Same Conformation (same + conformation)

Distribution by Scientific Domains


Selected Abstracts


1H chemical shifts in NMR: Part 22,,Prediction of the 1H chemical shifts of alcohols, diols and inositols in solution, a conformational and solvation investigation

MAGNETIC RESONANCE IN CHEMISTRY, Issue 8 2005
Raymond J. Abraham
Abstract The 1H NMR spectra of a number of alcohols, diols and inositols are reported and assigned in CDCl3, D2O and DMSO- d6 (henceforth DMSO) solutions. These data were used to investigate the effects of the OH group on the 1H chemical shifts in these molecules and also the effect of changing the solvent. Inspection of the 1H chemical shifts of those alcohols which were soluble in both CDCl3 and D2O shows that there is no difference in the chemical shifts in the two solvents, provided that the molecules exist in the same conformation in the two solvents. In contrast, DMSO gives rise to significant and specific solvation shifts. The 1H chemical shifts of these compounds in the three solvents were analysed using the CHARGE model. This model incorporates the electric field, magnetic anisotropy and steric effects of the functional group for long-range protons together with functions for the calculation of the two- and three-bond effects. The long-range effect of the OH group was quantitatively explained without the inclusion of either the CO bond anisotropy or the COH electric field. Differential , and , effects for the 1,2-diol group needed to be included to obtain accurate chemical shift predictions. For DMSO solution the differential solvent shifts were calculated in CHARGE on the basis of a similar model, incorporating two-bond, three-bond and long-range effects. The analyses of the 1H spectra of the inositols and their derivatives in D2O and DMSO solution also gave the ring 1H,1H coupling constants and for DMSO solution the CHOH couplings and OH chemical shifts. The 1H,1H coupling constants were calculated in the CHARGE program by an extension of the cos2, equation to include the orientation effects of electronegative atoms and the CHOH couplings by a simple cos2, equation. Comparison of the observed and calculated couplings confirmed the proposed conformations of myo -inositol, chiro -inositol, quebrachitol and allo -inositol. The OH chemical shifts were also calculated in the CHARGE program. Comparison of the observed and calculated OH chemical shifts and CH. OH couplings suggested the existence of intramolecular hydrogen bonding in a myo -inositol derivative. Copyright © 2005 John Wiley & Sons, Ltd. [source]


Grp94, the endoplasmic reticulum Hsp90, has a similar solution conformation to cytosolic Hsp90 in the absence of nucleotide

PROTEIN SCIENCE, Issue 9 2009
Kristin A. Krukenberg
Abstract The molecular chaperone, Hsp90, is an essential eukaryotic protein that assists in the maturation and activation of client proteins. Hsp90 function depends upon the binding and hydrolysis of ATP, which causes large conformational rearrangements in the chaperone. Hsp90 is highly conserved from bacteria to eukaryotes, and similar nucleotide-dependent conformations have been demonstrated for the bacterial, yeast, and human proteins. There are, however, important species-specific differences in the ability of nucleotide to shift the conformation from one state to another. Although the role of nucleotide in conformation has been well studied for the cytosolic yeast and human proteins, the conformations found in the absence of nucleotide are less well understood. In contrast to cytosolic Hsp90, crystal structures of the endoplasmic reticulum homolog, Grp94, show the same conformation in the presence of both ADP and AMPPNP. This conformation differs from the yeast AMPPNP-bound crystal state, suggesting that Grp94 may have a different conformational cycle. In this study, we use small angle X-ray scattering and rigid body modeling to study the nucleotide free states of cytosolic yeast and human Hsp90s, as well as mouse Grp94. We show that all three proteins adopt an extended, chair-like conformation distinct from the extended conformation observed for the bacterial Hsp90. For Grp94, we also show that nucleotide causes a small shift toward the crystal state, although the extended state persists as the major population. These results provide the first evidence that Grp94 shares a conformational state with other Hsp90 homologs. [source]


A benzene-rich pseudopolymorph of bis[,-1,3-bis(pentafluorophenyl)propane-1,3-dionato]-,3O,O,:O,;,3O:O,O,-bis{aqua[1,3-bis(pentafluorophenyl)propane-1,3-dionato-,2O,O,]nickel(II)} benzene tetrasolvate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009
Akiko Hori
The title complex comprises two Ni2+ ions, four fluorinated ligands and two water molecules in a centrosymmetric dinuclear complex. This compound was crystallized from benzene,CH2Cl2, and two types of crystals, viz. the title benzene tetrasolvate, [Ni2(C15HF10O2)4(H2O)2]·4C6H6, (I), and the previously reported benzene disolvate, [Ni2(C15HF10O2)4(H2O)2]·2C6H6, (II) [Hori et al. (2009). Bull. Chem. Soc. Jpn, 82, 96,98], were obtained as pseudopolymorphs. In the crystal structure of (I), the four benzene solvent molecules interact closely with all the pentafluorophenyl groups of the complex through arene,perfluoroarene interactions. The molecular structures of the two compounds show essentially the same conformation, although the benzene molecules are accommodated in a columnar packing in (I), while they are isolated from each other in (II). [source]


6-(2-Chloro­acetamido)­hexa­noic acid

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2006
Carolina Gastone
Crystals of the title compound, C8H14ClNO3, belong to the space group Cc and are characterized by an asymmetric unit containing two mol­ecules, both with a twisted conformation. The mol­ecular packing is stabilized by N,H,O=C hydrogen bonds between the amide groups of mol­ecules with the same conformation. In addition, hydrogen-bonded cyclic carboxylic acid dimers are established between mol­ecules with a different conformation. The ClCH2,CONH bond has a cis conformation in order to favour an intra­molecular Cl,HN electrostatic inter­action. Weak intra- and inter­molecular CH2,O=C inter­actions are also present. [source]


Bis(tetraethylammonium) hydrogensulfate dihydrogenphosphate at 292 and 150,K

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2003
Jan Fábry
The title compound, 2C8H20N+·HSO4,·H2PO4,, was crystallized in a desiccator over P4O10 from a water solution of stoichiometric amounts of tetraethyl­ammonium hydroxide and sulfuric and phosphoric acids. The compound is deliquescent. The structure contains two symmetry-independent cations in nearly the same conformation, as well as two symmetry-independent anions, the central atoms of which are equally occupied by P and S. The anions are interconnected by short O,O hydrogen bonds into one-dimensional chains. The distances and angles between some of the methyl or methyl­ene groups and anionic O atoms indicate the presence of C,H,O hydrogen bonds. The structure was determined from data at 292,(2) and 150,(2) K. These room- and low-temperature structures are virtually the same, with the exception of the localization of the H atoms that participate in the symmetry-restricted O,O hydrogen bonds. A differential scanning calorimetry experiment indicated no phase transition below the temperature at which the compound started to decompose (353,K), down to 93,K. [source]


The structure of human deoxycytidine kinase in complex with clofarabine reveals key interactions for prodrug activation

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2006
Yan Zhang
Clofarabine [2-chloro-9-(2-deoxy-2-fluoro-,- d -arabinofuranosyl)-9H -purin-6-amine] is a hybrid of the widely used anticancer drugs cladribine and fludarabine. It is the precursor of an effective chemotherapeutic agent for leukemias and other hematological malignancies and received accelerated approval by the FDA for the treatment of pediatric patients with relapsed or refractory acute lymphoblastic leukemia. Clofarabine is phosphorylated intracellularly by human deoxycytidine kinase (dCK) to the 5,-monophosphate, which is the rate-limiting step in activation of the prodrug. dCK has a broad substrate specificity, with a much higher activity to deoxycytidine than to deoxyadenosine and deoxyguanosine. As a purine-nucleoside analog, clofarabine is a better substrate of dCK than deoxycytidine. The crystal structure of dCK has been solved previously in complex with pyrimidine nucleosides and ADP [Sabini et al. (2003), Nature Struct. Biol.10, 513,519]. In the current study, the crystal structure of clofarabine- and ADP-bound dCK was solved to 2.55,Å by molecular replacement. It appears that the enzyme takes the same conformation as in the structures of the pyrimidine nucleoside-bound complexes. The interactions between 2-Cl and its surrounding hydrophobic residues contribute to the high catalytic efficiency of dCK for clofarabine. [source]


Structure of an elastin-mimetic polypeptide by solid-state NMR chemical shift analysis

BIOPOLYMERS, Issue 2 2003
M. Hong
Abstract The conformation of an elastin-mimetic recombinant protein, [(VPGVG)4(VPGKG)]39, is investigated using solid-state NMR spectroscopy. The protein is extensively labeled with 13C and 15N, and two-dimensional 13C- 13C and 15N- 13C correlation experiments were carried out to resolve and assign the isotropic chemical shifts of the various sites. The Pro 15N, 13C,, and 13C, isotropic shifts, and the Gly-3 C, isotropic and anisotropic chemical shifts support the predominance of type-II ,-turn structure at the Pro-Gly pair but reject a type-I ,-turn. The Val-1 preceding Pro adopts mostly ,-sheet torsion angles, while the Val-4 chemical shifts are intermediate between those of helix and sheet. The protein exhibits a significant conformational distribution, shown by the broad line widths of the 15N and 13C spectra. The average chemical shifts of the solid protein are similar to the values in solution, suggesting that the low-hydration polypeptide maintains the same conformation as in solution. The ability to measure these conformational restraints by solid-state NMR opens the possibility of determining the detailed structure of this class of fibrous proteins through torsion angles and distances. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 158,168, 2003 [source]