Structural and electrostatic characterization of Pariacoto virus: Implications for viral assembly

We present the first all‐atom model for the structure of a T = 3 virus, pariacoto virus (PaV), which is a nonenveloped, icosahedral RNA virus and a member of the Nodaviridae family. The model is an extension of the crystal structure, which reveals about 88% of the protein structure but only about 35% of the RNA structure. New modeling methods, combining coarse‐grained and all‐atom approaches, were required for developing the model. Evaluation of alternative models confirms our earlier observation that the polycationic N‐ and C‐terminal tails of the capsid proteins must penetrate deeply into the core of the virus, where they stabilize the structure by neutralizing a substantial fraction of the RNA charge. This leads us to propose a model for the assembly of small icosahedral RNA viruses: nonspecific binding of the protein tails to the RNA leads to a collapse of the complex, in a fashion reminiscent of DNA condensation. The globular protein domains are excluded from the condensed phase but are tethered to it, so they accumulate in a shell around the condensed phase, where their concentration is high enough to trigger oligomerization and formation of the mature virus. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 530–538, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Predicting Important Residues and Interaction Pathways in Proteins Using Gaussian Network Model: Binding and Stability of HLA Proteins

A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric activities of ten structures of HLA Class I proteins of the immune system are studied by the Gaussian Network Model. Five of these models are associated with inflammatory rheumatic disease and the remaining five are properly functioning. In the Gaussian Network Model, the protein structures are modeled as an elastic network where the inter-residue interactions are harmonic. Important residues and the interaction pathways in the proteins are identified by focusing on the largest eigenvalue of the residue interaction matrix. Predicted important residues match those known from previous experimental and clinical work. Graph perturbation is used to determine the response of the important residues along the interaction pathway. Differences in response patterns of the two sets of proteins are identified and their relations to disease are discussed.     

VitAL: Viterbi Algorithm for de novo Peptide Design

Background

Drug design against proteins to cure various diseases has been studied for several years. Numerous design techniques were discovered for small organic molecules for specific protein targets. The specificity, toxicity and selectivity of small molecules are hard problems to solve. The use of peptide drugs enables a partial solution to the toxicity problem. There has been a wide interest in peptide design, but the design techniques of a specific and selective peptide inhibitor against a protein target have not yet been established.

Methodology/Principal Findings

A novel de novo peptide design approach is developed to block activities of disease related protein targets. No prior training, based on known peptides, is necessary. The method sequentially generates the peptide by docking its residues pair by pair along a chosen path on a protein. The binding site on the protein is determined via the coarse grained Gaussian Network Model. A binding path is determined. The best fitting peptide is constructed by generating all possible peptide pairs at each point along the path and determining the binding energies between these pairs and the specific location on the protein using AutoDock. The Markov based partition function for all possible choices of the peptides along the path is generated by a matrix multiplication scheme. The best fitting peptide for the given surface is obtained by a Hidden Markov model using Viterbi decoding. The suitability of the conformations of the peptides that result upon binding on the surface are included in the algorithm by considering the intrinsic Ramachandran potentials.

Conclusions/Significance

The model is tested on known protein-peptide inhibitor complexes. The present algorithm predicts peptides that have better binding energies than those of the existing ones. Finally, a heptapeptide is designed for a protein that has excellent binding affinity according to AutoDock results.     

Evidence of fast serotonin transmission in frog slowly adapting type 1 responses

The Merkel cell-neurite (MCN) complex generates slowly adapting type 1 (SA1) response when mechanically stimulated. Both serotonin (5-HT) and glutamate have been implicated in the generation of normal SA1 responses, but previous studies have been inconclusive as to what their roles are or how synaptic transmission occurs. In this study, excised dorsal skin patches from common water frogs (Rana ridibunda) were stimulated by von Frey hairs during perfusion in a tissue bath, and single-unit spike activity was recorded from SA1 fibres. Serotonin had no significant effect on the SA1 response at low (10?μM) concentration, significantly increased activity in a force-independent manner at 100?μM, but decreased activity with reduced responsiveness to force at 1?mM. Glutamate showed no effect on the responsiveness to force at 100?μM. MDL 72222 (100?μM), an ionotropic 5-HT3 receptor antagonist, completely abolished the responsiveness to force, suggesting that serotonin is released from Merkel cells as a result of mechanical stimulation, and activated 5-HT3 receptors on the neurite. The metabotropic 5-HT2 receptor antagonist, ketanserin, greatly reduced the SA1 fibre's responsiveness to force, as did the non-specific glutamate receptor antagonist, kynurenic acid. This supports a role for serotonin and glutamate as neuromodulators in the MCN complex, possibly by activation and/or inhibition of signalling cascades in the Merkel cell associated with vesicle release. Additionally, it was observed that SA1 responses contained a force-independent component, similar to a dynamic response observed during mechanical vibrations.     

First Report of Fungal Strains from Afşin–Elbistan Mine for Microbial Lignite Process

Abstract

Today, the need for energy is increasing and fossil fuels are constituting one of the most important energy sources in the world. Therefore, the efficient use of fossil fuels has become inevitable. In order to better use the opportunities offered by nature, we have turned to nature’s own resources. In this study, fungal strains of potential use in coal processing technology, isolated from Turkey’s largest lignite mine and identified. Our goal was to obtain active isolates for the biotechnological applications using the mine’s own source. For this aim, lignite samples were collected from different regions of the Af?in–Elbistan lignite mine, isolation studies were done and eventually, distinguished fungal isolates were identified by using conventional and molecular techniques. Hereby, fungal biodiversity of Turkey’s largest lignite mine has been investigated for the first time. Furthermore, 20 fungal isolates belong to Alternaria, Aspergillus, and Penicillium genera were cultured to provide resources for the development of future biotechnological coal processing techniques.     

Adipocyte Lipid Chaperone aP2 Is a Secreted Adipokine Regulating Hepatic Glucose Production

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Expression of regulatory receptors on γδ T Cells and their cytokine production in Behcet's disease

Introduction

Behcet''s disease (BD) is a multi-systemic disorder with muco-cutaneous, ocular, arthritic, vascular or central nervous system involvement. The role of γδ T cells is implicated in BD. The activation status of γδ T cells and their cytokine secretion against phosphoantigens are evaluated in BD.

Methods

NKG2A, NKG2C, NKG2D, CD16 and CCR7 molecules on γδ T cells were analyzed in 70 BD, 27 tuberculosis (TB) patients and 26 healthy controls (HC). Peripheral γδ T cells were expanded with a phosphoantigen (BrHPP) and IL-2, restimulated with BrHPP and a TLR3 ligand, and cytokine production was measured.

Results

γδ T cells were not increased in both BD and TB patients, but the proportions of TCRVδ2⁺ T cells were lower (58.9 and 50.7 vs. 71.7%, P = 0.04 and P = 0.005) compared to HC. Higher proportion of TCRVδ2⁺ T cells were CD16⁺ (26.2 and 33.9 vs. 16.6%, P = 0.02 and P = 0.001) and CCR7^- (32.2 and 27.9 vs. 17.7%, P < 0.0001 and P = 0.014) in BD and TB patients compared to HC. NKG2C⁺ γδ⁺ T cells were relatively increased (0.5 and 0.6 vs. 0.3%, P = 0.008 and 0.018), whereas NKG2D positivity was decreased in patients with BD and TB (77.7 and 75.8 vs. 87.5%, P = 0.001 and 0.004). Expansion capacity of γδ T cells in BD and TB as well as production of IL-13, IFN-γ, granulocyte monocyte colony stimulating factor (GM-CSF), TNF-α, CCL4 and CCL5 in BD was lower compared to HC, when restimulated by TLR3 ligand and BrHPP.

Conclusion

The changes on γδ T cells of BD as well as TB patients implicate that γδ T cells have already been exposed to regulatory effects, which changed their activity. Lower cytokine response of γδ T cells implicates down modulation of these cells in BD.     

His74 conservation in the bilin reductase PcyA family reflects an important role in protein-substrate structure and dynamics

Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the proton-coupled four-electron reduction of biliverdin IXα’s two vinyl groups to produce phycocyanobilin, an essential chromophore for phytochromes, cyanobacteriochromes and phycobiliproteins. Previous site directed mutagenesis studies indicated that the fully conserved residue His74 plays a critical role in the H-bonding network that permits proton transfer. Here, we exploit X-ray crystallography, enzymology and molecular dynamics simulations to understand the functional role of this invariant histidine. The structures of the H74A, H74E and H74Q variants of PcyA reveal that a “conserved” buried water molecule that bridges His74 and catalytically essential His88 is not required for activity. Despite distinct conformations of Glu74 and Gln74 in the H74E and H74Q variants, both retain reasonable activity while the H74A variant is inactive, suggesting smaller residues may generate cavities that increase flexibility, thereby reducing enzymatic activity. Molecular dynamic simulations further reveal that the crucial active site residue Asp105 is more dynamic in H74A compared to wild-type PcyA and the two other His74 variants, supporting the conclusion that the Ala74 mutation has increased the flexibility of the active site.     

The effects of endothelial lipase gene (LIPG) variants on inflammation marker levels and atherosclerosis development

Atherosclerosis is a major pathological process related with several important adverse vascular events including coronary artery disease, stroke, and peripheral arterial disease. Endothelial lipase is an enzyme the activity of which affects all of lipoproteins, whereas HDL is the main substrate. The purpose of our study was to investigate the effects of endothelial lipase gene polymorphism and inflammation markers (CRP, IL-1β, IL-6, IL-8 and TNF-α) in the atherosclerosis. 104 patients with atherosclerosis and 76 healthy individuals were included in the study. LIPG ?584C/T polymorphism gene polymorphisms were assessed with PCR–RFLP method. The serum CRP levels were measured by turbidimetric method using a biochemistry autoanalyzer, whereas serum IL-1β, IL-6, IL-8, TNF-α levels were determined by enzyme-linked immunosorbent assay. In this study, we found that the frequencies of TC genotype are more prevalent in patients than controls. We found a statistically significant difference of IL-6 levels between patient and control group. Our findings suggest that T allele might play a potential role in the susceptibility to atherogenesis in the Turkish population.     

Vibrotactile thresholds of the Non-Pacinian I channel: II. Predicting the effects of contactor location on the phalanx

The firing-rate-based population model for rapidly-adapting (RA) mechanoreceptive fibers by Güçlü and Bolanowski (Güçlü B, Bolanowski SJ. 2002. Modeling population responses of rapidly-adapting mechanoreceptive fibers. Journal of Computational Neuroscience 12:201–218.) is extended by including temporal-response properties of RA fibers. This representation allows for the generation of action-potential (spike) times for each fiber when a sinusoidal, steady-state stimulus is applied onto the skin. Signal detection theory was used to predict human psychophysical thresholds. Specifically, the effects of sensorineural innervation pattern, stimulus-contactor location and selected decision rules on the model predictions were studied. The predicted thresholds were lowest when the decision rule was one spike and highest when many active fibers were required for detection. These predictions were empirically tested by measuring vibrotactile thresholds of the Non-Pacinian I (NP I) channel, which required the special techniques discussed in the preceding article. Although the model predicted thresholds to decrease distally due to the known innervation density which is higher distally, the thresholds of the NP I psychophysical channel were found to be approximately constant (20–25?dB re 1?µm peak amplitude) from the proximal site on the terminal phalanx to the most distal portion. Interestingly, the mechanical impedance of the skin was found not to be constant along the proximo-distal axis. This latter result implies that the space-invariant mechanical attenuation function used in the model may not be valid at every location on the fingertip. Because of this, the discrepancy between the model's predictions and the psychophysical results may be reconciled.