Catalytic Mechanism and Product Specificity of Protein Arginine Methyltransferase PRMT7: A Study from QM/MM Molecular Dynamics and Free Energy Simulations.

QM/MM molecular dynamics and potential of mean force (PMF) free-energy simulations are performed for wild-type PRMT7 and E172Q, E181Q, and Q329A mutants in this work, and the catalytic mechanism, product specificity, and the role of key residues for the PRMT7 activity are investigated. The main strategies of PRMT7 in reducing the activation barrier for methyl transfer that are found in this study include (1) formation of reactive (near attack) conformations for the substrate Arg, (2) strengthening the active-site interactions at the transition state, and (3) generation of more effective nucleophiles by changing charge distributions on the target Arg through active-site interactions. More importantly, it is shown that it is a combination of these different factors that determines the PRMT7 methylation activity and substrate/product specificity.

Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study.

The mesophilic inorganic pyrophosphatase from Escherichia coli (EcPPase) retains function at 353 K, the physiological temperature of hyperthermophilic Thermococcus thioreducens, whereas the homolog protein (TtPPase) from this hyperthermophilic organism cannot function at room temperature. To explain this asymmetric behavior, we examined structural and dynamical properties of the two proteins using molecular dynamics simulations. The global flexibility of TtPPase is significantly higher than its mesophilic homolog at all tested temperature/pressure conditions.

Carotenoids promote lateral packing and condensation of lipid membranes.

Carotenoids are pigment molecules that protect biomembranes against degradation and may be involved in the formation of functional bacterial membrane microdomains. Little is known on whether different types of carotenoids have different effects on the membrane or if there is any concentration dependence of these effects. In this work, we present results from molecular dynamics simulations of phospholipid bilayers containing different amounts of either β-carotene or zeaxanthin.

Enhancing the Light Coverage of Photosynthetic Bacteria to Augment Photosynthesis by Conjugated Polymer Nanoparticles.

By coating photosynthetic bacteria of with conjugated polymers nanoparticles modified with positively charged peptide TAT (CPNs-TAT), a bio-optical hybrid composite of /CPNs-TAT has been constructed. /CPNs-TAT augments the light coverage of to broaden the absorption due to excellent light-harvesting properties of CPNs-TAT, especially in the ultraviolet region. It leads to converting ultraviolet light to visible light that could be absorbed by , allowing antenna systems around the reaction center (RC) of the photosynthetic membrane to absorb more photons, thus photons are excited and transferred to the RC where the electron-hole separation occurs.

Graphene Oxide Composite for Selective Recognition, Capturing, Photothermal Killing of Bacteria over Mammalian Cells.

The multifunctional photothermal therapy (PTT) platform with the ability to selectively kill bacteria over mammalian cells has received widespread attention recently. Herein, we prepared graphene oxide-amino(polyethyleneglycol) (GO-PEG-NH) while using the hydrophobic interaction between heptadecyl end groups of 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethyleneglycol)] (DSPE-PEG-NH) and graphene oxide (GO). Based on GO-PEG-NH, the versatile PTT system was constructed with simultaneous selective recognition, capturing, and photothermal killing of bacteria.

Near-Infrared Light Regulation of Tumor PI3K/Akt Signaling Pathway for Enhancing Cancer Cell Apoptosis through Conjugated Polymer Nanoparticles.

Calmodulin (CaM), as a calcium binding protein involved in the signal pathways of many life activities such as cell proliferation and apoptosis, can be regulated with the near-infrared (NIR) light-based photothermal conversion. Here, we build a conjugated polymer nanoparticle (CPNs-C) by assembling polypyrrole dione and dipalmitoyl phosphatidylethanolamine-polyethylene glycol-maleimide with a calmodulin antibody modified on the surface, which is NIR light-responsive for photothermally inducing apoptosis of cancer cells. Under near-infrared light irradiation, protein kinase B (Akt) and phosphatidylinositol 3-kinase, which bind to CaM, reduce the degree of phosphorylation due to the photothermal effect of CPNs-C, thus inhibiting the recruitment of Akt on the cell membrane.

Capturing Deuteration Effects in a Molecular Mechanics Force Field: Deuterated THF and the THF-Water Miscibility Gap.

Deuteration is a common chemical modification used in conjunction with experiments such as neutron scattering, NMR, and Fourier-transform infrared for the study of molecular systems. Under the Born-Oppenheimer (BO) approximation, while the underlying potential energy surface remains unchanged by isotopic substitutions, isotopic substitution still alters intramolecular vibrations, which in turn may alter intermolecular interactions. Molecular mechanics (MM) force fields used in classical molecular dynamics simulations are assumed to represent local approximations of the BO potential energy surfaces, and hence, MD simulations using simple isotopic mass substitutions should capture BO-compatible isotope effects.

Periodic Mesoporous Organosilica Nanoparticles with BOC Group, towards HIFU Responsive Agents.

Periodic Mesoporous Organosilica Nanoparticles (PMONPs) are nanoparticles of high interest for nanomedicine applications. These nanoparticles are not composed of silica (SiO). They belong to hybrid organic-inorganic systems.

Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold.

Multidrug efflux is a major contributor to antibiotic resistance in Gram-negative bacterial pathogens. Inhibition of multidrug efflux pumps is a promising approach for reviving the efficacy of existing antibiotics. Previously, inhibitors targeting both the efflux transporter AcrB and the membrane fusion protein AcrA in the Escherichia coli AcrAB-TolC efflux pump were identified.

The relation between lignin sequence and its 3D structure.

Background: Lignin, the second most abundant biopolymer on earth, plays a major structural role in plants, conferring mechanical strength and regulating water conduction. Understanding the three-dimensional structure of lignin is important for fundamental reasons as well as engineering plants towards lignin valorization. Lignin lacks a specific primary sequence, making its average chemical composition the focus of most recent studies.

Treatment of hypoxia-dependent cardiovascular diseases by myo-inositol trispyrophosphate (ITPP)-enhancement of oxygen delivery by red blood cells.

Heart failure is a consequence of progression hypoxia-dependent tissue damages. Therapeutic approaches to restore and/or protect the healthy cardiac tissue have largely failed and remain a major challenge of regenerative medicine. The myo-inositol trispyrophosphate (ITPP) is a modifier of haemoglobin which enters the red blood cells and modifies the haemoglobin properties, allowing for easier and better delivery of oxygen by the blood.

Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets.

Selecting peptides that bind strongly to the major histocompatibility complex (MHC) for inclusion in a vaccine has therapeutic potential for infections and tumors. Machine learning models trained on sequence data exist for peptide:MHC (p:MHC) binding predictions. Here, we train support vector machine classifier (SVMC) models on physicochemical sequence-based and structure-based descriptor sets to predict peptide binding to a well-studied model mouse MHC I allele, H-2D.

An Atomistic Molecular Dynamics Study of Titanium Dioxide Adhesion to Lipid Bilayers.

Titanium dioxide (TiO) nanoparticles are found in an array of consumer and industrial products, and human exposure to these nanoparticles involves interaction with biological membranes. To understand the effect of the membrane lipid composition on bilayer perturbation by TiO, we performed all-atom molecular dynamics simulations of nanosized TiO interacting with three single component bilayers differing only in their headgroup composition: the zwitterionic DOPC, which is overall neutral containing negatively charged phosphate and positively charged choline in its head, DOPG, which is overall anionic containing negatively charged phosphate and neutral glycerol, and the anionic DOPS, containing negatively charged phosphate attached to the hydroxyl side-chain of the amino acid, serine containing negatively charged carboxyl and positively charged ammonium. The nanoparticle adheres to all three bilayers causing a negative curvature on their top leaflet.

Four countries for science.

A personal retrospect is given on four decades in science in four countries - the UK, France, Germany and the USA. Some historical observations are made together with a time transect through scientific systems and institutions in the four countries.

Odd haemoglobins in odd-toed ungulates: Impact of selected haemoglobin characteristics of the white rhinoceros (Ceratotherium simum) on the monitoring of the arterial oxygen saturation of haemoglobin.

Background: Due to the current poaching crisis in Africa, increasing numbers of white rhinoceroses (Ceratotherium simum) require opioid immobilisation for medical interventions or management procedures. Alarmingly, the results of both blood gas analysis and pulse oximetry regularly indicate severe hypoxaemia. Yet, the recovery of the animals is uneventful.

Probing the critical nucleus size for ice formation with graphene oxide nanosheets.

Water freezing is ubiquitous and affects areas as diverse as climate, the chemical industry, cryobiology and materials science. Ice nucleation is the controlling step in water freezing and has, for nearly a century, been assumed to require the formation of a critical ice nucleus. But there has been no direct experimental evidence for the existence of such a nucleus, owing to its transient and nanoscale nature.

A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins.

The mer operon in bacteria encodes a set of proteins and enzymes that impart resistance to environmental mercury toxicity by importing Hg and reducing it to volatile Hg(0). Because the reduction occurs in the cytoplasm, mercuric ions must first be transported across the cytoplasmic membrane by one of a few known transporters. MerF is the smallest of these, containing only two transmembrane helices and two pairs of vicinal cysteines that coordinate mercuric ions.

The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation.

To assess the chemical reactivity, toxicity, and mobility of pollutants in the environment, knowledge of their species distributions is critical. Because their direct measurement is often infeasible, speciation modeling is widely adopted. Mercury (Hg) is a representative pollutant for which study of its speciation benefits from modeling.

Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e.

Use of MRI, metabolomic, and genomic biomarkers to identify mechanisms of chemoresistance in glioma.

Gliomas are the most common form of central nervous system tumor. The most prevalent form, glioblastoma multiforme, is also the most deadly with mean survival times that are less than 15 months. Therapies are severely limited by the ability of these tumors to develop resistance to both radiation and chemotherapy.

Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly.

Multidrug efflux pumps of pathogenic, Gram-negative bacteria comprise an innate resistance mechanism and are key contributors to the emerging global pandemic of antibiotic resistance. Several increasingly detailed cryo-electron microscopy maps have been resolved of an entire efflux pump complex, AcrAB-TolC, resulting in atomistic structural models. Using a recent model, we have carried out nearly 40 μs of molecular dynamics simulations to study one of the key components of the protein complex AcrA, the membrane fusion protein that connects the inner-membrane-bound AcrB to the outer-membrane-bound TolC.

Ligand-Dependent Sodium Ion Dynamics within the A Adenosine Receptor: A Molecular Dynamics Study.

Sodium ions have long been known to reduce the binding of agonists in many class-A GPCRs while having little effect on antagonist binding. Here, using long-time scale classical all-atom molecular dynamics simulations, we explore, in atomic detail, the motion of sodium ions within the ligand-binding pocket of the A adenosine receptor (A2A-AR) both in the presence and absence of ligands and in the active and inactive state. We identify novel secondary ion binding sites within the pocket and find that the types of ion motions within the pocket are highly dependent on the presence and type of ligand within the pocket.

Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins.

Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) play important roles in many aspects of normal cell physiology, such as signal transduction and transcription, as well as pathological states, including Alzheimer's, Parkinson's, and Huntington's disease. Unlike their globular counterparts that are defined by a few structures and free energy minima, IDP/IDR comprise a large ensemble of rapidly interconverting structures and a corresponding free energy landscape characterized by multiple minima. This aspect has precluded the use of structural biological techniques, such as X-ray crystallography and nuclear magnetic resonance (NMR) for resolving their structures.