Biology subjects

Khan, T.

Publications and source records attributed to Khan, T..

4 recordsLinked to original sources

bioRxiv2017

ProLego: tool for extracting and visualizing topological modules in protein structures

BackgroundIn protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intuitive and efficient way to scan the protein topology space.\n\nResultWe have implemented in-house developed \"topological representation\" in an automated-pipeline to extract protein topology from given protein structure. Using the topology string, ProLego, compares topology against a non-redundant extensive topology database (ProLegoDB) as well as extracts constituent topological modules. The platform offers interactive topology visualization graphs.\n\nConclusionProLego, provides an alternative but comprehensive way to scan and visualize protein topology along with an extensive database of protein topology.\n\nProLego can be found at http://www.proteinlego.com

bioinformatics↗

bioRxiv2017

Quinary structure kinetically controls protein function and dysfunction

Protein self-assemblies modulate protein activities over biological time scales that can exceed the lifetimes of the proteins or even the cells that harbor them. We hypothesized that these time scales relate to kinetic barriers inherent to the nucleation of ordered phases. To investigate nucleation barriers in living cells, we developed Distributed Amphifluoric FRET (DAmFRET). DAmFRET exploits a photoconvertible fluorophore, heterogeneous expression, and large cell numbers to quantify via flow cytometry the extent of a proteins self-assembly as a function of cellular concentration. We show that kinetic barriers limit the nucleation of ordered self-assemblies, and that the persistence of the barriers with respect to concentration relates to structure. Supersaturation resulting from sequence-encoded nucleation barriers gave rise to prion behavior, and enabled a prion-forming protein, Sup35 PrD, to partition into dynamic intracellular condensates or to form toxic aggregates. Our results suggest that nucleation barriers govern cytoplasmic inheritance, subcellular organization, and proteotoxicity.\n\nHighlightsO_LIDistributed Amphifluoric FRET (DAmFRET) quantifies nucleation in living cells\nC_LIO_LIDAmFRET rapidly distinguishes prion-like from non-prion phase transitions\nC_LIO_LINucleation barriers allow switch-like temporal control of protein activity\nC_LIO_LISequence-intrinsic features determine the concentration-dependence of nucleation barriers\nC_LI

biophysics↗

bioRxiv2017

Indoril: An I-PV Add-On For Visualization Of Point Mutations On 3D Cartesian Coordinates

SummaryOne of the main goals of proteomics is to understand how point mutations impact on the protein structure. Visualization and clustering of point mutations on user-defined 3 dimensional space can allow researchers to have new insights and hypothesis about the mutations mechanism of action.\n\nAvailability and ImplementationWe have developed an interactive I-PV add-on called INDORIL to visualize point mutations. Indoril can be downloaded from http://www.i-pv.org.\n\nContactibrahim.tanyalcin@i-pv.org [boxV] support@i-pv.org\n\nSupplementary InformationPlease refer to the supplementary section and http://www.i-pv.org.

bioinformatics↗

bioRxiv2017

Assessing the causal role of body mass index on cardiovascular health in young adults: Mendelian randomization and recall-by-genotype analyses

BackgroundMendelian randomization (MR) studies of body mass index (BMI) and cardiovascular health in mid-to-late life suggest causal relationships, but the nature of these has not been explored systematically at younger ages. Using complementary MR and recall-by-genotype (RbG) methodologies, our objective was to estimate the causal effect of BMI on detailed measures of cardiovascular health in a population of young healthy adults.\n\nMethods and FindingsData from the Avon Longitudinal Study of Parents and Children were used. For MR analyses, a genetic risk score (GRS) comprising 97 independent single nucleotide polymorphisms (SNPs) and constructed using external weighting was used as an instrument to test the causal effect of each unit increase in BMI (kg/m2) on selected cardiovascular phenotypes measured at age 17 (N=7909). An independent enriched sample from the same cohort participated in a RbG study at age 21, which enabled more detailed cardiovascular phenotyping (N=418; 191/227 from the lower/upper [~]30% of a genome-wide GRS distribution predicting variation in BMI). The causal effect of BMI on the additional cardiovascular phenotypes was assessed by comparing the two recalled groups. Difference in mean BMI between RbG groups was 3.85kg/m2 (95% CI: 2.53, 4.63; P=6.09x1011). In both MR and RbG analyses, results indicated that higher BMI causes higher blood pressure (BP) and left ventricular mass (indexed to height2.7, LVMI) in young adults (e.g. difference in LVMI per kg/m2 using MR: 1.07g/m2.7; 95% CI: 0.62, 1.52; P=3.87x10-06 and per 3.58kg/m2 using RbG: 1.65g/m2.7 95% CI: 0.83, 2.47; P=0.0001). Additionally, RbG results indicated a causal role of higher BMI on higher stroke volume (SV; difference per 3.58kg/m2: 1.49ml/m2.04; 95% CI: 0.62, 2.35; P=0.001) and cardiac output (CO; difference per 3.58kg/m2: 0.11l /min/m1.83; 95% CI: 0.03, 0.19; P=0.01). Neither analysis supported a causal role of higher BMI on heart rate.\n\nConclusionsComplementary MR and RbG causal methodologies, together with a range of appropriate sensitivity analyses, showed that higher BMI is likely to cause worse cardiovascular health, specifically higher BP and LVMI, even in youth. These consistent results support efforts to prevent or reverse obesity in the young.

epidemiology↗