A5045824126- Enzyme Structure and Function
- X-ray Spectroscopy and Fluorescence Analysis
- Protein Structure and Dynamics
- Advanced NMR Techniques and Applications
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Advanced biosensing and bioanalysis techniques
- Crystallography and Radiation Phenomena
- DNA and Nucleic Acid Chemistry
- RNA modifications and cancer
- Nuclear Physics and Applications
- Advanced X-ray Imaging Techniques
- RNA Interference and Gene Delivery
- nanoparticles nucleation surface interactions
- Protein Kinase Regulation and GTPase Signaling
- DNA Repair Mechanisms
- Advanced Electron Microscopy Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Metal-Organic Frameworks: Synthesis and Applications
- Hereditary Neurological Disorders
- Advanced Biosensing Techniques and Applications
- Cell Image Analysis Techniques
- RNA regulation and disease
- Heat shock proteins research
Illinois Institute of Technology
2019-2025
Argonne National Laboratory
2020-2025
Cornell University
2011-2017
Cornell High Energy Synchrotron Source
2016-2017
European Molecular Biology Laboratory
2017
European Molecular Biology Laboratory
2017
Lockheed Martin (United States)
2015
Oberlin College
2008-2011
Boehringer Ingelheim (United States)
1997
Eindhoven University of Technology
1995
BioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software designed biological SAXS data enables creation plotting one-dimensional profiles from two-dimensional detector images, standard operations such as averaging subtraction radius gyration molecular weight, advanced calculation inverse Fourier transforms envelopes. It also allows easy processing inline size-exclusion...
Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity active site enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but extent which different these residues are correlated unclear. Here we compare conformational ensembles CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The...
Abstract Compartmentalization by liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mechanism underlying the organization of biomolecules in space and time. Here, we combine rapid-mixing time-resolved small-angle X-ray scattering (SAXS) approaches to characterize assembly kinetics prototypical prion-like domain with equilibrium techniques that its boundaries size distribution clusters prior separation. We find two kinetic regimes on micro- millisecond timescale are...
BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in version 2 are described. These include improved data reduction using pyFAI ; updated automated Guinier fitting D max finding algorithms; series ( e.g. size-exclusion chromatography coupled X-ray or SEC-SAXS) buffer- sample-region linear integral baseline correction series; deconvolution regularized alternating least squares REGALS );...
Ubiquitin‐binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48‐ K63‐linked polyubiquitin chains, respectively. comprises self‐associating regions that drive its homotypic liquid–liquid phase separation (LLPS). Specific one of these ubiquitin inhibit LLPS. Here, we show that, unlike ubiquitin, the effects multivalent chains on LLPS are highly dependent chain types. Specifically, K11‐Ub4 K48‐Ub4 generally LLPS, whereas...
Intrinsically disordered proteins (IDPs) perform a broad range of functions in biology, suggesting that the ability to design IDPs could help expand repertoire with novel functions. Computational specific conformational properties has, however, been difficult because their substantial dynamics and structural complexity. We describe general algorithm for designing properties. demonstrate power by generating variants naturally occurring differ compaction, long-range contacts, propensity phase...
Diffuse reflectance infrared (IR) spectroscopy performed over a wide temperature range (35-298 K) is used to study the dynamics of H(2) adsorbed within isostructural metal-organic frameworks M(2)L (M = Mg, Mn, Co, Ni and Zn; L 2,5-dioxidobenzene-1,4-dicarboxylate) referred as MOF-74 CPO-27. Spectra collected at concentrations ranging from 0.1 3.0 per metal cation reveal that strongly red-shifted vibrational modes arise isolated bound available coordination site. The red shift bands...
Abstract We report on higher-order G-quadruplex structures adopted by long promoter sequences obtained an iterative integrated structural biology approach. Our approach uses quantitative biophysical tools (analytical ultracentrifugation, small-angle X-ray scattering, and circular dichroism spectroscopy) combined with modeling molecular dynamics simulations, to derive self-consistent models. The formal resolution of our is 18 angstroms, but in some cases features only a few nucleotides can be...
Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these embedded within duplexes, their presumed genomic environment. Here, we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, small-angle X-ray...
A series of studies that provide a consistent and illuminating picture global radiation damage to protein crystals, especially at temperatures above ∼200 K, are described. The sensitivity shows transition near 200 which it appears be limited by solvent-coupled diffusive processes. Consistent with this interpretation, component proceeds on timescales several minutes 180 decreasing seconds room temperature. As result, data collection times order 1 s allow up half outrun 260 K. Much larger...
Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations technique, such as minimum required sample volume, and experimental design, flow cells, are necessary because samples sensitive to damage from X-rays. Radiation typically manifests aggregation sample, which makes collected data unreliable. However, there has been little systematic...
Diffuse reflectance infrared spectroscopy is used to measure the quantum dynamics of molecular hydrogen adsorbed in microporous material MOF-5. Low-temperature spectra reveal at least three distinct binding sites. The induced redshifts vibrational mode frequencies allow estimation site-specific energies ranging from 2.5 4 kJ/mol. Splittings rovibrational sidebands are consistent with existing theories and indicate that ${\text{H}}_{2}$ relatively freely rotating even temperatures as low 10...
SARS-CoV-2, a human coronavirus, is the causative agent of COVID-19 pandemic. Its genome translated into two large polyproteins subsequently cleaved by viral papain-like protease and main (Mpro). Polyprotein processing essential yet incompletely understood. We studied Mpro-mediated nsp7-11 polyprotein, whose mature products include cofactors replicase, identified order cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange cross-linking) x-ray...
Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four neutron (SANS) instruments, 171 SAXS 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase xylose isomerase) were acquired. From these data, the solvent-subtracted protein profiles shown to be reproducible, with caveat additive constant adjustment was required account small errors in solvent subtraction. Further, major features of...
Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in folding hybrid 1 2 telomeric G-quadruplex structures. The collapse, initiated by pH jump, is characterized exponential decrease radius gyration from 24.3 to 12.6 Å. monophasic complete <600 ms. Additional hand-mixing pH-jump kinetic studies show slower steps follow collapse. folded states at equilibrium...
The General Stress Response promotes survival of bacteria in adverse conditions, but how sensor proteins transduce species-specific signals to initiate the response is not known. serine/threonine phosphatase RsbU initiates B. subtilis upon binding a partner protein (RsbT) that released from sequestration by environmental stresses. We report RsbT activates inducing otherwise flexible linkers form short coiled-coil dimerizes and domains. Importantly, we present evidence related dimers diverse...