaenoic acid (DHA, sn22:6) is particularly vital in human brain cell membranes. There is considerable interest in DHA because low-level DHA has been associated with declined cognitive function and poor visual acuity. In this work, atomistic molecular dynamics simulations were used to investigate the effects of free protonated DHA (DHAP) in molar fractions of 0, 17, 30, and 38% in a realistic model of a healthy brain cell membrane comprising 26 lipid types. Numerous flip-flop events of DHAP were observed and categorized as successful or aborted. Novel use of the machine learning technique, density-based spatial clustering of applications with noise (DBSCAN), effectively identified flip-flop events by way of clustering. Our data show that increasing amounts of DHAP in the membrane disorder the bilayer packing, fluidize the membrane, and increase the rates of successful flip-flop from k = 0.2 μs^-1 (17% DHAP) to 0.8 μs^-1 (30% DHAP) and to 1.3 μs^-1 (38% DHAP). In addition, we also provided a detailed understanding of the flip-flop mechanism of DHAP across this complex membrane. Interestingly, we noted the role of hydrogen bonds in two distinct coordinated flip-flop phenomena between two DHAP molecules: double flip-flop and assisted flip-flop. Understanding the effects of various concentrations of DHAP on the dynamics within a lipid membrane and the resulting structural properties of the membrane are important when considering the use of DHAP as a dietary supplement or as a potential therapeutic.

Low-frequency vibrations of water molecules in DNA minor groove

Water molecules around the DNA form the hydration shell having different structural and dynamical features in different regions of the double helix. In the DNA minor groove, water molecules are highly ordered and in the case of AT nucleotide sequence, the formation of a hydration spine is observed. In the present research, the vibrations of the hydration spine have been studied to establish the mode of translational vibrations of water molecules in the DNA low-frequency spectra (water-spine vibrations). Using the developed phenomenological model with the parameters determined for different nucleotides of the DNA fragment CGCGAATTCGCG, the frequencies of vibrations of the hydration spine have been obtained within 185 ± 20 cm[Formula: see text] depending on type of nucleotide. The obtained frequencies are in the same region as the translational vibrations of water molecules in the bulk. To select the mode of water-spine vibrations from those modes that are present in the bulk water, the dynamics of DNA with different nucleotide contents has been analyzed, and the possible influence of heavy water has been estimated. The determined features of the mode of water vibrations in the hydration spine of DNA minor groove indicate that this mode may be observed in the experimental spectra.

Molecular dynamics simulation for membrane separation and porous materials: A current state of art review

Computational frameworks have been under specific attention within the last two decades. Molecular Dynamics (MD) simulations, identical to the other computational approaches, try to address the unknown question, lighten the dark areas of unanswered questions, to achieve probable explanations and solutions. Owing to their complex microporous structure on one side and the intricate biochemical nature of various materials used in the structure, separative membrane materials possess peculiar degrees of complications. More notably, as nanocomposite materials are often integrated into separative membranes, thin-film nanocomposites and porous separative nanocomposite materials could possess an additional level of complexity with regard to the nanoscale interactions brought to the structure. This critical review intends to cover the recent methods used to assess membranes and membrane materials. Incorporation of MD in membrane technology-related fields such as desalination, fuel cell-based energy production, blood purification through hemodialysis, etc., were briefly covered. Accordingly, this review could be used to understand the current extent of MD applications for separative membranes. The review could also be used as a guideline to use the proper MD implementation within the related fields.

Solvent effect on the 195Pt NMR properties in pyridonate-bridged PtIII dinuclear complex derivatives investigated by ab initio molecular dynamics and localized orbital analysis

An ab initio molecular dynamics investigation of the solvent effect (water) on the structural parameters, ¹⁹⁵Pt NMR spin-spin coupling constants (SSCCs) and chemical shifts of a series of pyridonate-bridged Pt^III dinuclear complexes is performed using Kohn-Sham (KS) Car-Parrinello molecular dynamics (CPMD) and relativistic hybrid KS NMR calculations. The indirect solvent effect (via structural changes) has a dramatic effect on the ¹J_PtPt SSCCs. The complexes exhibit a strong trans influence in solution, where the Pt-Pt bond lengthens with increasing axial ligand σ-donor strength. In the diaqua complex, where the solvent effect is more pronounced, the SSCCs averaged for CPMD configurations with explicit plus implicit solvation agree much better with the experimental data, while the calculations for static geometry and CPMD unsolvated configurations show large deviations with respect to experiment. The combination of CPMD with hybrid KS NMR calculations provides a much more realistic computational model that reproduces the large magnitudes of ¹J_PtPt and ¹⁹⁵Pt chemical shifts. An analysis of ¹J_PtPt in terms of localized and canonical orbitals shows that the SSCCs are driven by changes in the s-character of the natural atomic orbitals of Pt atoms, which affect the 'Fermi contact' mechanism.

Effect of RNA on Morphology and Dynamics of Membraneless Organelles

Membraneless organelles (MLOs) are spatiotemporally regulated structures that concentrate multivalent proteins or RNA, often in response to stress. The proteins enriched within MLOs are often classified as high-valency "scaffolds" or low-valency "clients", with the former being associated with a phase-separation promoting role. In this study, we employ a minimal model for P-body components, with a defined protein-protein interaction network, to study their phase separation at biologically realistic low protein concentrations. Without RNA, multivalent proteins can assemble into solid-like clusters only in the regime of high concentration and stable interactions. RNA molecules promote cluster formation in an RNA-length-dependent manner, even in the regime of weak interactions and low protein volume fraction. Our simulations reveal that long RNA chains act as superscaffolds that stabilize large RNA-protein clusters by recruiting low-valency proteins within them while also ensuring functional "liquid-like" turnover of components. Our results suggest that RNA-mediated phase separation could be a plausible mechanism for spatiotemporally regulated phase separation in the cell.

Molecular dynamics study of the competitive binding of hydrogen peroxide and water molecules with DNA phosphate groups

The interaction of hydrogen peroxide molecules with the DNA double helix is of great interest for understanding the mechanisms of anticancer therapy utilising heavy ion beams. In the present work, a molecular dynamics study of competitive binding of hydrogen peroxide and water molecules with phosphate groups of the DNA double helix backbone was carried out. The system of DNA double helix in a water solution with hydrogen peroxide molecules and Na[Formula: see text] counterions was simulated. The results show that the hydrogen peroxide molecules bind to oxygen atoms of the phosphate groups of the double helix backbone replacing water molecules of its hydration shell. The complexes of hydrogen peroxide molecules with the phosphate groups are stabilized by one or two hydrogen bonds and by Na[Formula: see text] counterions, forming ion-mediated contacts between phosphate groups and hydrogen peroxide molecules. The complex characterized by one H-bond between the hydrogen peroxide molecule and phosphate group is dominant, the other complexes are rare. The hydrogen peroxide molecule bound to the phosphate group of the double helix backbone can inhibit the formation of hydrogen bonds indispensable for the DNA biological functioning.