Shiv Nadar University

About: Shiv Nadar University is a education organization based out in Dadri, Uttar Pradesh, India. It is known for research contribution in the topics: Population & Graphene. The organization has 1015 authors who have published 1924 publications receiving 18420 citations.

Identification of Glucose-Binding Pockets in Human Serum Albumin Using Support Vector Machine and Molecular Dynamics Simulations

Abstract: Human Serum Albumin (HSA) has been suggested to be an alternate biomarker to the existing Hemoglobin-A1c (HbA1c) marker for glycemic monitoring. Development and usage of HSA as an alternate biomarker requires the identification of glycation sites, or equivalently, glucose-binding pockets. In this work, we combine molecular dynamics simulations of HSA and the state-of-art machine learning method Support Vector Machine (SVM) to predict glucose-binding pockets in HSA. SVM uses the three dimensional arrangement of atoms and their chemical properties to predict glucose-binding ability of a pocket. Feature selection reveals that the arrangement of atoms and their chemical properties within the first 4A from the centroid of the pocket play an important role in the binding of glucose. With a 10-fold cross validation accuracy of 84 percent, our SVM model reveals seven new potential glucose-binding sites in HSA of which two are exposed only during the dynamics of HSA. The predictions are further corroborated using docking studies. These findings can complement studies directed towards the development of HSA as an alternate biomarker for glycemic monitoring.

Cytosolic aggregates in presence of non-translocated proteins perturb endoplasmic reticulum structure and dynamics.

Abstract: Presence of cytosolic protein aggregates and membrane damage are two common attributes of neurodegenerative diseases. These aggregates delay degradation of non-translocated protein precursors leading to their persistence and accumulation in the cytosol. Here, we find that cells with intracellular protein aggregates (of cytosolic prion protein or huntingtin) destabilize the endoplasmic reticulum (ER) morphology and dynamics when non-translocated protein load is high. This affects trafficking of proteins out from the ER, relative distribution of the rough and smooth ER and three-way junctions that are essential for the structural integrity of the membrane network. The changes in ER membranes may be due to high aggregation tendency of the ER structural proteins-reticulons, and altered distribution of those associated with the three-way ER junctions-Lunapark. Reticulon4 is seen to be enriched in the aggregate fractions in presence of non-translocated protein precursors. This could be mitigated by improving signal sequence efficiencies of the proteins targeted to the ER. These were observed using PrP variants and the seven-pass transmembrane protein (CRFR1) with different signal sequences that led to diverse translocation efficiencies. This identifies a previously unappreciated consequence of cytosolic aggregates on non-translocated precursor proteins-their persistent presence affects ER morphology and dynamics. This may be one of the ways in which cytosolic aggregates can affect endomembranes during neurodegenerative disease.

Trapping of Light in Nonlinear 1-D Photonic Crystal

Abstract: Theoretical studies on the group velocity of light wave in 1-D polystyrene/SiO2 nonlinear photonic crystal is investigated. The speed of light wave through these multilayered structures is calculated in the absence as well as in the presence of a high intensity controlling wave by using the transfer matrix method. This letter shows that we can trap a light wave inside the nonlinear 1-D photonic crystal by switching off the controlling wave.

Facile and Green Engineering Approach for Enhanced Corrosion Resistance of Ni-Cr-Al2O3 Thermal Spray Coatings.

Abstract: Thermal spray coatings (TSCs) are widely utilized for limiting degradation of structural components. However, the performance of TSCs is significantly impaired by its inherent non-homogeneous micro...