Coronary heart disease (CHD)2 is one of the prime causes of an increase in the mortality rate worldwide. Over the past few years, various epidemiological studies have provided ample evidence that increased levels of HDL, by transporting cholesterol from atherosclerotic plaques to liver for excretion, can arrest the progression of CHD (1, 2). Subsequent preclinical studies on overexpression of apolipoprotein A-I (apoA-I), the major protein constituent of HDL, have reported significant reduction in CHD risk (3, 4). Although raising HDL levels is a longstanding strategy for mitigating CHD risk, the current lipidtargeted therapies, including the usage of statins, fibrates, and niacin, have shown reduced therapeutic potential (5-7). Hence, there is a continuous requirement for new strategies that can elevate HDL levels to halt the progression of CHD.Cholesteryl ester transfer protein (CETP), a plasma glycoprotein with 476 residues, has been found to mediate the transfer of cholesteryl esters (CEs) from HDL to LDL and VLDL as well as the reciprocal transfer of triglycerides (TGs) from LDL and VLDL to HDL (8, 9). The identification of deficient CETP gene levels and correlated high HDL levels in a Japanese population (10 -13) brought CETP into focus as a therapeutic target for controlling HDL levels. Preclinical animal model studies have further substantiated these findings by showing an elevated level of HDL in mice with non-expressing CETP (14 -16). Since then, the inhibition of CETP activity by small molecule inhibitors has been pursued as an active approach to prevent atherosclerosis with varying levels of success at clinical trial phases (17)(18)(19)(20). Given the complexity of lipid metabolism and the pivotal role of CETP in the process, understanding CETP structure, CETP inhibition, and the mechanism by which CETP transfers neutral lipids is of prime importance. The last decade, therefore, has seen the employment of sophisticated techniques, like cryo-EM (21, 22), x-ray (23, 24), and MD simulations (25-28) on this front. Nevertheless, the story of CETP remains far from complete.The crystal structure of CETP (Protein Data Bank entry 2OBD) has been solved with four bound lipid molecules (23). The structure shows two ␤-barrel domains at the N and C termini, each with a twisted ␤-sheet and a long ␣-helix; a central ␤-sheet between the two ␤-barrels; a C-terminal ␣-helix; and a 60-Å-long hydrophobic tunnel occupied by two CE molecules. Additionally, there were two plug-in dioleoylphosphatidylcholine molecules with polar headgroups exposed to plasma and acyl chains buried in the hydrophobic tunnel of CETP. Interestingly, one of the CEs in the hydrophobic tunnel was in the bent conformation, whereas the second CE molecule was in the linear conformation. Recent cryopositive staining EM and optimized negative-staining electron microscopy (OpNS-EM) protocols combined with CETP C terminus-specific polyclonal antibody studies have suggested that CETP penetrates its C-terminal ␤-barrel domain into LDL or VLDL and its N-termi...

Cholesteryl ester transfer protein (CETP) facilitates the transfer of cholesteryl esters (CEs) from antiatherogenic high-density lipoproteins to proatherogenic low-density lipoproteins. Inhibition of CETP is therefore being pursued as a potential strategy to reduce cardiovascular risk. The crystal structure of CETP has revealed the existence of two neutral CEs and two charged phospholipids (PLs) in its hydrophobic tunnel. This is in direct contrast to the other lipid-binding proteins that contain only two bound lipids. Moreover, previous animal studies on mice showed no detectable PL-transfer activity of CETP. Thus, the role of bound PLs in CETP is completely unknown. Here, we employ molecular dynamics simulations and free-energy calculations to unravel the primary effects of bound PLs on CETP structure and dynamics and attempt to correlate the observed changes to its function. Our results suggest that the structure of CETP is elastic and can attain different conformations depending on the state of bound PLs. In solution, these PLs maintain CETP in a bent-untwisted conformation that can uphold neutral lipids in its core tunnel. Results also suggest that although both PLs complement each other in their action, the C-terminal PL (C-PL) imparts greater influence on CETP by virtue of its tighter binding. Our finding fits very well with the recent inhibitor-bound CETP crystal structure, where the inhibitor displaced the N-terminal PL for binding to CETP's central domain without disrupting the binding of C-PL. We speculate that the observed increased flexibility of CETP in the absence of PLs could play a crucial role in its binding with lipoproteins and subsequent lipid-transfer activity.

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Rapid spread of ZIKA virus (ZIKV) and its association with severe birth defects have raised worldwide concern. Recent studies have shown that ZIKV retains its infectivity and remains structurally stable at temperatures up to 40 °C, unlike dengue and other flaviviruses. In spite of recent cryo-EM structures that showed similar architecture of ZIKA and dengue virus (DENV) E protein shells, little is known that makes ZIKV so temperature insensitive. Here, we attempt to unravel the molecular basis of greater thermal stability of ZIKV over DENV2 by executing atomistic molecular dynamics (MD) simulations on the viral E protein shells at 37 °C. Our results suggest that ZIKA E protein shell retains its structural integrity through stronger inter-raft communications facilitated by a series of electrostatic and H-bonding interactions among multiple inter-raft residues. In comparison, the DENV2 E protein shell surface was loosly packed that exhibited holes at all 3-fold vertices, in close agreement with another EM structure solved at 37 °C. The residue-level information obtained from our study could pave way for designing small molecule inhibitors and specific antibodies to inhibit ZIKV E protein assembly and membrane fusion.

: Nipah virus (NiV) is a zoonotic virus of the paramyxovirus family that sporadically breaks out from livestock and spread in human through breathing resulting in indication of encephalitis syndrome. In the current study, T cell epitopes with the NiV W protein antigens were predicted. Modelling of unavailable 3D structure of W protein followed by docking studies of respective Human MHC - class I and MHC - class II alleles predicted was carried out for the highest binding rates. In the computational analysis, epitopes were assessed for immunogenicity, conservation, and toxicity analysis. T – cell based vaccine development against NiV was screened for eight epitopes of Indian - Asian origin. Two epitopes SPVIAEHYY, LVNDGLNII, have been screened and selected for further docking study based on toxicity and conservancy analyses. These epitopes showed a significant score of -1.19 kcal/mol, 0.15 kcal/mol with HLA- B*35:03, HLA- DRB1 * 07:03, allele - Class I and Class II using AutoDock. These two peptides predicted by reverse vaccinology approach are likely to induce immune response mediated by T – cells. Simulation using GROMACS has revealed LVNDGLNII epitope forms more stable complex with HLA molecule and will be useful in developing epitope-based Nipah virus vaccine.