Irina El Khoury | Environmental Molecular Sciences Laboratory

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using microcrystal electron diffraction (MicroED)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

Project type

Cryo-EM Only

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain…

Cell-free synthesis of Influenza Virus-like particles (VLPs) as prototyping platform for vaccine development and variant characterization

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Irina El Khoury

We aim to combine wheat germ cell-free protein expression platform with active microsomes of different origin to synthesize influenza virus-like particles (VLPs). These particles will undergo…

The molecular basis for the role of apolipoprotein A-II in cholesterol and triglyceride metabolism

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Melchior

Project type

Cryo-EM Only

Apolipoprotein (apo)A-II is an abundant human plasma protein primarily in high-density lipoproteins (HDL) but also in very low density lipoproteins (VLDL) and chylomicrons. Despite a large literature…

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using microcrystal electron diffraction (MicroED)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain…

Unraveling New Pathways for Carbon Capture to Enhance Lipid-Biomass Feedstocks

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Organisms have evolved a number of spatially localized processes to efficiently break down, absorb, and use necessary metabolites. Although progress has been made in identifying the genes that are…

Determining structural mechanisms of transporters and signaling networks in cellular stress responses

Lead Institution

University of Arizona

Principal Investigator

Thomas Tomasiak

Rapidly dividing or invasive cells tied to diseases such as cancer, fungal or bacterial infection require responses that enable their survival during nutrient deprivation and drug therapy. Tightly…

Structure determination of transthyretin amyloid fibrils extracted from amyloidosis patients

Lead Institution

University of Texas Southwestern Medical Center

Principal Investigator

Lorena Saelices

Here, we aim to use cryo-electron microscopy to determine the structures of full-length transthyretin fibrils extracted from autopsied or explanted hearts from ATTR patients carrying either a wild…

Novel serine peptidases regulate the NLRP1 and CARD8 inflammasomes

Lead Institution

Boston Children's Hospital

Principal Investigator

Hao Wu

The inflammatory response provides an absolutely essential host defense mechanism that, if perturbed, can itself cause a large number of human diseases. Collectively, innate immune responses…

Opportunities linking omics and structural biology at PNNL: Excelling at Cryo-EM

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

We were recently funded jointly by EMSL and DOE/BER to purchase, install and operate a new Krios G3i cryo-TEM at EMSL. By funding the system jointly, the new microscope would become available to EMSL…

Synthesis and Structural Probing of Protein Networks in Vitamin B6 Biosynthesis.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Irina El Khoury

We propose to develop a multi-modal experimental pipeline, integrating multiple existing and emerging EMSL capabilities, including cell-free protein expression, Native Mass Spectrometry (Native MS),…

Manganese biomineralization by the bacterial protein complex Mnx

Lead Institution

University of Washington

Principal Investigator

Bradley Tebo

Project type

Large-Scale EMSL Research

Manganese-oxide mineral formation by bacterial oxidation of dissolved Mn(II) is an important process in aquatic and soil environments and is a key part of the global Mn cycle. The Mn bio-oxides…

Structural studies of large clostridium toxins

Lead Institution

University of California, Irvine

Principal Investigator

Rongsheng Jin

Bacterial toxins are virulence factors that manipulate host cell functions and cause a myriad of serious diseases. We propose two aims to study the structure and function of Clostridium difficile…

Novel biochemical methods for facilitating GPCR tertiary and quaternary structure determination by cryo-EM.

Lead Institution

Oregon Health & Science University

Principal Investigator

David Farrens

GPCRs are the largest family of membrane proteins in the human genome, and a major target of pharmaceutical drugs. However, relatively few GPCR structures are known. Moreover, many GPCRs are known…

Mechanisms of DNA damage access within the nucleosome during Base Excision Repair

Lead Institution

University of Kansas Medical Center

Principal Investigator

Bret Freudenthal

Despite the packaging of eukaryotic DNA into chromatin through repeating units known as the nucleosomes, it is constantly damaged via reactive oxygen species (ROS). 8oxo-guanine (8oxoG) is a common…

Collaborative Access Team: Pacific Northwest Cryo-EM Center (PNCC)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

PNNL will create and operate the Pacific Northwest Center for Cryo-EM (PNCC), a state-of-the-art national center for cryo-electron microscopy (Cryo-EM) that will rapidly and efficiently collect and…

Structure of the first purified manganese oxidase Mnx

Lead Institution

University of Washington

Principal Investigator

Bradley Tebo

Microbial production of manganese oxide (MnO2) is a globally important biomineralization process. MnO2 is a key component of the Mn cycle, which supports life through the Mn catalytic centers of many…

Structure determination of diversity-generating retroelements ribonucleoprotein complex by Cryo-EM

Lead Institution

University of California, San Diego

Principal Investigator

Partho Ghosh

Diversity-generating retroelements (DGRs) are unique and unparalleled generators of massive protein sequence diversity. DGRs diversify proteins through a fundamentally different mechanism than the…

Structural basis for SidJ-catalyzed polyglutamylation of the SidE all-in-one ubiquitin ligases

Lead Institution

University of Texas Southwestern Medical Center

Principal Investigator

Vincent Tagliabracci

Enzymes with a protein kinase fold transfer phosphate from ATP to substrates in a process known as phosphorylation. We have discovered that the Legionella meta-effector SidJ adopts a protein kinase…

Structure / Function Analysis of Positive-Strand RNA Virus Replication Complexes

Lead Institution

University of Wisconsin, Madison

Principal Investigator

Paul Ahlquist

SARS-CoV-2, Zika, Dengue, and many other dangerous viruses belong to the positive-strand RNA((+)RNA) viruses. Our group first used cryo-electron tomography (cryo-ET) to reveal the organization of…

Cryo-EM studies of heteromeric epithelial sodium channels

Lead Institution

Oregon Health & Science University

Principal Investigator

Isabelle Baconguis

Epithelial sodium channels (ENaCs) are members of the ENaC/DEG superfamily of trimeric voltage-independent, Na+-selective and amiloride-sensitive ion channels. ENaCs assemble as heterotrimers that…

Solving the Structure of Eukaryotic Type III Glutamine Synthetase Assembles

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

There are three major classes of the enzyme Glutamine Synthetase (GS) that share widely conserved active-site residues but vary in average protein length, oligomeric assembly state and cofactor…

Cryo-EM studies of DNA damage response proteins

Lead Institution

Mayo Clinic

Principal Investigator

Georges Mer

DNA double-strand breaks (DSBs) are toxic lesions associated with cancer. In chromatin, a complex of DNA and histone proteins that forms nucleosomes, DSBs can be repaired by two different pathways…

Nuclear import of histone H2A-H2B and histone chaperone Nap1 by Kap114

Lead Institution

University of Texas Southwestern Medical Center

Principal Investigator

Yuh Chook

Core histones organize DNA in the nucleus. Histones are synthesized in the cytoplasm and are be transported by to the nucleus by Karyopherin nuclear transport receptors. In the cytoplasm, histones…

Cryo-EM studies of drug transporters

Lead Institution

Duke University

Principal Investigator

Seok-Yong Lee

The SLC superfamily of membrane transporters play critical roles in many aspects of human physiology and pharmacology. Several SLC transporters play roles in drug transport. Of note, nucleoside…

Development of an Integrated Structural Mass Spectrometry Platform for Unveiling the Structure of an Unknown Protein Complex Machinery in Lignin Synthesis

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mowei Zhou

Multiple distinct Lignin-Forming Complexes (LFC) are proposed to be templates and catalysts that orchestrate lignin synthesis in plants. It is hypothesized that each LFC consists of one or more…

Structural basis for recognition of receptor CSPG4 by Clostridium difficile toxin B

Lead Institution

University of California, Irvine

Principal Investigator

Rongsheng Jin

Clostridium difficile (C. diff) is an opportunistic pathogen, which establishes in the colon when the gut microbiota is disrupted by antibiotics or diseases. C. difficile infection (CDI) leads to…

Development of Copper Storage Protein Csp1 as an Electron-Dense “Bio Tag” for Facilitating Structural Determination of Small (< 100 kDa) Proteins by single-particle Cryo EM Methods.

Lead Institution

Oregon Health & Science University

Principal Investigator

David Farrens

Small (< 100 kDa) proteins are challenging to study by standard single-particle cryo-EM techniques, due to their very low signal to noise ratios in images. Heavy atoms could potentially overcome…

COVID19: Structure of COVID19 SARS-CoV-2 Spike protein in complex with monoclonal antibodies.

Lead Institution

Fred Hutchinson Cancer Research Center

Principal Investigator

Marie Pancera

The ongoing global outbreak of atypical pneumonia (COVID-19) is caused by a newly emerged zoonotic beta coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (1). On March 11th,…

Nuclear export of phosphorylated proteins by Karyopherin MSN5

Lead Institution

University of Texas Southwestern Medical Center

Principal Investigator

Yuh Chook

MSN5 is the 142 kDa S. cerevisiae exportin, which exports many different protein cargoes from the nucleus to the cytoplasm in response to cellular environmental changes. Peptide signals in several…

Structure and Function of Adenylyl Cyclase

Lead Institution

Oregon Health & Science University

Principal Investigator

Matt Whorton

Adenylyl cyclases (ACs) are a family of proteins that convert ATP to the second messenger cyclic AMP (cAMP). They are widely expressed and involved in numerous biological processes. The…

Structural Mechanisms of Renal Sensory and Transport Proteins

Lead Institution

University of Utah

Principal Investigator

Erhu Cao

The kidneys regulate blood composition, pressure, and volume, balance electrolytes and acid-base, and reabsorb most salts and nutrients from the initial renal filtrate while excreting metabolic…

Structural basis of synaptic receptor trafficking by PICK1

Lead Institution

University of Pennsylvania

Principal Investigator

Roberto Dominguez

Our goal is to determine the structural-functional mechanism by which the BAR domain protein PICK1 controls the trafficking of synaptic receptors, including AMPA and the dopamine transporter…

Structure and function of the membrane-bound copper-dependent methane monooxygenase in lipid nanodiscs

Lead Institution

Northwestern University

Principal Investigator

Amy Rosenzweig

Particulate methane monooxygenase (pMMO) is the primary enzyme used for methane metabolism by methane-consuming bacteria known as methanotrophs. pMMO is a copper-dependent, membrane-bound…

Structure and function of connexin-46/50 gap junction channels

Lead Institution

Portland State University

Principal Investigator

Steve Reichow

The gap junctions are a class of membrane channel proteins that form direct pathways for cell-to-cell communication. Dynamic mechanisms of channel gating are required to control these communication…

Structure / Function Analysis of Positive-Strand RNA Virus Replication Complexes

Lead Institution

University of Wisconsin, Madison

Principal Investigator

Paul Ahlquist

Positive-strand RNA ((+)RNA) viruses, the largest genetic class of viruses, include numerous major pathogens such as the Zika, MERS, SARS and hepatitis C viruses. A key target for understanding and…

Mechanistic elucidation of inflammasome biology

Lead Institution

Boston Children's Hospital

Principal Investigator

Hao Wu

Innate immunity comprises ancient and evolutionarily conserved biological pathways that are imperative for the recognition of pathogens and endogenous damage. One such major signaling pathway…

Understanding the structural basis of RFX complex in regulating MHC gene expression

Lead Institution

Oregon Health & Science University

Principal Investigator

Liman Zhang

The Major Histocompatibility complex (MHC) is critical in immune system for T cell maturation and self vs nonself discrimination, thus expression of MHC genes has to be tightly regulated. Active…

COVID-19: Structural analysis of SARS-CoV-2 proteins to understand virus immunogenicity and develop therapeutic interventions for COVID19

Lead Institution

La Jolla Institute for Immunology

Principal Investigator

Erica Saphire

Effective and rapid responses to the ongoing COVID-19 pandemic must involve vaccination, therapies and serology. Our laboratory has the required expertise to produce and manage significant volumes of…

Determine the structural basis of splicing modulation by small molecules

Lead Institution

University of Colorado Anschutz Medical Campus

Principal Investigator

Rui Zhao

Aberrant pre-mRNA splicing contributes to 10-15 % of genetic disorders, including Spinal Muscular Atrophy (SMA). SMA is a potentially lethal neurodegenerative disorder caused by loss of function…

KATP channel structures

Lead Institution

Oregon Health & Science University

Principal Investigator

Show-Ling Shyng

ATP-sensitive potassium (KATP) channels couple cell metabolism to membrane excitability and are important for regulating hormone secretion, neuronal activity, vascular tone, and adaptive response to…

Structure of the TRAMP RNA surveillance complex

Lead Institution

Utah State University

Principal Investigator

Sean Johnson

This proposal seeks access to the PNCC cryo-EM facility in order to obtain structural information for the TRAMP (Trf4-Air2-Mtr4 polyadenylation) complex. The goal is to better understand assembly of…

Structural Mechanism of Jordan's Syndrome

Lead Institution

University of Wisconsin, Madison

Principal Investigator

Yongna Xing

Protein phosphatase 2A (PP2A) is an essential and major serine/threonine phosphatase in all eukaryotic cells, and regulates multiple cellular processes and signaling events. Deregulation of PP2A and…

Elucidating the structure of C. elegans TMC1 and TMC2

Lead Institution

Oregon Health & Science University

Principal Investigator

Eric Gouaux

Transmembrane channel-like (TMC) proteins are a unique family of channel-like proteins that are conserved from humans to C. elegans. Vertebrates express eight isoforms, two of which are essential for…

Impact of apolipoprotein E isoforms on brain lipoproteins

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Melchior

Cerebrovascular dysfunction leads to the deposition of amyloid plaques and neurofibrillary tangles in the brain which underlie the development of Alzheimer’s disease (AD); an epidemic that…

Structure and function of the gap junctions

Lead Institution

Portland State University

Principal Investigator

Steve Reichow

The gap junctions are a class of membrane channel proteins that form direct pathways for cell-to-cell communication. Dynamic mechanisms of channel gating are required to control these communication…

Cryo-EM studies of TRP channels

Lead Institution

Duke University

Principal Investigator

Seok-Yong Lee

Transient receptor potential (TRP) channels are a superfamily of calcium-permeable ion channels that are involved in diverse physiological processes. A subset of TRP channels that are known as the…

CryoEM structural determinations of Bacterial Restriction-Modification systems

Lead Institution

Fred Hutchinson Cancer Research Center

Principal Investigator

Betty Shen

Nuclease enzymes are of enormous importance for a wide range of biological and biotechnology disciplines that require site-specific DNA manipulations. Bacterial R-M systems consist of a restriction…

Cryo-EM structural analysis of Glucose-6-phosphatase catalytic subunit, G6PC1

Lead Institution

Vanderbilt University

Principal Investigator

Hassane Mchaourab

The catalytic subunit of glucose-6-phosphatase, G6PC1, functions as a gatekeeper of glucose production in the liver by catalyzing the hydrolysis of glucose-6-phosphate. Dysregulation of G6PC1 gene…

The molecular basis for the role of apolipoprotein A-II in cholesterol and triglyceride metabolism

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Melchior

Apolipoprotein (apo)A-II is an abundant human plasma protein primarily in high-density lipoproteins (HDL) but also in very low density lipoproteins (VLDL) and chylomicrons. Despite a large literature…

Structure and mechanism of neurotransmitter-gated ion channels

Lead Institution

Oregon Health & Science University

Principal Investigator

Eric Gouaux

The objectives of this research are to elucidate the structures of mammalian neurotransmitter receptors by single particle cryo-EM in multiple distinct conformational states in which the receptors…

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