Planarity and out-of-plane vibrational modes of tryptophan and tyrosine in biomolecular modeling

Tryptophan and tyrosine are aromatic amino acids that play significant roles in the folding processes of proteins at water-membrane interfaces because of their amphipathic structures. Employing appropriate heteroaromatic molecular structures are essential for obtaining accurate dynamics and predictive capabilities in molecular simulations of these amino acids. In this study, molecular dynamics simulations that applied the most recent version of the CHARMM36 force field were conducted on aqueous solutions of tryptophan and of tyrosine. Geometric analysis and dynamics quantified how aromatic rings deviated from planar structures and exhibited out-of-plane fluctuations. Radial distribution functions showed possible biological significance because extent of ring planarity slightly affected local water concentrations near aromatic rings. Instantaneous all-atom normal mode analysis (NMA) and Fourier transformation of time autocorrelation functions of out-of-plane displacements were applied to study out-of-plane vibrations of atoms in those rings. NMA started with minimum energy configurations and then averaged over fluctuations in aqueous solution. The frequencies and frequency patterns that were obtained for tryptophan and tyrosine with CHARMM36 differed from literature reports of Raman spectra, infrared spectra, and frequencies calculated using quantum mechanics, with some out-of-plane modes found at higher frequencies. Effects of imposing improper torsion potentials and changing torsion angle force constants were investigated for all atoms in the rings of tryptophan and tyrosine. Results show that these coarse force fields variations only affect planarity and out-of-plane vibrations of atoms within the rings, not other vibrations. Although increasing improper torsion force constants reduced deviations from aromatic ring planarity significantly, it increased out-of-plane mode frequencies. Reducing torsion angle force constants (with and without improper torsions) shifted modes to lower frequencies. A combination of decreasing most torsion angle force constants for ring atoms in both amino acids and including improper torsion forces attained frequencies and frequency patterns for out-of-plane normal modes that were more similar to literature spectra. These force field variations decreased the extents of out-of-plane vibrations within the heteroaromatic rings of tryptophan, especially around the nitrogen atom in the ring, but not within the heteroaromatic ring of tyrosine. Conclusions were unaffected by peptide endgroup, water, or simulation ensemble

Computing Individual Area per Head Group Reveals Lipid Bilayer Dynamics

Lipid bilayers express a range of phases from solid-like to gel-like to liquid-like as a function of temperature and lipid surface concentration. The area occupied per lipid head group serves as one useful indicator of the bilayer phase, in conjunction with the two-dimensional radial distribution function (i.e., structure factor) within the bilayer. Typically, the area per head group is determined by dividing the bilayer area equally among all head groups. Such an approach is less satisfactory for a multicomponent set of diverse lipids. In this work, area determination is performed on a lipid-by-lipid basis by attributing to a lipid the volume that surrounds each atom. Voronoi tessellation provides this division of the interfacial region on a per-atom basis. The method is applied to a multicomponent system of water, NaCl, and 19 phospholipid types that was devised recently [Langmuir 2022, 38, 9481–9499] as a computational representation of the Gram-positive Staphylococcus aureus phospholipid bilayer. Results demonstrate that lipids and water molecules occupy similar extents of area within the interfacial region; ascribing area only to head groups implicitly incorporates assumptions about head group hydration. Results further show that lipid tails provide non-negligible contributions to area on the membrane side of the bilayer–water interface. Results for minimum and maximum area of individual lipids reveal that spontaneous fluctuations displace head groups more than 10 Å from the interfacial region during an NPT simulation at 310 K, leading to a zero contribution to total area at some times. Total area fluctuations and fluctuations per individual lipid relax with a correlation time of ∼10 ns. The method complements density profile as an approach to quantify the structure and dynamics of computational lipid bilayers

Collagen Gel Formation in the Presence of a Carbon Nanobrush

Type I, bovine skin collagen was allowed to gel in the presence of various concentrations of a carbon nanotube material covered with a polystyrene/polyaniline copolymer, called a carbon nanobrush (CNB). The rate of collagen gelation was enhanced by the presence of the CNB in a dose dependent manner. The extent of collagen gelation was due to the concentration of collagen and not the amount of CNB. Collagen D-periodicity, and average fibril diameter were unchanged by the CNB material as seen in transmission electron micrographs. Gel tensile strength was reduced by the presence of the CNB in a dose related manner. The collagen-CNB mixture may have a role in the repair and reconstruction of wounds or degenerated connective tissue

Salinity Effects on Growth and Nutritional Content of Newly Isolated Microalgal with Potential Use in The Shrimp-Hatcheries

A two-week batch experiment was conducted on three newly isolated Indonesian microalgal strains (Kb1-2 identified as Chaetoceros sp., Kb1-3 and Kb1-5) and Tisochrysis lutea to determine salinity effects upon the growth, proximate composition and ω-3, eicosapentaenoic acidand docosahexaenoic acid, (EPA and DHA) and ω-6 (arachidonic acid /ARA) fatty acids. Salinity within each strain growth of all microalgae tested. The highest cell densities were observed in Indonesian strains, Kb1-3 on day 8 at 25 psu and Kb1-5 on day 10 at 35 psu. Salinity significantly affected the lipid, protein and carbohydrate content in all microalgae cultured. The highest total lipid content was found in T. lutea cultured at 30 psu (28.3 %) followed by Kb1-2 cultured at 20 psu (25.0 %) and T. lutea at 35 psu (24.8 %). Kb1-3 produced highest protein when cultured at 20 and 25 psu, decreasing at higher salinities of 30 and 35 psu, 44.7 and 39.2 % to 31.5 and 32.6 %, respectively, similar to T. lutea. Kb1-5 had higher protein at both 25 and 35 psu but showed lower protein levels at 20 and 30 psu. Indonesian strains showed almost a similar content of carbohydrate across culture salinities similar to T. lutea. Although all Indonesian microalgae contained important ω-3 (EPA and DHA) and ω-6 (ARA) fatty acids, concentrations were low in comparison to T. lutea. All Indonesian microalgal strains also contained the dicarboxylic acid (DCA), phthalic acid, which was not present in T. lutea

Matrix quality and disturbance frequency drive evolution of species behavior at habitat boundaries

Previous theoretical studies suggest that a species' landscape should influence the evolution of its dispersal characteristics, because landscape structure affects the costs and benefits of dispersal. However, these studies have not considered the evolution of boundary crossing, that is, the tendency of animals to cross from habitat to nonhabitat ("matrix"). It is important to understand this dispersal behavior, because of its effects on the probability of population persistence. Boundary-crossing behavior drives the rate of interaction with matrix, and thus, it influences the rate of movement among populations and the risk of dispersal mortality. We used an individual-based, spatially explicit model to simulate the evolution of boundary crossing in response to landscape structure. Our simulations predict higher evolved probabilities of boundary crossing in landscapes with more habitat, less fragmented habitat, higher-quality matrix, and more frequent disturbances (i.e., fewer generations between local population extinction events). Unexpectedly, our simulations also suggest that matrix quality and disturbance frequency have much stronger effects on the evolution of boundary crossing than either habitat amount or habitat fragmentation. Our results suggest that boundary-crossing responses are most affected by the costs of dispersal through matrix and the benefits of escaping local extinction events. Evolution of optimal behavior at habitat boundaries in response to the landscape may have implications for species in human-altered landscapes, because this behavior may become suboptimal if the landscape changes faster than the species' evolutionary response to that change. Understanding how matrix quality and habitat disturbance drive evolution of behavior at boundaries, and how this in turn influences the extinction risk of species in human-altered landscapes should help us identify species of conservation concern and target them for management

HCMV Infection of Human Trophoblast Progenitor Cells of the Placenta Is Neutralized by a Human Monoclonal Antibody to Glycoprotein B and Not by Antibodies to the Pentamer Complex

Human cytomegalovirus (HCMV) is the major viral cause of congenital infection and birth defects. Primary maternal infection often results in virus transmission, and symptomatic babies can have permanent neurological deficiencies and deafness. Congenital infection can also lead to intrauterine growth restriction, a defect in placental transport. HCMV replicates in primary cytotrophoblasts (CTBs), the specialized cells of the placenta, and inhibits differentiation/invasion. Human trophoblast progenitor cells (TBPCs) give rise to the mature cell types of the chorionic villi, CTBs and multi-nucleated syncytiotrophoblasts (STBs). Here we report that TBPCs are fully permissive for pathogenic and attenuated HCMV strains. Studies with a mutant virus lacking a functional pentamer complex (gH/gL/pUL128-131A) showed that virion entry into TBPCs is independent of the pentamer. In addition, infection is blocked by a potent human neutralizing monoclonal antibody (mAb), TRL345, reactive with glycoprotein B (gB), but not mAbs to the pentamer proteins pUL130/pUL131A. Functional studies revealed that neutralization of infection preserved the capacity of TBPCs to differentiate and assemble into trophospheres composed of CTBs and STBs in vitro. Our results indicate that mAbs to gB protect trophoblast progenitors of the placenta and could be included in antibody treatments developed to suppress congenital infection and prevent disease

Personalized Epigenomic Signatures That Are Stable Over Time and Covary with Body Mass Index

International audienc

Homeoviscous response of Clostridium pasteurianum to butanol toxicity during glycerol fermentation

Clostridium pasteurianum ATCC 6013 achieves high n-butanol production when glycerol is used as the sole carbon source. In this study, the homeoviscous membrane response of C. pasteurianum ATCC 6013 has been examined through n-butanol challenge experiments. Homeoviscous response is a critical aspect of n-butanol tolerance and has not been examined in detail for C. pasteurianum. Lipid membrane compositions were examined for glycerol fermentations with n-butanol production, and during cell growth in the absence of n-butanol production, using gas chromatography–mass spectrometry (GC–MS) and proton nuclear magnetic resonance (1H-NMR). Membrane stabilization due to homeoviscous response was further examined by surface pressure–area (π–A) analysis of membrane extract monolayers. C. pasteurianum was found to exert a homeoviscous response that was comprised of an increase lipid tail length and a decrease in the percentage of unsaturated fatty acids with increasing n-butanol challenge. This led to a more rigid or stable membrane that counteracted n-butanol fluidization. This is the first report on the changes in the membrane lipid composition during n-butanol production by C. pasteurianum ATCC 6013, which is a versatile microorganism that has the potential to be engineered as an industrial n-butanol producer using crude glycerol