A5079741689- Enzyme Structure and Function
- Light effects on plants
- Photosynthetic Processes and Mechanisms
- Protein Structure and Dynamics
- Photoreceptor and optogenetics research
- Biochemical and Molecular Research
- Computational Drug Discovery Methods
- Vitamin C and Antioxidants Research
- Cultural Heritage Materials Analysis
- Plant Gene Expression Analysis
- Photovoltaic System Optimization Techniques
- Machine Learning in Materials Science
- bioluminescence and chemiluminescence research
- Vitamin K Research Studies
- Solar Thermal and Photovoltaic Systems
- Phenothiazines and Benzothiazines Synthesis and Activities
- Tuberculosis Research and Epidemiology
- Plant Molecular Biology Research
- Antibiotic Resistance in Bacteria
- Advanced Electron Microscopy Techniques and Applications
- Synthesis and biological activity
- solar cell performance optimization
- Antibiotics Pharmacokinetics and Efficacy
- Biocrusts and Microbial Ecology
- Crystallization and Solubility Studies
University of Wisconsin–Milwaukee
2020-2024
Kathmandu University
2022
Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase enzymatic cycle is observed with near-atomic resolution using most advanced X-ray source currently available: European XFEL (EuXFEL). high repetition rate EuXFEL combined our mix-and-inject technology enables ceftriaxone binding to
Abstract For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing positions in real-time. Our work builds possibilities unleashed mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, reactions are triggered mixing substrate or ligand solutions with enzyme microcrystals. Here, we report detail (between 2.2 and 2.7 Å resolution) room-temperature, time-resolved millisecond time-resolution...
Abstract Charge-transfer reactions in proteins are important for life, such as photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report changes that take place while electrons transfer along a chain four conserved tryptophans Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction flavin by first tryptophan causes directed responses at key asparagine, salt bridge,...
Phytochromes are red-light photoreceptors discovered in plants with homologs bacteria and fungi that regulate a variety of physiological responses. They display reversible photocycle between two distinct states: red-light-absorbing Pr state far-red light-absorbing Pfr state. The photoconversion regulates the activity an enzymatic domain, usually histidine kinase (HK). molecular mechanism explains how light controls HK is not understood because structures unmodified bacterial phytochromes...
With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating structure of transient states along coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review recent developments, opportunities, and challenges pump-probe at XFELs.
The upgrade of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France to an Extremely Brilliant Source (EBS) is expected enable time-resolved synchrotron serial crystallography (SSX) experiments with sub-millisecond time resolution. ID29 a new beamline dedicated SSX at ESRF–EBS. Here, we report emerging from initial phase user operation ID29. We first used microcrystals photoactive yellow protein as model system exploit potential microsecond pulses for SSX. Subsequently,...
Abstract Phytochromes are essential photoreceptor proteins in plants with homologs bacteria and fungi that regulate a variety of important environmental responses. They display reversible photocycle between two distinct states, the red-light absorbing Pr far-red light Pfr, each its own structure. The to Pfr photoconversion requires covalently bound bilin chromophore regulates activity C-terminal enzymatic domain, which is usually histidine kinase (HK). In plants, phytochromes translocate...
Abstract There is an urgent need for anti-viral agents that treat and/or prevent Covid-19 caused by SARS-Coronavirus (CoV-2) infections. The replication of the SARS CoV-2 dependent on activity two cysteine proteases, a papain-like protease, PL-pro, and 3C-like protease known as main Mpro or 3CLpro. shortest safest path to clinical use repurposing drugs with binding affinity PLpro 3CLpro have established safety profile in humans. Several studies reported crystal structures SARS-CoV-2 complex...
Here, a machine-learning method based on kinetically informed neural network (NN) is introduced. The proposed designed to analyze time series of difference electron-density maps from time-resolved X-ray crystallographic experiment. named KINNTREX (kinetics-informed NN for crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing levels complexity. For the simulations, data generated that mimic collected photocycle photoactive yellow protein. only...
For decades, researchers have been determined to elucidate essential enzymatic functions on the atomic lengths scale by tracing positions in real time. Our work builds new possibilities unleashed mix-and-inject serial crystallography (MISC) 1-5 at X-ray free electron laser facilities. In this approach, reactions are triggered mixing substrate or ligand solutions with enzyme microcrystals 6 . Here, we report detail and millisecond time-resolution how Mycobacterium tuberculosis BlaC is...
Abstract Here, a machine learning method based on kinetically informed neural network (NN) is introduced. The proposed designed to analyze time series of difference electron density (DED) maps from time-resolved X-ray crystallographic experiment. named KINNTREX (Kinetics Inspired NN for Time-Resolved Crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing level complexity. For the simulations, data was generated that mimic collected photocycle...
Abstract The SARS coronavirus 2 main protease 3CLpro tailor cuts various essential virus proteins out of long poly-protein translated from the RNA. If is inhibited, functional cannot form and replicate assemble. Any compound that inhibits therefore a potential drug to end pandemic. Here we show diffraction power crystals effectively destroyed by Ebselen. It appears Ebselen may be widely available, relatively cost effective way eliminate 2.
Abstract Phytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display reversible photocycle between the resting (dark) Pr state and activated Pfr state, signals received transduced as structural change through entire protein modulate activity protein. It is unknown how Pr-to-Pfr interconversion occurs structure intermediates remain notoriously elusive. Here, we present short-lived crystal structures...
Abstract In this study, we follow the diffusion and buildup of occupancy substrate ceftriaxone in M. tuberculosis β-lactamase BlaC microcrystals by structural analysis enzyme complex at single millisecond time resolution. We also show binding reaction an inhibitor, sulbactam, on a slower scale. use ‘mix-and-inject’ technique to initiate these reactions diffusion, determine resulting structures serial crystallography using ultrafast, intense X-ray pulses from European XFEL (EuXFEL) arriving...
Abstract Charge transfer reactions in proteins are fundamentally important for life, but it is currently not clear how protein structural dynamics control these electron reactions. Photolyases/cryptochromes, which repair DNA and signal all kingdoms of have a paradigm cascade. Here, photoreduction the flavin cofactor initiates charge along chain four conserved tryptophans. We report femtosecond X-ray crystallographic snap-shots Drosophila melanogaster (6-4) photolyase, revealing changes while...
Abstract For decades, researchers have been determined to elucidate essential enzymatic functions on the atomic lengths scale by tracing positions in real time. Our work builds new possibilities unleashed mix-and-inject serial crystallography (MISC) 1-5 at X-ray free electron laser facilities. In this approach, reactions are triggered mixing substrate or ligand solutions with enzyme microcrystals 6 . Here, we report detail and millisecond time-resolution how Mycobacterium tuberculosis BlaC...