A5030920869- Enzyme Structure and Function
- Biochemical and Molecular Research
- Amino Acid Enzymes and Metabolism
- Microbial Natural Products and Biosynthesis
- Photoreceptor and optogenetics research
- Metal complexes synthesis and properties
- Advanced Fluorescence Microscopy Techniques
- Synthesis and Characterization of Heterocyclic Compounds
- Protein Structure and Dynamics
- Photosynthetic Processes and Mechanisms
- bioluminescence and chemiluminescence research
- Cancer, Hypoxia, and Metabolism
- Bacteriophages and microbial interactions
- Enzyme Production and Characterization
- Enzyme Catalysis and Immobilization
- SARS-CoV-2 and COVID-19 Research
- Pancreatic function and diabetes
- HIV/AIDS drug development and treatment
- Antibiotic Resistance in Bacteria
- Monoclonal and Polyclonal Antibodies Research
- Crystal structures of chemical compounds
- Spectroscopy and Quantum Chemical Studies
- Peptidase Inhibition and Analysis
- Inorganic and Organometallic Chemistry
- Click Chemistry and Applications
Stanford Synchrotron Radiation Lightsource
2016-2025
Stanford University
2014-2024
SLAC National Accelerator Laboratory
2013-2024
Fermi National Accelerator Laboratory
2012-2024
Lawrence Berkeley National Laboratory
2021
Los Alamos National Laboratory
2021
University of California, San Francisco
2021
University of Nebraska–Lincoln
2021
Linac Coherent Light Source
2021
Menlo School
2017
The task of protein sequence design is central to nearly all rational engineering problems, and enormous effort has gone into the development energy functions guide design. Here, we investigate capability a deep neural network model automate sequences onto backbones, having learned directly from crystal structure data without any human-specified priors. generalizes native topologies not seen during training, producing experimentally stable designs. We evaluate generalizability our method de...
Abstract Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 essential for viral replication. In addition, PLpro dysregulates the host immune response cleaving ubiquitin and interferon-stimulated gene 15 protein proteins. As a result, promising target inhibition small-molecule therapeutics. Here we design series...
Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this on genomic scale, novel methods and technologies must be developed determine large numbers of structures. We describe the design implementation high-throughput structural pipeline its application proteome thermophilic bacterium Thermotoga maritima. By using pipeline, we successfully cloned attempted expression 1,376 predicted 1,877 genes (73%) have identified...
The x-ray crystal structure of a 194-kDa fragment from module 5 the 6-deoxyerythronolide B synthase has been solved at 2.7 Å resolution. Each subunit homodimeric protein contains full-length ketosynthase (KS) and acyl transferase (AT) domain as well three flanking “linkers.” linkers are structurally defined contribute extensively to intersubunit or interdomain interactions, frequently by means multiple highly conserved residues. also reveals that active site residue Cys-199 KS is separated...
Adenosine kinase (AK) is a key enzyme in the regulation of extracellular adenosine and intracellular adenylate levels. Inhibitors elevate to levels that activate nearby receptors produce wide variety therapeutically beneficial activities. Accordingly, AK promising target for new analgesic, neuroprotective, cardioprotective agents. We determined structure human by X-ray crystallography using MAD phasing techniques refined 1.5 Å resolution. The consisted one large α/β domain with nine...
Significance The extremely short and bright X-ray pulses produced by free-electron lasers unlock new opportunities in crystallography-based structural biology research. Efficient methods to deliver crystalline material are necessary due damage or destruction of the crystal pulse. Crystals for first experiments were 5 µm smaller size, delivered a liquid injector. We describe highly automated goniometer-based approach, compatible with crystals larger varied sizes, accessible at cryogenic...
Electrostatics guide chromophore twist Photoisomerization—the twisting of bonds in a molecule response to absorption light—is exploited biology sense light and can influence the photophysical properties fluorescent proteins used imaging applications. Romei et al. studied this behavior by introducing unnatural amino acids into photoswitchable green protein Dronpa2, thus systematically altering electronic (see Perspective Hu ). Crystal structures spectroscopic analyses series these variants...
The AXL receptor and its activating ligand, growth arrest–specific 6 (GAS6), are important drivers of metastasis therapeutic resistance in human cancers. Given the critical roles that GAS6 play refractory disease, this signaling axis represents an attractive target for intervention. However, strong picomolar binding affinity between promiscuity small molecule inhibitors represent challenges faced by current anti-AXL therapeutics. Here, we have addressed these obstacles engineering a...
V-domain immunoglobulin (Ig) suppressor of T cell activation (VISTA) is an immune checkpoint protein that inhibits the response against cancer. Similar to PD-1 and CTLA-4, a blockade VISTA promotes tumor clearance by system. Here, we report 1.85 Å crystal structure elusive human extracellular domain, whose lack homology necessitated combinatorial MR-Rosetta approach for determination. We highlight features make variable (IgV)-like fold unique among B7 family members, including two additional...
Lymphocyte activation gene-3 (LAG-3) is an inhibitory receptor expressed on activated T cells and emerging immunotherapy target. Domain 1 (D1) of LAG-3, which has been purported to directly interact with major histocompatibility complex class II (MHCII) fibrinogen-like protein (FGL1), the focus for development therapeutic antibodies that inhibit LAG-3 receptor-ligand interactions restore cell function. Here, we present a high-resolution structure glycosylated mouse ectodomain, identifying...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystallographic Structures of Thrombin Complexed with Receptor Peptides: Existence Expected and Novel Binding ModesI. I. Mathews, K. P. Padmanabhan, V. Ganesh, A. Tulinsky, M. Ishii, J. Chen, C. W. Turck, S. R. Coughlin, Fenton, IICite this: Biochemistry 1994, 33, 11, 3266–3279Publication Date (Print):March 22, 1994Publication History Published online1 May 2002Published inissue 22 March...
Prolyl endopeptidases (PEPs) are a unique class of serine proteases with considerable therapeutic potential for the treatment celiac sprue. The crystal structures two didomain PEPs have been solved in alternative configurations, thereby providing insights into mode action these enzymes. structure Sphingomonas capsulata PEP, and refined to 1.8-A resolution, revealed an open configuration active site. In contrast, inhibitor-bound PEP from Myxococcus xanthus was crystallized (1.5-A resolution)...
Complete automation of the macromolecular crystallography experiment has been achieved at SSRL through combination robust mechanized experimental hardware and a flexible control system with an intuitive user interface. These highly reliable systems have enabled experiments to be carried out from researchers' home institutions other remote locations while retaining complete over even most challenging systems. A breakthrough component system, Stanford Auto-Mounter (SAM), efficient mounting...
The unusual architecture of the enzyme (MsAcT) isolated from Mycobacterium smegmatis forms mechanistic basis for favoring alcoholysis over hydrolysis in water. Unlike hydrolases that perform only under anhydrous conditions, MsAcT demonstrates substantially aqueous media and, presence hydrogen peroxide, has a perhydrolysis:hydrolysis ratio 50-fold greater than best lipase tested. crystal structures apoenzyme and an inhibitor-bound form have been determined to 1.5 Å resolution. is octamer...
Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, spontaneous especially one that includes effects of protein environment. In this work, we study correlations among from...
One of the simplest organisms to divide asymmetrically is bacterium Caulobacter crescentus. The DivL pseudo-histidine kinase, positioned at one cell pole, regulates cell-fate by controlling activation global transcription factor CtrA via an interaction with response regulator (RR) DivK. uniquely contains a tyrosine histidine phosphorylation site, and can achieve these regulatory functions in vivo without kinase activity. Determination crystal structure biochemical analysis wild-type...
Type I modular polyketide synthases are homodimeric multidomain assembly line enzymes that synthesize a variety of natural products by performing chain extension and β-keto group modification reactions. We determined the 2.4-angstrom-resolution x-ray crystal structure 3.1-angstrom-resolution cryo–electron microscopy Lsd14 synthase, stalled at transacylation condensation steps, respectively. These structures revealed how constituent domains positioned relative to each other, they rearrange...
In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate host response. Here, vitro assays show that 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of 2.50 Å resolution crystal structure C145S bound
The 1.51 Å resolution X-ray crystal structure of the trans-acyltransferase (AT) from "AT-less" disorazole synthase (DSZS) and that its acetate complex at 1.35 are reported. Separately, comprehensive alanine-scanning mutagenesis one acyl carrier protein substrates (ACP1 DSZS) led to identification a conserved Asp45 residue on ACP, which contributes substrate specificity this unusual enzyme. Together, these experimental findings were used derive model for selective association DSZS AT ACP...
Significance The electronic structure of oxyhemoglobin has been under intense scrutiny since the geometric this bent, end-on bound Fe-O 2 species was first determined over three decades ago, but a consensus description not yet reached. Here, solution and crystalline X-ray absorption spectroscopies have combined with time-dependent density functional theory calculations to demonstrate dominantly (ferric-superoxide) character oxyhemoglobin. It is also shown that, in crystallo , Fe 2+ -O...