Arjun Ray

• Ph.D.
• Professor (Assistant) at Indraprastha Institute of Information Technology Delhi

Hydration forces exerted by water in the form of hydrogen bonding networks or electrostatic interactions play an essential role in protein structure and function. These interactions often govern chemical catalysis, ion transport, protein stability, and folding. While water's role as a biological solvent and on the protein surface is widely studied,...

CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates of on-target DNA cleavage. This study compares the dynamics of the highly specific Cas9 from Francise...

Targeted proteomics using multiple reaction monitoring (MRM) assays enables fast and sensitive detection of a preselected set of target peptides. This technique utilizes the specificity of precursors to product transitions for quantitative analysis of multiple proteins in a single sample. The success of an MRM experiment depends on the selection of...

Breast cancer (BC) is one of the most prevalent cancers in the world and is one of the major reasons for the death of women worldwide. BC is majorly categorized based on the presence or absence of three cell receptors ER, PR and HER2. The latest treatment for BC involves interfering with the production and action of hormones such as estrogen and pr...

Atherosclerosis is a major contributor to the onset and progression of cardiovascular disease (CVD). Cholesterol-loaded foam cells play a pivotal role in forming atherosclerotic plaques. Induction of cholesterol efflux from these cells may be a promising approach in treating CVD. The reverse cholesterol transport (RCT) pathway delivers cholesteryl...

The triple helix structure at the 3′ end of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long non-coding RNA, has been considered to be a target to modulate the oncogenic functions of MALAT1. This study examines the binding of quercetin- a known triplex binding molecule- to the MALAT1 triplex. By employing UV-visible spectrosc...

The introduction of CRISPR/Cas9 based gene editing has greatly accelerated therapeutic genome editing. However, the off-target DNA cleavage by CRISPR/Cas9 protein hampers its clinical translation, hindering its widespread use as a programmable genome editing tool. Although Cas9 variants with better mismatch discrimination have been developed, they...

India confines more than 17% of the world’s population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) containing limited samples for Indian ethnicity. Such databases are critical for the pharmaceutical an...

Targeted therapies against HER2 subtype breast cancer (BC) like Trastuzumab and Neratinib, often become futile as patients relapse with aggressive disease. Receptor switching to other HER family members in Lapatinib resistance and HER2 receptor tyrosine kinase domain mutations have been elaborated in promoting resistance. Here we studied the struct...

Lipid compositions of cells, tissues, and bio-fluids are complex, with varying concentrations and structural diversity making their identification challenging. Newer methods for comprehensive analysis of lipids are thus necessary. Herein, we propose a targeted-mass spectrometry based lipidomics screening method using a combination of variable reten...

Significance Hsp60/10 chaperonins are critical for cellular proteostasis in all kingdoms of life. In this study, we present that Hsp60/10 across different species have differences in the cavity properties and correlatively in their capability to remove entropic traps in folding pathways of GroEL/ES substrates; this is affected majorly by difference...

CRISPR/Cas system, a newly but extensively investigated genome-editing method, harbors practical solutions for various genetic problems. It relies on short guide RNAs (gRNAs) to recruit the Cas9 protein, a DNA cleaving enzyme, to its genomic target DNAs. The Cas9 enzyme exhibits some unique properties, like the ability to differentiate self vs. non...

Background Viral infections have a history of abrupt and severe eruptions through the years in the form of pandemics. And yet, definitive therapies or preventive measures are not present. Herbal medicines have been a source of various antiviral compounds such as Oseltamivir, extracted using shikimic acid from star anise ( Illicium verum ) and Acycl...

The double-membrane-bound architecture of mitochondria, essential for ATP production, sub-divides the organelle into inter-membrane space (IMS) and matrix. IMS and matrix possess contrasting oxido-reductive environments and discrete protein quality control (PQC) machineries resulting inherent differences in their protein folding environments. To un...

The introduction of CRISPR/Cas9 based gene editing has greatly accelerated therapeutic genome editing. However, the off-target DNA cleavage by CRISPR/Cas9 protein hampers its clinical translation thereby hindering its widespread use as a programmable genome editing tool. Although Cas9 variants with better mismatch discrimination have been developed...

Triglycerides (TG) are transported packaged inside lypophillic particles. Several lipid exchange/transfer proteins interact with these lipoproteins and facilitate lipid exchange amongst lipoproteins, to maintain a constant flux in RCT. During this process, these neutral lipids are inadvertently exposed to the bulk water. Previous studies have eluci...

Motivation Internal cavities in proteins are of critical functional importance. They can serve as substrate/ligand-binding sites, pave path for movement of biomolecules and even mediate structural conformations occurring between domain interfaces during structural transitions. Yet, there is a paucity of computational tools that can accurately and r...

ATP Binding Cassette Transporter A1 (ABCA1) plays an integral part in Reverse Cholesterol Transport (RCT) and is critical for maintaining lipid homeostasis. One theory of lipid efflux by the transporter (alternating access) proposes that ABCA1 harbours two different conformations that provide alternating access for lipid binding and release. This i...

Activity modulation of proteins is an essential biochemical process in cell. The interplay of the protein, as receptor, and it's corresponding ligand dictates the functional effect. It is imperative to decipher the receptor-ligand functional effect for understanding native biochemical processes as well as for drug discovery. Experimental activity d...

Bioactive fractions obtained from medicinal plants which have been used for the treatment of multiple diseases could exert their effects by targeting common pathways. Prior knowledge of their usage could allow us to identify novel molecular links. In this study, we explored the molecular basis of action of one such herbal formulation Cissampelos pa...

Long non-coding RNAs (lncRNAs) are emerging as key regulators of endothelial cell function. Here, we investigated the role of a novel vascular endothelial-associated lncRNA (VEAL2) in regulating endothelial permeability. Precise editing of veal2 loci in zebrafish (veal2gib005Δ8/+ ) induced cranial hemorrhage. In vitro and in vivo studies revealed t...

The population diversity in India contains a treasure of clinically relevant rare mutations which may have evolved differently in different subpopulations. While there are many sub-groups present in the nation, the publicly available database like the 1000 Genome data (1KG) contains limited samples for indian ethnicity. Such databases are critical...

ABCA1 plays an integral part in Reverse Cholesterol Transport (RCT) and is critical for maintaining lipid homeostasis. One theory of lipid efflux by the transporter (alternating access) proposes that ABCA1 harbors two different conformations that provide alternate access for lipid binding and release, leading to sequestration via a direct interacti...

In traditional systems, a single herbal formulation is often used in the treatment of diverse diseases, including some that are newly emergent and prevalent today. We provide here a multi-omics framework to probe the molecular basis of a multicomponent example herb, Cissampelos pareira L. (Cipa) used in the treatment of hormonal disorders and fever...

Neuroserpin (NS) is an inhibitory protein of serpin super family, its shutter region variants have high propensity to aggregate leading to pathological disorders like familial encephalopathy with NS inclusion bodies (FENIB). Helix F and β-sheet A of NS participate in the tissue plasminogen activator (tPA) inhibition but the mechanism is not yet com...

Lipids are highly diverse group of biomolecules that play a pivotal role in biological processes. Lipid compositions of bio-fluids are complex, reflecting a wide range of concentration of different lipid classes with structural diversity within lipid species. Varying degrees of chemical complexity makes their identification and quantification chall...

The epithelial cell adhesion molecule (EpCAM) is a transmembrane cell adhesion glycoprotein, which primarily contributes to stemness, proliferation, and metastasis properties of tumor cells. Regulated intramembrane proteolysis by ADAM proteases and γ-secretase cleaves EpCAM into an ∼27 kDa soluble extracellular and an ∼4 kDa cytoplasmic domain (EpI...

Internal cavities in proteins are of critical functional importance. They can serve as substrate/ligand binding sites, pave path for movement of bio-molecules and even mediate structural conformations occurring between domain interfaces during structural transitions. Yet, there is a paucity of computational tools that can accurately, and reliably c...

In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to det...

The complex double-membrane architecture of mitochondria is essential for its ATP synthesis function and divides the organelle into two sub-mitochondrial compartments, inter-membrane space (IMS) and matrix. The folding environments of IMS and matrix are significantly different owing to its dissimilar oxido-reductive environments and distinctly dive...

In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel corona virus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation is key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to det...

In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel corona virus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation is key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to det...

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) is mediated via the initial interaction of the virus’s spike (S-) protein with a human receptor protein called angiotensin-converting enzyme 2 (hACE2). Interference in this association can have immense therapeutic importance. We used an in-silico combinatorial approach involving homo...

Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off...

Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off...

In eukaryotes, Hsp110s are unambiguous cognates of the Hsp70 chaperones, in primary sequence, domain organization, and structure. Hsp110s function as nucleotide exchange factors (NEFs) for the Hsp70s although their apparent loss of Hsp70‐like chaperone activity, nature of interdomain communication, and breadth of domain functions are still puzzling...

Genome editing using the CRISPR Cas9 system has been used to manipulate eukaryotic DNA and make precise heritable changes. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain, regarding their putat...

An increased level of homocysteine, a reactive thiol amino acid, is associated with several complex disorders and is an independent risk factor for cardiovascular disease. A majority (>80%) of circulating homocysteine is protein bound. Homocysteine exclusively binds to protein cysteine residues via thiol disulfide exchange reaction, the mechanism o...

Proteins typically adopt a multitude of flexible and rapidly interconverting conformers, many of which are governed by specific protein interaction domains. While disc-shaped oligomeric HDL and its major protein component ApoA1 have been the focus of several investigations, yet the structural properties of monomeric ApoA1 remain poorly understood....

Proteins typically adopt a multitude of flexible and rapidly interconverting conformers, many of which are governed by specific protein interaction domains. While disc-shaped oligomeric HDL and its major protein component ApoA1 have been the focus of several investigations, yet the structural properties of monomeric ApoA1 remain poorly understood....

Epithelial to mesenchymal transition (EMT) is a process in which epithelial cells lose cell polarity and cell–cell adhesion and gain migratory and invasive properties to become mesenchymal cells that are very vital for development, wound healing and stem cell behavior and contribute pathologically to fibrosis and cancer progression. miR21, a potent...

Biological membranes are remarkably heterogeneous, composed of diverse lipid mixtures with distinct chemical structure and composition. By combining molecular dynamics simulations and the newly developed Lipid-Force Distribution Analysis (L-FDA), we explore force transmission in complex multi-component membrane models mimicking eukaryotic organelle...

Cardiac hypertrophy and associated heart fibrosis remain a major cause of death worldwide. Phytochemicals have gained attention as alternative therapeutics for managing cardiovascular diseases. These include the extract from the plant Terminalia arjuna which is a popular cardioprotectant and may prevent or slow progression of pathological hypertrop...

Editing in microRNAs, particularly in seed can significantly alter the choice of their target genes. We show that out of 13 different human tissues, different regions of brain showed higher adenosine to inosine (A-to-I) editing in mature miRNAs. These events were enriched in seed sequence (73.33%), which was not observed for cytosine to uracil (17....

The covalent attachment of lipids to proteins is a fundamental property of all living cells. These lipidated or lipid-modified proteins are directly targeted to the membranes and display diverse functional roles that are critical to cell function, such as membrane signaling and trafficking. All lipidated proteins have been classified by the type of...

Waste management is a pressing problem in the crowded urban and semi-rural residential colonies of Indian cities. Wet waste (vegetable peels, leftover food, etc.) rot very fast and necessitates regular disposal, often resulting in overflowing dustbins and litter piles in drains and open spaces on the roadside. The use of plastic garbage bags furthe...

miRNAs are important components of regulatory networks that control gene expression and have implications in various diseases including cancer. Targeting oncogenic miRNAs with small molecules is currently being explored to develop cancer therapeutics. Here, we report the development of dual binding neomycin-bisbenzimidazole conjugates that target o...

miRNAs are nodal regulators of gene expression and deregulation of miRNAs is causally associated with different diseases, including cancer. Modulation of miRNA expression is thus of therapeutic importance. Small molecules are currently being explored for their potential to downregulate miRNAs. Peptides have shown to have better potency and selectiv...

Background Employing methods to assess the quality of modeled protein structures is now standard practice in bioinformatics. In a broad sense, the techniques can be divided into methods relying on consensus prediction on the one hand, and single-model methods on the other. Consensus methods frequently perform very well when there is a clear consens...

Learning-based model quality assessment programs have been quite successful at discriminating between high- and low-quality protein structures. Here, we show that it is possible to improve this performance significantly by restricting the learning space to a specific context, in this case membrane proteins. Since these are among the most important...