Deciphering molecular basis of pesticide-induced recurrent pregnancy loss: insights from transcriptomics analysis.

Recent studies have revealed a notable connection between pesticide exposure and Recurrent Pregnancy Loss (RPL), yet the precise molecular underpinning of this toxicity remains elusive. Through the alignment of Differentially Expressed Genes (DEGs) of healthy and RPL patients with the target genes of 9 pesticide components, we identified a set of 12 genes responsible for RPL etiology. Interestingly, biological process showed that besides RPL, those 12 genes also associated with preeclampsia and cardiovascular disease.

Exploring polyamine interactions and binding pockets in SARS-CoV-2 ORF3a.

Ongoing global pandemic caused by coronavirus (COVID-19) requires urgent development of vaccines, treatments, and diagnostic tools. Open reading frame 3a (ORF3a) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is considered to be a potential drug target for COVID-19 treatment. ORF3a is an accessory protein that plays a significant role in virus-host interactions and in facilitating host immune responses.

Effect of pH on stability of dimer structure of the main protease of coronavirus-2.

The viral main protease (M) from a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a key enzyme essential for viral replication and has become an attractive target for antiviral drug development. The M forms a functional dimer and exhibits a pH-dependent enzyme activity and dimerization. Here, we report a molecular dynamics (MD) investigation to gain insights into the structural stability of the enzyme dimer at neutral and acidic pH.

Interaction fingerprint of transmembrane segments in voltage sensor domains.

Voltage sensor domain (VSD) in channel and non-channel membrane proteins shares a common function in the detection of changes in the transmembrane electric potential. The VSD is made of four helical transmembrane segments (S1-S4) that form a structurally conserved scaffold through inter-transmembrane residue-residue interactions. Details about these interactions are yet to be fully understood in the context of the unique structural and physical characteristics of the voltage sensor unit.

Self-Organized Morphology and Multiscale Structures of CoVE Proteins.

Self-organizing structures of CoVE proteins have been investigated using a coarse-grained model in Monte Carlo simulations as a function of temperature () in a range covering the native (low ) to denatured (high ) phases. The presence of even a few chains accelerates the very slow dynamics of an otherwise free protein chain in the native phase. The radius of gyration depends nonmonotonically on temperature and increases with the protein concentration in both the native and denatured phase.

Dynamics and Environmental Characteristics of Spin Labels in a KvAP Voltage Sensor by Molecular Dynamics Simulations.

The nitroxide spin label is the most widely used probe for electron paramagnetic resonance (EPR) spectroscopy studies of the structure and function of biomolecules. However, the role of surrounding environments in determining the dynamics of nitroxide spin labels in biological complex systems remains to be clarified. This study aims to characterize the dynamics and environmental structure of spin labels in the voltage-sensing domain (VSD) of a KvAP potassium channel by means of molecular dynamics (MD) studies.

Thermally induced structural organization of nanodiscs by coarse-grained molecular dynamics simulations.

Membrane scaffold proteins (MSP) nanodiscs have been extensively used in structural study of membrane proteins. In cryo-EM, an incorporation of target proteins into nanodiscs is conducted under a rapid change from cryogenic to ambient temperatures. We present a coarse-grained molecular dynamics (CGMD) study for investigating an effect of temperature on the structural organization of DPPC-nanodisc and POPC-nanodisc.

Conformation, flexibility and hydration of hyaluronic acid by molecular dynamics simulations.

Hyaluronic acid (HA) is a biopolymer of disaccharide with two alternate glycosidic bonds, β(1,3) and β(1,4). A molecular dynamics study presented here unveiled conformational variability in association with the flexibility of the glycosidic linkers, which depends on the number of disaccharide units. HA chain maintains a rigid rod-like conformation with short chain lengths.

Inferring the three-dimensional structures of the X-chromosome during X-inactivation.

The Hi-C experiment can capture the genome-wide spatial proximities of the DNA, based on which it is possible to computationally reconstruct the three-dimensional (3D) structures of chromosomes. The transcripts of the long non-coding RNA (lncRNA) Xist spread throughout the entire X-chromosome and alter the 3D structure of the X-chromosome, which also inactivates one copy of the two X-chromosomes in a cell. The Hi-C experiments are expensive and time-consuming to conduct, but the Hi-C data of the active and inactive X-chromosomes are available.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation.

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f).

Asymmetry in structural response of inner and outer transmembrane segments of CorA protein by a coarse-grain model.

Structure of CorA protein and its inner (i.corA) and outer (o.corA) transmembrane (TM) components are investigated as a function of temperature by a coarse-grained Monte Carlo simulation.

Aggregation and network formation in self-assembly of protein (H3.1) by a coarse-grained Monte Carlo simulation.

Multi-scale aggregation to network formation of interacting proteins (H3.1) are examined by a knowledge-based coarse-grained Monte Carlo simulation as a function of temperature and the number of protein chains, i.e.

Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach.

Binding of a solvated peptide A1 ((1)E (2)P (3)L (4)Q (5)L (6)K (7)M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of temperature (T). Quantitative differences (e.

Conformational response to solvent interaction and temperature of a protein (Histone h3.1) by a multi-grained monte carlo simulation.

Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.

Distinction in binding of peptides (P2E) and its mutations (P2G, P2Q) to a graphene sheet via a hierarchical coarse-grained Monte Carlo simulation.

A hierarchical coarse-grained approach is used to study the binding of peptides (P2E: (1)E(2)P(3)L(4)Q(5)L(6)K(7)M) and variants (P2G: (1)G(2)P(3)L(4)Q(5)L(6)K(7)M and P2Q: (1)Q(2)L(3)P(4)M(5)E(6)K(7)L) with a graphene sheet. Simulation-based residue-substrate and hydropathy index-based residue-residue interaction is used as input to a phenomenological interaction potential for peptide chains to execute the stochastic motion with a graphene sheet at the center of a box. Large-scale Monte Carlo simulations are performed at a range (low to high) of temperatures to identify peptides binding with the graphene sheet with a constant peptide concentration (Cp = 0.

A hierarchical coarse-grained (all-atom-to-all-residue) computer simulation approach: self-assembly of peptides.

A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 ((1)H (2)S (3)S (4)Y (5)W (6)Y (7)A (8)F (9)N (10)N (11)K (12)T) is considered as an example to illustrate the utility.

Variation in structure of a protein (H2AX) with knowledge-based interactions.

The structure of a protein (H2AX) as a function of temperature is examined by three knowledge-based phenomenological interactions, MJ (Miyazawa and Jernigan), BT (Betancourt and Thirumalai), and BFKV (Bastolla et al.) to identify similarities and differences in results. Data from the BT and BFKV residue-residue interactions verify finding with the MJ interaction, i.

Random coil to globular thermal response of a protein (H3.1) with three knowledge-based coarse-grained potentials.

The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.

Fenestration closure in a calcified ventricular septal defect patch.

Ventricular septal defect closure with a fenestrated patch is a recognized rescue maneuver to decrease the risk of right ventricular failure after complete repair in patients with pulmonary atresia. If the fenestration needs surgical closure, severe calcification of the patch may make it extremely difficult. We describe the closure of such a defect in a 6-year-old boy, using a double Dacron patch sandwich.

Scaffolding of an antimicrobial peptide (KSL) by a scale-down coarse-grained approach.

A coarse-grained approach with enhanced representation of amino acid (involving four components, i.e. a central alpha carbon and its side group along with C and N terminals) is used to study the multi-scale assembly of an antimicrobial peptide (KSL) in an explicit solvent (in a scale-down hierarchy of Eby et al.

Survival and precopulatory guarding behavior of Hyalella azteca (Amphipoda) exposed to nitrate in the presence of atrazine.

Nitrate is one of the most commonly detected contaminants found in aquatic systems with other pesticides such as atrazine. The current study examined potential combined effects of nitrate and atrazine on adults of the freshwater amphipod Hyalella azteca, using survival and precopulatory guarding behavior as toxic endpoints. Although significant differences in acute toxicity with nitrate alone and in binary combination with atrazine (200 µg/L) in water-only tests were not consistently observed for each time point, potential biologically relevant trends in the data were observed.

Supramolecular assembly of a biomineralizing antimicrobial peptide in coarse-grained Monte Carlo simulations.

Monte Carlo simulations are used to model the self-organizing behavior of the biomineralizing peptide KSL (KKVVFKVKFK) in the presence of phosphate. Originally identified as an antimicrobial peptide, KSL also directs the formation of biosilica through a hypothetical supramolecular template that requires phosphate for assembly. Specificity of each residue and the interactions between the peptide and phosphate are considered in a coarse-grained model.

Biofunctionalization and immobilization of a membrane via peptide binding (CR3-1, S2) by a Monte Carlo simulation.

A coarse-grained computer simulation model is used to study the immobilization of a dynamic tethered membrane (representation of a clay platelet) in a matrix of mobile peptide chains CR3-1: 1Trp-2Pro-3Ser-4Ser-5Tyr-6Leu-7Ser-8Pro-9Ile-10Pro-11Tyr-12Ser and S2: 1His-2Gly-3Ile-4Asn-5Thr-6Thr-7Lys-8Pro-9Phe-10Lys-11Ser-12Val on a cubic lattice. Each residue interacts with the membrane nodes with appropriate interaction and executes their stochastic motion with the Metropolis algorithm. Density profiles, binding energy of each residue, mobility, and targeted structural profile are analyzed as a function of peptide concentration.

Bioassembled layered silicate-metal nanoparticle hybrids.

Here we report on the bioenabled assembly of layered nanohybrids using peptides identified with regard to their affinity to the nanoparticle surface. A dodecamer peptide termed M1, determined from a phage peptide display library, was found to bind to the surface of a layered aluminosilicate (montmorillonite, MMT). Fusion of a metal binding domain to the M1 peptide or the M1 peptide by itself was able to direct the growth of metal nanoparticles, such as gold and cobalt-platinum, respectively, on the MMT.