PubMed Health⌕ Search

Biomedical subjects

R A Atkinson

Publications and source records attributed to R A Atkinson.

31 records · Page 2Linked to original sources
PubMed1991

1H NMR and circular dichroism studies of the N-terminal domain of cyclic GMP dependent protein kinase: a leucine/isoleucine zipper.

Cyclic GMP dependent protein kinase exists as a dimer in its native form. A peptide corresponding to the dimerization domain in the N-terminal segment has been characterized by circular dichroism, ultracentrifugation, and 1H NMR spectroscopy. The peptide (G-kinase1-39 amide) is shown to be dimeric in solution. Determination of the molecular weight of the species in solution from the sedimentation coefficient and diffusion coefficient yields a value more than twice that of the monomeric species. Circular dichroism studies show G-kinase1-39 amide to be largely helical in aqueous solution and stable over a wide range of pH and temperature. The conformational stability is found to be concentration dependent, the peptide having a melting temperature of 75 degrees C (at 20 microM and pH 4.0). The assignment of the 1H NMR spectrum and analysis of the patterns of nuclear Overhauser enhancements confirm the helical nature of the conformation. Distance geometry calculations result in a well-defined helical structure containing a kink near Ser 26. The dimerization of G-kinase is most likely to occur through the hydrophobic interaction of leucine and isoleucine side chains located on one face of a helical structure with supporting electrostatic interactions between flanking side chains. The dimerization domain of G-kinase is clearly analogous to the "leucine zipper" motifs found in a number of DNA transcriptional activators.

Amino Acid Sequence↗
PubMed1991

Three-dimensional structure of echistatin, the smallest active RGD protein.

Echistatin is a 49 amino acid protein isolated from the venom of a viper (Echis carinatus) and is one of the smallest natural adhesive ligands that interacts with integrin-type receptors through an Arg-Gly-Asp (RGD) sequence. The structure of echistatin in aqueous solution has been determined by nuclear magnetic resonance spectroscopy. Nuclear Overhauser spectra yielded 490 interatomic distance constraints, which were used in distance geometry calculations. The chain is shown to fold in a series of irregular loops to form a rigid core stabilized by four cystine cross-links. From this core an irregular hairpin and the C-terminus protrude. The core and the hairpin are further stabilized by a network of hydrogen bonds. The RGD sequence is located in a mobile loop at the tip of the hairpin. The mobility and its significance for activity are discussed.

Amino Acid Sequence↗
PubMed1991

Topological mirror images in protein structure computation: an underestimated problem.

When calculating three-dimensional structures from NMR data, alternative solutions with very large RMS deviation can be obtained. Sometimes local or global inversions of the protein folding can be observed. We call these different solutions topological mirror images, as they keep the correct amino acid chirality. They are observed when the number of restraints is insufficient and represent different solutions from the same scalar information. Therefore they are common in small peptides where the NMR data are often limited and the secondary structure is not very well defined. They can also be observed in large molecules in regions of higher flexibility. In our experience the observation of topological mirror images is independent of the efficiency of sampling of the algorithm used. We present four examples of proteins with different size and folding. We also discuss ways to distinguish among the different solutions.

Acid Anhydride Hydrolases↗
PubMed1990

Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry.

Kringle 4 is an autonomous structural and folding domain within the proenzyme plasminogen. Homologous domains are found throughout the blood clotting and fibrinolytic proteins. In this paper, we present the almost complete assignment of the 1H nuclear magnetic resonance (n.m.r.) spectrum of the kringle 4 domain of human plasminogen. A detailed structural analysis has been completed. The sequential pattern of nuclear Overhauser enhancements indicated little regular secondary structure but rather a series of turns and loops connecting beta-strands. A small stretch of antiparallel beta-sheet was identified between the residues 61 to 63 and 71 to 73 and the close proximity of other strands was determined from two-dimensional nuclear Overhauser enhancement spectra. Slowly exchanging amide (NH) resonances were found to be associated with residues of the beta-sheet and neighbouring strands that support the hydrophobic core of the domain. A total of 526 interproton distance constraints and two hydrogen bonds were specified as input to the distance geometry program DISGEO. Tertiary structures were produced that were consistent with the n.m.r. data. The structures were compared with that of our earlier model based on n.m.r. studies and with that of prothrombin fragment 1 determined crystallographically.

Amino Acid Sequence↗
PubMed1989

Identification and description of alpha-helical regions in horse muscle acylphosphatase by 1H nuclear magnetic resonance spectroscopy.

It has been proposed that combination of intraresidue, sequential and longer range nuclear Overhauser enhancements occurring in 1H nuclear magnetic resonance spectra of protein chains folded in a helix show a regular characteristic pattern. As a test case the spectra of horse muscle acylphosphatase were searched for this pattern together with other typical signs of a helical conformation (i.e. chemical shift, coupling constants and slow 2H-H exchange). Two amino acid sequences complying with these requirements were found. Just a few amino acid spin system assignments were then sufficient to locate the two segments within the primary structure (residues 22 to 35 and 55 to 66), thus providing the sequential assignment. The assignment of the side-chains was completed and a list of all nuclear magnetic resonance constraints within the two segments (126 intra- and 180 interresidue distances, 21 torsion angles phi and 19 hydrogen bonds) was produced. Distance geometry calculation shows that each segment forms an alpha-helix. The mutual orientation of the two helices was established subsequently.

Acid Anhydride Hydrolases↗
PubMed1988

Two-dimensional NMR as a probe of structural similarity applied to mutants of cytochrome c.

Using site-directed mutagenesis, it is possible to prepare many mutants of a protein in a short time, and to uncover differences in function. To understand the changes in function, it is essential to understand the effect(s) of the mutation in terms of structural and dynamic changes. It is particularly important to establish a rapid method for comparing the structure of the mutants with that of the wild-type protein. We propose that a combination of overlayed and difference two-dimensional NOE spectra between the wild-type and mutant protein provide a rapid method for determination of structural similarity. The observation of differences other than those due directly to the field effects of the exchanged side chain allow both local and distant conformational changes to be assessed. Here we compare NOESY spectra from a mutant of yeast iso-1-ferrocytochrome c in which the invariant residue Phe-82 has been changed to a Tyr. We conclude that NMR can show subtle changes in protein structure. Specifically, we show the change must involve the reorientation of the side chain of Leu-85 which is proximal to the mutation. The dynamics of the aromatic side chain at position 82 are shown not to give rise to measurable differences between the wild-type and mutant protein. Structural changes are not propagated to a measurable degree in other parts of the protein.

Binding Sites↗
PubMed1976

[Headache in the pathology of small cerebral blood vessels: study of patients with systemic lupus erythematosus].

Seventy-two records of patients with systemic lupus erythematosus were reviewed retrospectively. Sixty-one fulfilled the criteria for the disease. Forty-six percent had clinical evidence of central nervous system involvement. The incidence of headache was compared in those with and without central nervous system lupus. No difference in the frequency of headache in the two groups was found and the incidence of hypertension, renal disease and steroid therapy was equally distributed among those with and without headache. A significantly higher incidence of hypertension was found in patients with central nervous system lupus erythematosus. We conclude that headache in systemic lupus erythematosus in the absence of neurologic symptoms or signs is no indication of central nervous system involvement by the process and that small vessel disease of the brain is not a cause of headache.

Adolescent↗
PubMedDate not supplied

Methohexital activation of epileptogenic foci during acute electrocorticography.

Methohexital was used as an activating agent in 62 patients undergoing focal cortical resections of epileptogenic foci and in six patients undergoing chronic electroencephalogram (EEG)/video monitoring with intracranial strip electrodes. In 87% of cases, methohexital caused selective activation of the epileptogenic focus during acute electrocorticography (ECoG). This activation appeared to be specific for the epileptogenic focus and did not cause epileptiform spiking from adjacent nonepileptogenic cortex. This ECoG activation occurred whether patients received local or general anesthesia. Sixty-five percent of patients demonstrated adequate activation with as little as 25 mg of drug. Methohexital is a safe and reliable method of activating epileptogenic foci during acute ECoG recordings and can decrease the time for ECoG recordings during surgery.

Brain↗