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Biomedical subjects

A K Dunker

Publications and source records attributed to A K Dunker.

At least 37 records · Page 2Linked to original sources
PubMed1996

Quaternion contact ribbons: a new tool for visualizing intra- and intermolecular interactions in proteins.

Protein side chain interactions between residues separated by at least one loop or turn or break in the amino acid sequence are called 'nonlocal contacts' in this manuscript, and contiguous sets of such interactions located between segments of secondary structure are called 'contact zones.' A new interactive program, the quaternion contact ribbon tool, has been developed to help protein chemists identify, straighten if twisted, and display contact zones between two neighboring segments of helix.

Binding Sites↗
PubMed1996

An introductory course in computation molecular biology: rationale, history, observations, and course description.

A course called "Molecular Biology Computer Techniques" was implemented in 1987 and has been evolving ever since. Currently the semester-long three credit course consists of thirty hours of lecture (three hours/week for the first ten weeks of the semester) and a minimum of 45 hours of laboratory instruction (three hours/week). The lectures survey both bioinformatics and structure based methods. The laboratory has two tracks, one that can be described loosely as "sequence analysis" and the other as "molecular modelling." Most students choose one of the two laboratory tracks, although a small number have done both, either simultaneously or in successive years. For each student, the goal of the course is the completion of a student-initiated research project. The culmination of the course is the presentation of the completed projects at a "Poster Session Final." During this final, which is conducted like a poster session at a typical biological science meeting, students are examined, not only by the instructors in the course, but also by a diverse cross-section of the university community at large, including non-scientists (who are specially invited to attend). Questioning by non-scientists provides opportunity for the students to improve their communication skills with the lay public. In this manuscript we discuss our views regarding the rationale for the development of formal courses in computational molecular biology, relate our experiences in the development of our course, and describe the course as it stood the last time it was taught, which was in the Fall of 1994.

Base Sequence↗
PubMed1994

Evidence that the A2 fragment of Shiga-like toxin type I is required for holotoxin integrity.

Escherichia coli Shiga-like toxin type I (SLT-I) is a potent cytotoxin consisting of an enzymatically active A subunit and a pentameric B subunit that mediates toxin binding to susceptible eukaryotic cells. Evidence that the carboxy-terminal 38 amino acids of the A subunit are involved in holotoxin 1A:5B association is presented. We compared the ability of purified recombinant SLT-I B subunit (Slt-IB) to combine in vitro with purified recombinant SLT-I A subunit (Slt-IA; full-length subunit A includes amino acids 1 to 293) and its ability to combine with purified recombinant SLT-I A1 subunit (Slt-IA1; truncated subunit A includes amino acids 1 to 255). Each mixture was analyzed for biological and physical evidence of toxin assembly. Although Slt-IA successfully combined with Slt-IB to form a molecular species similar to holotoxin that was detectable by nondenaturing polyacrylamide gel electrophoresis and immunoblotting and yielded a molecule which was cytotoxic to cultured Vero cells, Slt-IA1 did not have this ability. Slt-IA1 was 36-fold more active than Slt-IA in an in vitro protein synthesis inhibition assay. These findings suggest that the Slt-IA2 fragment is crucial for formation of SLT holotoxin and stabilizes the interaction between the A and B subunits.

Animals↗
PubMed1993

Ca(2+)-induced folding and aggregation of skeletal muscle sarcoplasmic reticulum calsequestrin. The involvement of the trifluoperazine-binding site.

Calsequestrin is an intermediate affinity, high capacity Ca(2+)-binding protein found in the lumen of the sarcoplasmic reticulum of both skeletal and cardiac muscle cells. Previous sequence analysis suggested that calsequestrin may contain a hydrophobic binding site for the drug trifluoperazine, a site shared by the calmodulin family and shown to play a role in calmodulin/calmodulin receptor interaction. Previous studies showed that, upon Ca2+ binding, calsequestrin undergoes a conformational change, burying the trifluoperazine-binding site, folding into a more compact structure that is trypsin-resistant, and increasing the negative ellipticity of the circular dichroism spectrum. In this study, the structural and functional roles of the trifluoperazine-binding site in the Ca(2+)-induced conformational change of calsequestrin are further studied using the calmodulin antagonists trifluoperazine and melittin. If trifluoperazine or melittin is added to calsequestrin prior to Ca2+ addition, then Ca(2+)-induced folding is inhibited as determined by the changes in circular dichroism spectra and protein sensitivity to trypsin digestion. If, however, Ca2+ is added prior to trifluoperazine or melittin, calsequestrin remains resistant to trypsin digestion, just as if the calmodulin antagonists are not present, suggesting that the conformational change is not affected. Aggregates of calsequestrin that exhibit high Ca2+ binding capacity have previously been shown to occur at high Ca2+ and calsequestrin concentrations. By preventing a prerequisite folding step, trifluoperazine or melittin also prevents the Ca(2+)-induced aggregation of calsequestrin, thus decreasing the maximal Ca2+ binding by calsequestrin. These data suggest that the trifluoperazine-binding site is critically involved in the Ca(2+)-induced intramolecular folding step required for the intermolecular interactions leading to high capacity Ca(2+)-binding by calsequestrin.

Amino Acid Sequence↗
PubMed1993

Structural changes accompanying chloroform-induced contraction of the filamentous phage fd.

Contact with a chloroform/water interface at 2 degrees C induces contraction of fd filamentous phage into rodlike I-forms; this contraction is accompanied by a decrease in the magnitude of circular dichroism spectral intensity near 222 nm and an increase near 210 nm. Comparisons with circular dichroism spectra of 100% helical poly-L-lysine and N-bromosuccinimide-oxidized fd phage indicate that the spectral change accompanying the fd to I-forms transition is due primarily to a change in the contributions from the single tryptophan (W26) of the major coat protein, with probably no significant change in the alpha-helix content. Further contraction of the rodlike I-forms to spherical S-forms at 25 degrees C is accompanied by a substantial general decrease in the magnitude of the ellipticity throughout the 230-210-nm region, which is indicative of a decrease in the alpha-helix content of the major coat protein. The similarity of the circular dichroism spectrum of S-forms with that of coat protein in detergents suggests that the S-form coat protein resembles the coat protein in lipid bilayers. The intrinsic fluorescence of W26 is quenched without red-shift (but perhaps a barely detectable blue-shift) following fd contraction to I-forms and S-forms. The accessibility of W26 to aqueous quenchers does not change significantly upon contraction. However, interaction with hydrophobic quenchers is dramatically altered in the contracted forms in a manner suggesting that the environment surrounding the tryptophan changes from native-protein-like in the fd filament to molten globule-like in the I-form rods and S-form spheroids. As discussed herein, certain features of these data support previous suggestions that chloroform-induced filamentous phage contraction may provide information about phage penetration and assembly in vivo.

Capsid↗
PubMed1992

Tryptophan contributions to the unusual circular dichroism of fd bacteriophage.

The circular dichroism (CD) spectrum of fd bacteriophage has a deep minimum at 222 nm characteristic of highly alpha-helical protein, but there is a shoulder at 208 nm rather than a minimum, with a 222/208-nm amplitude ratio near 1.5 rather than near 1. Oxidation of fd phage with the tryptophan reagent N-bromosuccinimide (NBS) changes the ratio. In this report, the NBS titration of fd is followed by CD and three other spectroscopies, the results of which yield an explanation of the unusual CD spectrum. Absorbance, fluorescence, and Raman data show the oxidation to have two phases, the first of which involves the destruction of tryptophan and the second, tryptophan and tyrosine. Raman spectra reveal the invariance of an environmentally-sensitive tyrosine Fermi resonance doublet during the first oxidative phase. Raman spectra also show that little or no change of alpha-helicity occurs in the first or second oxidation phase, although very slight changes in the helix parameters might be occurring. Concurrent with the destruction of tryptophan during the first phase is the appearance in CD difference spectra ([theta]NBS-treated fd - [theta]native fd) of positive maxima at 208-210 nm and negative maxima at 224 nm, with crossovers at 217 nm. Enormous difference ellipticities, per oxidized subunit of 50 amino acids, of +490,000 +/- 80,000 deg cm2 dmol-1 at 208 nm and -520,000 +/- 110,000 deg cm2 dmol-1 at 224 nm have been derived from the data.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriophages↗
PubMed1992

Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure.

The conditional probability, P(sigma/x), is a statement of the probability that the value of sigma will be found given the prior information that a value of x has been observed. Here sigma represents any one of the secondary structure types, alpha, beta, tau, and rho for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N-cap and C-cap values; (4) Chou-Fasman conformational parameters for helix, P alpha, for sheet, P beta, and for turn, P tau; and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, I alpha, for sheet, I beta, for turn, I tau, and for random structure, I rho. Plots of P(sigma/x) vs. x are demonstrated to provide information about the correlation between structure and attribute, sigma and x. The separations between different P(sigma/x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P(alpha/x), P(beta/x), P(tau/x) and P(rho/x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix greater than P alpha much greater than N-cap greater than C-cap approximately I alpha approximately I tau. The information value for turns, I tau, was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: I beta much greater than P beta approximately hydropathy greater than I rho approximately hydrophobic moment assuming sheet. Three attributes, at their low values, were found to give significant discrimination for the absence of helix: I alpha approximately P alpha approximately hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: P beta much greater than I rho approximately hydropathy. Indications of the absence of sigma could be as useful for some applications as the indication of the presence of sigma.

Amino Acid Sequence↗
PubMed1991

A model for fd phage penetration and assembly.

Below 15 degrees C, chloroform causes fd phage to contract to I-forms, which are compact structures about 1/3 as long as the original phage. Above 15 degrees C, chloroform causes I-forms to contract to even more compact spheroidal S-forms. Here we show that the coat protein structure in I-forms is the same as the protein structure in the phage and the protein structure in S-forms is the same as the protein structure in bilayers. The conversions from fd----I-forms----S-forms are therefore suggested to mimic steps in fd penetration. The same conversions, in reverse order, are suggested to mimic steps in fd assembly.

Bacteriophages↗
PubMed1991

Proposed molten globule intermediates in fd phage penetration and assembly.

The fd filamentous phage can be contracted to short rods called I-forms and to spheroidal particles called S-forms. The conversions from fd----I-forms----S-forms were previously suggested to mimic steps in fd penetration. The same conversions, in reverse order, were suggested to mimic steps in fd assembly. The I-forms and S-forms bind the hydrophobic probe, 1-anilino-napthalene-8-sulfonate (ANS); under the same conditions, fd binds this probe very poorly. Rigidly packed side chains in fd and nonrigidly packed side chains in I-forms and S-forms would explain the differences in ANS binding. A compilation of the properties of I-forms and S-forms indicate that: (i) they have compact structures; (ii) they have secondary structures of the same type as native phage; (iii) they have non-native morphologies; and (iv) they may have nonrigid side chain packing. These are the properties of molten globules.

Anilino Naphthalenesulfonates↗
PubMed1987

Limited nucleosome migration can completely randomize DNA repair patches in intact human cells.

Following irradiation of human cells with ultraviolet light, DNA repair patches are initially inserted near the 5' and 3' ends of nucleosome core DNA leaving a "gap" in repair synthesis (of approximately 50 bases) near the center of the core DNA. With time, however, these same repair patches become randomized, apparently by nucleosome migration. We have developed both an analytical expression and a computer algorithm (which simulates nucleosome migration along DNA) to determine the average distance nucleosomes must migrate to change the initial, non-uniform distribution of repair patches in nucleosomes to a random distribution. Both of these methods yielded the same result: nucleosomes must migrate an average of about 50 base-pairs in either direction to produce the randomization observed.

Cell Movement↗
PubMed1987

Characterization of hepatic carnitine palmitoyltransferase. Use of bromoacyl derivatives and antibodies.

Carnitine palmitoyltransferase (CPT) is a mitochondrial-inner-membrane enzyme, with activities located on both the outer and inner sides of the membrane. The inhibition of CPT by bromopalmitate derivatives was studied in intact hepatic mitochondria (representing CPT-A activity, the outer enzyme), in inverted submitochondrial vesicles (representing CPT-B, the inner enzyme), and in purified hepatic CPT. Bromopalmitoyl-CoA had an I50 (concentration giving 50% inhibition of CPT activity) of 0.63 +/- 0.08 microM in intact mitochondria and 2.44 +/- 0.86 microM in inverted vesicles. Preincubation of mitochondria with bromopalmitoyl-CoA decreased V max. for both CPT-A and CPT-B. Sonication decreased sensitivity to bromopalmitoyl-CoA, and solubilization with Triton abolished sensitivity at the concentrations used (0-10 microM). Purified CPT had a bromopalmitoyl-CoA I50 of 353 microM in aqueous buffer, 67 microM in 20% dimethyl sulphoxide, 45 microM in phosphatidylcholine liposomes and 26 microM in cardiolipin liposomes. Increasing [carnitine] at constant bromopalmitoyl-CoA concentrations or increasing [bromopalmitoyl-CoA] in the preincubation resulted in increased inhibition of purified CPT. 2-Tetradecylglycidyl-CoA and malonyl-CoA did not offer measurable protection against bromopalmitoyl-CoA inhibition of the purified CPT, suggesting a different site of interaction of bromopalmitoyl-CoA with CPT. The data suggest that the sensitivity of CPT to bromopalmitoyl-CoA may be modulated by membrane environment and assay conditions.

Acyl Coenzyme A↗
PubMed1987

Comparison of lipid/gramicidin dispersions and cocrystals by Raman scattering.

Gramicidin crystals, dimyristoylphosphatidylcholine (DMPC)/gramicidin dispersions, and DMPC/gramicidin cocrystals were examined by Raman scattering to determine lipid/gramicidin stoichiometries and lipid organization. Calibrations of the choline (716-cm-1) and tryptophan (756-cm-1) peaks indicate that the cocrystals contain two lipids for each gramicidin monomer, a result confirmed by chemical analyses of washed crystals. In dispersions with high lipid/gramicidin ratios (e.g., 25:1), the lipid is ordered but becomes increasingly disordered as the gramicidin content is increased. Paradoxically, the DMPC/gramicidin cocrystals have highly ordered lipids that possibly contain no gauche bonds at all, despite their low lipid/gramicidin ratio. In addition, the polypeptide amide I peak position near 1670 cm-1 is found to be independent of the lipid/gramicidin ratio in the complexes and may indicate a beta-helix-type secondary structure at all ratios. However, the amide I peak broadens significantly at low lipid/gramicidin ratios and broadens still further in the cocrystals, suggesting that protein-protein interactions may induce band-broadening distortions of the polypeptide structure.

Choline↗
PubMed1984

Raman spectroscopy and deuterium exchange of the filamentous phage fd.

The filamentous phage fd has been investigated using the techniques of Raman spectroscopy and deuterium exchange. Despite the rather uniform secondary structure of the fd phage coat protein, which is predominantly alpha-helix, the deuterium exchange is complex. A substantial fraction of the helical peptides exchange deuterium by 8 h at room temperature, yet another substantial fraction does not exchange following an additional 5 months at 4 degrees C. Heating the phage to 70 degrees C for several hours leads to additional deuterium exchange compared to samples soaked for 5 months in heavy water. We suggest that the wide variation in peptide exchange rates may be related to the phage protein quaternary structure, which has been shown to be a double layer of tightly packed helices. The accomplishment of enhanced exchange by reaction at high temperature combined with digital difference spectroscopic methods has enabled us to define the structure of the amide III and III' bands. The complexity of these bands is unexpected for a simple helical protein, but we suggest that the complexity arises at least in part from end-effects that become important in short alpha-helices.

Amides↗
PubMed1983

Evidence that trypsin digestion exposes a channel in the sarcoplasmic reticulum membrane.

We present evidence that proteolytic digestion of sarcoplasmic reticulum membranes with trypsin exposes an ionophore that is capable of translocating calcium across the membrane of preloaded vesicles. Net transport of calcium appears to stop when the chemical potential of the ion on both sides of the membrane is equal. The temperature coefficient of steady-state leakage suggests that the ionophore is of the channel or pore type. We suggest that tryptic digestion exposes a channel in sarcoplasmic reticulum membranes through which calcium, and perhaps other ions as well, can diffuse down concentration gradients.

Adenosine Triphosphate↗