Investigating role of positively selected genes and mutation sites of ERG11 in drug resistance of Candida albicans.

The steep increase in acquired drug resistance in Candida isolates has posed a great challenge in the clinical management of candidiasis globally. Information of genes and codon sites that are positively selected during evolution can provide insights into the mechanisms driving antifungal resistance in Candida. This study aimed to create a manually curated list of genes of Candida spp.

Structural Significance of Conformational Preferences and Ribose-Ring-Puckering of Hyper Modified Nucleotide 5'-Monophosphate 2-Methylthio Cyclic N-Threonylcarbamoyladenosine (p-msctA) Present at 37th Position in Anticodon Loop of tRNA.

Structural significance of conformational preferences and ribose ring puckering of newly discovered hyper modified nucleotide, 5'-monophosphate 2-methylthio cyclic N-threonylcarbamoyladenosine (p-msctA) have been investigated using quantum chemical semi-empirical RM1 and molecular dynamics simulation techniques. Automated geometry optimization of most stable structure of p-msctA has also been carried out with the help of abinitio (HF SCF, DFT) as well as semi empirical quantum chemical (RM1, AM1, PM3, and PM6) methods. Most stable structure of p-msctA is stabilized by intramolecular interactions between N(3)…HC(2'), N(1)…HC(16), O(13)…HC(15), and O(13)…HO(14).

Structural insights and inhibition mechanism of TMPRSS2 by experimentally known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride to control SARS-coronavirus-2: A molecular modeling approach.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been responsible for the cause of global pandemic Covid-19 and to date, there is no effective treatment available. The spike 'S' protein of SARS-CoV-2 and ACE2 of the host cell are being targeted to design new drugs to control Covid-19. Similarly, a transmembrane serine protease, TMPRSS2 of the host cell plays a significant role in the proteolytic cleavage of viral 'S' protein helpful for the priming of ACE2 receptors and viral entry into human cells.

Molecular modeling approach to identify inhibitors of Rv2004c (rough morphology and virulent strain gene), a DosR (dormancy survival regulator) regulon protein from .

Being a part of dormancy survival regulator (DosR) regulon, Rv2004c (rough morphology and virulent strain gene) has been identified in earlier experimental studies as an indispensable protein required for the growth and survival of . This protein was predicted to have a role in inhibition of phospholipase A2 activity related to immuno-defence and other membrane-related events. Thus, considering significance of Rv2004c protein, a structure-based drug designing strategy was followed to identify potential inhibitors to this novel target.

Role of Wybutosine and Mg Ions in Modulating the Structure and Function of tRNA: A Molecular Dynamics Study.

Transfer RNA remains to be a mysterious molecule of the cell repertoire. With its modified bases and selectivity of codon recognition, it remains to be flexible inside the ribosomal machinery for smooth and hassle-free protein biosynthesis. Structural changes occurring in tRNA due to the presence or absence of wybutosine, with and without Mg ions, have remained a point of interest for structural biologists.

Preferences of AAA/AAG codon recognition by modified nucleosides, τmsU and tA present in tRNA.

Deficiency of 5-taurinomethyl-2-thiouridine, τmsU at the 34th 'wobble' position in tRNA causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNA, recognizes AAA/AAG codons during protein biosynthesis process. Its preference to identify cognate codons has not been studied at the atomic level.

Conformational preferences and structural analysis of hypermodified nucleoside, peroxywybutosine (o2yW) found at 37 position in anticodon loop of tRNA and its role in modulating UUC codon-anticodon interactions.

Hypermodified bases present at 3'-adjacent (37) position in anticodon loop of tRNA are well known for their contribution in modulating codon-anticodon interactions. Peroxywybutosine (o2yW), a wyosine family member, is one of such tricyclic modified bases observed at the 37 position in tRNA. Conformational preferences and three-dimensional structural analysis of peroxywybutosine have not been investigated in detail at atomic level.

Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm5U present at 'wobble' position in anticodon loop of tRNALeu: A molecular modeling approach.

Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the 'wobble' 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level.

Comparative Structural Dynamics of tRNA(Phe) with Respect to Hinge Region Methylated Guanosine: A Computational Approach.

Transfer RNAs (tRNAs) contain various uniquely modified nucleosides thought to be useful for maintaining the structural stability of tRNAs. However, their significance for upholding the tRNA structure has not been investigated in detail at the atomic level. In this study, molecular dynamic simulations have been performed to assess the effects of methylated nucleic acid bases, N (2)-methylguanosine (m(2)G) and N (2)-N (2)-dimethylguanosine (m 2 (2) G) at position 26, i.

Homology modeling, molecular docking and DNA binding studies of nucleotide excision repair UvrC protein from M. tuberculosis.

Mycobacterium tuberculosis is a Gram positive, acid-fast bacteria belonging to genus Mycobacterium, is the leading causative agent of most cases of tuberculosis. The pathogenicity of the bacteria is enhanced by its developed DNA repair mechanism which consists of machineries such as nucleotide excision repair. Nucleotide excision repair consists of excinuclease protein UvrABC endonuclease, multi-enzymatic complex which carries out repair of damaged DNA in sequential manner.