Andrew Lipton

Analysis of zinc environments in singlet oxygen-responsive proteins

Lead Institution

University of Wisconsin, Madison

Principal Investigator

Timothy Donohue

Project type

Capability Research

This project will use solid state NMR to probe the binding and environment of zinc ligands in the ChrR protein from the photosynthetic bacterium Rhodobacter sphaeroides. ChrR is a zincmetalloprotein…

Metal Binding by Melanin Biopolymers

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Eric Walter

The ubiquitous biopolymer melanin has important and unique materials properties, yet these very properties have prevented elucidation of its basic structure. MAS-NMR capabilities at EMSL will probe…

Investigation of Dynamics of Villin Headpiece Subdomain by Solid-State NMR with the Use of Single-Site Labeling.

Lead Institution

University of Alaska at Anchorage

Principal Investigator

Liliya Vugmeyster

Project type

Large-Scale EMSL Research

Villin headpiece protein subdomain (HP36) is extensively used as a model system for protein folding. A mutation of F58 residue was shown to rupture the native fold. Yet a double mutant involving two…

Multinuclear Solid-State NMR Studies of Environmental and Biological Systems

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Karl Mueller

My research team at EMSL carries out a number of studies that utilize a combination of high-resolution, solid-state nuclear magnetic resonance (NMR) spectroscopy and computational chemistry to…

Correlation of Structure and Function of Zinc Metalloproteins Via Solid-state NMR Methods

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

As early as 1869 it was known that zinc is an essential element for eukaryotes, it is the second most abundant trace element in humans after iron. About half of all proteins contain metal cations,…

Solid-State 67Zn NMR of Synthetic Metalloprotein Models

Lead Institution

Columbia University

Principal Investigator

Gerard Parkin

Project type

Capability Research

It is the invention of this proposal to describe studies that will be undertaken in order to aid our understanding of the structures and mechanisms of zinc enzymes. Such knowledge will be obtained…

Advancing soil C characterization using HRMS and NMR

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Nancy Hess

Soil organic matter consists of diverse and complex mixture of hundreds to thousands biological and metabolic products that are poorly characterized using current techniques. We seek to develop a…

Correlation of Structure and Function of Zinc Metalloproteins Via Solid-state NMR Methods

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

As early as 1869 it was known that zinc is an essential element for eukaryotes, it is the second most abundant trace element in humans after iron. About half of all proteins contain metal cations,…

Low Temperature (10K) 25Mg Solid-State NMR of DNA Repair Proteins and Their
Complexes

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Paul Ellis

Project type

Large-Scale EMSL Research

The chemistry central to the function of the DNA repair proteins apurinic/apyrimidic endonuclease 1 (APE1) and polymerase &#946; (Pol &#946;) is the chemistry of water activated by Mg2+…

Multinuclear Solid-State NMR Studies of Biological, Environmental, and Energy Systems

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Karl Mueller

My research team at EMSL carries out a number of studies that utilize a combination of high-resolution, solid-state nuclear magnetic resonance (NMR) spectroscopy and computational chemistry to…

Correlation of Structure and Function of Zinc Metalloproteins Via Solid-state NMR Methods

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

As early as 1869 it was known that zinc is an essential element for eukaryotes, it is the second most abundant trace element in humans after iron. About half of all proteins contain metal cations,…

Correlating the active site structure of copper metalloproteins with their spectroscopic and chemical properties

Lead Institution

University of Nebraska - Lincoln

Principal Investigator

Gerard Harbison

Project type

Large-Scale EMSL Research

We propose to implement 63Cu and 65Cu, in combination with quantum chemical calculations, to study the metal sites of blue copper proteins, oxidase enzymes, and copper chaperones. Living systems &…

Development of Solid-state NMR Methods for Characterization of Biological Materials, Catalytic Systems, Disordered Solids and Terrestrial Carbon.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

This proposal covers the development of advanced solid-state NMR techniques for a variety of purposes. The first is toward the detection of quadrupolar nuclides. These challenging nuclei (ie. Zn, Mg…

Correlation of Structure and Function of Zinc Metalloproteins Via Solid-state NMR Methods

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

As early as 1869 it was known that zinc is an essential element for eukaryotes, it is the second most abundant trace element in humans after iron. About half of all proteins contain metal cations,…

43Ca NMR Spectroscopy of Ca2+ Dependent Proteins and models

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Paul Ellis

Project type

Large-Scale EMSL Research

We are exploring the application and utility of low temperature solid-state NMR methods to the observation of 43Ca in Ca2+ dependent proteins. Our first application is to the protein calbindin D9k …

Molecular Phenotyping of Brachypodium to Provide Metabolic and Functional Linkages to the Plant-Atmosphere-Soil-Systems (iPASS) Model

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

This proposal aims to provide the fundamental molecular characterization necessary to develop a model which ultimately links phenotypic measurements to the atmospheric processes and soil…

Investigation of the role of Mg2+ in DNA repair proteins APE1, Pol ?, and FEN1

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

Nuclear DNA is continuously damaged by endogenous sources, such as the reactive free radicals produced during oxidative metabolism, or by exogenous sources, such as ionizing radiation. It has been…

Probing the Mechanism of the Alkaline Phosphatase Reaction by 67Zn and 25Mg NMR

Lead Institution

Boston College

Principal Investigator

Evan Kantrowitz

Project type

Capability Research

Alkaline phosphatase (AP) is a ubiquitous enzyme, which is extremely important in mammals. The enzyme catalyzes the hydrolysis of phosphomonoesters providing the cell with the free alcohol and…

Extracellular Research Thrust for EMSL SSA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

This project will develop a conceptual framework that defines the biotic and abiotic mechanisms regulating the persistence of mineral associated organic matter (OM). The specific goals are to…

Investigation of the role of Mg2+ in DNA repair proteins APE1, Pol ?, and FEN1

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

Nuclear DNA is continuously damaged by endogenous sources, such as the reactive free radicals produced during oxidative metabolism, or by exogenous sources, such as ionizing radiation. It has been…

Probing the Mechanism of the Alkaline Phosphatase Reaction by 67Zn and 25Mg NMR

Lead Institution

Boston College

Principal Investigator

Evan Kantrowitz

Project type

Capability Research

Alkaline phosphatase (AP) is a ubiquitous enzyme, which is extremely important in mammals. The enzyme catalyzes the hydrolysis of phosphomonoesters providing the cell with the free alcohol and…

Development of Methodologies to Speciate Soil Nitrogen Using Solid-state NMR

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

I am proposing to develop new methods for identifying nitrogen species utilizing solid-state NMR (ssNMR). These methods will not require extraction and can be used on whole soils (or minerals)…

Investigation of the role of Mg2+ in DNA repair proteins APE1, Pol ?, and FEN1

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

Nuclear DNA is continuously damaged by endogenous sources, such as the reactive free radicals produced during oxidative metabolism, or by exogenous sources, such as ionizing radiation. It has been…

Determine 3d-structure of chemokine in apo form and in complex with its native receptor by solid state NMR

Lead Institution

Bristol-Myers Squibb

Principal Investigator

Luciano Mueller

Project type

Exploratory Research

Structural biology has significantly accelerated the development of drug leads in protein targets for which 3d structures could be obtained either by XRAY crystallography or by NMR spectroscopy…

Development of Solid-state NMR Methods for Characterization of Biological Materials, Catalytic Systems, Disordered Solids and Terrestrial Carbon.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

This proposal covers the development of advanced solid-state NMR techniques for a variety of purposes. The first is toward the detection of quadrupolar nuclides. These challenging nuclei (ie. Zn, Mg,…

Investigation of the role of Mg2+ in DNA repair proteins APE1, Pol ?, and FEN1

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Paul Ellis

Project type

Capability Research

We propose to utilize unique capabilities within the EMSL (low temperature solid-state NMR and the mpp2 super computer) to investigate Mg2+ binding to two DNA repair proteins Pol ? and APE1. In the…

Probing the Dynamics of a Protein Hydrophobic Core at Low Temperatures

Lead Institution

University of Alaska at Anchorage

Principal Investigator

Liliya Vugmeyster

Project type

Exploratory Research

Hydrophobic cores are found in the interior of globular proteins and are essential for the formation of the folded state. The core represents a complex dynamical medium reflecting the existence of a…

Carriers for Transporting and Storing Hydrogen

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Autrey

This proposal will determine the mechanistic and thermodynamic understanding required to address bottlenecks in materials capable of storing or transporting hydrogen. We propose a series of…

Correlation of Structure and Function of Zinc Metalloproteins Via Solid-state NMR Methods

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

This project will utilize ab initio molecular orbital theory to aid in the interpretation of the measured field gradients and shielding tensors. These calculations utilize NWCHEM (developed in the…

Determine 3d-structure of chemokine in apo form and in complex with its native receptor by solid state NMR

Lead Institution

Bristol-Myers Squibb

Principal Investigator

Luciano Mueller

Project type

Large-Scale EMSL Research

Structural biology has significantly accelerated the development of drug leads in protein targets for which 3d structures could be obtained either by XRAY crystallography or by NMR spectroscopy…

Development of Solid-state NMR Methods for Characterization of Biological Materials, Catalytic Systems, Disordered Solids and Terrestrial Carbon

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

This proposal covers the development of advanced solid-state NMR techniques for a variety of purposes. The first is toward the detection of quadrupolar nuclides. These challenging nuclei (ie. Zn, Mg…

Sensitivity Enhancing NMR of
Strontium-87 Nuclei in Clays, Zeolites, and Waste Cleanup Technologies

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Karl Mueller

Project type

Capability Research

Our proposal is to use DFS-QCPMG NMR at 21.14 T to study the binding sites of strontium nuclei in clays, zeolites, and proposed waste remediation technologies. The only stable NMR-active isotope of…

Correlation of Structure and Function of Zinc Metalloproteins Via a Combined NMR/Molecular Theory Approach

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Large-Scale EMSL Research

One of the most significant challenges in the metallobiochemistry of Zn2+ is the a priori determination of how the metal center will facilitate a particular chemical reaction. Two examples…

Building an automation-ready multimodal workflow for comprehensive 3D characterization of intact soil structures.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Odeta Qafoku

3-dimensional (3D) characterization of intact soil structures (i.e. macro and microaggregates) will provide understandings on how soil physical, mineralogical, biotic heterogeneities control long…

The Mechanism of Action of Carbonic Anhydrase and LpxC

Lead Institution

University of Michigan

Principal Investigator

Carol Fierke

Project type

Capability Research

Zinc binding sites in proteins play diverse roles, including enhancement or inhibition of catalysis, stabilization and assembly of protein structures, and regulation of metal concentration. Further…

The affinity and structure of biomolecules immobilized on a 3-D substrate: Time-resolved EPR detection during mobile phase gradients

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Eric Walter

We propose the development of a new magnetic resonance technique to monitor the interactions of biomolecules with binding partners and their environment. Physically, this will be implemented by…

Invesitgation of the role of Mg2+ in DNA repair proteins

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

The chemistry central to the function of the DNA repair proteins APE1, Pol b and FEN1 is the chemistry of water activated by a magnesium ion. Further, Mg2+ also facilitates the organization of the…

Correlation of Structure and Function of Zinc Metalloproteins Via a Combined NMR/Molecular Theory Approach

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Large-Scale EMSL Research

One of the most significant challenges in the metallobiochemistry of Zn2+ is the a priori determination of how the metal center will facilitate a particular chemical reaction. Two examples…

Cryogenic NMR and Advanced Electronic Structure Theory as a Unique EMSL Capability for Complex Systems:
Application to the Photosynthetic Energy Conversion Systems

Lead Institution

Los Alamos National Laboratory

Principal Investigator

Ping Yang

The goal of this proposal is to demonstrate a unique capability to be enabled in the EMSL, the integration of leading-edge cryogenic NMR measurements and advanced electronic structure computations,…

Invesitgation of the role of Mg2+ in DNA repair proteins

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

The chemistry central to the function of the DNA repair proteins APE1, Pol b and FEN1 is the chemistry of water activated by a magnesium ion. Further, Mg2+ also facilitates the organization of the…

Correlation of Structure and Function of Zinc Metalloproteins Via a Combined NMR/Molecular Theory Approach

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

The critical nature of zinc in biology requires a detailed understanding of the chemistry, structure, and bondings of these zinc complexes and how, in turn, these manifestations alter the chemistry…

Magnesium NMR of DNA Repair Proteins

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Exploratory Research

The chemistry central to the function of the DNA repair proteins apurinic/apyrimidic endonuclease 1 (APE1) and polymerase beta (pol beta) is the chemistry of water activated by a magnesium ion. …

Correlation of Structure and Function of Zinc metalloproteins via Solid-state NMR Methods

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Capability Research

In the past, we have utilized surrogate probes to address structure/function relationships for zinc. At a qualitative level the surrogate strategy works well. However, the critical nature of zinc…

SGI Altix Allocation for Advanced Computing Technology Lab

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jarek Nieplocha

This is a placeholder proposal to manage time allocation under EMSL resource tracking system.

Experimental and Computational Characterization of the Structure and Electronic Properties of Novel Porphyrins for Solar Cells

Lead Institution

Portland State University

Principal Investigator

Carl Wamser

Project type

Exploratory Research

The proposed project will be primarily computational studies carried out in collaboration with Dr. Niri Govind, Dr. Kenneth Lopata, and Dr. Karol Kowalski (PNNL/EMSL Molecular Science Computing). …

Projects