A5086079209- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- X-ray Spectroscopy and Fluorescence Analysis
- Advanced X-ray Imaging Techniques
- Trace Elements in Health
- RNA modifications and cancer
- Computational Drug Discovery Methods
- Advanced Electron Microscopy Techniques and Applications
- Photoacoustic and Ultrasonic Imaging
- Radiation Dose and Imaging
- Bacterial Genetics and Biotechnology
- Advanced MRI Techniques and Applications
- Lanthanide and Transition Metal Complexes
- Microbial Metabolic Engineering and Bioproduction
- Biochemical and biochemical processes
- Optical Imaging and Spectroscopy Techniques
- Protein Structure and Dynamics
- Biotin and Related Studies
- Photodynamic Therapy Research Studies
- Radiation Therapy and Dosimetry
- Genomics and Phylogenetic Studies
- Heavy Metal Exposure and Toxicity
- Iron Metabolism and Disorders
- Advanced X-ray and CT Imaging
- thermodynamics and calorimetric analyses
McMaster University
2014-2024
SLAC National Accelerator Laboratory
2015-2023
Linac Coherent Light Source
2022
Stanford University
2019
The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for includes: (1) designing a vaccine future protection; (2) de novo drug discovery; (3) identifying existing drugs repurpose them immediate treatments. To assist repurposing design, we determine two apo structures severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial...
Abstract Structural information about biological macromolecules near the atomic scale provides important insight into functions of these molecules. To date, X-ray crystallography has been predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection diffraction before onset damage, yet majority solved at FELs phased...
The Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS) is seventh and newest world's first hard X-ray free-electron laser. It was designed with a primary focus on structural biology, employing ultrafast pulses of X-rays from LCLS atmospheric conditions to overcome radiation damage limitations in biological measurements. also capable performing various time-resolved MFX design consists versatile base system supporting multiple methods,...
The SARS-CoV-2 main protease of (Mpro) is an important target for related drug repurposing and development studies. Here, we describe the steps structural characterization Mpro, starting from plasmid preparation protein purification. We detail crystallization using sitting drop, microbatch (under oil) approach. Finally, cover data collection structure determination serial femtosecond crystallography. For complete details on use execution this protocol, please refer to Durdagi et al. (2021).
Abstract Objectives A major challenge in non‐small cell lung cancer surgery is the occurrence of positive tumor margins. This may lead to need for additional surgeries and has been linked poor patient prognosis. study aims develop an vivo surgical tool that can differentiate cancerous from noncancerous tissue at margin. Methods time‐resolved fluorescence diffuse reflectance bimodal device was used measure lifetime, spectra, intensities endogenous fluorophores as well optical properties...
Abstract Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric complexes. Also, it offers versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, first one ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution second cryogenic (Apo-Cryo) 1.1 resolution. These structures mostly...
Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient CO2-fixing enzymes described to date. However, molecular mechanisms underlying extraordinary catalytic activity ECRs on level protein assembly remain elusive. Here we used a combination ambient-temperature X-ray free electron laser (XFEL) and cryogenic synchrotron experiments study structural organization ECR from Kitasatospora setae. The K. setae is homotetramer that differentiates into pair dimers open- closed-form...
The bacterial 30S ribosomal subunit is a primary antibiotic target. Despite decades of discovery, the mechanisms by which binding induces dysfunction are not fully understood. Ambient temperature crystallographic techniques allow more biologically relevant investigation how local site interactions trigger global rearrangements that perturb protein synthesis. Here, structural effects 2-deoxystreptamine (paromomycin and sisomicin), novel sisomicin derivative, N1-methyl sulfonyl (N1MS)...
Prostatic zinc content is a known biomarker for discriminating normal healthy tissue from benign prostatic hyperplasia (BPH) and prostate cancer (PCa). Given that not readily measured without biopsy, we have been exploring noninvasive imaging methods to detect these diagnostic differences using zinc-responsive MRI contrast agent. During studies in mice, observed bolus of glucose stimulates secretion the fasted mice. This discovery allowed use Gd-based sensor differential regions versus...
The ribosome translates nucleotide sequences of messenger RNA to proteins through selection cognate transfer according the genetic code. To date, structural studies ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New light sources like X-ray free electron laser (XFEL) enabled collection from macromolecular crystals ambient temperature. Here, we report an crystal structure Thermus thermophilus 30S subunit...
Routine tissue sample preparation using chemical fixatives is known to preserve the morphology of being studied. A competitive method, cryofixation followed by freeze drying, involves no agents and maintains biological function tissue. The possible effects both techniques in terms distribution bio-metals (calcium (Ca), copper (Cu) zinc (Zn), iron (Fe) specifically) human skin samples was investigated. Micro synchrotron radiation x-ray fluorescence (μSRXRF) used map bio-metal epidermal dermal...
Breast cancer is the most common and ovarian 8th affecting women worldwide. This study highlights changes of trace element levels accompanied by progression from ductal carcinoma in situ (DCIS) to invasive (IDC) breast, using micro probe Synchrotron Radiation X-ray Fluorescence (μSRXRF). The average values for increase Ca, Fe Zn tumour regions with respect surrounding DCIS samples were significantly higher compared IDC (P <0.01).This was also carried out find a connection between breast...
Abstract Objective This work aims to develop a clinically compatible system that can perform breast tissue analysis in more time efficient process than conventional histopathological assessment. The potential for such be used vivo the operating room or surgical suite improve patient outcome is investigated. Method In this work, 80 matched pairs of invasive ductal carcinoma and adjacent normal were measured combined time‐resolved fluorescence diffuse reflectance (DA) system. Following...
Abstract We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at Linac Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as model system its high affinity between biotin and streptavidin where sulfur atom in molecule (C 10 H 16 N 2 O 3 S) is substituted with selenium. The dataset collected three different...
Abstract Initiation factor 1 (IF1) is one of multiple key ligands involved in the initiation mRNA translation, a highly dynamic and carefully-orchestrated process. However, details surrounding IF1 transient interactions with small 30S ribosomal subunit remain incompletely understood despite characterization unbound fully-bound states. Improvements X-ray light sources crystallographic techniques are now enabling time-resolved structural studies at near-physiological temperature near-atomic...
Abstract The COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for includes: i) designing a vaccine as future protection; ii) structure-based drug design; iii) identifying existing drugs repurpose them immediate treatments. To assist repurposing design, we determined two apo structures of Severe Acute Respiratory Syndrome CoronaVirus-2 main protease at ambienttemperature by Serial Femtosecond X-ray...
Previous studies have shown that the zinc-responsive MRI probe, GdL1, can distinguish healthy versus malignant prostate tissues based upon differences in zinc content and secretion. In this study, mice were fed chow containing low, normal, or high for 3 weeks before imaging glucose stimulated secretion (GSZS) by MRI. The distribution of tissue these three groups was imaged synchrotron radiation X-ray fluorescence (SR-XRF). A deficiency caused systemic organ-level dysregulation, weight loss,...
<title>Abstract</title> The long-term goal of this work is to use glucose-stimulated zinc secretion (GSZS) MRI in men undergoing scans for prostate cancer. Given that dietary choices may affect an individual’s content we examined how impacts cancer detection via GSZS healthy and TRAMP mice. Mice were fed a low, normal, high diet. was evaluated by MRI, tissue synchrotron radiation X-ray fluorescence (SR-XRF), bioavailability ICP-MS serum. Results showed deficiency caused systemic organ-level...
Previous studies have shown that the combination of X‐ray fluorescence and diffraction data can be used as a histopathological characterization tool for breast tissue. Recent advances in energy‐dispersive techniques allowed benchtop systems to produce useful results reasonable time frame, allowing clinical implementation realized. Using polarized system optimized measuring soft tissues, 38 tissue samples (19 normal 19 diseased) were interrogated. The measured elemental concentrations adipose...
During space missions, astronauts are exposed to a stream of energetic and highly ionizing radiation particles that can suppress immune system function, increase cancer risks even induce acute syndrome if the exposure is large enough. As human exploration goals shift from missions in low-Earth orbit (LEO) long-duration interplanetary protection remains one key technological issues must be resolved. In this work, we introduce NEUtron DOSimetry & Exploration (NEUDOSE) CubeSat mission, which...
In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment these samples was conducted at the X-ray Pump Probe end-station Linac Coherent Light Source (LCLS) recently introduced instrumentation. These were genetically engineered to omit 26-residue protein, Thx, which is present in wild-type Thermus thermophilus subunit. We are primarily...
ABSTRACT Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric complexes. Also, it offers versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, first one ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution second cryogenic (Apo-Cryo) 1.1 resolution. These structures mostly...
ABSTRACT The ribosome translates nucleotide sequences of messenger RNA to proteins through selection cognate transfer according the genetic code. To date, structural studies ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New lightsources like X-ray free electron laser (XFEL) enabled collection from macromolecular crystals ambient temperature. Here, we report an crystal structure Thermus thermophilus 30S...