Irina El Khoury

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…

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…

EMSL Science Overview

Irina El Khoury

Projects

Structural characterization of essential enzymes in bacterial wall teichoic acid biogenesis

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

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

Structure determination of transthyretin amyloid fibrils extracted from amyloidosis patients

Novel serine peptidases regulate the NLRP1 and CARD8 inflammasomes

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

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

Manganese biomineralization by the bacterial protein complex Mnx

Structural studies of large clostridium toxins

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

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

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

Structure of the first purified manganese oxidase Mnx

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

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

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

Cryo-EM studies of heteromeric epithelial sodium channels

Solving the Structure of Eukaryotic Type III Glutamine Synthetase Assembles

Cryo-EM studies of DNA damage response proteins

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

Cryo-EM studies of drug transporters

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

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

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.

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

Nuclear export of phosphorylated proteins by Karyopherin MSN5

Structure and Function of Adenylyl Cyclase

Structural Mechanisms of Renal Sensory and Transport Proteins

Structural basis of synaptic receptor trafficking by PICK1

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

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