We study the possibility of producing axion dark matter (DM) via misalignment mechanisms in a non-standard cosmological era dominated by ultra-light primordial black holes (PBH). While effect PBH domination on production vacuum is known assuming evaporation to proceed according Hawking's semi-classical (SC) approximation, we go beyond these simplest possibilities include kinetic and backreaction emitted particles themselves, referred as memory-burden (MB) effect. show that, depending upon...

The unprecedented worldwide pandemic caused by COVID-19 has motivated several research groups to develop machine-learning based approaches that aim automate the diagnosis or screening of COVID-19, in large-scale. gold standard for detection, quantitative-Real-Time-Polymerase-Chain-Reaction (qRT-PCR), is expensive and time-consuming. Alternatively, haematology-based detections were fast near-accurate, although those less explored. external-validity COVID-19-predictions on diverse populations...

Abstract Two iridium(III) diimine complexes [mono(1,10‐phenanthroline)bis(triphenylphosphine)(dihydrido)iridium(III) hexafluorophosphate ( 1 ) and mono(1,10‐phenanthroline)bis(triphenylphosphine)(hydrido)(chloro)iridium(III) 2 )] have been synthesized from a single two‐step reaction. The structures of both adopt distorted octahedral geometries, as established by single‐crystal X‐ray diffraction. complexes, upon irradiation with UV light at 365 nm, emit faint in solution bright the solid...

We have demonstrated earlier that protein microenvironments were conserved around disulfide-bridged cystine motifs with similar functions, irrespective of diversity in sequences. Here, cysteine thiol modifications characterized based on microenvironments, secondary structures and specific functions. Protein microenvironment an amino acid was defined as the summation hydrophobic contributions from surrounding fragments solvent molecules present within its first contact shell. Cysteine...

Proteins involved in proton-/electron-transfer processes often possess "functional" aspartates/aspartic acids (Asp) with variable protonation states. The mechanism of Asp protonation–deprotonation within proteins is unclear. Two questions were asked—the possible types determinants responsible for and the spatial arrangements leading to selective stabilization. analyzed using nine different solvent models, which scanned complete protein dielectric range, four illustrated around Asp, termed as...

In this work, we present the wetting property of edges a monatomic step on graphite. We have used frictional force microscope to experimentally investigate these edges. carried out quantum chemical calculations model system nanographene characterize hydrogen-bonding interactions between water and two different graphene, namely, zigzag arm-chair edges, explain our experimental results. clearly observed distinct properties along steps graphite surface under varying conditions humidity. The...

Quinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide that yields therapeutically effective quinolone and acridone compounds. Addressing the structural molecular underpinnings of AmQNS its substrate interaction in terms high selectivity specificity can aid development numerous novel This paper presents high-resolution crystal structure explains mechanistic role synthetic selectivity. Additionally, we provide model framework to comprehend constraints on ketide insertion...

Abstract A general method has been developed to characterize the hydrophobicity or hydrophilicity of microenvironment (MENV), in which a given amino acid side chain is immersed, by calculating quantitative property descriptor (QPD) based on relative (to water) MENV. Values QPD were calculated for test set 733 proteins analyze modulating effects residue properties MENV they are imbedded. The values and solvent accessibility used derive partitioning residues hydrophobicities. From this...

Abstract It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross‐strand bifurcated or Extra Watson–Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity DNA double helices certain sequences. The strengths these are debatable, however, as they do not have standard linear geometry criterion. We therefore carried out detailed ab initio quantum chemical studies using RHF/6‐31G(2d,2p)...

Role of Magnesium ion is well substantiated in DNA structure and function though the appropriate nature magnesium interaction still not fully established. We have analyzed available crystal structures presence ion, which show experimental evidences for various modes between molecule ion. Two preferred are found: direct coordinating electronegative atoms, secondary mode via formation hydrogen bonds. This qualitative data further supported by ab initio quantum chemical calculations using...

In our previous study, we have shown that the microenvironments around conserved amino acids are also in protein families (Bandyopadhyay and Mehler, Proteins 2008; 72:646-659). this hypothesized perform similar functions when embedded a certain type of microenvironment. We tested hypothesis on disulfide-bridged cysteines from high-resolution crystal structures. Although such cystines mainly play structural role proteins, enzymes they participate catalysis redox reactions. performed report...

Abstract Cysteine (Cys) is the most reactive amino acid participating in a wide range of biological functions. In‐silico predictions complement experiments to meet need functional characterization. Multiple Cys function prediction algorithm scarce, contrast specific algorithms. Here we present deep neural network‐based multiple prediction, available on web‐server (DeepCys) ( https://deepcys.herokuapp.com/ ). DeepCys model was trained and tested two independent datasets curated from protein...

Mutations conferring susceptibility to complex disorders also occur in healthy individuals but at significantly lower frequencies than patients, indicating that these mutations are not completely penetrant. Therefore, it is important estimate the penetrance or likelihood of developing a disease presence mutation. Recently, method calculate and its credible intervals was developed on basis Bayesian since been used literature. However, present form, this approach demands programming skills for...

Nonstructural (NS1) protein is mainly involved in virulence and replication of several viruses, including influenza virus A (H1N1); surveillance the latter started India 2009. The objective this study was to identify new substitutions NS1 from (H1N1) pandemic 2009 (pdm09) strain isolated India.The sequences proteins A(H1N1) pdm09 strains were obtained publicly available databases. Multiple sequence alignment phylogeny analyses performed confirm "consistent substitutions" on H1N1 Indian...

It is generally believed that base-pair stacking interaction in DNA double helix one of the strongest interactions governs sequence directed structural variability. However, X-ray crystal structures some base-paired doublet sequences have been seen to adopt different when flanked by base-pairs. database, however, still too small make good statistical inference about effect such flanking residues. Influence neighboring residue on local helical geometry a B-DNA has investigated here using...

Computational characterization of multiple Histidine (His) post-translational-modifications (PTM) at enzyme active sites complements tedious experimental in proteins-of-unknown-functions (PUFs) and domain-of-unknown-functions (DUFs). There are only a handful Histidine-PTM-prediction-tools those also annotate single function. Here, we addressed the problem using artificial neural networks on functional histidine dataset curated from (protein) sequences available UniProt database (sample size...

Experimental characterization of amino acid functions Domains Unknown Function (DUF) proteins is expensive, and time-consuming which could be complemented by computational methods. Cysteine, being the second most reactive at catalytic sites enzymes, was selected for functional annotation on DUF proteins. Earlier we reported Cysteine belonging to COX-II family. However, holistic not known, best our knowledge. Here, annotated characterized post-translational modifications (PTMs) based...

Influenza A (H1N1) virus has been one of the most common threats to humankind since 1918. The viral genome is frequently substituted, leading new strains and recurrent pandemics. Despite knowing effects single amino acid substitutions on individual proteins, collective infection remain elusive. Here, we addressed whether 'consistent substitutions' occur in a consortium functional domains protein-protein interaction (PPI) sites, impacting overall host immune responses. By definition, 'all'...

Effect of flanking base pairs on CA and AA dinluceotide step-geometry has been studied using molecular dynamics method. Sixteen dodecameric sequences are constructed for each doublet with all possible bases at their 5' 3' positions along complementary sequences. Structural parameter, formation Extra Watson Crick bifurcated hydrogen bonds or across the strands effect sodium ions these It is found that geometry step perturbed by neighboring pairs, which might be due to inherent flexibility...