A5012789413- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Advanced NMR Techniques and Applications
- Enzyme Structure and Function
- Molecular spectroscopy and chirality
- Signaling Pathways in Disease
- RNA regulation and disease
- RNA Research and Splicing
- Electron Spin Resonance Studies
- Peptidase Inhibition and Analysis
- Mass Spectrometry Techniques and Applications
- Toxin Mechanisms and Immunotoxins
- Spectroscopy and Quantum Chemical Studies
- DNA and Nucleic Acid Chemistry
- Force Microscopy Techniques and Applications
- Cancer, Hypoxia, and Metabolism
- NMR spectroscopy and applications
- Photosynthetic Processes and Mechanisms
- Hemoglobin structure and function
- Glycosylation and Glycoproteins Research
- RNA modifications and cancer
- interferon and immune responses
- Trypanosoma species research and implications
- Viral Infections and Immunology Research
- Microtubule and mitosis dynamics
University of Colorado Anschutz Medical Campus
2017-2025
University of Colorado Denver
2017-2024
The University of Texas at Austin
2024
University of Houston
2024
ETH Zurich
2005-2021
Goethe University Frankfurt
2021
Tokyo Metropolitan University
2021
Uppsala University
2021
École Polytechnique Fédérale de Lausanne
2004-2016
National Institutes of Health
2006-2014
Significance The nucleotide-binding domain, leucine-rich containing family, pyrin domain-containing-3 (NLRP3) inflammasome, an intracellular complex that regulates maturation and release of interleukin (IL)-1β, is active in biopsies metastatic melanoma. Here, we demonstrate NLRP3 activation melanoma cells drives tumor progression mice. Subsequent to cells, IL-1β induces melanoma-associated inflammation, resulting immunosuppression. Oral administration a single inhibitor (OLT1177) reduces...
A general method to enhance the sensitivity of multidimensional NMR experiments performed at high-polarizing magnetic field via significant reduction longitudinal proton relaxation times is described. The based on use two vast pools "thermal bath" 1H spins residing hydrogens covalently attached carbon and oxygen atoms in 13C,15N labeled fully protonated or fractionally deuterated proteins uniformly 1HN concomitantly multipulse experiments. proposed optimization implemented 2D...
3JHN,Hα, 3JHN,Cβ, and 3JHN,C' couplings, all related to the backbone torsion angle φ, were measured for third immunoglobulin binding domain of protein G, or GB3. Measurements carried out using both previously published methods novel sequences based on multiple-quantum principle, which limit attenuation experimental couplings caused by finite lifetimes spin states passive spins. High reproducibility between conventional approaches confirms accuracy measurements. With few exceptions, close...
A highly active, monomeric chorismate mutase, obtained by topological redesign of a dimeric helical bundle enzyme from Methanococcus jannaschii, was investigated NMR and various other biochemical techniques, including H/D exchange. Although structural disorder is generally considered to be incompatible with efficient catalysis, the monomer, unlike its natural counterpart, unexpectedly possesses all characteristics molten globule. Global conformational ordering, observed upon binding...
The N−H bond length in backbone peptide groups of the protein GB3 has been studied by liquid-crystal NMR, using five structurally conserved mutants this protein. In absence additional information, impact dynamic fluctuations vector orientation on 15N−1H dipolar interaction cannot be separated from a change length. However, directly impacts C′−H vectors group, and simultaneous analysis 13C′−HN 15N−HN residual couplings, measured under different alignment orientations, permits modelfree...
It is proposed to convert nuclear Overhauser effects (NOEs) into relatively precise distances for detailed structural studies of proteins. To this purpose, it demonstrated that the measurement NOE buildups between amide protons in perdeuterated human ubiquitin using a designed (15)N-resolved HMQC-NOESY experiment enables determination (1)H(N)-(1)H(N) up 5 A with high accuracy and precision. These NOE-derived have an experimental random error approximately 0.07 A, which smaller than pairwise...
Abstract Adenosine-to-inosine (A-to-I) editing of eukaryotic cellular RNAs is essential for protection against auto-immune disorders. Editing carried out by ADAR1, whose innate immune response-specific cytoplasmic isoform possesses a Z-DNA binding domain (Zα) unknown function. Zα also binds to CpG repeats in RNA, which are hallmark Z-RNA formation. Unexpectedly, has been predicted — and some cases even shown bind specific regions within mRNA rRNA devoid such repeats. Here, we use NMR,...
The gut microbiota is essential for human health. Microbial supply of short-chain fatty acids (SCFAs), particularly butyrate, a well-established contributor to homeostasis and disease resistance. Reaching millimolar luminal concentrations, butyrate sequestered utilized in the colon as favored energy source intestinal epithelia. Given steep oxygen gradient across anoxic lumen highly oxygenated lamina propria, provides interesting environment study sensing. Previous studies have shown that...
The nucleocapsid protein is one of four structural proteins encoded by SARS-CoV-2 and plays a central role in packaging viral RNA manipulating the host cell machinery, yet its dynamic behavior promiscuity nucleotide binding has made standard methods to address atomic-resolution details difficult. To begin addressing interactions with both along behavior, we have specifically focused on folded N-terminal domain (NTD) flanking regions using nuclear magnetic resonance solution studies. Studies...
A novel iterative procedure is described that allows both the orientation and dynamics of internuclear bond vectors to be determined from direct interpretation NMR dipolar couplings, measured under at least three orthogonal alignment conditions. If five alignments are available, approach also yields information on degree motional anisotropy direction in which largest amplitude internal motion each vector takes place. The method demonstrated for backbone 15N−1H, 13Cα−1Hα, 13Cα−13C'...
All animal cells use the motor cytoplasmic dynein 1 (dynein) to transport diverse cargo toward microtubule minus ends and organize position arrays such as mitotic spindle. Cargo-specific adaptors engage with recruit activate motor, but molecular mechanisms remain incompletely understood. Here, we structural dynamic nuclear magnetic resonance (NMR) analysis demonstrate that C-terminal region of human light intermediate chain (LIC1) is intrinsically disordered contains two short conserved...
Abstract Recent methodological advances in solution NMR allow the determination of multi-state protein structures and provide insights into structurally dynamically correlated sites at atomic resolution. This is demonstrated present work for well-studied PDZ2 domain human tyrosine phosphatase 1E which allostery had been predicted. Two-state were calculated both free form complex with RA-GEF2 peptide using exact nuclear Overhauser effect (eNOE) method. In apo protein, an allosteric...
NMR structure determination is usually based on distance restraints extracted semiquantitatively from cross peak volumes or intensities in NOESY spectra. The recent introduction of exact NOEs (eNOE) by Vogeli et al. opens an avenue for the ensemble-based proteins basis eNOE-derived quantitative restraints. We present approach to extract eNOE build-up curve intensities. For eNOEs, spin diffusion a major source errors. A full relaxation matrix analysis used calculate contribution peaks each...
The motions of biological macromolecules are tightly coupled to their functions. However, while the study fast has become increasingly feasible in recent years, slower, biologically important remains difficult. Here, we present a method construct native state ensembles proteins by combination physical force fields and experimental data through modern statistical methodology. As an example, use NMR residual dipolar couplings determine ensemble extensively studied third immunoglobulin binding...
Structural snapshots characterize six hundred million years of evolution intrinsically disordered proteins.
Amyloid-β (Aβ) peptide is the major component found in senile plaques of Alzheimer's disease patients. The 42-residue fragment Aβ(1-42) proposed to be one most pathogenic species therein. Here, soluble were analyzed by various liquid-state NMR methods. Transient formation a micelle was observed at onset aggregation kinetics. This dissolved after approximately day. Subsequent loss this and protofibrils are route fibril formation. Consequently, suggested on an off-pathway mechanism....
We have recently developed an NMR protocol to extract exact distances between nuclei in proteins from interpretation of NOESY buildup intensities (eNOEs). This enabled us calculate multistate structural ensembles that exhibit realistic spatial sampling and long-range correlations. Our initial studies were laborious required a deep understanding the underlying spin dynamics. Here, we present MatLab package integrates all data processing steps convert assigned peaks series into upper lower...
We provide an atomic-level description of the structure and dynamics UUCG RNA stem-loop by combining molecular simulations with experimental data. The integration exact nuclear Overhauser enhancements data allowed us to characterize two distinct states this molecule. most stable conformation corresponds consensus three-dimensional structure. second state is characterized absence peculiar non-Watson-Crick interactions in loop region. By using machine learning techniques we identify a set...
During episodes of acute inflammation, polymorphonuclear leukocytes (PMNs) are actively recruited to sites inflammation or injury where they provide anti-microbial and wound-healing functions. One enzyme crucial for fulfilling these functions is myeloperoxidase (MPO), which generates hypochlorous acid from Cl- hydrogen peroxide. The potential exists, however, that uncontrolled the extracellular generation by MPO can cause bystander tissue damage inhibit healing response. Previous work...