Search PubMed⌕ Search

Biomedical subjects

D A Case

Publications and source records attributed to D A Case.

At least 19 recordsLinked to original sources
PubMed1992

High-resolution X-ray study of deoxyhemoglobin Rothschild 37 beta Trp----Arg: a mutation that creates an intersubunit chloride-binding site.

The mutation site in hemoglobin Rothschild (37 beta Trp----Arg) is located in the "hinge region" of the alpha 1 beta 2 interface, a region that is critical for normal hemoglobin function. The mutation results in greatly reduced cooperativity and an oxygen affinity similar to that of hemoglobin A [Gacon, G., Belkhodja, O., Wajcman, H., & Labie, D. (1977) FEBS Lett. 82, 243-246]. Crystal were grown under "low-salt" conditions [100 mM Cl- in 10 mM phosphate buffer at pH 7.0 with poly(ethylene glycol) as a precipitating agent]. The crystal structure of deoxyhemoglobin Rothschild and the isomorphous crystal structure of deoxyhemoglobin A were refined at resolutions of 2.0 and 1.9 A, respectively. The mutation-induced structural changes were partitioned into components of (1) tetramer rotation, (2) quaternary structure rearrangement, and (3) deformations of tertiary structure. The quaternary change involves a 1 degree rotation of the alpha subunit about the "switch region" of the alpha 1 beta 2 interface. The tertiary changes are confined to residues at the alpha 1 beta 2 interface, with the largest shifts (approximately 0.4 A) located across the interface from the mutation site at the alpha subunit FG corner-G helix boundary. Most surprising was the identification of a mutation-generated anion-binding site in the alpha 1 beta 2 interface. Chloride binds at this site as a counterion for Arg 37 beta. The requirement of a counterion implies that the solution properties of hemoglobin Rothschild, in particular the dimer-tetramer equilibrium, should be very dependent upon the concentration and type of anions present.

Anions↗
PubMed1991

Unfolding of an alpha-helix in water.

We describe a 1 ns molecular dynamics simulation of an 18-residue peptide (corresponding to a portion of the H helix of myoglobin) in water. The initial helical conformation progressively frays to a more disordered structure, with the loss of internal secondary structure generally proceeding from the C-terminus toward the N-terminus. Although a variety of mechanisms are involved in the breaking of helical hydrogen bonds, the formation of transient turn structures, with i----i + 3 hydrogen bonds, and bifurcated hydrogen-bond structures intermediate between alpha and turn or 3(10) structures is a common motif. In some cases a single water molecule is inserted into an internal hydrogen bond, but it is also common to have several water molecules involved in transient intermediates. Overall, the results provide new information about the detailed mechanisms by which helices are made and broken in aqueous solution.

Amino Acid Sequence↗
PubMed1991

High-resolution solution structure of reduced French bean plastocyanin and comparison with the crystal structure of poplar plastocyanin.

The three-dimensional solution structure of reduced (CuI) plastocyanin from French bean leaves has been determined by distance geometry and restrained molecular dynamics methods using constraints obtained from 1H n.m.r. (nuclear magnetic resonance) spectroscopy. A total of 1244 experimental constraints were used, including 1120 distance constraints, 103 dihedral angle constraints and 21 hydrogen bond constraints. Stereospecific assignments were made for 26 methylene groups and the methyls of 11 valines. Additional constraints on copper co-ordination were included in the restrained dynamics calculations. The structures are well defined with average atomic root-mean-square deviations from the mean of 0.45 A for all backbone heavy atoms and 1.08 A for side-chain heavy atoms. French bean plastocyanin adopts a beta-sandwich structure in solution that is similar to the X-ray structure of reduced poplar plastocyanin; the average atomic root-mean-square difference between 16 n.m.r. structures and the X-ray structure is 0.76 A for all backbone heavy atoms. The conformations of the side-chains that constitute the hydrophobic core of French bean plastocyanin are very well defined. Of 47 conserved residues that populate a single chi 1 angle in solution, 43 have the same rotamer in the X-ray structure. Many surface side-chains adopt highly preferred conformations in solution, although the 3J alpha beta coupling constants often indicate some degree of conformational averaging. Some surface side-chains are disordered in both the solution and crystal structures of plastocyanin. There is a striking correlation between measures of side-chain disorder in solution and side-chain temperature factors in the X-ray structure. Side-chains that form a distinctive acidic surface region, believed to be important in binding other electron transfer proteins, appear to be disordered. Fifty backbone amide protons form hydrogen bonds to carbonyls in more than 60% of the n.m.r. structures; 45 of these amide protons exchange slowly with solvent deuterons. Ten hydrogen bonds are formed between side-chain and backbone atoms, eight of which are correlated with decreased proton exchange. Of the 60 hydrogen bonds formed in French bean plastocyanin, 56 occur in the X-ray structure of the poplar protein; two of the missing hydrogen bonds are absent as a result of mutations. It appears that molecular dynamics refinement of highly constrained n.m.r. structures allows accurate prediction of the pattern of hydrogen bonding.

Amino Acid Sequence↗
PubMed1990

Computational methods for determining protein structures from NMR data.

The general procedures by which solution structures of proteins may be deduced from distance and angular constraints derived from NMR are reviewed, with an emphasis on practical aspects of the calculations. In addition, novel methods based on chemical shift calculations and on quantitative fits to nuclear Overhauser effect intensities are presented; these should provide improved understanding of the limits of our ability to simulate complex spectra, and may permit higher precision structures to be determined.

Macromolecular Substances↗
PubMed1990

Three-dimensional solution structure of the reduced form of Escherichia coli thioredoxin determined by nuclear magnetic resonance spectroscopy.

The three-dimensional solution structure of reduced (dithiol) thioredoxin from Escherichia coli has been determined with distance and dihedral angle constraints obtained from 1H NMR spectroscopy. Reduced thioredoxin has a well-defined global fold consisting of a central five-strand beta-sheet and three long helices. The beta-strands are packed in the sheet in the order beta 1 beta 3 beta 2 beta 4 beta 5, with beta 1, beta 3, and beta 2 parallel and beta 2, beta 4, and beta 5 arranged in an antiparallel fashion. Two of the helices connect strands of the beta-sheet: alpha 1 between beta 1 and beta 2 and alpha 2 between beta 2 and beta 3. Strands beta 4 and beta 5 are connected by a short loop that contains a beta-bulge. Strands beta 3 and beta 4 are connected by a long loop that contains a series of turn-like or 3(10) helical structures. The active site Cys-Gly-Pro-Cys sequence forms a protruding loop between strand beta 2 and helix alpha 2. The structure is very similar overall to that of oxidized (disulfide) thioredoxin obtained from X-ray crystal structure analysis but differs in the local conformation of the active site loop. The distance between the sulfurs of Cys 32 and Cys 35 increases from 2.05 A in the disulfide bridge to 6.8 +/- 0.6 A in the dithiol of reduced thioredoxin, as a result of a rotation of the side chain of Cys 35 and a significant change in the position of Pro 34. This conformational change has important implications for the mechanism of thioredoxin as a protein disulfide oxidoreductase.

Amino Acid Sequence↗
PubMed1990

Enhanced sexual behavior in exercising men.

The effects of 9 months of aerobic exercise on aerobic work capacity (physical fitness), coronary heart disease risk factors, and sexuality were studied in 78 sedentary but healthy men (mean age, 48 years). The men exercised in supervised groups 60 min per day, 3.5 days per week on average. Peak sustained exercise intensity was targeted at 75-80% of maximum aerobic working capacity. A control group of 17 men (mean age, 44 years) participated in organized walking at a moderate pace 60 min per day, 4.1 days per week on average. Each subject maintained a daily diary of exercise, diet, smoking, and sexuality during the first and last months of the program. Beneficial effects of chronic, vigorous exercise on fitness and coronary heart disease risk factors were obtained in close agreement with prior studies. Analysis of diary entries revealed significantly greater sexuality enhancements in the exercise group (frequency of various intimate activities, reliability of adequate functioning during sex, percentage of satisfying orgasms, etc.). Moreover, the degree of sexuality enhancement among exercisers was correlated with the degree of their individual improvement in fitness.

Anxiety↗
PubMed1990

Observing behavior in a computer game.

Contingencies studied in lever-pressing procedures were incorporated into a popular computer game, "Star Trek," played by college students. One putative reinforcer, the opportunity to destroy Klingon invaders, was scheduled independently of responding according to a variable-time schedule that alternated unpredictably with equal periods of Klingon unavailability (mixed variable time, extinction schedule of reinforcement). Two commands ("observing responses") each produced stimuli that were either correlated or uncorrelated with the two components. In several variations of the basic game, an S-, or bad news, was not as reinforcing as an S+, or good news. In addition, in other conditions for the same subjects observing responses were not maintained better by bad news than by an uninformative stimulus. In both choices, more observing tended to be maintained by an S- for response-independent Klingons when its information could be (and was) used to advantage with respect to other types of reinforcement in the situation (Parts 1 and 2) than when the information could not be so used (Part 3). The findings favor the conditioned reinforcement hypothesis of observing behavior over the uncertainty-reduction hypothesis. This extends research to a more natural setting and to multialternative concurrent schedules of events of seemingly intrinsic value.

Adult↗
PubMed1989

Three-dimensional solution structure of a single zinc finger DNA-binding domain.

The three-dimensional solution structure of a zinc finger nucleic acid binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. Spectra of a synthetic peptide corresponding to a single zinc finger from the Xenopus protein Xfin yielded distance and dihedral angle constraints that were used to generate structures from distance geometry and restrained molecular dynamics calculations. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding.

Amino Acid Sequence↗
PubMed1989

Harmonic dynamics of a DNA hexamer in the absence and presence of the intercalator ethidium.

Vibrational normal mode calculations are presented for a DNA hexanucleoside pentaphosphate, d(CpGpCpGpCpG)2, and for its complex with the cationic intercalator ethidium. Two intercalation sites are modeled that differ in DNA backbone torsion angles. Normal mode frequencies for the DNA fragment itself are significantly lower than those reported earlier using different force fields, but an analysis of "effective" frequencies suggests that somewhat higher frequencies are more appropriate. Intercalation leads to significant lowering of mobility for the base pairs adjacent to the drug; in this sequence, the ethidium binding affects the guanosine atoms more strongly than the cytosine atoms. Motions of the bases and the intercalator are analyzed in terms of "twist" about the local helix axis and a "tilt" angle relative to this axis, and the results are compared to fluorescence studies of ethidium-DNA complexes.

DNA↗
PubMed1989

A combined 2D-NMR and molecular dynamics analysis of the structure of the actinomycin D: d(ATGCAT)2 complex.

We present a comparative analysis of an NMR experiment and molecular and harmonic dynamics simulations of an actinomycin D: d(ATGCAT)2 complex. A comparison of NOE measurements and 1/R6 weighted proton-proton distances confirm the general correctness of the Actinomycin D-DNA model proposed by Sobell. There are, however, some substantial differences between the proton-proton distances inferred from the NOE results and the molecular and harmonic dynamics simulations. The remaining discrepancies could either come from contributions of other conformations to the average properties of the complex or from uncertainties in the NMR distance analysis. An analysis of the molecular dynamics helix properties, sugar puckers, hydrogen bonding, rms fluctuations and torsional properties are qualitatively consistent with those from previous simulations, but the presence of an intercalated drug leads to some new structural and dynamical features.

Chemical Phenomena↗
PubMed1988

Three-dimensional solution structure of plastocyanin from the green alga Scenedesmus obliquus.

The solution conformation of plastocyanin from the green alga Scenedesmus obliquus has been determined from distance and dihedral angle constraints derived by nuclear magnetic resonance (NMR) spectroscopy. Structures were generated with distance geometry and restrained molecular dynamics calculations. A novel molecular replacement method was also used with the same NMR constraints to generate solution structures of S. obliquus plastocyanin from the x-ray structure of the homologous poplar protein. Scenedesmus obliquus plastocyanin in solution adopts a beta-barrel structure. The backbone conformation is well defined and is similar overall to that of poplar plastocyanin in the crystalline state. The distinctive acidic region of the higher plant plastocyanins, which functions as a binding site for electron transfer proteins and inorganic complexes, differs in both shape and charge in S. obliquus plastocyanin.

Calorimetry↗
PubMed1986

Computational studies of the interaction of myoglobin and xenon.

Computational studies are used to investigate the energies of xenon binding to myoglobin and to describe pathways through the protein interior for a metmyoglobin-xenon complex. Empirical energy calculations indicate a favorable enthalpic contribution of 0.6 to 4.2 kcal/mol to xenon binding for four experimentally determined xenon sites. These calculated enthalpies help to explain the different xenon occupancies observed experimentally. A fifth site, modeled in place of the iron co-ordinated water molecule in the distal cavity, is also predicted to bind xenon. The largest contribution to the binding energy is from van der Waals' interactions with smaller contributions from polarization and protein strain terms. Ligand trajectory calculations as well as a new geometric algorithm define a connecting network of channel-like pathways through the static protein structure. One or two pathways appear to lead most easily from each major internal cavity to the protein surface. The importance of these channels in protein dynamics and their implications as routes for ligand motion are discussed.

Algorithms↗
PubMed1986

Dynamic simulations of oxygen binding to myoglobin.

We report dynamic simulations of the process by which a dioxygen molecule enters or leaves the heme pocket region of myoglobin along a path between the distal histidine (E7) and valine (E11). Our reaction coordinate measures the distance of the ligand from a "dividing plane" defined by three protein atoms. The equilibrium probability distribution as a function of this coordinate is determined by a series of molecular-dynamic simulations with overlapping "umbrella" constraining potentials; the resulting potential of mean force has a barrier of about 7 kcal/mol for exit from the heme pocket. A comparison of this free energy profile with the corresponding potential energy profile suggests that entropy effects dominate the kinetic barrier. Reactive trajectories are generated from dynamic simulations beginning at the top of the potential of mean force; only a small fraction of these recross the dividing surface, indicating that transition state theory may be a good approximation for this process.

Computer Simulation↗
PubMed1985

Human observing: maintained by negative informative stimuli only if correlated with improvement in response efficiency.

Two experiments investigated the effect of observing responses that enabled college students to emit more efficient distributions of reinforced responses. In Experiment 1, the gains of response efficiency enabled by observing were minimized through use of identical low-effort response requirements in two alternating variable-interval schedules. These comprised a mixed schedule of reinforcement; they differed in the number of money-backed points per reinforcer. In each of three choices between two stimuli that varied in their correlation with the variable-interval schedules, the results showed that subjects preferred stimuli that were correlated with the larger average amount of reinforcement. This is consistent with a conditioned-reinforcement hypothesis. Negative informative stimuli--that is, stimuli correlated with the smaller of two rewards--did not maintain as much observing as stimuli that were uncorrelated with amount of reward. In Experiment 2, savings in effort made possible by producing S- were varied within subjects by alternately removing and reinstating the response-reinforcement contingency in a mixed variable-interval/extinction schedule of reinforcement. Preference for an uncorrelated stimulus compared to a negative informative stimulus (S-) decreased for each of six subjects, and usually reversed when observing permitted a more efficient temporal distribution of the responses required for reinforcement; in this case, the responses were pulls on a relatively high-effort plunger. When observing the S- could not improve response efficiency, subjects again chose the control stimulus. All of these results were inconsistent with the uncertainty-reduction hypothesis.

Attention↗