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Biomedical subjects

D Kristofferson

Publications and source records attributed to D Kristofferson.

16 recordsLinked to original sources
PubMed1992

GenBank.

The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 85,000,000 nucleotides in 67,000 entries from a total of 3,000 organisms. The input stream of data coming into the database is primarily as direct submissions from the scientific community on electronic media, with little or no data being keyboarded from the printed page by the databank staff. The data are maintained in a relational database management system and are made available in flatfile form through on-line access, and through various network and off-line computer-readable media. The data are also distributed in relational form through satellite copies at a number of institutions in the U.S. and elsewhere. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service.

Animals↗
PubMed1991

GenBank.

The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 56,000,000 nucleotides in 45,000 entries. The input stream of data coming into the database has largely been shifted to direct submissions from the scientific community on electronic media. The data have been installed in a relational database management system and are made available in this form through on-line access, and through various network and off-line computer-readable media. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service.

Base Sequence↗
PubMed1991

A mechanism for maintaining an up-to-date GenBank database via Usenet.

In this paper, we describe an automated system for distributing updates to the GenBank nucleic acid sequence database, using the Usenet news system as the underlying transport mechanism. Our system allows new loci to be distributed as soon as the sequences are available, over existing networks, using existing Usenet software and infrastructure currently available on a wide range of computer systems.

Amino Acid Sequence↗
PubMed1988

New developments at BIONET.

BIONET has made considerable progress in developing communication links among molecular biologists and biochemists worldwide. We describe these efforts and also note the many new enhancements to the BIONET system itself.

Amino Acid Sequence↗
PubMed1986

Direct observation of steady-state microtubule dynamics.

Different types of unusual dynamic behavior have been reported for steady-state microtubules. While almost all earlier reports relied on kinetic measurements of bulk polymerization, we have directly visualized the steady-state addition of subunits to individual microtubules through the use of tubulin derivitized with biotin. Biotinylated tubulin was used both as an internal "seed" for polymerization and as a marker for assembly onto the ends of microtubules composed of purified tubulin. Biotinylated segments were distinguished from unmodified tubulin by double-label immunofluorescence. Microtubule lengths, number concentrations, and segment lengths have been monitored with time at steady state under two buffer conditions. The results indicate that the microtubule steady state under these conditions is a balance between a majority of slowly growing microtubules and a minority of rapidly depolymerizing ones as described by the "dynamic instability" model (Mitchison T., and M. Kirschner, 1984, Nature (Lond.)., 312:232-242). Microtubules show no evidence of treadmilling; instead most show progressive growth off both ends at steady state. Although solvent conditions markedly influence the growth rates, qualitatively the behavior is unchanged.

Alkanesulfonates↗
PubMed1983

Subunit organization and structure of an acetylcholine receptor.

We have learned the positions of the alpha-subunits around the AChR rosette and the location of the toxin on the synaptic crest. A charge/hydrophobic character map of the 40 A X 30 A receptor surface that binds alpha-bungarotoxin has been constructed. A beta-structure domain surrounds the agonist binding site on the alpha-subunits, as predicted by amphipathic Fourier sequence analysis. The ion channel may be constructed from five amphipathic helices, which insert into the bilayer as the alpha2 beta gamma delta subunits come together. They form a water-filled channel on one side and interface with hydrophobic helices in each subunit on the other.

Amino Acid Sequence↗
PubMed1980

Calcium ion induces endwise depolymerization of bovine brain microtubules.

Calcium ion induces rapid depolymerization of microtubules, and the mechanism of interaction of Ca2+ with cytoskeletal components may be metabolically significant. The sufficiency of an endwise depolymerization model for describing calcium-induced disassembly was demonstrated by three criteria: (a) correlation of the observed time course of disassembly with the initial polymer length distribution using a kinetic model described elsewhere (Kristofferson, D., Karr, T. L., and Purich, D. L. (1980) J. Biol. Chem. 255, 8567-8572); (b) observation that the initial rate of calcium-induced disassembly parallels the microtubule number of concentration which is experimentally manipulated by mechanical shearing; and (c) determination of the average polymer length, microtubule number concentration, and extent of depolymerization at various levels of added calcium ion to achieve successive partial disassembly extents. The rate constant for protomer release and other aspects of the disassembly mechanisms are also presented. Critical concentration measurements at low calcium ion levels are also consistent with endwise interactions.

Animals↗
PubMed1980

Dynamics of linear protein polymer disassembly.

This report presents a kinetic model for endwise depolymerization of linear, self-assembling protein systems. We develop a reliable method for predicting the shape of depolymerization curves (remaining polymer weight versus time) on the basis of the initial polymer length distribution. Computer simulations are used to illustrate changes in the polymer length distribution and average polymer weight during disassembly. In addition, our method provides an accurate determination of the microscopic rate constant for subunit release. Application of this analysis to dilution-induced and cold induced disassembly of microtubules is illustrated in the preceding paper (Karr, T.L., Kristofferson, D., and Purich, D.L. (1980) J. Biol. Chem. 255, 8560-8566). A survey of other possible applications of this treatment to microtubules, flagella, F-actin, and tobacco mosaic virus protein is included.

Actins↗
PubMed1980

Mechanism of microtubule depolymerization. Correlation of rapid induced disassembly experiments with a kinetic model for endwise depolymerization.

Microtubule disassembly has been studied using a rapid dilution technique (Karr, T.L., and Purich, D.L. (1979) J. Biol. Chem. 254, 10885-10888). Disassembly curves, generated by computer from the solution of series first order differential equations (see following paper), were fit to experimental data with excellent agreement when the diluted microtubules contained no microtubule-associated proteins. The rate constant for dimer release from microtubules was found to be 154 s-1. Assuming a critical tubulin concentration of 8 to 9 x 10(-6) M, the apparent bimolecular rate constant (2 x 10(7) M-1 s-1) for assembly is near the diffusion limit. It was also possible to use the rapid dilution technique for quantitatively correlating the disassembly rate to the number concentration of microtubule ends. These findings suggest that the dynamics of tubulin interactions with microtubules may be characterized in terms of an endwise depolymerization model. A re-evaluation of cold induced depolymerization kinetics (see miniprint supplement) is also fully consistent with our analysis of disassembly dynamics.

Kinetics↗