John Cort

Pentosan Polysulfate Sodium Profiling with Mass Spectrometry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

PPS is a semisynthetic heterogeneous sulfated polysaccharide derived from xylan, the β-1,4-linked polymer of xylose that is the backbone structural component of hemicellulose in most types of wood…

Pentosan Polysulfate Profiling with NMR Spectroscopy

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

The proposed research will apply a heteronuclear nuclear magnetic resonance (NMR) spectroscopy method for profiling the molecular composition of pentosan polysulfate (PPS) in its pure active…

Pentosan Polysulfate Sodium Profiling with Mass Spectrometry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

PPS is a semisynthetic heterogeneous sulfated polysaccharide derived from xylan, the β-1,4-linked polymer of xylose that is the backbone structural component of hemicellulose in most types of wood…

Structure of the binding interface between tropomodulin and tropomyosin

Lead Institution

Washington State University

Principal Investigator

Alla Kostyukova

In striated muscles, actin thin filament architecture is critical for efficient contractile activity, and alterations in the thin filament length are linked to severe and often lethal muscle diseases…

1H AND 13C NMR STUDY OF BRODIFACOUM STEREOCHEMISTRY AND STRUCTURE

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

Project type

Exploratory Research

Brodifacoum is a lipid-soluble warfarin derivative that inhibits vitamin K epoxide reductase (VKOR) and exhibits potent anticoagulant activity. Because of its chemical stability and use in numerous…

Signature Discovery in Organic Compounds

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

This project will survey physical and chemical characteristics of organic compounds of interest in chemical forensics applications.The goal is to develop chemical attribution signatures (CAS’s) for…

Integrated multi-modal approach for structure and function determination of lignin-forming protein complexes isolated from plants

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

We propose to apply an integrated multi-modal structural biology approach to investigate a biosynthetic protein complex in plants that is hypothesized to organize and guide lignin biosynthesis via…

A Systems Biology Approach to Infectious Diseases Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

Project type

Exploratory Research

We describe an integrated program for coupling advanced capabilities in high-throughput transcriptomics, proteomics, and metabolomics with a comprehensive informatics infrastructure and a…

Statistical Methodology for Characterization of Macromolecular Similarity

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

As with any drug, approval of generic versions of macromolecular drugs requires rigorous evaluation of therapeutic equivalence to the reference drug in order to assure similar efficacy and safety…

Backfilling the Natural Products Magnetic Resonance Database with DFT Calculated NMR Chemical Shifts

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Ryan Renslow

The gold standard for unequivocal identification of a novel natural product (NP) or other small molecule is structure elucidation by NMR spectroscopy. Although, over 100,000 natural products have…

Study of temperature-sensitive mutants of yeast guanylate kinase

Lead Institution

Washington State University

Principal Investigator

Ping Ye

Project type

Limited Scope

The ability to switch genes on and off spatially and temporally is important for understanding individual gene function in complex biological processes. Despite the fact that a variety of conditional…

Deciphering Microbial Communication Through Metabolites

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

This project will establish a Metabolomics Center at PNNL that will develop the advanced measurement capabilities necessary to define the metabolic processes of microbiomes and determine how these…

Structural characterization of polycyclopropanated high energy biofuels produced by fermentation

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

This project will use NMR spectroscopy and mass spectrometry to elucidate structures and profile mixtures of novel fatty acids produced by engineered microorganisms.

Exploring Microbe-Microbe and Microbe-Environment Interactions in Acidiphilium cryptum and Acidithiobacillus ferrooxidans: A Model Contaminant Metal Redox Cycling System

Lead Institution

Idaho State University

Principal Investigator

Timothy Magnuson

Project type

Large-Scale EMSL Research

Dissimilatory metal-respiring bacteria (DIRB) of widely differing phylogenetic and ecophysiologic affiliation share one distinct physiologic feature-the copious production of redox-active…

Undiagnosed Diseases Network Metabolomics Core

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

A state of the art metabolomics core will be a vital part of the Undiagnosed Diseases Network (UDN). However, in order for the UDN to realize it’s the full potential it is essential that the…

Pentosan Polysulfate Profiling with NMR Spectroscopy

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

The proposed research will apply a heteronuclear nuclear magnetic resonance (NMR) spectroscopy method for profiling the molecular composition of pentosan polysulfate (PPS) in its pure active…

A Systems Biology Approach to Infectious Diseases Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

Project type

Exploratory Research

We describe an integrated program for coupling advanced capabilities in high-throughput transcriptomics, proteomics, and metabolomics with a comprehensive informatics infrastructure and a…

Structure of the binding interface between leiomodin and tropomyosin.

Lead Institution

Washington State University

Principal Investigator

Alla Kostyukova

Project type

Limited Scope

Cardiac muscle cells contain two types of protein filaments composed of either actin or myosin. The filaments slide past one another and produce force in the heart muscle. For healthy heart…

PNNL/NESG Structural Genomics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

Project type

Capability Research

PNNL is a member of the Northeast Structural Genomics Consortium (NESG), a NIH-funded pilot project intended to explore the feasability of and technical challenges presented by high-throughput…

Characterization of Effector and Host Proteins Involved in Host-Pathogen Interactions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

Project type

Exploratory Research

The multiple mechanisms by which pathogenic enterobacteria of the genus Salmonella infect their host indicate a complex host-pathogen relationship. The pathogen secretes dozens of proteins, termed &…

The Lignin Enigma: Turning the Corner

Lead Institution

Washington State University

Principal Investigator

Norman Lewis

Project type

Large-Scale EMSL Research

Lignins (Nature's second most abundant terrestrial plant substances) provide structural support for plants to stand upright, to conduct water/nutrients, and as barriers to opportunistic…

GC-MS Analysis of Alkaline Cellulose Degradation Products

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

Project type

Exploratory Research

Degradation of cellulose and other polysaccharides in alkaline conditions and at elevated temperatures yields mixtures of compounds containing carboxylic acid and/or alcohol functional groups. These…

NMR profiling of monoclonal antibodies

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

High resolution solution state NMR spectroscopy will be used to profile monoclonal antibodies. Two antibodies will be studied, 1) a candidate NIST standard Fab domain, and 2) trastuzumab, an FDA…

Dirigent Protein Structure and Mechanism

Lead Institution

Washington State University

Principal Investigator

Norman Lewis

Project type

Large-Scale EMSL Research

The biochemistry of vascular plants has evolved in such a way as to rely extensively upon unique phenoxy radical coupling reactions thereby generating substances for structural support, for formation…

Statistical Methodology for Characterization of Macromolecular Similarity

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

As with any drug, approval of generic versions of macromolecular drugs requires rigorous evaluation of therapeutic equivalence to the reference drug in order to assure similar efficacy and safety…

Structural Genomics Collaborative Access Team (CAT)

Lead Institution

Miami University

Principal Investigator

Michael Kennedy

The Structural Genomics CAT will carry out research focused in structural genomics and related research areas with a primary goal of increasing throughput, maximizing efficiency of existing resources…

NMR-based metabolomics of the enteropathogens Salmonella and Yersinia

Lead Institution

Washington State University Tri-Cities

Principal Investigator

Kathleen McAteer

Project type

Large-Scale EMSL Research

The goal of this research is to analyze and reconstruct intercellular and intracellular networks in Salmonella and Yersinia using multiple types of -omics data. Although we hope to gain a more…

Using Mass Spectrometry and 2D-NMR to characterize biomass-derived liquid and solid streams

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Mariefel Olarte

This proposal aims to generate a deeper understanding of bio-oils and lignin samples through characterization using advanced chromatography (LC and GC), mass spectrometry (MS) and nuclear magnetic…

Source Attribution of Biological Weapons (Ricin and Associated Metabolites) Using NMR Spectroscopy

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Garry Buchko

Project type

Capability Research

This project will study variations in the chemical and isotopic composition of biological weapons with the goal of developing a robust forensics method for deducing the origins and relatedness of…

Quantitative Characterization of Biomass Deconstruction

Lead Institution

Washington State University Tri-Cities

Principal Investigator

Bin Yang

Project type

Exploratory Research

The objective of this research is to apply advanced characterization techniques to gain a deeper understanding of lignocellulosic biomass conversion to biofuels. The proposed research will take…

Using Mass Spectrometry and 2D-NMR to characterize biomass-derived liquid and solid streams

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Mariefel Olarte

This proposal aims to generate a deeper understanding of bio-oils and lignin samples through characterization using advanced chromatography (LC and GC), mass spectrometry (MS) and nuclear magnetic…

Protein Interactions and Interfaces

Lead Institution

Rutgers University

Principal Investigator

Gaetano Montelione

Project type

Large-Scale EMSL Research

All proteins interact with other molecules: ligands, metals, membranes, surfaces or other proteins. Such interactions are intrinsic to protein function. We propose to leverage our successful program…

Detection and identification of counterions in biologically active organic compounds

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

Project type

Limited Scope

Organic compounds containing acidic or basic functional groups, such as carboxylic acids or amines, frequently occur as the salt of the neutral compound. The characteristics of the counterion in…

Proteomic Assessment of Genes of Unknown Function

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

Understanding the full repertoire of biological functions has proven elusive, hampering our ability to predict outcomes of biological processes, such as infections or impacts of toxins. PNNL will…

Structure of Allochromatium vinosum DsrC protein

Lead Institution

Los Alamos National Laboratory

Principal Investigator

Thomas Terwilliger

Project type

Capability Research

Project Description: The dsrC gene codes for the 12.7 kDa protein DsrC, also known as the gamma subunit of dissimilatory sulfite reductase, and occurs in all sulfate-reducing bacteria (e.g…

Characterization of Effector and Host Proteins Involved in Host-Pathogen Interactions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The multiple mechanisms by which pathogenic enterobacteria of the genus Salmonella infect their host indicate a complex host-pathogen relationship. The pathogen secretes dozens of proteins, termed &…

Statistical Methodology for Characterization of Macromolecular Similarity

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

As with any drug, approval of generic versions of macromolecular drugs requires rigorous evaluation of therapeutic equivalence to the reference drug in order to assure similar efficacy and safety…

NMR and EPR Structural Characterization of c-Type Cytochromes and their Complexes from Contaminant Metal Remediating Iron-Respiring Bacteria

Lead Institution

Idaho State University

Principal Investigator

Timothy Magnuson

Project type

Exploratory Research

Abstract: While significant progress has been made regarding the genetics and genomics of dissimilatory metal-transforming bacteria and the redox proteins they possess, very little has yet been done…

Discovery of Host Proteins Involved in Host-Pathogen Interactions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The multiple mechanisms by which pathogenic enterobacteria of the genus Salmonella infect their host indicate a complex host-pathogen relationship. The pathogen secretes dozens of proteins, termed &…

Deciphering Lignin-forming Supramolecular Protein Complexes for Facile Biomass Deconstruction

Lead Institution

Washington State University

Principal Investigator

Norman Lewis

Project type

Large-Scale EMSL Research

Our overall aim is to further identify, dissect, and exploit dirigent protein (DP) mediated supramolecular protein complexes for macromolecular lignin assembly in order to ultimately achieve facile…

Proton and Carbon Chemical Shift Assignments of Brodifacoum

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

Project type

Limited Scope

We are making complete proton and carbon chemical shift assignments of both diastereomers of the potent vitamin K epoxide reductase (VKOR) inhibitor brodifacoum ((3-[3-[4-(4-bromophenyl)phenyl]-1,2,3…

Signature Discovery in Organic Compounds

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

This project will survey physical and chemical characteristics of organic compounds of interest in chemical forensics applications.The goal is to develop chemical attribution signatures (CAS’s) for…

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…

Evaluating the role of DsrC as a key protein in dissimilatory sulfur metabolism

Lead Institution

Instituto de Tecnologia Quimica e Biologica

Principal Investigator

Ines Pereira

Project type

Large-Scale EMSL Research

The dissimilatory reduction of sulfur compounds is one of the earliest energy metabolisms detected on Earth, at ~3.5 billion years ago. Sulfate reducing bacteria (SRB) are prominent among sulfur…

How Dirigent Proteins Guide Assembly of Lignans and Lignin in Vascular Plants

Lead Institution

Washington State University

Principal Investigator

Norman Lewis

Project type

Large-Scale EMSL Research

Vascular plants use a class of proteins termed dirigent proteins (from Latin dirigere, to guide or steer) to direct the regio- and stereospecificity of radical-radical coupling reactions of…

Proteomic Assessment of Genes of Unknown Function

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

Understanding the full repertoire of biological functions has proven elusive, hampering our ability to predict outcomes of biological processes, such as infections or impacts of toxins. PNNL will…

High-Throughput Structure Determination of Proteins and Protein Complexes

Lead Institution

Rutgers University

Principal Investigator

Gaetano Montelione

Project type

Large-Scale EMSL Research

The Northeast Structural Genomics Consortium (NESGC, www.nesg.org) is one of four large protein structure production centers supported by the NIH Protein Structure Initiative II (the PSI II). The…

Discovery of Host Proteins Involved in Host-Pathogen Interactions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The multiple mechanisms by which pathogenic enterobacteria of the genus Salmonella infect their host indicate a complex host-pathogen relationship. The pathogen secretes dozens of proteins, termed &…

Pentosan Polysulfate Sodium Profiling with Ion Mobility Mass Spectrometry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

Pentosan polysulfate sodium, known as PPS, is the active pharmaceutical ingredient in the prescription drug Elmiron, and is indicated for interstitial cystitis, a painful bladder condition caused by…

Projects