A5081187194- Protein Structure and Dynamics
- Biochemical and Structural Characterization
- RNA and protein synthesis mechanisms
- Antimicrobial Peptides and Activities
- Computational Drug Discovery Methods
- Monoclonal and Polyclonal Antibodies Research
- Helicobacter pylori-related gastroenterology studies
- Geochemistry and Geologic Mapping
- Advanced Electron Microscopy Techniques and Applications
- Radioactivity and Radon Measurements
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Radioactive element chemistry and processing
- Probiotics and Fermented Foods
- Stock Market Forecasting Methods
- Gastrointestinal disorders and treatments
- Chemical Synthesis and Analysis
- Toxin Mechanisms and Immunotoxins
- Microbial Metabolism and Applications
- Microbial Natural Products and Biosynthesis
- Antibiotic Resistance in Bacteria
- Diatoms and Algae Research
- Drug-Induced Adverse Reactions
- Forensic Entomology and Diptera Studies
- Immunotherapy and Immune Responses
M S Ramaiah University of Applied Sciences
2023-2025
St. Xavier's College (Autonomous)
2023-2025
St Xavier’s College
2023-2025
University of Washington
2021-2022
Indian Institute of Science Bangalore
2013-2022
Seattle University
2021
University of Birmingham
2020
Bangalore University
2017-2018
Abstract A wooden house frame consists of many different lumber pieces, but because the regularity these building blocks, structure can be designed using straightforward geometrical principles. The design multicomponent protein assemblies, in comparison, has been much more complex, largely owing to irregular shapes structures 1 . Here we describe extendable linear, curved and angled as well inter-block interactions, that conform specified geometric standards; assemblies blocks inherit their...
There is a pressing need for new therapeutics to combat multidrug- and carbapenem-resistant bacterial pathogens. This challenge prompted us use long short-term memory (LSTM) language model understand the underlying grammar, i.e. arrangement frequencies of amino acid residues, in known antimicrobial peptide sequences. According output our LSTM network, we synthesized 10 peptides tested them against All these displayed broad-spectrum activity, validating LSTM-based design approach. Our two...
Ω76 is a promising drug with remarkably low toxicity, which may be used in the future for treating highly resistant infections.
Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale architectures with internal degrees of freedom is an outstanding challenge for computational design. Here we explore the de novo construction machinery from designed axle and rotor cyclic or dihedral symmetry. We find axle-rotor systems assemble in vitro vivo as designed. Using cryo-electron microscopy, these populate conformationally variable...
Many bacterial genomes exclusively display an N4-methyl cytosine base (m4C), whose physiological significance is not yet clear. Helicobacter pylori a carcinogenic bacterium and the leading cause of gastric cancer in humans. strain 26695 harbors single m4C methyltransferase, M2.HpyAII which recognizes 5′ TCTTC 3′ sequence methylates first residue. To understand role modification, M2.hpyAII deletion was constructed. Deletion displayed lower adherence to host AGS cells reduced potential induce...
Antimicrobial resistance (AMR) is one of the most important global health challenges, driven by ability bacteria to produce β-lactamase enzymes that hydrolyze β-lactam antibiotics and, therefore, neutralize their effects. This poses a challenge in inhibitor development because classes A, B, C, and D β-lactamases show distinct catalytic mechanisms. In this study, silico approaches involving protein modelling 20 proteins, molecular docking have been used design pentapeptides inhibitors. The...
Chintamani village, Chikkaballapura district, Karnataka, India was found to possess high aquifer uranium concentrations. Geologically, village is located on bedrock that rich in elements like potassium (K) naturally contain levels of radioactive elements, such as and thorium, due the presence alkali-feldspar granites gneisses. Aquifer depletion has caused concentration these groundwater increase over time, posing a potential health hazard residents village. Here, we report sampling from 12...
Chintamani village, Chikkaballapura district, Karnataka, India was found to possess high aquifer uranium concentrations. Geologically, village is located on bedrock that rich in elements like potassium (K) naturally contain levels of radioactive elements, such as and thorium, due the presence alkali-feldspar granites gneisses. Aquifer depletion has caused concentration these groundwater increase over time, posing a potential health hazard residents village. Here, we report sampling from 12...
ABSTRACT Aspergillus niger strain melanoliber was isolated from the coastal region of Mumbai, Maharashtra, India. This secretes water-soluble melanin attached to peptides possessing metal-chelation properties. Here, we report whole-genome sequence melanoliber. The genome sequenced using Illumina Novaseq6000 giving a total size 3.86 Mb.
<ns3:p>Background Chintamani village, Chikkaballapura district, Karnataka, India was found to possess high aquifer uranium concentrations. Ge- ologically, village is located on bedrock that rich in elements like potassium (K) naturally contain levels of radioactive elements, such as and thorium, due the presence alkali-feldspar granites gneisses. Aquifer de- pletion has caused concentration these groundwater increase over time, posing a potential health hazard residents village. Methods...
Most of the biological processes are governed through specific protein–ligand interactions. Discerning different components that contribute toward a favorable protein– ligand interaction could significantly better understanding protein function, rationalizing drug design and obtaining principles for engineering. The Protein Data Bank (PDB) currently hosts structure ∼68 000 complexes. Although several databases exist classify proteins according to sequence structure, mere handful them...
<ns4:p>Most physiological processes in living systems are fundamentally regulated by protein–ligand interactions. Understanding the process of ligand recognition proteins is a vital activity molecular biology and biochemistry. It well known that residues present at binding site protein form pockets provide conducive environment for specific ligands. In many cases, boundaries these sites not defined. Here, we web-server to systematically evaluate important contribute towards through silico...
<ns4:p>Most physiological processes in living systems are fundamentally regulated by protein–ligand interactions. Understanding the process of ligand recognition proteins is a vital activity molecular biology and biochemistry. It well known that residues present at binding site protein form pockets provide conducive environment for specific ligands. In many cases, boundaries these sites not defined. Here, we web-server to systematically evaluate important contribute towards through silico...
Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins custom structures and functions. Such could find widespread medical industrial applications. Here, we have adapted algorithms from Rosetta software suite to much larger proteins, based on ideal geometric topological criteria. Furthermore, developed techniques incorporate symmetry into designed structures. For our first attempt, targeted (α/β)8 TIM barrel scaffold. We gained...
Knowledge of protein-ligand interactions is essential to understand several biological processes and important for applications ranging from understanding protein function drug discovery engineering. Here, we describe an algorithm the comparison three-dimensional ligand-binding sites in structures. A previously described algorithm, PocketMatch (version 1.0) optimised, expanded, MPI-enabled parallel execution. 2.0) rapidly quantifies binding-site similarity based on structural descriptors...
Antimicrobial peptides are ubiquitous molecules that form the innate immune system of organisms across all kingdoms life. Despite their prevalence and early origins, they continue to remain potent natural antimicrobial agents. therefore promising drug candidates in face overwhelming multi-drug resistance conventional antibiotics. Over past few decades, thousands have been characterized vitro, efficacy data now available a multitude public databases. Computational peptide design attempts...
Abstract A wooden house frame consists of many different lumber pieces, but because the regularity these building blocks, structure can be designed using straightforward geometrical principles. The design multicomponent protein assemblies in comparison has been much more complex, largely due to irregular shapes structures 1 . Here we describe extendable linear, curved, and angled as well inter-block interactions that conform specified geometric standards; blocks inherit their extendability...
Heavy metal contamination of agricultural soils reduces crop yields, contaminates groundwater and disrupts local ecosystems. Here, we describe a novel, water-soluble form melanin (peptidomelanin) capable chelating heavy metals in large quantities. Peptidomelanin is composed an L-DOPA core polymer that solubilized via short, heterogeneous peptide chains with mean amino acid length ∼2.6. It secreted by the spores Aspergillus niger melanoliber during germination. was found to chelate quantities...
Abstract While many computational methods accurately predict destabilizing mutations, identifying stabilizing mutations has remained a challenge, due to their relative rarity. We tested ΔΔG 0 predictions from predictors such as Rosetta, ThermoMPNN, RaSP, and DeepDDG, using eighty-two mutants of the bacterial toxin CcdB test case. On this dataset, best predictor is ThermoMPNN which identifies with precision 68%. However, average increase in T m for these predicted was only 1°C CcdB, were...
Melanin is an amorphous, highly heterogeneous polymer found across all kingdoms of life. Although the properties melanin can greatly vary, most forms are insoluble and strongly absorb light, appearing dark brown to black. Here, we describe a water-soluble form (peptidomelanin) secreted by spores Aspergillus niger (strain: melanoliber) during germination. Peptidomelanin composed L-DOPA core that solubilized via short, copolymerized peptide chains forming "corona" with mean amino acid length...
While many computational methods accurately predict destabilizing mutations, identifying stabilizing mutations has remained a challenge, because of their relative rarity. We tested ΔΔG
Megaselia scalaris, commonly known as the scuttle fly, is a cosmopolitan species in family Phoridae. It an easily cultured fly that emerging model organism fields of genetics and developmental biology. Its affinity for carrion its predictable life cycle makes it useful field forensic science estimating post-mortem interval (PMI) human remains. Cases myasis caused by M. scalaris have also been reported medical literature. Despite ubiquitous prevalence relevance across multiple fields,...