A5084372867- SARS-CoV-2 and COVID-19 Research
- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Animal Virus Infections Studies
- Monoclonal and Polyclonal Antibodies Research
- Bat Biology and Ecology Studies
- SARS-CoV-2 detection and testing
- vaccines and immunoinformatics approaches
- COVID-19 Clinical Research Studies
- Influenza Virus Research Studies
- Plant Molecular Biology Research
- RNA Research and Splicing
- Viral gastroenteritis research and epidemiology
- Caveolin-1 and cellular processes
- Plant Reproductive Biology
- Neurobiology and Insect Physiology Research
- Genomics and Chromatin Dynamics
- Biofuel production and bioconversion
- Membrane Separation Technologies
- Nanopore and Nanochannel Transport Studies
- Viral Infections and Vectors
- Metabolomics and Mass Spectrometry Studies
- Advanced Sensor and Energy Harvesting Materials
- Proteoglycans and glycosaminoglycans research
Pennsylvania State University
2020-2025
Indian Institute of Technology Kharagpur
2019-2024
Bioenergy Life Science (United States)
2022
The association of the receptor binding domain (RBD) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme (hACE2) represents first required step for cellular entry. SARS-CoV-2 has continued to evolve emergence several novel variants, and amino acid changes in RBD have been implicated increased fitness potential immune evasion. Reliably predicting effect on ability interact more strongly hACE2 can help assess implications public...
Estimation of enzymatic activities still heavily relies on experimental assays, which can be cost and time-intensive. We present CatPred, a deep learning framework for predicting in vitro enzyme kinetic parameters, including turnover numbers (kcat), Michaelis constants (Km), inhibition (Ki). CatPred addresses key challenges such as the lack standardized datasets, performance evaluation sequences that are dissimilar to those used during training, model uncertainty quantification. explore...
SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by binding with the cell surface receptor – angiotensin converting enzyme (ACE2). We computationally contrasted interactions between ACE2 and coronavirus spike protein domain (RBD) of 2002 epidemic-causing SARS-CoV-1, SARS-CoV-2, bat RaTG13 using Rosetta energy function. find that RBD optimized achieve very strong (hACE2) consistent its enhanced infectivity. forms most stable complex hACE2 compared SARS-CoV-1...
There is mounting evidence of SARS-CoV-2 spillover from humans into many domestic, companion, and wild animal species. Research indicates that have infected white-tailed deer, deer-to-deer transmission has occurred, indicating deer could be a wildlife reservoir source novel variants. We examined the hypothesis Omicron variant actively asymptomatically infecting free-ranging New York City. Between December 2021 February 2022, 155 on Staten Island, York, were anesthetized for gross...
Retro-biosynthetic approaches have made significant advances in predicting synthesis routes of target biofuel, bio-renewable or bio-active molecules. The use only cataloged enzymatic activities limits the discovery new production routes. Recent retro-biosynthetic algorithms increasingly novel conversions that require altering substrate cofactor specificities existing enzymes while connecting pathways leading to a metabolite. However, identifying and re-engineering for desired are currently...
Novel vapor-permeable materials are sought after for applications in protective wear, energy generation, and water treatment. Current impermeable effectively block harmful agents but trap heat due to poor vapor transfer. Here we present a new class of materials, permeable dehydrated nanoporous biomimetic membranes (DBMs), based on channel proteins. This application is unexpected as proteins were assumed be unstable under dry conditions. DBMs mimic human skin's structure offer both high...
The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods design potentially neutralizing antibodies (Abs) to counter immune evasion by virus. Here, we report on de novo computational high-affinity Ab variable regions (Fv) through recombination VDJ genes targeting most solvent-exposed hACE2-binding residues spike receptor binding domain (RBD) protein using software tool OptMAVEn-2.0. Subsequently, carried out affinity maturation...
Clostridium thermocellum is a promising candidate for consolidated bioprocessing because it can directly ferment cellulose to ethanol. Despite significant efforts, achieved yields and titers fall below industrially relevant targets. This implies that there still exist unknown enzymatic, regulatory, and/or possibly thermodynamic bottlenecks throttle back metabolic flow. By (i) elucidating internal fluxes in wild-type C. grown on cellobiose via 13C-metabolic flux analysis (13C-MFA), (ii)...
Abstract Quantification of enzymatic activities still heavily relies on experimental assays, which can be expensive and time-consuming. Therefore, methods that enable accurate predictions enzyme activity serve as effective digital twins. A few recent studies have shown the possibility training machine learning (ML) models for predicting turnover numbers ( k cat ) Michaelis constants K m using only features derived from sequences substrate chemical topologies by in vitro measurements....
Extradenticle (EXD) is a partner protein of the HOX transcription factors and plays an important role in development Drosophila. It confers increased affinity specificity DNA-binding to proteins. However, homeodomain EXD has significantly weaker DNA compared homeodomains. Here, we show that glycine residue (G290) middle helix primarily results this binding. Glycine destabilizes helices. To probe its stability function protein, G290 was mutated alanine. The intrinsic G290A mutant as observed...
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), believed to have originated from a bat species, can infect wide range of non-human hosts. Bats are known harbor hundreds coronaviruses capable spillover into human populations. Recent studies shown significant variation in the susceptibility among species SARS-CoV-2 infection. We show that little brown bats (LBB) express angiotensin-converting enzyme 2 receptor and transmembrane serine protease 2, which accessible support binding....
Multiple domestic and wild animal species are susceptible to SARS-CoV-2 infection. Cattle swine experimental The unchecked transmission of in hosts could lead virus adaptation the emergence novel variants. In addition, spillover subsequent livestock significantly impact food security as well public health. Therefore, it is essential monitor for spillover. We developed optimized species-specific indirect ELISAs (iELISAs) detect anti-SARS-CoV-2 antibodies cattle, swine, chickens using spike...
Background There is mounting evidence that SARS-CoV-2 spills over from humans into many domestic, companion, and wild animal species. Indeed, there the potential for to evolve novel variants within non-human hosts could subsequently reinfect humans. Current work indicates White-tailed deer have repeatedly received infections humans, subsequent onward deer-to-deer transmission so potentially act as a wildlife reservoir source of new variants. We examined hypothesis Omicron variant actively...
ABSTRACT The association of the receptor binding domain (RBD) SARS-CoV-2 viral spike with human angiotensin converting enzyme (hACE2) represents first required step for entry. Amino acid changes in RBD have been implicated increased infectivity and potential immune evasion. Reliably predicting effect amino ability to interact more strongly hACE2 can help assess public health implications spillover adaptation into other animals. Here, we introduce a two-step framework that relies on 48...
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Abstract Quantification of enzymatic activities still heavily relies on experimental assays, which can be expensive and time-consuming. Therefore, methods that enable accurate predictions enzyme activity serve as effective digital twins. A few recent studies have shown the possibility training machine learning (ML) models for predicting turnover numbers ( k cat ) Michaelis constants K m using only features derived from sequences substrate chemical topologies by in vitro measurements....
Abstract The emergence of SARS-CoV-2 is responsible for the pandemic respiratory disease known as COVID-19, which emerged in city Wuhan, Hubei province, China late 2019. Both vaccines and targeted therapeutics treatment this are currently lacking. Viral entry requires binding viral spike receptor domain (RBD) with human angiotensin converting enzyme (hACE2). In an earlier paper 1 , we report on specific residue interactions underpinning event. Here de novo computational design high affinity...
The cellular entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the association its receptor binding domain (RBD) with human angiotensin converting enzyme (hACE2) as first crucial step. Efficient and reliable prediction RBD-hACE2 affinity changes upon amino acid substitutions can be valuable for public health surveillance monitoring potential spillover adaptation into non-human species. Here, we introduce a convolutional neural network (CNN) model trained on...
Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), believed to have originated from a bat species, can infect wide range of non-human hosts. Bats are known harbor hundreds coronaviruses capable spillover into human populations. Earlier studies showed significant variation in susceptibility among species SARS-CoV-2 infection. The ability spike protein bind the angiotensin-converting enzyme 2 (ACE2) receptor is crucial determinant host infection.Methods:...