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K E Lind

Publications and source records attributed to K E Lind.

12 recordsLinked to original sources
PubMed1999

Structural properties of DNA:RNA duplexes containing 2'-O-methyl and 2'-S-methyl substitutions: a molecular dynamics investigation.

The physical properties of a DNA:RNA hybrid sequence d(CCAACGTTGG)*(CCAACGUUGG) with modifications at the C2'-positions of the DNA strand by 2'-O-methyl (OMe) and 2'-S-methyl (SMe) groups are studied using computational techniques. Molecular dynamics simu-lations of SMe_DNA:RNA, OMe_DNA:RNA and standard DNA:RNA hybrids in explicit water indicate that the nature of the C2'-substituent has a significant influence on the macromolecular conformation. While the RNA strand in all duplexes maintains a strong preference for C3'-endo sugar puckering, the DNA strand shows considerable variation in this parameter depending on the nature of the C2'-substituent. In general, the preference for C3'-endo puckering follows the following trend: OMe_DNA>DNA>SMe_DNA. These results are further corroborated using ab initio methods. Both gas phase and implicit solvation calculations show the C2'-OMe group stabilizes the C3'-endo conformation while the less electronegative SMe group stabilizes the C2'-endo conformation when compared to the standard nucleoside. The macromolecular conformation of these nucleic acids also follows an analogous trend with the degree of A-form character decreasing as OMe_DNA:RNA>DNA:RNA>SMe_DNA:RNA. A structural analysis of these complexes is performed and compared with experimental melting point temper-atures to explain the structural basis to improved binding affinity across this series. Finally, a possible correlation between RNase H activity and conformational changes within the minor groove of these complexes is hypothesized.

Base Sequence↗
PubMed1998

Structural characteristics of 2'-O-(2-methoxyethyl)-modified nucleic acids from molecular dynamics simulations.

The structure and physical properties of 2'-sugar substituted O -(2-methoxyethyl) (MOE) nucleic acids have been studied using molecular dynamics simulations. Nanosecond simulations on the duplex MOE[CCAACGTTGG]-r[CCAACGUUGG] in aqueous solution have been carried out using the particle mesh Ewald method. Parameters for the simulation have been developed from ab initio calculations on dimethoxyethyl fragments in a manner consistent with the AMBER 4.1 force field database. The simulated duplex is compared with the crystal structure of the self-complementary duplex d[GCGTATMOEACGC]2, which contains a single modification in each strand. Structural details from each sequence have been analyzed to rationalize the stability imparted by substitution with 2'- O -(2-methoxyethyl) side chains. Both duplexes have an A-form structure, as indicated by several parameters, most notably a C3' endo sugar pucker in all residues. The simulated structure maintains a stable A-form geometry throughout the duration of the simulation with an average RMS deviation of 2.0 A from the starting A-form structure. The presence of the 2' substitution appears to lock the sugars in the C3' endo conformation, causing the duplex to adopt a stable A-form geometry. The side chains themselves have a fairly rigid geometry with trans , trans , gauche +/- and trans rotations about the C2'-O2', O2'-CA', CA'-CB' and CB'-OC' bonds respectively.

Base Sequence↗
PubMed1978

Enzymatically active Ca2+ ATPase from sarcoplasmic reticulum membranes, solubilized by nonionic detergents. Role of lipid for aggregation of the protein.

The present study provides data on the properties of Ca2+-dependent Atpase of sarcoplasmic reticulum in states intermediary between the fully detergent-solubilized and vesicular form. After solubilization of ATPase vesicles by dodecyloctaoxyethylene glycol monoether (C12E8), the protein is mainly present as a monomer exhibiting enzymatic activity. Gel chromatography in presence or absence of Tween 80 gives rise to formation of oligomers of various size and smaller amounts of monomeric ATPase. Only the oligomeric species retain enzymatic activity (half-life, 3 to 4 days), while the gel chromatographic monomer is enzymatically inactive. Teteramers or trimers of ATPase, containing approximately 22 mol of phospholipid/mol of ATPase, are the smallest enzymatically active units after gel chromatography. Formation of larger sized particles and vesicles of ATPase appears to depend on the presence of sufficient lipid to make a cohesion between the tetrameric or trimeric units. The protein appears to be partially deaggregated by a relatively high Tween 80 concentration in the eluant (0.5 mg/ml) and under these conditions, phospholipid binding is reduced to a low level (approximately 11 mol/mol of protein). The data indicate that any bonds between ATPase polypeptide chains are easily disrupted by detergent and that lipid also may play a role in mediating contact between individual polypeptide chains in the tetrameric or trimeric units. Phospholipid analysis and exchange experiments indicate that the phospholipid left on ATPase after solubilization has a similar composition to that of the whole membrane. The binding of Tween 80 by soluble ATPase above the critical micellar concentration is 0.23 to 0.29 g/g of protein. The inactive monomer of ATPase binds phospholipid and Tween 80 to about the same extent, but has a slightly different circular dichroism spectrum, than oligomeric ATPase.

Animals↗
PubMed1978

The functional unit of calcium-plus-magnesium-ion-dependent adenosine triphosphatase from sarcoplasmic reticulum. The aggregational state of the deoxycholate-solubilized protein in an enzymically active form.

Vesicles consisting of (Ca(2+)+Mg(2+))-dependent ATPase (adenosine triphosphatase), and lipid were prepared from sarcoplasmic reticulum of rabbit skeletal muscle. As with non-ionic detergents [le Maire, Møller & Tanford (1976) Biochemistry15, 2336-2342] the (Ca(2+)+Mg(2+))-dependent ATPase after solubilization by deoxycholate showed a pronounced tendency to form oligomers in gel-chromatographic experiments, when eluted in the presence of deoxycholate and phosphatidylcholine. To evaluate the functional significance of oligomer formation the properties of enzymically active preparations of ATPase, solubilized by deoxycholate, were studied. Such preparations were obtained at a protein concentration of 2.5mg/ml in the presence of a high salt concentration (0.4m-KCl) and sucrose (0.3m) in the solubilization medium. Analytical ultracentrifugation of solubilized ATPase showed one protein boundary moving at the same rate as gel-chromatographically prepared monomeric ATPase (s(20,w)=6.0S). From simultaneous measurements of the diffusion coefficient an apparent molecular weight of 133000 was calculated, consistent with solubilization of ATPase in predominantly monomeric form. The enzymic activity of deoxycholate-solubilized ATPase when measured directly in the solubilization medium at optimal Ca(2+) and MgATP concentrations was about 35-50% of that of vesicular ATPase. The dependence of enzymic activity on MgATP concentration indicated that the solubilized ATPase retained high-affinity binding of MgATP, but the presence of high concentrations of the nucleotide did not stimulate activity further, in contrast with that of vesicular ATPase. The dependence of enzymic activity on the free Ca(2+) concentration was essentially the same for both solubilized and vesicular forms, indicating that interaction of ATPase with more than one molecule of Ca(2+) is required for enzyme activity. Solubilized enzyme at 20 degrees C was phosphorylated to about the same degree as vesicular ATPase. It is concluded that the catalytic activity of monomeric ATPase retains most of the features of vesicular ATPase and that extensive oligomer formation in gel-chromatographic experiments in the presence of deoxycholate probably reflects processes taking place during inactivation and delipidation of the protein.

Adenosine Triphosphatases↗
PubMed1976

Ligand-apomyoglobin interactions. Configurational adaptability of the haem-binding site.

1. The interaction of the haem-binding region of apomyoglobin with different ligands was examined by ultrafiltration, equilibrium dialysis and spectrophotometry, to study unspecific features of protein-ligand interactions such as they occur in, for example, serum albumin binding. 2. Apomyoglobin, in contrast with metmyoglobin, binds at pH 7, with a high affinity, one molecule of Bromophenol Blue, bilirubin and protoporphyrin IX, two molecules of n-dodecanoate and n-decyl sulphate and four molecules of n-dodecyl sulphate and n-tetradecyl sulphate. 3. The number of high-affinity sites and/or association constants for the alkyl sulphates are enhanced by an increase of hydrocarbon length, indicating hydrophobic interactions with the protein. 4. Measurements of the temperature-dependence of the association constants of the high-affinity sites imply that the binding processes are largely entropy-driven. 5. Binding studies in the presence of two ligands show that bilirubin plus Bromophenol Blue and dodecanoate plus Bromophenol Blue can be simultaneously bound by apomyoglobin, but with decreased affinities. By contrast, the apomyoglobin-protoporphyrin IX complex does not react with Bromophenol Blue. 6. Optical-rotatory-dispersion measurements show that the laevorotation of apomyoglobin is increased towards that of metmyglobin in the presence of haemin and protoporphyrin IX. Small changes in the optical-rotatory-dispersion spectrum of apomyoglobin are observed in the presence of the other ligands. 7. It is concluded that the binding sites on apomyoglobin probably do not pre-exist but appear to be moulded from predominantly non-polar amino acid residues by reaction with hydrophobic ligands. 8. Comparison with data in the literature indicates that apomyoglobin on a weight basis has a larger hydrophobic area avaialble for binding of ligands than has human serum albumin. On the other hand, the association constants of serum for the ligands used in this study are generally somewhat larger than those of apomyoglobin.

Apoproteins↗