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Shiv Nadar University

(SoNS) School of Natural Sciences

The cellular membranes are composed of hundreds of components such as lipids, proteins, and sterols that are chemically and physically distinct from each other. The lipid–lipid and lipid–protein interactions form domains in this membrane, which play vital roles in membrane physiology. The hybrid lipids (HLs) with one saturated and one unsaturated chain can control the shape and size of these domains, ensuring the thermodynamic stability of a membrane. In this study, the thermodynamics of mixing of a HL and its structural effects on the phase separated domains in a model membrane composed of a saturated and an unsaturated lipid have been investigated. The HL is observed to mix into an unsaturated lipid reducing the Gibbs free energy, whereas the mixing is unfavorable in a saturated lipid. The presence of an HL in an unsaturated lipid tends to increase its area fraction, which is reflected in the enhanced correlation length across the bilayers in a multilayered sample. There is a feeble effect on the domain structure of the saturated lipid due to the presence of the HLs at the phase boundary. This study concludes that the HLs preferentially participate in the unsaturated lipid regions compared to that of a saturated lipid. © 2021 The Authors. Published by American Chemical Society

World University root node

Physics

ACS Omega

Partitioning of a Hybrid Lipid in Domains of Saturated and Unsaturated Lipids in a Model Cellular Membrane

The Bures distance holds a special place among various distance measures due to its several distinguishing features and has applications in diverse problems in quantum information theory. It is related to fidelity, and among other things, it serves as a bona fide measure for quantifying the separability of quantum states. In this work, we calculate exact analytical results for the mean root fidelity and mean-square Bures distance between a fixed density matrix and a random density matrix and also between two random density matrices. In the course of derivation, we also obtain the spectral density for the product of the above pairs of density matrices. We corroborate our analytical results using Monte Carlo simulations. Moreover, we compare these results with the mean-square Bures distance between reduced density matrices generated using coupled kicked tops and find very good agreement. © 2021 American Physical Society.

Physical Review A

Random density matrices: Analytical results for mean root fidelity and the mean-square Bures distance

In this paper, we prove an extension of the Helson–Lowdenslager theorem for L2(T) for sub - Hilbert spaces under certain axioms. Furthermore, we provide an alternate proof of characterization of shift invariant sub-Hilbert spaces contained in H2(D) satisfying similar axioms. © 2021, Tusi Mathematical Research Group (TMRG).

Mathematics

Advances in Operator Theory

On extension of Beurling–Helson–Lowdenslager theorem

A uni-molecular layer of lipids at air-water interface mimicking one of the leaflets of the cellular membrane provides a simple model to understand the interaction of any foreign molecules with the membrane. Here, the interactions of protein Kalata B1 (KB1) of cyclotide family with the phospholipids 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol) sodium salt (DPPG), and 1,2-distearoyl-sn-glycero-3-ethylphosphocholine chloride salt (DSEPC) have been investigated. The addition of KB1 induces a change in pressure of the lipid monolayers. The characteristic time of the change in pressure is found to be dependent on the electrostatic nature of the lipid. Even though the protein is weakly surface active, it is capable of modifying the phase behavior and elastic properties of lipid monolayers with differences in their strength and nature making the layers more floppy. The KB1-lipid interaction has been quantified by calculating the excess Gibb's free energy of interaction and the 1-anilino-8-naphthalenesulfonate (ANS) binding studies. The interaction with zwitterionic DPPC and negatively charged DPPG lipids are found to be thermodynamically favorable whereas the protein shows a weaker response to positively charged DSEPC lipid. Therefore, the long ranged electrostatic is the initial driving force for the KB1 to recognize and subsequently attach to a cellular membrane. Thereafter, the hydrophobic region of the protein may penetrate into the hydrophobic core of the membrane via specific amino acid residues. © 2021 Elsevier B.V.

International Journal of Biological Macromolecules

Interaction of cyclotide Kalata B1 protein with model cellular membranes of varied electrostatics

CD4-mimetic HIV-1 entry inhibitors are small sized molecules which imitate similar conformational flexibility, in gp120, to the CD4 receptor. However, the mechanism of the conformational flexibility instigated by these small sized inhibitors is little known. Likewise, the effect of the antibody on the function of these inhibitors is also less studied. In this study, we present a thorough inspection of the mechanism of the conformational flexibility induced by a CD4-mimetic inhibitor, NBD-557, using Molecular Dynamics Simulations and free energy calculations. Our result shows the functional importance of Asn425 in substrate induced conformational dynamics in gp120. The MD simulations of Asn425Gly mutant provide a less dynamic gp120 in the presence of NBD-557 without incapacitating the binding enthalpy of NBD-557. The MD simulations of complexes with the antibody clearly show the enhanced affinity of NBD-557 due to the presence of the antibody, which is in good agreement with experimental Isothermal Titration Calorimetry results (Biochemistry2006, 45, 10973-10980).

Chemical Engineering

(SoE) School of Engineering

Chemistry

Fulltext

Molecules (Basel, Switzerland)

Does Antibody Stabilize the Ligand Binding in GP120 of HIV-1 Envelope Protein? Evidence from MD Simulation

Graphene-based nano-technology is the future of biomedical devices including biosensors and, hence, it is essential to unravel the interaction of graphene oxide (GO) with cellular membrane. Here, the structural reorganization of lipid molecules, which are the building blocks of a cellular membrane, has been demonstrated in presence of GO flakes. The membrane is mimicked by forming a stack of lipid bilayers of zwitterionic phospholipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and its structures have been probed by X-ray reflectivity and grazing incidence X-ray diffraction techniques. Lipid-GO composites have exhibited two sets of lamellar diffraction peaks illustrating GO-rich micro-domains in the matrix of phospholipid bilayers (GO-poor phase). In these domains, the GO flakes are observed to penetrate into hydrophobic core of the bilayer altering the thickness along with the overall electron density profile of the lipid layer. The GO-poor bilayer is closely related to the phase formed by pristine lipid molecules. The lattice parameters of a body-centred rectangular unit cell formed by chains of saturated phospholipids are found to be modified in presence of GO with a significant effect on molecular tilt. The structural description of GO-membrane interaction may pave the way of discerning the physical behaviour of the composites. © 2020 Elsevier B.V.

Applied Surface Science

Unravelling the structural changes of phospholipid membranes in presence of graphene oxide

The Jacobi ensemble is one of the classical ensembles of random matrix theory. Prominent in applications are properties of the eigenvalues at the spectrum edge, specifically the distribution of the largest (e.g. Roy’s largest root test in multivariate statistics) and smallest (e.g. condition numbers of linear systems) eigenvalues. We identify three ranges of parameter values for which the gap probability determining these distributions is a finite sum with respect to particular bases, and moreover make use of a certain differential–difference system fundamental in the theory of the Selberg integral to provide a recursive scheme to compute the corresponding coefficients. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.

Ramanujan Journal

Computable structural formulas for the distribution of the β -Jacobi edge eigenvalues

Ionospheric response during the annular solar eclipse of June 21, 2020, has been examined in terms of the Total Electron Content (TEC) obtained from six Global Positioning System (GPS) receivers positioned in the Chinese-Taiwanese region. We have shown TEC variation from satellites designated by PRNs (Pseudo-Random Noise code) 2, 6, and 19. PRN wise TEC trend was observed to depend upon satellite-pass trajectory to the receiver's location during the eclipse period. A time lag of ~15–30 min is also observed in maximum TEC decrement after the phase of maximum eclipse. Instead of the percentage of eclipse magnitude, a reduction in TEC is seen more for the station for which the orbital track of respective satellites was in closer view relative to receivers for more hours of eclipse window. Additionally, the eclipse day diurnal variations are compared with the pre-eclipse day TEC trend, and observed results show a clear decrease in TEC values at all chosen stations after the eclipse onset then reached the lowest value a few minutes afterward the maximum eclipse phase. © 2021 COSPAR

Life Sciences

Advances in Space Research

A study on TEC reduction during the tail phase of the 21st June 2020 annular solar eclipse

In the present study, various solar and atmospheric parameters, namely solar radiation, surface ozone, relative humidity, air temperature, and wind speed, have been studied first time for the annular solar eclipse of June 21, 2020, at seven Indian stations simultaneously. All the seven different stations are selected along the solar eclipse path having the maximum eclipse magnitude of 92% and above. The various atmospheric parameters have shown the change in behavior during the solar eclipse duration. The incoming solar radiation has a maximum 95.97% decrease at Ludhiana at the time of maximum obscuration compared to the previous day. The surface ozone concentration has shown a decrease for all the seven stations during the maximum obscuration period. A maximum of 9.25% decrease in surface temperature has been observed nearly after 30 min of the time of maximum obscuration of the eclipse. Relative humidity started increasing at all the stations and showed an inverse trend from temperature. The wind speed was found to suppress during the maximum solar eclipse which may be attributed to stabilization of atmospheric boundary layer due to cooling. © 2021, Indian Association for the Cultivation of Science.

Indian Journal of Physics

Changes in atmospheric parameters due to annular solar eclipse of June 21, 2020, over India

One of the major barriers in the prevention and control of malaria programs worldwide is the growing emergence of multidrug resistance in Plasmodium parasites, and this necessitates continued efforts to discover and develop effective drug molecules targeting novel proteins essential for parasite survival. In recent years, epigenetic regulators have evolved as an attractive drug target option owing to their crucial role in survival and development of Plasmodium at different stages of its life cycle. PfMYST, a histone acetyltransferase protein, is known to regulate key cellular processes, such as cell cycle progression, DNA damage repair, and antigenic variation, that facilitate parasite growth, adaptation, and survival inside its host. With the aim of assessing the therapeutic potential of PfMYST as a novel drug target, we examined the effect of NU9056 (an HsTIP60 inhibitor) on the rate of parasite growth and survival. In the present study, by using a yeast complementation assay, we established that PfMYST is a true homolog of TIP60 and showed that NU9056 can inhibit PfMYST catalytic activity and kill P. falciparum parasites in culture. Inhibiting the catalytic activity of PfMYST arrests the parasite in the trophozoite stage and inhibits its further transition to the schizont stage, eventually leading to its death. Overall, our study provides proof of concept that PfMYST catalytic activity is essential for parasite growth and survival and that PfMYST can be a potential target for antimalarial therapy. © 2020 American Society for Microbiology. All Rights Reserved.