Irina El Khoury

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…

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…

Development of in vitro glycosylation toolkit to study eukaryotic glycoproteins

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Irina El Khoury

When working with glycoproteins from native sources, biochemical analysis is often hampered by sample heterogeneity and glycan-postprocessing structural diversity. It is therefore desirable to create…

Structure of the first purified manganese oxidase Mnx

Lead Institution

University of Washington

Principal Investigator

Bradley Tebo

This project aims to obtain high-resolution atomic structure of the first purified bacterial manganese-oxidizing complex, Mnx. This complex, containing the novel multicopper oxidase MnxG enzyme, has…

Toward the visualization of eukaryotic transcription machineries by cryo-EM

Lead Institution

Northwestern University

Principal Investigator

Yuan He

Eukaryotic genomes are modulated by different types of chromatin remodeling complexes and transcribed by multiple RNA polymerases. Of the three polymerases, Pol I-III, that produce RNA required for…

Validation and functional characterization of transcription factors in wheat using cell-free protein
expression and high-throughput sequencing technologies

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Irina El Khoury

This study aims to validate and functionally characterize a family of transcription factors to understand the differences in their deoxyribonucleic acid binding preferences and their potential impact…

The structure of pseudoenzyme PDX1.2 and its complex with active enzyme PDX1.3

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Aim - Determine the high-resolution structure of the protein PDX1.2 alone and in complex with PDX1.3. PDX1.2 is an important pseudo-enzyme with regulatory roles in vitamin B6 biosynthesis. It…

Interactions of Adeno-associated virus (AAV) with its Cellular Receptor, RAAV

Lead Institution

University of Missouri - Columbia

Principal Investigator

Michael Chapman

AAV is a leading vector for gene therapy, and, through genomic screening, we recently identified the cellular receptor, AAVR. Biochemistry, and early cryo-EM indicate that the different serotype…

CryoEM structures of pancreatic KATP channels

Lead Institution

Oregon Health & Science University

Principal Investigator

Show-Ling Shyng

The ATP-sensitive potassium (KATP) channel formed by four Kir6.2 and four SUR1 subunits regulate insulin secretion in ?-cells by coupling glucose metabolism with membrane excitability. Mutations in…

Determination of inner hair cell stereocilia widening mechanism

Lead Institution

Oregon Health & Science University

Principal Investigator

Peter Barr-Gillespie

Hair cells are the sensory cells of the inner ear, and use the mechanically sensitive hair bundle to detect sound and head movements. Bundles are composed of a hundred or so stereocilia, each of…

Structure, function and aggregation of the lens alpha-crystallins

Lead Institution

Portland State University

Principal Investigator

Steve Reichow

We are applying emerging methods in single particle CryoEM to advance our understanding the molecular mechanisms leading to cataract formation (the leading cause of blindness in the world). The focus…

Structural Analysis of human retinal ABCA4 using single particle cryo-electron microscopy

Lead Institution

University of British Columbia

Principal Investigator

Robert Molday

Stargardt disease (STGD1) is an autosomal recessive, early-onset macular dystrophy associated with reduced visual acuity and a progressive loss in vision. The gene responsible for STGD1 encodes ABCA4…

Structural characterization of BlaR1: A key regulator of beta-lactam resistance in Staphylococcus aureus

Lead Institution

University of British Columbia

Principal Investigator

Natalie Strynadka

Our vision is to develop and use structural biology methods to characterize membrane-associated protein assemblies relevant to antibiotic resistance and bacterial pathogenicity. We are particularly…

Cryo-EM studies of the prothrombinase:prothrombin complex and the protein C anti-coagulant complex

Lead Institution

Saint Louis University

Principal Investigator

Enrico Di Cera

The objective of this study, funded by 2 active NIH grants, is to elucidate the structures of key proteins and their interacting partners of the prothrombinase:prothrombin complex and the protein C…

Cryo-EM studies of the human biogenic amine transporters

Lead Institution

Oregon Health & Science University

Principal Investigator

Eric Gouaux

The aims of the proposed research are to elucidate the first structure of the human dopamine transporter (hDAT) as well as to determine multiple structures of the human serotonin transporter (hSERT)…

Cryo-EM study of alpha-synuclein fibrils with hereditary disease mutation

Lead Institution

University of California, Los Angeles

Principal Investigator

Lin Jiang

With recent advances of cryo-EM technologies, including direct electron detecting cameras, we are now able to probe a broad scope of amyloid fibril structures to a level of molecular detail that has…

Structural study of full-length SARS-Cov-2 Spike proteins by Cryo-EM

Lead Institution

Oregon Health & Science University

Principal Investigator

Liman Zhang

As of February 25th, 2020 there were 80,146 confirmed cases of SARS-Cov-2 infection across the globe. However, no vaccine or drug is available to prevent or treat the infection. Spike protein of SARS…

Structural characterization of protozoa Hsp100 by single-particle cryo-transmission electron microscopy (Cryo-TEM).

Lead Institution

Sao Carlos Institute of Chemistry, University of São Paulo

Principal Investigator

Julio Borges

Chaperones, such as Hsp100, can help maintain cellular homeostasis and adaptation playing an important role for different organisms. The Hsp100 has a disaggregase action, acting with other proteins…

Correlative Imaging and Spectroscopy of Biological Systems and Structural Dynamics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

The overall objective of this project is to create an integrative capability for combining dynamic transmission electron microscopy with femtosecond x-ray diffraction, in situ and automated secondary…

Structural characterization of immunogens in complex with antibodies for structure-based vaccine design

Lead Institution

Fred Hutchinson Cancer Research Center

Principal Investigator

Marie Pancera

Although to-date numerous vaccines exist, their mechanism of protection is not always understood. Additionally, there are pathogens such as HIV and Malaria for which vaccines do not exist. Our…

Determination of RAD52 and replication fork DNA complex

Lead Institution

University of Iowa

Principal Investigator

Maria Spies

RAD52 is an emerging target for drug discovery targeting DNA repair-deficient tumors. The exact cellular functions and structural mechanisms of RAD52, however, remain unresolved. This proposed…

Toward the visualization of NHEJ DNA repair machineries by cryo-EM

Lead Institution

Northwestern University

Principal Investigator

Yuan He

Among all different types of DNA damages, double strand breaks (DSBs) are viewed as the most toxic ones that lead to genome instability. Non-homologous end-joining (NHEJ) pathway, in which the two…

Cryo-EM structural study of mammalian DNA methylation

Lead Institution

University of California, Riverside

Principal Investigator

Jikui Song

The eukaryotic genome is organized into different functional compartments, with euchromatin representing an open and transcriptionally active state and heterochromatin representing a more compact and…

Systems Biology Through an Integrated Multimodal Imaging and Analysis Framework

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…

Native Mass Spectrometry Enabled Electron Microscopy for Visual Proteomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jared Shaw

Develop a soft-landing capability for native protein complexes coupled with electron microscopy (EM) to enable visual proteomics. Sample heterogeneity greatly limits the resolution of 3D structures…

Structural studies of chromatin complexes involved in human diseases

Lead Institution

Pennsylvania State University

Principal Investigator

Song Tan

The nucleosome is a fundamental unit of chromatin and the target of a host of gene regulatory chromatin enzymes and proteins. It consists of DNA wrapped around a protein core, composed of histones…

Structure and mechanism of human diacylglycerol O-acyltransferase-1

Lead Institution

Baylor College of Medicine

Principal Investigator

Ming Zhou

Diacylglycerol O-acyltransferase-1 (DGAT1) synthesizes triacylglycerides and is required for dietary fat absorption and fat storage in mammals. DGAT1 belongs to the superfamily of membrane-bound O…

Structural studies on AAA+ chaperone complexes

Lead Institution

University of Toronto

Principal Investigator

Walid Houry

Cells have evolved various mechanisms for harnessing the energy from nucleotide hydrolysis and directing it towards useful work. One class of proteins using such a mechanism is the P-loop NTPases,…

Systems Biology Through an Integrated Multimodal Imaging and Analysis Framework

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…

Single-particle cryo-EM structural analysis of Q-dependent transcription antitermination

Lead Institution

Rutgers University

Principal Investigator

Richard Ebright

The transcription antitermination factor Q, produced by lambdoid bacteriophages, is a textbook example of a regulator of gene expression that functions at the level of transcription termination. Q…

Structure and activation mechanism of TMEM206

Lead Institution

Oregon Health & Science University

Principal Investigator

Eric Gouaux

Proton activated channels are ion-permeable channels that are rapidly activated by extracellular acidification. With their activation levels falling well below physiological pH, these channels…

Elucidating HIV-1 capsid interactions with host cofactors

Lead Institution

Yale University

Principal Investigator

Yong Xiong

Human immunodeficiency virus type 1 (HIV-1) infection is a global epidemic. Between the point of entry into the cell and integration of the HIV-1 genome into the host genome, the virus encounters…

Structural characterization of essential enzymes in bacterial wall teichoic acid biogenesis

Lead Institution

University of British Columbia

Principal Investigator

Natalie Strynadka

Wall teichoic acid (WTA) is a Gram-positive bacterial cell wall polymer with roles in host cell adherence and coordination of essential physiological processes including cell division and…

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…

Projects