Conformational stability in dinucleoside phosphate crystals. Semiempirical potential energy calculations for uridylyl-3'-5'-adenosine monophosphate (UpA) and guanylyl-3',5'-cytidine monophosphate (GpC)

Classical potential energy calculations were performed for the dinucleoside phosphates UpA and GpC. Two widely accessible low-energy regions of conformation space were found for the w', w pair. That of lowest energy contains conformations similar to helical RNA, with w' and w in the vicinity of 300° and 280°, respectively. All five experimental observations of crystalline GpC, two of ApU, and the helical fragment of ApApA fall in this range. The second lowest region has w' and w at about 20° and 80°, respectively, which is in the general region of one experimentally observed crystalline conformer of UpA, and the nonhelical region of ApApA. It is concluded that GpC and ApU, which were crystallized as either sodium or calcium salts, are shielded from each other in the crystal by the water of hydration and are therefore free to adopt their predicted in vacuo minimum energy helical conformations. By contrast, crystalline UpA had only 1/2 water per molecule, and was forced into higher energy conformations in order to maximize intermolecular hydrogen bonding

Structure of guanylyl-3′,5′-cytidine monophosphate. II. Description of the molecular and crystal structure of the calcium derivative in space group P2₁

The structural features of calcium guanosine-3′,5′-cytidine monophosphate (GpC) have been elucidated by X-ray diffraction analysis. The molecule was crystallized in space group P2₁ with cell constants of a = 21.224 Å, b = 34.207 Å, c = 9.327 Å, and β = 90.527°, Z = 8. The hydration of the crystal is 21% by weight with 72 water molecules in the unit cell. The four GpC molecules in the asymmetric unit occur as two Watson-Crick hydrogen-bonded dimers related by a pseudo-C face centering. Each dimer consists of two independent GpC molecules whose bases are hydrogen bonded to each other in the traditional Watson-Crick fashion. Each dimer possesses a pseudo twofold axis broken by a calcium ion and associated solvent. The four molecules are conformationally similar to helical RNA, but are not identical to it or to each other. Instead, values of conformational angles reflect the intrinsic flexibility of the molecule within the range of basic helical conformations. All eight bases are anti, sugars are all C3′-endo, and the C4′-C5′ bond rotations are gauche-gauche. The R factor is 12.6% for 2918 observed reflections at 1.2-Å resolution

The crystal and molecular structure of a calcium salt of guanylyl-3',5'-cytidine (GpC)

The calcium salt, Ca(C_19H_24N_8O_I2P)_2.18H_20, of guanylyl-3',5'-cytidine (GpC) has been refined to an R of 8·2 % for 2918 observed reflections (11% for 4237 reflections, including unobserved). The molecule crystallized in space group P2_1 with a=21·224, b=34·207, c=9·327 Å, β=90·527°, Z=4. The asymmetric unit contains four GpC, 36 waters and two Ca^2+ ions, for a total of 198 non-hydrogen atoms. The four GpC occur as two dimers related by a pseudo C-face-centering. Each dimer consists of two crystallographically independent GpC as Watson-Crick base-pairs, and possesses a pseudo twofold axis broken by a Ca^2+ ion and associated solvent. The structure was solved by an unusual series of steps including semi-empirical potential-energy methods, packing analysis, rigid-body refinement, least-squares and difference Fourier techniques, and direct-methods tangent-formula phase refinement. The four GpC have conformational angles in the range of helical RNA, but are not identical. The different crystallographic environments perturb the GpC from exact symmetry and demonstrate the range of the basic helical conformations. All eight bases are anti, sugars are all C(3’) endo, the C(4')-C(5') bond rotations are gauche-gauche, and the ω', ω angle pair about the O-P bonds is gauche—gauche-

Conformation of Guanosine Cytidine 3',5'-Monophosphate (GpC)

A brief communication of preliminary results of solution of dinucleoside phosphate GpC

Structure of guanosine-3′,5′-cytidine monophosphate. I. Semi-empirical potential energy calculations and model-building

The conformation and packing scheme for guanosine-3’,5’-cytidine monophosphate, GpC, were computed by minimizing the classical potential energy. The lowest energy conformation of the isolated molecule had dihedral angles in the range of helical RNA’s, and the sugar pucker was C3‘ endo. This was used as the starting conformation in a packing search over orientation space, the dihedral angles being flexible in this step also. The packing search was restricted by constraints from our x-ray data, namely, (1) the dimensions of the monoclinic unit cell and its pseudo-C2 symmetry (the real space group is P21), (2) t,he location of the phosphorous atom, and (3) the orientation of the bases. In addition, a geometric function was devised to impose Watson-Crick base pairing. Thus, a trial structure could be sought without explicit inclusion of intermolecular potentials. An interactive computer graphics system was used for visualizing the calculated structures. The packing searches yielded two lowest energy schemes in which the molecules had the same conformation (similar to double-helical RNA) but different orientations within the unit cell. One of these was refined by standard x-ray methods to a discrepancy index of 14.4% in the C2 pseudocell. This served as the starting structure for the subsequent refinement in the real P21 cell

Positional, Reorientational and Bond Orientational Order in DNA Mesophases

We investigate the orientational order of transverse polarization vectors of long, stiff polymer molecules and their coupling to bond orientational and positional order in high density mesophases. Homogeneous ordering of transverse polarization vector promotes distortions in the hexatic phase, whereas inhomogeneous ordering precipitates crystalization of the 2D sections with different orientations of the transverse polarization vector on each molecule in the unit cell. We propose possible scenarios for going from the hexatic phase, through the distorted hexatic phase to the crystalline phase with an orthorhombic unit cell observed experimentally for the case of DNA.Comment: 4 pages, 2 figure

Generation of unique protein specifiic MRM signatures; using peptide information from alternate scanning LC-MS data to drive MRM development

Comunicaciones a congreso

Neutron reflection from the liquid helium surface.

The reflection of neutrons from a helium surface has been observed for the first time. The 4He surface is smoother in the superfluid state at 1.54 K than in the case of the normal liquid at 2.3 K. In the superfluid state we also observe a surface layer ~200 Å thick which has a subtly different neutron scattering cross-section, which may be explained by an enhanced Bose-Einstein condensate fraction close to the helium surface. The application of neutron reflectometry described in this paper creates new and exciting opportunities for the surface and interfacial study of quantum fluids