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Thermodynamic Quantities for the Ionization Reactions of Buffers in Water

December 1, 2002

Author(s)

Robert N. Goldberg, N Kishore, R M. Lennen

This table contains selected values for the pK, standard molar enthalpy of reaction {Δ} rH , and standard molar heat-capacity change {Δ} rC p for the ionization reactions of 64 buffers many of which are relevant to biochemistry and to biology. The values

Reaction Mechanism of Chorismate Mutase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics

November 21, 2002

Author(s)

Y. S. Lee, S. E. Worthington, Morris Krauss, B R. Brooks

The reaction path for the rearrangement of chorismate to prephenate has been determined in a QM/MM study including the entire protein environment while treating the reaction with ab initio quantum chemistry. In addition to the reactant, chorismate, the

Nanometer-Scale Pores: Potential Applications for Analyte Detection and DNA Characterization

October 1, 2002

Author(s)

John J. Kasianowicz

Several classes of transmembrane protein ion channels function in vivo as sensitive and selective detection elements for analytes. Recent studies on single channels reconstituted into planar lipid bilayer membranes suggest that nanometer-scale pores can be

Importance of Product Inhibition in the Kinetics of the Acylase Hydrolysis Reaction by Differential Stopped Flow Microcalorimetry

September 15, 2002

Author(s)

M Stodeman, Frederick P. Schwarz

The hydrolysis of N-acetyl-L-methionine, N-acetylglycine, N-acetyl-L-phenylalanine, and N-acetyl-L-alanine at 298.35 K by porcine kidney acylase I (EC 3.5.1.14) was monitored by the heat released upon mixing of the substrate and enzyme in a differential

The Cockayne Syndrome Group B Gene Product is Involved in Cellular Repair of 8-Hydroxyadenine in DNA

August 23, 2002

Author(s)

J Tuo, Pawel Jaruga, H Rodriguez, Miral M. Dizdar, V. Bohr

Cockayne syndrome (CS) is a human disease characterized by sensitivity to sunlight, severe neurological abnormalities and accelerated aging. CS has two complementation groups, CS-A and CS-B. The CSB gene encodes the CSB protein with 1493 amino acids. We

A New NIST Mitochondrial DNA Interactive Website

August 1, 2002

Author(s)

Barbara C. Levin, L A. Tully, Diane K. Hancock, Frederick P. Schwarz, M S. Lee

Every human cell has from a few dozen to several thousand mitochondria each of which contain mitochondrial DNA (mtDNA). The sequence of the entire human mtDNA (16,569 base pairs) was determined and published by Anderson et al. in 1981. A mtDNA standard

Cell Membrane Hybrid Bilayers Containing the G-Protein-Coupled Receptor CCR5

August 1, 2002

Author(s)

N M. Rao, Vitalii I. Silin, K D. Ridge, John T. Woodward IV, Anne L. Plant

A hybrid bilayer membrane is a planar model membrane that is formed at an alkanethiol monolayer-coated gold surface by the spontaneous reorganization of phospholipid vesicles. Membrane vesicles from monkey kidney COS-cells also reorganize at an alkanethiol

Crystal Structure of the YjeE Protein from Haemophilus Influenzae: A Putative Atpase Involved in Cell Wall Synthesis

August 1, 2002

Author(s)

A Teplyakov, G Obmolova, M Tordova, N Thanki, N Bonander, E Eisenstein, A J. Howard, G L. Gilliland

A hypothetical protein encoded by the gene YjeE of Haemophilus influenzae was selected as part of a structural genomics project, for X-ray analysis to assist with the functional assignment. The protein is considered essential to bacteria since the gene is

Electrophoretic Capture of Circular DNA in Gels - A Review

August 1, 2002

Author(s)

B. Akerman, Kenneth D. Cole

Results on electrophoretic capture of circular DNA in porous gels are reviewed. Processes, which cause arrest of circular forms of DNA during electrophoresis, can provide a very efficient separation mechanism for the purification of plasmids and bacterial

Mechanism of Ionic Current Blockades During Polymer Transport Through Pores of Nanometer Dimensions

June 1, 2002

Author(s)

D W. Deamer, H Olsen, M Akeson, John J. Kasianowicz

Linear anionic polymers driven through the α-hemolysin channel produce ionic current blockades. Three parameters of the blockades can be measured, including blockade amplitude, duration and modulations of amplitude within a single event to test the

The Biological Macromolecule Crystallization Database: Crystallization Procedures and Strategies

June 1, 2002

Author(s)

G L. Gilliland, Michael Tung, Jane E. Ladner

The Biological Macromolecule Crystallization Database (BMCD) archives crystallization data from published reports for all forms of biological macromolecules that have produced crystals suitable for x-ray diffraction studies. The information includes the

A Strategy for Examining Complex Mixtures of Deoxyoligonucleotides Using Ion-Pair Reverse-Phase High-Performance Liquid Chromatography, Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry, and Informatics

May 15, 2002

Author(s)

Peter M. Vallone, J. M. Devaney, M A. Marino, John M. Butler

Cellular Biomarkers Used to Detect Damage in Tissue-Engineered Medical Products

May 1, 2002

Author(s)

H Rodriguez

Tissue engineering is an emerging new area of biotechnology that will provide replacement tissues for patients, as well as complex, functional biological systems for research and testing in the pharmaceutical industry. However, a lack of a formal

Grafting Segments from the Extracellular Surface of CCR5 onto a Bacteriorhodopsin Transmembrane Scaffold Confers HIV-1 Corcceptor Activity

April 1, 2002

Author(s)

N G. Abdulaev, T T. Strassmaier, T Ngo, R W. Chen, H Lueke, D D. Oprian, K D. Ridge

The G-protein coupled receptor CCR5 binds three distinct B-chemokines on the solvent exposed segments of the extracellular surface. This same region of CCr5 also interacts with certain macrophage-tropic strains of HIV-1. To investigate structural features

Synchrotron White-Beam X-Ray Topography of Ribonuclease S Crystals

April 1, 2002

Author(s)

W M. Vetter, David Travis Gallagher, M Dudley

With careful experimental design indexed synchrotron white-beam X-ray topographs of ribonuclease S crystals at ambient temperature could be recorded with a definition and contrast comparable to that of monochromatic beam topographs of other proteins

Identification and Characterization of a Human DNA Glycosylase for Repair of Modified Bases in Oxidatively Damaged DNA

March 19, 2002

Author(s)

T. K. Hazra, T. Izumi, I Boldough, B Imhoff, Y W. Kow, Pawel Jaruga, Miral M. Dizdar, Somenath Mitra

8-oxoguanine (8-oxoG), ring-opened purines (formamidopyrimidines or Fapys), and other oxidized DNA base lesions generated by reactive oxygen species, are often mutagenic and toxic, and have been implicated in the etiology of many diseases including cancer

Mass Spectrometric Assays for the Tandem Lesion 8,5'- Cyclo-2' Deoxyguanosine in Mammalian DNA

March 19, 2002

Author(s)

Pawel Jaruga, M Birincioglu, H Rodriguez, M Miral Dizdar

8,5'-Cyclopurine-2'-deoxynucleosides are among major lesions in DNA that are formed by attack of hydroxyl radical. These compounds represent a concomitant damage to both sugar and base moieties of the same nucleoside and thus can be considered tandem

DNA Electrophoresis in Gellan Gels. The Effect of Electroosmosis and Polymer Additives

March 7, 2002

Author(s)

M. Markstrom, Kenneth D. Cole, B. Akerman

The polysacharide gellan forms hydrogels if a divalent ion such as calcium is added at millimolar concentrations. The gel can be reversed to solution by adding EDTA, which makes it a promising candidate for preparative electrophoretic separation of

Cytonectin Expression in Alzheimer's Disease

March 1, 2002

Author(s)

S J. Anderson, Peter E. Barker, M G. Hadfield

Cytonectin is a novel 35,000 molecular weight protein that displays remarkable ion-independent adherence properties. This consigns it to a family of well-known adherence molecules essential for cell communication and the development of 3-dimensional tissue

Chlorella Virus Pyrimidine Dimer Glycosylase Excises Ultraviolet Radiation- and Hydroxyl Radical-Induced Products 4,6-Diamino-5-Formamidopyrimidine and 2,6-Diamino-4-Hydroxy-5-Formamidopyrimidine from DNA

February 1, 2002

Author(s)

Pawel Jaruga, R Jabil, Amanda K. McCullough, H Rodriguez, M Miral Dizdar, R S. Lloyd

A DNA glycosylase specific for UV radiation-induced pyrimidine dimers has been identified from chlorella virus Paramecium bursaria chlorella virus-1. This enzyme (Chlorella virus Pyrimidine dimer glycosylase [cv-pdgl) exhibits a 41% amino acid identity

Chorismate Lyase: Kinetics and Engineering for Stability

January 31, 2002

Author(s)

Marcia J. Holden, M P. Mayhew, David T. Gallagher, V L. Vilker

By removing the enolpyruvyl group from chorismate, chorismate lyase (CL) produces p-hydroxybenzoate (p-HB) for the ubiquinone biosynthetic pathway. We have analyzed CL by several spectroscopic and chemical techniques and measured its kinetic (k cat = 1.7x

Determination of Active Site Residues in Escherichia Coli Endonuclease VIII

January 25, 2002

Author(s)

S. M. Burgess, Pawel Jaruga, M L. Dodson, Miral M. Dizdar, R S. Lloyd

Endonuclease VIII from Escherichia coli is a DNA glycosylase/lyase that removes oxidatively damaged bases. EndoVIII is a functional homologue of endonuclease III, but a sequence homologue of formamidopyrimidine DNA glycosylase (Fpg). Using multiple

Effects of Metal Ligation and Oxygen on the Reversibility of the Thermal Denaturation of Pseudomonas Aeruginosa Azurin

January 22, 2002

Author(s)

A Sandberg, J Leckner, Y. Shi, Frederick P. Schwarz, B G. Karlsson

Thermodynamic equilibrium transition models in DSC are only applicable to reversible processes, but reversibility of the thermal transitions of proteins is comparatively rare because of intermolecular aggregation of denatured proteins and the degradation

Mutual Recognition of Measurements: Its Potential Impact on International Trade in IVDs

January 1, 2002

Author(s)

Hratch G. Semerjian, Ellyn S. Beary

International agreements and decisions concerning global trade, the environment and health care increasingly call for mutual recognition of measurements and standards between nations. Such mutual recognition can remove technical barriers to trade

Physics of DNA Threading Through a Nanometer Pore and Applications to Simultaneous Multianalyte Sensing

January 1, 2002

Author(s)

John J. Kasianowicz, S. E. Henrickson, Martin Misakian, H H. Weetall, B Robertson, Vincent M. Stanford

Polymer transport is central to many biological processes, including protein translocation, bacterial gene transduction and some modes of viral infection. To better understand the mechanisms of macromolecular transport, we are studying the ability of