PubMed Health⌕ Search

Biomedical subjects

S S Danyluk

Publications and source records attributed to S S Danyluk.

At least 19 recordsLinked to original sources
PubMed1980

Conformational flexibility of the 3' acceptor end of transfer ribonucleic acid.

The intimate details of the conformational features and dynamics of the trinucleoside diphosphates CpCpA and ApCpC in aqueous solution have been arrived at by the complete analysis of their proton magnetic resonance spectra. In addition to the right-handed stacked species in which the phosphodiester torsions conform to the gauche-gauche domains, sugar puckers 3E, C4'-C5 approximately equal to 60 degrees, C5'-O5' approximately 180 degrees, C3'-O3' approximately equal to 205 degrees, and chi CN approximately equal to 40 degrees, the trimers display a variety of spatial configurations, an important one being a bulged configuration in which the central nucleotide unit is bulged out, enabling stacking interactions between the end units. It is further shown that the 3' acceptor end of tRNA, CpCpA, displays considerable flexibility for the terminal adenine nucleotide unit. Theoretical NMR calculations demonstrate that the predominant solution conformation does not conform to the CCA terminus of tRNA as reported by four independent crystallographic studies of tRNAPhe. It is shown that the preferred intramolecular order of CCA in solution is such that chi 1 = chi 2 = chi 3 = 40 degrees, all the three sugars are in 3E, psi 1 = psi 2 = psi 3 = 60 degrees, phi 2 and phi 3 = 170 and 180 degrees, respectively, phi 1 = phi 2' = 205 degrees, and omega 1/omega 1 and omega 2/omega 2' = 240/205 degrees and 295/265 degrees, respectively.

Base Sequence↗
PubMed1980

13C nuclear magnetic resonance study of the complexation of calcium by taurine.

13C Nuclear magnetic resonance chemical shifts, 1JC-C scalar coupling constants, spin-lattice relaxation times, and nuclear Overhauser effects were determined for taurine-[1,2 13C] and a taurine-[1 13C] and taurine-[2 13C] mixture in the presence and absence of calcium. Ionization constants for taurine amino and sulfonic acid groups and chemical shifts of N-methylene and S-methylene carbons of the taurine cation, zwitterion, and anion were obtained from simultaneous least squares analysis of 13C titration curves of both taurine carbons. Comparison of taurine titration shifts to values for related compounds reveals some unusual electronic properties of the taurine molecule. Stability constants of 1:1 calcium complexes with taurine zwitterions and anions, as well as their 13C chemical shifts, were obtained by least squares analysis of titration curves measured in the presence of calcium. The stability constants of calcium-taurine complexes were significantly lower than previous values and led to estimates that only approximately one percent of intracellular calcium of mammalian myocardial cells would exist in a taurine complex. The implications of these results with respect to the effect of taurine on calcium ion flux are discussed.

Calcium↗
PubMed1978

Spin label detection of intermolecular interactions in carbonmonoxy sickle hemoglobin.

With recently developed spin label techniques for monitoring macromolecular rotational motion, heme-liganded sickle cell hemoglobin in the presence of inositol hexaphosphate is shown to exhibit restricted motional freedom as compared to liganded normal adult human hemoglobin. This motional restriction is dependent on both hemoglobin concentration and temperature.

Adult↗
PubMed1977

Conformational properties of purine-pyrimidine and pyrimidine-purine dinucleoside monophosphates.

The detailed conformational features and dynamics of heterodinucleoside monophosphates ApU, ApC, GpU, GpC, UpA, CpA, UpG, and CpG have been studied in aqueous solution by high field nuclear magnetic resonance (NMR) spectroscopy. Analysis of the resultant NMR parameters leads to a number of discernible trends throughout the series. Thus the ribose rings of the dimers exist as equilibrium mixtures of C(2')-endo(2E) in equilibrium C(3')-endo(3E) conformers with a proclivity for the 3E pucker in most cases; the C(4')-C(5') bonds of both nucleotidyl units show significant preference (74-96%) for a gg conformation and the dominant conformer (85-89%) about C(5')-O(5') is g'g'. Orientation about the C(3')-O(3') bond is coupled to the ribose conformational equilibrium and the system exists with a bias for the 3Eg- coupled conformation in which the H(3')-C(3')-O(3')-P dihedral angle occupies the narrow range of 33-35 degrees. Dimerization, on the average, causes about 10% increase in gg and g'g' populations and the g-domain becomes increasingly populated about the C(3')-O(3') bond. The ribose equilibrium 2E in equilibrium 3E shifts in favor of 3E upon dimerization, the effect being very conspicuous for the pu-py series (similar to 40 yields 60%) and less noticeable for the py-pu systems (similar to 47 yields 58%), clearly suggesting a correlation between sequence and ribose conformational equilibrium. The temperature and dimerization data for the heterodinucleoside monophosphates show that the transition 2E yields 3E is directly related to XCN changes induced by dimerization and stacking. Analysis of the ribose coupling data shows that the percentage populations of stacked species vary from dimer to dimer with GpC displaying a maximum of 45% stacked population and UpG about 10%. However, in general, the pu-py dimers show a higher preference (27-45%) for stacked conformations than py-pu dimers (10-25%). It is proposed that the pronounced deshielding of H(5') of the 5'-nucleotidyl units upon dimerization is associated with the presence of right-handed stacks (g-g-), whereas the chemical shift trends of H(5') and H(5') of 3'-nucleotidyl units are due to the presence of left-handed stacks (g+g+) in all the dimers. In pu-py dimers, the population of the g-g- species is found to be greater than that of g+g+. Also the population of g-g- stacks in pu-py dimers is generally greater than in their corresponding matched py-pu dimers. Thus the base sequence has not only an explicit effect on the overall populations of stacked species, but also on the handedness of the stacks. The present results further confirm the interdependence of conformational bonds throughout the nucleotidyl framework.

Deuterium↗
PubMed1976

Conformational properties of dinucleoside monophosphates in solution: dipurines and dipyrimidines.

In order to obtain information about the conformational features in a polyribonucleotide at the nearest neighbor level, detailed nuclear magnetic resonance studies of the dinucleoside monophosphates ApA, ApG, GpA, UpU, CpC, UpC, and CpU were undertaken. Proton spectra were recorded at 100, 220, 270, or 300 MHz for D2O solutions, 0.01-0.03 M, pD 7.4 at 20+/-2 degrees C. Spectra of ApA, ApG, UpU, and UpC were also recorded in the temperature range of 70-90 degrees C. Unambiguous signal assignments of all proton resonances were made with the aid of selectively deuterated dimers. Complete, accurate sets of nuclear magnetic resonance (NMR) parameters were derived for each nucleotidyl unit by simulation-iteration methods. A complete set of chemical shift and coupling constant data was also obtained for all the constituent monomeric units at a concentration and ionization state comparable to that of the dimers. Conformational properties were evaluated quantitatively for most of the bonds in the dinucleoside monophosphates using procedures developed in earlier studies. All of the dimers have a flexible conformational framework in aqueous solution. While flexibility is allowed and alternate conformations are accessible, these molecules nevertheless attempt to achieve conformational identity by showing preferences--sometimes overwhelming preferences--for certain orientations. Thus the ribose rings exist as equilibrium mixtures of C2'-endo in equilibrium C3'-endo conformers with a bias for the C3'-endo pucker in most cases. The C4'-C5' bonds of both nucleotidyl units show significant preference (70-85%) for a gg conformation. Similarly, the dominant conformer (80-90%) about C5'-O5' is g'g'. Even though an unambiguous determination of the orientation about C3'-O3' cannot be made, there is suggestive evidence that the orientation of the 3' phosphate group is coupled to the ribose conformational equilibrium and it is likely that a 3Eg- in equilibrium 2Eg+ equilibrium exists with a bias for the 3Eg- coupled conformation in which the H3'-C3'-O3'-P dihedral angle is about 34-38 degrees. The individual nucleotidyl units in the dimers differ in several key ways from corresponding monomer conformations. Specifically, the ribose equilibrium C2'-endo in equilibrium C3'-endo shifts in favor of C3'-endo upon dimerization, the only exception being UpU. The C4'-C5' and C5'-O5' bonding network in the dimer forms a stable conformational unit and no correlation exists in the dimers between the conformational preference of this fragment and ribose conformer population. The temperature data for the dimers and dimerization data clearly indicate that the transition C2'-endo leads to C3'-endo is directly related to XCN changes brought about by dimerization and stacking...

Magnetic Resonance Spectroscopy↗
PubMed1976

Conformational properties of adenylyl-3' leads to 5'-adenosine in aqueous solution.

A detailed 220-MHz NMR study has been made of the conformational properties for the homodinucleotide adenylyl-3' leads to 5'-adenosine, ApA, in D2O. Unambiguous signal assignments of all proton signals were made with the aid of selectively deuterated nucleotidyl units, ApA, ApA, and D-8ApA, and complete, accurate sets of NMR parameters were derived by simulation-iteration methods. Sets of limiting chemical shifts and coupling values were also obtained for ApA and constituent monomers 3'-AMP and 5'-AMP at infinite dilution and at identical ionization states for assessment of dimerization effects. Conformational properties were evaluated quantitatively for most of the conformational bonds of ApA and these are consistent with two compact folded dynamically averaged structures, a base-stacked right helical structure, I, characterized as anti, C3'-endo, g-, w,w' (320,330 degrees), g'g', gg, C3'-endo, anti, and a more loosely base-stacked loop structure, II, with anti, C3'-endo, g-, w,w' (80 degrees, 50 degrees), g'g', gg, C3'-endo, anti orientations. Dimerization produces a number of nucleotidyl conformational changes including a shift in ribose equilibrium C2'-endo (S) in equilibrium C3'-endo (N) in favor of C3'-endo in both Ap- and -pA (60:40 vs. 35:65 in monomers), a change in glycosidic torsion angle chiCN toward 0 degrees, and a greater locking-in of rotamers along bonds involved in the phosphodiester backbone. Moreover, there is clear evidence that the transitions from S leads to N forms and chiCN leads to 0 degrees are directly related to base stacking in ApA. Finally, ApA exists in solution as an equilibrium between I, II and an unstacked form(s) with as yet undetermined conformational features. Since C4'-C5', C5'-O5', and C3'-O3' bonds possess exceptional conformational stabilities, it is proposed that destacking occurs primarily by rotation about P-O5' and/or O3'-P. Predominant factors influencing the overall ApA conformation are thus base-base interaction and flexibility about P-O5' and O3'-P, with change of ribose conformation occurring in consequence of an alteration of chiCN, the latter in turn being governed by the need for maximum eta overlap of stacked adenine rings.

Adenine Nucleotides↗
PubMed1976

The effect of (2'-5') and (3'-5') phosphodiester linkages on conformational and stacking properties of cytidylyl-cytidine in aqueous solution.

Conformational properties of (2'-5') and (3'-5') CpC have been determined by proton magnetic resonance spectroscopy at 220 MHz. The ribose ring structures are predominantly 3E with the exception of the ring from the 2'-phosphate fragment of C(2'-5')pC which exhibits an 2E pucker. Bases are oriented anti with respect to the ribose and the conformations about C4'-C5', C5'-O5', C3'-O3' (C2'-O2') are gg, g'g', and g+ in equilibrium g-, respectively. The dimers exist as mixtures of stacked (g+g+ and g-g- about the P-O(C) bonds) and unstacked species at 20 degrees C. Stacking is estimated to be 35% in both dimers.

Cytosine↗
PubMed1975

Nuclear magnetic resonance studies of 2'- and 3'-ribonucleotide structures in solution.

A systematic 220-MHz proton nuclear magnetic resonance (nmr) study has been made of all common purine and pyrimidine 2'(3')-ribonucleotides in D2O solutions at 20 plus or minus 2 degrees. Spectra for the entire series were measured under similar conditions of concentration, temperature, and ionic strength, thereby facilitating intercomparisons of spectral properties. Spectral assignments were accomplished with the aid of selected 31P-1H decoupling experiments and accurate values of nmr parameters were derived by simulation-iteration procedures. A detailed analysis of the coupling constants and chemical shifts permitted a determination of conformational properties for ribose rings, exocyclic carbinol and phosphate groups, and the orientation of base-ribose rings. Following procedures described elsewhere, an evaluation was made of ribose ring pseudorotational parameters for each 2'(3')-nucleotide. The results show that both the degree of pucker and pseudorotational angle vary only slightly throughout the entire series of molecules, and lie within the ranges found in the crystalline state. Furthermore, the ribose rings are in rapid equilibrium between N type (C(3')-ENDO, C(2')-exo) and S type (C(2')-endo, C(3')-exo) conformers, N forms and is formed by S, with an S type conformer favored in purine 2'(3')-ribonucleotides (-60:40) while pyrimidines exhibit approximately equal compositions. Thus, the phosphate location on the ring has less of an effect on ring properties than the nature of the base ring. An analysis is also reported of rotamer equilibria about C(4')-C(5'), C(2')-O(2'), and C(3')-O(3') bonds. For the former the nmr coupling constant data are consistent with a predominant gg rotamer (-70%) with gt and tg rotamers populated to the extent of -20 and -10%, respectively. No correlation of the type seen for 5'-nucleotides appears to exist between C(4')-C(5') gg population and ribose ring equilibrium composition. For 2'-nucleotides the 31P-H(2') coupling data indicate a preferred C(3')g, C(1')t conformer about C(2')-O(2') in agreement with 13C nmr results. A less definitive rotamer analysis follows from observed J31P,H(3') values, but when these results are combined with relevant chemical shift data for deoxynucleosides and nucleotides the evidence strongly points to essentially free rotation and approximately equal rotamer populations about C(3')-O(3'). Chemical shift differences between purine and pyrimidine 2'(3')-ribonucleotides are qualitatively accounted for by "in-plane" purine diamagnetic anisotropy effects. Also, the greater magnitude for purine deshieldings in 2'(3')-nucleotides relative to 5'-nucleotides is explained by a more favored syn:anti ratio in the former in line with recent nucle

Deuterium↗
PubMed1975

An NMR relaxation study of polynucleotide - nucleotide interactions.

A study has been made of the influence of polyuridylic acid (poly U)-adenosine (A) interactions upon the NMR proton relaxation behavior of H2O protons in aqueous solutions doped with Mn++ ions. Factors investigated included the effect of adenine oligonucleotide chain length, nucleoside concentration, and temperature upon the relaxation behavior of H2O. The results show that in all cases where solution and temperature conditions favor 2 poly U:A triple strand formation, a significant enhancement in H2O relaxation rate occurs over that for poly U or nucleotide solutions alone. Moreover, plots of relaxation enhancement versus temperature show well-defined transition regions with the enhancement approaching values for free poly U above the transition temperature, TM. The data also show that TM increases with increasing adenosine concentration and oligomer chain length. No comparable changes were observed for poly U solutions containing guanosine or cytidine derivatives. The increased relaxation rate in 2 poly U:A solutions is consistent with a more rigid secondary structure in the complex than in poly U; melting of this structure leads to an increase in polymer segmental mobility and a corresponding decrease in relaxation rate. The "melting" transitions and variation of TM with concentration and chain length have been interpreted quantitatively in terms of recent statistical models and yield values of delta H = -20 plus or minus 3 kcal/mol (base triplet) and delta S = -63 plus or minus 10 cal/mole degrees K (base triplet) in satisfactory agreement with results of optical studies.

Adenine Nucleotides↗