Structural insights into transient receptor potential vanilloid type 1 (TRPV1) from homology modeling,flexible docking,and mutational studies

The transient receptor potential vanilloid subtype 1 (TRPV1) is a non-selective cation channel composed of four monomers with six transmembrane helices (TM1–TM6). TRPV1 is found in the central and peripheral nervous system, and it is an important therapeutic target for pain relief. We describe here the construction of a tetrameric homology model of rat TRPV1 (rTRPV1). We experimentally evaluated by mutational analysis the contribution of residues of rTRPV1 contributing to ligand binding by the prototypical TRPV1 agonists, capsaicin and resiniferatoxin (RTX). We then performed docking analysis using our homology model. The docking results with capsaicin and RTX showed that our homology model was reliable, affording good agreement with our mutation data. Additionally, the binding mode of a simplified RTX (sRTX) ligand as predicted by the modeling agreed well with those of capsaicin and RTX, accounting for the high binding affinity of the sRTX ligand for TRPV1. Through the homology modeling, docking and mutational studies, we obtained important insights into the ligand-receptor interactions at the molecular level which should prove of value in the design of novel TRPV1 ligands.     

Recent advances in the MS analysis of glycoproteins: Theoretical considerations

Protein glycosylation is involved in a broad range of biological processes that regulate protein function and control cell fate. As aberrant glycosylation has been found to be implicated in numerous diseases, the study and large-scale characterization of protein glycosylation is of great interest not only to the biological and biomedical research community, but also to the pharmaceutical and biotechnology industry. Due to the complex chemical structure and differing chemical properties of the protein/peptide and glycan moieties, the analysis and structural characterization of glycoproteins has been proven to be a difficult task. Large-scale endeavors have been further limited by the dynamic outcome of the glycosylation process itself, and, occasionally, by the low abundance of glycoproteins in biological samples. Recent advances in MS instrumentation and progress in miniaturized technologies for sample handling, enrichment and separation, have resulted in robust and compelling analysis strategies that effectively address the challenges of the glycoproteome. This review summarizes the key steps that are involved in the development of efficient glycoproteomic analysis methods, and the latest innovations that led to successful strategies for the characterization of glycoproteins and their corresponding glycans. As a follow-up to this work, we review innovative capillary and microfluidic-MS workflows for the identification, sequencing and characterization of glycoconjugates.     

Integration of ground aerogel particles as chromatographic stationary phase into microchip

C16 modified and ground monolithic silica aerogel particles in submicrometer size, as a new type of stationary phase was prepared and integrated in polydimethylsiloxane (PDMS) microchip. The aerogel particles were packed into the microfluidic channel using a simple procedure, which does not require any special frit or fabrication step to retain the particles. The subnanoliter volume of samples can be transported through the porous, short length of packing with low pressure (< 3 bar). Food dyes as test components could be separated using low pressure within 6s. A 50-fold preconcentration could be achieved by retaining 100 nL volume of sample on the packing and elution with methanol.     

Investigation of gas transport through porous membranes based on nonlinear frequency response analysis

Theoretical development of a new experimental method for investigation of mass transport in porous membranes, based on the principle of the modified Wicke-Kallenbach diffusion cell and the nonlinear frequency response analysis is presented. The method is developed to analyze the transport of a binary gas mixture in a porous membrane. The mixture is assumed to consist of one adsorbable and one inert component. Complex mass transfer mechanism in the membrane, where bulk or transition diffusion in the pore volume and surface diffusion take place in parallel, is assumed. Starting from the basic mathematical model equations and following a rather standardized procedure, the frequency response functions (FRFs) up to the second order are derived. Based on the derived FRFs, correlations between some characteristic features of these functions on one side, and the whole set of equilibrium and transport parameters of the system, on the other, are established. As the FRFs can be estimated directly from different harmonics of the measured outputs, these correlations give a complete theoretical basis for the proposed experimental method. The method is illustrated by quantifying the transport of helium (inert gas) and C₃H₈ and CO₂ (adsorbable gases) through a porous Vycor glass membrane.     

The optimal MR acquisition strategy for exponential decay constants estimation

Estimating the relaxation constant of an exponentially decaying signal from experimental MR data is fundamental in diffusion tensor imaging, fractional anisotropy mapping, measurements of transverse relaxation rates and contrast agent uptake. The precision of such measurements depends on the choice of acquisition parameters made at the design stage of the experiments. In this report, chi(2) fitting of multipoint data is used to demonstrate that the most efficient acquisition strategy is a two-point scheme. We also conjecture that the smallest coefficient of variation of the decay constant achievable in any N-point experiment is 3.6 times larger than that in the image intensity obtained by averaging N acquisitions with minimal exponential weighting.     

Conditions of Formation of Calcite Crystals of Tabular and Acute Rhombohedral Habits

Calcite crystals are grown under pure conditions by the method of counterdiffusion of calcium and carbonate ions in water. An extension of the diffusion method is used making possible the crystallization of calcite in a medium containing calcium or carbonate ions in excess of their stoichiometric amounts in calcite. Calcite crystals grown in the presence of an excess of Ca²⁺ ions exhibit an elongated habit determined by the prevailing development of some of the acute negative rhombohedra φ. {022 1}, θ. {044 1} or π. {088 1}, whereas with an excess of CO ions the habit varies from thick -to fine-tabular due to the considerable development of the pinacoid (c {0001}). The habit of crystals grown in a medium in which both ions are approximately in stoichiometric amounts or in which the excess of one of them frequently alternates with an excess of the other, is determined by the supersaturation and varies from basic rhombohedron to acute rhombohedron m. {404 1}. The results are discussed in the light of some of the existing theoretical ideas on the influence of admixtures on habit. It is shown that the order of morphological importance which can be derived on the basis of various extensions of Bravais' law agrees neither with the experimental results nor with the observations in nature. The particular habits observed in experiments, tabular and acute rhombohedral, are exactly those which Kalb had included in his morphogenetic order of calcite crystals as first and fifth habit types. Since they are the result of specific conditions in the medium they ought to deviate from the general order. The remaining three habit types, therefore, will determine the habit variations of calcite due to the decrease of supersaturation.