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Protein Research

15:57 EST 20th January 2019 | BioPortfolio

The Muscle Protein Synthetic Response to Meal Ingestion Following Resistance-Type Exercise.

Protein ingestion following resistance-type exercise stimulates muscle protein synthesis rates and consequently enhances the skeletal muscle adaptive response to prolonged training. Ingestion of ~ 20 g of quickly digestible protein isolate optimizes muscle protein synthesis rates during the first few hours of post-exercise recovery. However, the majority of daily protein intake is consumed as...

A journey through the cytoskeleton with protein kinase CK2.

Substrate pleiotropicity, a very acidic phosphorylation consensus sequence, and an apparent uncontrolled activity, are the main features of CK2, a Ser/Thr protein kinase that is required for a plethora of cell functions. Not surprisingly, CK2 appears to affect cytoskeletal structures and correlated functions such as cell shape, mechanical integrity, cell movement and division. This review outlines...

Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO).

We developed a computational approach called Domain-architecture Aware Inference of Orthologs (DAIO) for the analysis of protein orthology by combining phylogenetic and protein domain-architecture information. Using DAIO, we performed a systematic study of the proteomes of all human Herpesviridae species to define Strict Ortholog Groups (SOGs). In addition to assessing the taxonomic distribution f...

Crowder induced structural modulation of a multi-domain protein during its early stages of aggregation: A FRET-based and protein solvation study.

Protein aggregation has been known for long to be the prime cause for several neurological disorders in human beings. While protein aggregation is itself a complex process, understanding the same in the context of a crowded cellular medium remains a challenge. In this work, using Förster resonance energy transfer (FRET) and solvation dynamics, we have tried to gain important insights into the str...

Protein contact dermatitis by flours in a pastry chef.

Protein contact dermatitis is a chronic, recurring dermatitis triggered by type I hypersensitivity to protein allergen . We report a case caused by flours in a pastry chef. This article is protected by copyright. All rights reserved.

A novel core-attachment based method to identify dynamic protein complexes based on gene expression profiles and PPI Networks.

Cellular functions are always performed by protein complexes. At present, many approaches have been proposed to identify protein complexes from protein-protein interaction (PPI) networks. Some approaches focus on detecting local dense sub-graphs in PPI networks which are regarded as protein complex cores, then identify protein complexes by including local neighbors. However, from gene expression p...

Molecular Sieving on the Surface of a Nano-Armored Protein.

The molecular sieving properties of protein surface-attached polymers are the central features in how polymers extend therapeutic protein lifetimes in vivo. Yet, even after thirty years of research, permeation rates of molecules through polymer-surrounded protein surfaces are largely unknown. As a result, the generation of protein-polymer conjugates remains a stochastic process, unfacilitated by k...

Significance of protein-substrate hydrogen bonding for the selectivity of P450 catalysed oxidations.

P450cin and P450cam are bacterial P450s that specifically hydroxylate bicyclic monoterpenes. Protein-substrate H-bonding has been previously proposed as crucial in the selectivity of P450cin oxidation, but not as essential for P450cam. To examine the difference in importance of H-bonds in these two model P450s, the P450-catalysed oxidation products from thiocamphor were compared. Surprisingly, bot...

Pathobiological role of cleft palate transmembrane protein 1 family proteins in oral squamous cell carcinoma.

Cleft palate transmembrane protein 1 (Clptm1) and its paralog protein, Cisplatin resistance-related protein 9 (CRR9) constitute a highly conserved protein family, from Caenorhabditis elegans to Homo sapiens. In the present study, we examined the clinicopathological and biological significance of Clptm1 and CRR9 expression in oral squamous cell carcinoma (OSCC).

Evaluating the evolution and function of the dynamic Venom Y protein in ectoparasitoid wasps.

Venom of the parasitoid wasp Nasonia vitripennis changes the metabolism and gene expression in its fly host Sarcophaga bullata to induce developmental arrest, suppression of the immune response, and various other venom effects. Yet, the venom of ectoparasitoid wasps has not been fully characterized. A major component of N. vitripennis venom is an uncharacterized, high-expressing protein referred t...

Small Noncoding 4.5SH and 4.5SI RNAs and Their Binding to Proteins.

The functions of small noncoding RNAs 4.5SH and 4.5SI found in murine-like rodents are unclear. These RNAs synthesized by RNA polymerase III are widely expressed in rodent organs and tissues. Using crosslinking assays, it was shown that approximately half of all 4.5SI and 4.5SH RNA molecules were bound to proteins provisionally called X and Y, respectively. An immunoprecipitation experiment showed...

Structure of Potato Virus A Coat Protein Particles and Their Dissociation.

This paper reports on a complex structural analysis of the potato virus A coat protein using a set of complementary physico-chemical methods. We have demonstrated previously that this protein does not exist as individual subunits in solution and undergoes association into oligomers with subsequent transition to β-conformation. The purpose of the present work was to study the possible mechanisms o...

Integrative data fusion for comprehensive assessment of a novel CHEK2 variant using combined genomics, imaging, and functional-structural assessments via protein informatics.

The CHEK2 gene and its encoded protein Chk2 have a well-known role in cancers, especially those related to breast cancer mediated through the BRCA1 gene. Additionally Chk2 has a crucial role in DNA repair, apoptosis and the cell cycle, which is why classification of variants of uncertain significance (VUS) is an area highly sought for a better elucidation of the "genomic effect" that results. Beca...

The role of conformational flexibility in Monte Carlo simulations of many-protein systems.

Efficient computational modeling of biological systems characterized by high concentrations of macromolecules often relies on rigid-body Brownian Dynamics or Monte Carlo (MC) simulations. However, the accuracy of rigid-body models is limited by the fixed conformation of the simulated biomolecules. Multi-conformation Monte Carlo (mcMC) simulations of protein solutions incorporate conformational fle...

Coarse-grained molecular dynamics study of wettability influence on protein translocation through solid nanopores.

Protein translocation through nanopores is widely involved in molecular sensing and analyzing devices, whereby nanopore surface properties are crucial. However, fundamental understanding of how these properties affect protein motion inside nanopores remains lacking. In this work, we study the influence of nanopore surface wettability on voltage-driven protein translocation through nanopores with c...

The Initial Dietary Pattern Should Be Considered when Changing Protein Food Portion Sizes to Increase Nutrient Adequacy in French Adults.

Patterns of protein food intake are undergoing a transition in Western countries, but little is known about how dietary changes to protein intake affect nutrient adequacy of the diet.

Palmitoylation of Claudin-5 Proteins Influences Their Lipid Domain Affinity and Tight Junctions Assembly at the Blood-Brain Barrier Interface.

Post-translational lipid modification of integral membrane proteins is recognized as a key mechanism to modulate protein-protein and membrane-protein associations. Despite numerous reports of lipid-modified proteins, molecular-level understanding of the influence of lipid-modification of key membrane proteins remains elusive. This study focuses on the lipid modification of one such protein-claudin...

CavVis - A field-of-view geometric algorithm for protein cavity detection.

Several geometric-based methods have been developed for the last two to three decades to detect and identify cavities (i.e., putative binding sites) on proteins, as needed to study protein-ligand interactions and protein docking. This paper introduces a new protein cavity method, called CavVis, which combines voxelization (i.e., a grid of voxels) and an analytic formulation of Gaussian surfaces th...

Exploring ligand-protein interaction: A laboratory exercise on herbicide binding to plasma transport protein.

A laboratory exercise on the interaction between the herbicide pendimethalin (PM) and goat serum albumin (GSA), a carrier protein present in mammalian blood circulation, is described. Fluorescence spectroscopy was used to study the binding reaction between PM and GSA. Titration of a constant amount of the protein (GSA) with increasing ligand (PM) concentrations produced a consecutive decrease in t...

Identification of evolutionary conserved DNA sequence and corresponding S21 ribosomal protein region for diagnostic purposes of all Borrelia spirochetes.

It is still under investigation, whether all Borrelia sp. causing Lyme borreliosis and other diseases are already identified and properly classified as human pathogens. For this reason, it is of great importance to develop a diagnostic ELISA test that detects all Borrelia sp. The aim of this study was to identify conserved DNA and protein regions present in all currently known Borrelia sp. In expe...

transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein-protein interaction.

Several freely available tools perform analysis using algorithms developed to identify significant variation of gene expression individually. The transcriptogramer R package uses protein-protein interaction to perform differential expression of functionally associated genes. The software assesses expression profile of entire genetic systems and reveals which biological systems are significantly al...

Protein modeling, molecular network and molecular dynamics study of newly sequenced interleukin-18 (IL-18) gene in Mus musculus.

Interleukin-18 (IL-18) belongs to the superfamily of IL-1 protein and exerts a pleiotropic pro-inflammatory effect on the body. Generally, this protein is significantly involved in immune defense during infection in cells, but sometimes its anomalous activities produce some inflammatory diseases like rheumatoid arthritis and Crohn's disease. In the present study, the IL-18 gene was isolated from m...

Improving Coarse-Grained Protein Force Fields with Small-Angle X-Ray Scattering Data.

Small-angle X-ray scattering (SAXS) experiments provide valuable structural data for biomolecules in solution. We develop a highly efficient maximum entropy approach to fit SAXS data by introducing minimal biases to a coarse-grained protein force field, the associative memory, water mediated, structure and energy model (AWSEM). We demonstrate that the resulting force field, AWSEM-SAXS, succeeds in...

Protein-protein binding supersites.

The lack of a deep understanding of how proteins interact remains an important roadblock in advancing efforts to identify binding partners and uncover the corresponding regulatory mechanisms of the functions they mediate. Understanding protein-protein interactions is also essential for designing specific chemical modifications to develop new reagents and therapeutics. We explored the hypothesis of...

The Vaccinia virion: Filling the gap between atomic and ultrastructure.

We have investigated the molecular-level structure of the Vaccinia virion in situ by protein-protein chemical crosslinking, identifying 4609 unique-mass crosslink ions at an effective FDR of 0.33%, covering 2534 unique pairs of crosslinked protein positions, 625 of which were inter-protein. The data were statistically non-random and rational in the context of known structures, and showed biologica...

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