Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Molecular Structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources
PubMed1983

Molecular structure of d(m5CGTAm5CG): TA pairs in Z-DNA and the consequences.

The hexamer d(m5CGTAm5CG) crystallizes as a left-handed Z-DNA molecule in a isomorphous lattice to d(m5CGm5CGm5CG). The three-dimensional structure has been determined by x-ray diffraction and refined to a final R value of 16% at 1.2A resolution. The molecular structure is similar to the Z-DNA structure seen in d(m5CGm5CGm5CG) and d(CGCGCG). The presence of TpA sequence in the middle of the molecule has resulted in slight changes in the helical twist angles, base pair stacking and twist angles of the base pair planes. The hydration structure is significantly changed from both of methylated and non-methylated d(CGCGCG). A large hole which has no water molecule tightly bound to the DNA molecule is found inside of the deep groove of the DNA helix at the TpA sequence. This deterioration of the hydration structure is associated with destabilization of the Z-DNA structure. These characteristic features of the structure are compared with another Z-DNA hexamer contains TpA sequence, d(br5CGTAbr5CG).

Base Sequence↗
PubMed2002

Molecular structure and biological function of the cancer-amplified nuclear receptor coactivator SRC-3/AIB1.

Nuclear hormone receptors are ligand-dependent transcription factors that require coactivators to regulate target gene expression. The steroid receptor coactivator-3 (SRC-3), also known as p/CIP, RAC3, AIB1, ACTR and TRAM-1, is a cancer-amplified coactivator in the SRC gene family that also contains SRC-1 and TIF2/GRIP1. SRC-3 interacts with nuclear receptors and certain other transcription factors, recruits histone acetyltransferases and methyltransferases for chromatin remodeling and facilitates target gene transcription. Accumulated results from both ex vivo and animal model studies indicate that SRC-3 plays important roles in many biological processes involving cell proliferation, cell migration, cell differentiation, somatic growth, sexual maturation, female reproductive function, vasoprotection and breast cancer. This article summarizes our current knowledge about SRC-3 under the following topics: molecular cloning and characterization; molecular structure and functional mechanisms; SRC-3 as a molecular target of growth factors and cytokines; organization and expression of the SRC-3 gene; generation and characterization of SRC-3 knockout mice; role of SRC-3 in the vasoprotective effects of estrogen; role of SRC-3 in cell migration, proliferation and cancers.

Acetyltransferases↗
PubMed1993

Molecular structural studies of effector functions of a mouse immunoglobulin G that lacks the entire CH1 domain: small-angle X-ray scattering, nanosecond fluorescence depolarization and stable isotope-aided NMR analyses.

Molecular structural studies are reported of a short-chain mouse IgG2a antibody that lacks the entire CH1 domain. We have recently shown that (1) this short-chain antibody comprises two components in which the inter light-chain disulfide bridge does and does not exist, and (2) these two components are different in the constitutive complement-activating activity [Mizutani et al. (1993) J. Immunol. 150, 131-138]. Structures were compared for these two components on the basis of small-angle X-ray scattering, nanosecond fluorescence depolarization and isotope-aided NMR data. It has been discussed how the presence and absence of the inter light-chain disulfide bridges affect the complement-activating activity of the two components of the short-chain antibody.

Animals↗
PubMed2003

Predicting the carcinogenic potential of pharmaceuticals in rodents using molecular structural similarity and E-state indices.

MDL QSAR (formerly SciVision QSAR IS) software is one of the several software systems under evaluation by the Informatics and Computational Safety Analysis Staff (ICSAS) of the FDA Center for Drug Evaluation and Research for regulatory and scientific decision support applications. MDL QSAR software contains an integrated set of tools for similarity searching, compound clustering, and modeling molecular structure related parameters that includes 240 electrotopological E-state, connectivity, and other descriptors. These molecular descriptors can be statistically correlated with toxicological or biological endpoints. The goal of this research was to evaluate the feasibility of using MDL QSAR software to develop structure-activity relationship (SAR) models that can be used to predict the carcinogenic potential of pharmaceuticals and organic chemicals. A validation study of 108 compounds that include 86 pharmaceuticals and 22 chemicals that were not present in a control rodent carcinogenicity data set of 1275 compounds demonstrated that MDL QSAR models had excellent coverage (93%) and good sensitivity (72%) and specificity (72%) for rodent carcinogenicity. The software correctly predicted 72% of non-carcinogenic compounds and compounds with carcinogenic findings. E-state descriptors contributed to more than half of the SAR models used to predict carcinogenic activity. We believe that electrotopological E-state descriptors and QSAR IS (MDL QSAR) software are promising new in silico approaches for modeling and predicting rodent carcinogenicity and may have application for other toxicological endpoints.

Algorithms↗
PubMed2004

Efficient and rapid method for extraction of intact phospholipids from sediments combined with molecular structure elucidation using LC-ESI-MS-MS analysis.

This paper presents the application of an efficient method for extraction and fractionation of intact phospholipids (PLs) from complex sediment matrices and elucidation of their molecular structure by normal-phase HPLC-ESI-MS-MS. Flow-blending extraction was tested with different solvent mixtures and the best recovery of all PLs classes from the sediment matrix was achieved by using methanol-dichloromethane-buffer, 2:1:0.8. The applied LC-ESI-MS system has linearity of R2=0.98 and a detection limit of 0.5 ng/PL, sufficient for reliable identification of complex mixtures of PLs. MS-MS analyses using a triple-quadrupole mass spectrometer enables detection of individual PL side-chain composition and, hence, characterization of the living organisms contributing to the sedimentary organic material. Parallel GC-MS analysis of the hydrolysed phospholipid fatty acids supports the characterized fatty acid patterns determined from intact PLs. The PL inventory of different investigated lacustrine surface sediments shows predominantly high abundance of phosphatidylglycerols and phosphatidylethanolamines and phosphatidyl-mono- and dimethyl-ethanolamines with fatty acyl side-chains typically known from bacteria. In a sample from Lake Baikal intense signals of bacterial 14:0-acyl-PGs were also identified, for the first time in sediments as far as we are aware.

Bacteria↗
PubMed2005

Microstructure control of iron hydroxide nanoparticles using surfactants with different molecular structures.

To control the morphology and crystal phase of iron oxide nanoparticles within several 10 nm in diameter, a microbial-derived surfactant (MDS) with a high carboxyl-group density and relatively low molecular weight (about 650 g/mol) or an artificially synthesized polyacrylic acid sodium salt (PAA) was added into the raw material aqueous solution before iron oxide particle synthesis by the gel-sol method. While pseudo-cubic hematite particles with a diameter of 500 nm were prepared without surfactant addition, spherical iron hydroxide nanoparticles with a diameter of 20 nm were prepared by MDS addition. In contrast, needle-type iron hydroxide nanoparticles with a length of 100 nm along the long axis were prepared by PAA addition. Complex formation due to the interaction between COO- groups in each surfactant and Fe3+ ions, as well as the template role prior to the synthesis of iron oxide in raw aqueous solution, inhibited the phase transition from iron hydroxide to hematite. Furthermore, the morphology of the iron hydroxide nanoparticles depended on the molecular structure of the surfactants.

Acrylic Resins↗
PubMed2002

Effect of molecular structure on the selective phototoxicity of triarylmethane dyes towards tumor cells.

In response to transmembrane potentials which are negative on the inner side of both the plasma and mitochondrial membranes, cationic dyes displaying appropriate structural features naturally accumulate in the cytosol and inside the mitochondria. Because enhanced mitochondrial membrane potential is a prevalent tumor cell phenotype, a number of cationic dyes preferentially accrue and are retained for longer periods in the mitochondria of tumor cells as compared to normal cells. The opportunities brought about by this phenomenon in chemo- and photochemotherapy of neoplastic diseases is highlighted by the observation that the phototoxic effects associated with some of the cationic photosensitizers known to accumulate in cell mitochondria are much more pronounced in tumor cells than in normal cells. However, the structural determinants of selective phototoxicity towards tumor cells are not well understood, and the lack of a robust model to describe the relationship between molecular structure and tumor selectivity has prevented mitochondrial targeting from becoming a more dependable therapeutic strategy. In this report we describe how the lipophilic/hydrophilic character of a series of cationic triarylmethane dyes affects the selectivity with which these photosensitizers mediate the destruction of tumor cells. Our results indicated that only the more hydrophilic triarylmethanes show tumor selectivity, presumably because these are the only dyes capable of staining energized mitochondria with a high degree of specificity. The partition of the more lipophilic dyes into a variety of extra-mitochondrial subcellular compartments occurs with comparable efficiencies in tumor and in normal cells, and this less specific subcellular localization precludes tumor selectivity from taking place.

Animals↗
PubMed2001

Capturing a photoexcited molecular structure through time-domain x-ray absorption fine structure.

The determination of the structure of transient molecules, such as photoexcited states, in disordered media (such as in solution) usually requires methods with high temporal resolution. The transient molecular structure of a reaction intermediate produced by photoexcitation of NiTPP-L2 (NiTPP, nickeltetraphenylporphyrin; L, piperidine) in solution was determined by x-ray absorption fine structure (XAFS) data obtained on a 14-nanosecond time scale from a third-generation synchrotron source. The XAFS measurements confirm that photoexcitation leads to the rapid removal of both axial ligands to produce a transient square-planar intermediate, NiTPP, with a lifetime of 28 nanoseconds. The transient structure of the photodissociated intermediate is nearly identical to that of the ground state NiTPP, suggesting that the intermediate adopts the same structure as the ground state in a noncoordinating solvent before it recombines with two ligands to form the more stable octahedrally coordinated NiTPP-L2.

Journal Article↗
PubMed1996

[Molecular structure and expression of ion channels in the heart].

Ion channels are essential for the generation and maintenance of the cardiac action potential. The successful cloning of ion channels has shed considerable light into their structure and function. The combination of molecular biological and electrophysiological studies has paved the ground to develop general concepts for understanding properties of these channels, such as gating mechanism, kinetics of activation and inactivation, ion selectivity and pharmacological properties. Recently, several cDNAs encoding cardiac inwardly rectifying K+ channels, including classical inwardly rectifying, G-protein-gated, and ATP-sensitive K+ channels, have been isolated. Identification of these molecular mechanisms may point to novel approaches to the treatment of cardiac arrhythmias. This review focuses on the molecular properties and functional roles of cardiac ion channels.

Adenosine Triphosphate↗
PubMed1992

Computational complexity of a problem in molecular structure prediction.

The computational task of protein structure prediction is believed to require exponential time, but previous arguments as to its intractability have taken into account only the size of a protein's conformational space. Such arguments do not rule out the possible existence of an algorithm, more selective than exhaustive search, that is efficient and exact. (An efficient algorithm is one that is guaranteed, for all possible inputs, to run in time bounded by a function polynomial in the problem size. An intractable problem is one for which no efficient algorithm exists.) Questions regarding the possible intractability of problems are often best answered using the theory of NP-completeness. In this treatment we show the NP-hardness of two typical mathematical statements of empirical potential energy function minimization of macromolecules. Unless all NP-complete problems can be solved efficiently, these results imply that a function minimization algorithm can be efficient for protein structure prediction only if it exploits protein-specific properties that prohibit the simple geometric constructions that we use in our proofs. Analysis of further mathematical statements of molecular structure prediction could constitute a systematic methodology for identifying sources of complexity in protein folding, and for guiding development of predictive algorithms.

Algorithms↗
PubMed1982

Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA.

The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA--RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.

DNA↗
PubMed2001

Molecular structure of the molybdenum oxo-diperoxo compound MoO(O(2))(2)(OPy)(H(2)O): a computational and X-ray study.

We have carried out a combined experimental and theoretical study of the molecular structure of the MoO(O(2))(2)(OPy)(H(2)O) coordination compound using X-ray crystallography and DFT-B3LYP computational method, respectively. The MoO(O(2))(2)(OPy)(H(2)O) complex crystallizes in the orthorhombic space group Pmna with Z = 4, a = 6.9001(9) A, b = 8.0471(1) A, c = 16.227(2) A, V = 901.0(2) A(3), and the X-ray data analysis yields a bipyramidal-pentagonal coordination polyhedron for the Mo atom. The pyridine N-oxide (OPy) ligand occupies the equatorial position, with the oxygen atom of this ligand being located in the same plane as the four peroxo oxygen atoms. The H(2)O ligand is situated trans to the oxo group, forming intermolecular hydrogen bonds with peroxo groups belonging to two adjacent complexes. In our theoretical approach these intermolecular interactions were taken into account by including two methanol molecules which form hydrogen bonds with the water ligand leading to a good agreement between the calculated and the experimental geometry. Our results suggest that it is necessary to take into account the presence of these interactions in order to reconcile the theoretical results to the experimental data, in particular the distance between Mo and the oxygen of water ligand. These results seem to be a general feature for analogous bis-peroxo complexes that have been reported in the literature.

Journal Article↗
PubMed2000

Preparation and molecular structures of 9,10-dihydrophenanthrenes: substituent effects on the long bond length

9,10-Dihydrophenanthrene derivatives 1-3 with electron-donating and/or -accepting groups at their 9,10-positions were prepared, and their precise molecular structures were determined by X-ray analyses at 203 K. The long C(9)-C(10) bond [1.646(4) A] in the hexaarylethane-type compound 1 with four electron-donating groups is mainly caused by steric interaction. Push-pull type substitution does not induce the elongation of the central bond in the present system; the corresponding distance in 9, 9-bis(4-dimethylaminophenyl)-10,10-dicyano derivative 2 [1.599(4) A] is intermediate between those of 1 and the tetracyano compound 3 [1. 587(2) A].

Journal Article↗
PubMed1999

Least-Squares Mass-Dependence Molecular Structures.

The major part of the difference between the zero-point and equilibrium moment of inertia of a molecule is a homogeneous function of degree 12 in the atomic masses. The use of explicit mathematical models of is studied here as a means of determining near-equilibrium molecular structures from the zero-point moments of inertia of a range of isotopomers. It is found that models with more than two parameters per axis generally give strongly correlated fits for the number of isotopomers typically available. The two-parameter model, where N is the number of atoms, mi are the atomic masses, and M is the molecular mass, usually gives well-conditioned fits with standard deviations in the parts-per-million range, and structures called that are often close to equilibrium structures. Laurie-type corrections for hydrogen atoms and parameters to describe isotopic rotations of the epsilon tensor can also be included. Copyright 1999 Academic Press.

Journal Article↗
PubMed2006

The molecular structure of Rv2074, a probable pyridoxine 5'-phosphate oxidase from Mycobacterium tuberculosis, at 1.6 angstroms resolution.

The crystal structure of a conserved hypothetical protein corresponding to open reading frame Rv2074 from Mycobacterium tuberculosis (Mtb) has been solved by the two-wavelength anomalous dispersion method. Refinement of the molecular structure at 1.6 angstroms resolution resulted in an R(work) of 0.178 and an R(free) of 0.204. The crystal asymmetric unit contains an Rv2074 monomer; however, the crystallographic twofold symmetry operation of space group P4(3)2(1)2 generates dimeric Rv2074. Each monomer folds into a six-stranded antiparallel beta-barrel flanked by two alpha-helices. The three-dimensional structure of Rv2074 is very similar to that of Mtb Rv1155, a probable pyridoxine 5'-phosphate oxidase (PNPOx), which corroborates well with the relatively high sequence similarity (52%) between the two. A structural comparison between Rv2074 and Rv1155 revealed that the core structure (a six-stranded beta-barrel) is also well conserved; the major differences between the two lie in the N- and C-termini and in the small helical domain. Two citric acid molecules were observed in the active site of Rv2074, the crystals of which were grown in 0.2 M sodium citrate buffer pH 5.0. The citric acid molecules are bound to Rv2074 by hydrogen-bonding interactions with Thr55, Gln60 and Lys61. One of the two citric acid molecules occupies the same spatial position that corresponds to the position of the phosphate and ribose sugar moieties of the flavin mononucleotide (FMN) in the Mtb Rv1155-FMN, Escherichia coli PNPOx-FMN and human PNPOx-FMN complex structures. Owing to its extensive structural similarity with Mtb Rv1155 and to the E. coli and human PNPOx enzymes, Rv2074 may be involved in the final step in the biosynthesis of pyridoxal 5'-phosphate (PLP; a vitamin B6).

Bacterial Proteins↗
PubMed2002

Prediction of peptide ion collision cross sections from topological molecular structure and amino acid parameters.

Quantitative structure-property relationships (QSPRs) have been developed to predict the ion mobility spectrometry (IMS) collision cross sections of singly protonated lysine-terminated peptides using information derived from topological molecular structure and various amino acid parameters. The primary amino acid sequence alone is sufficient to accurately predict the collision cross section. The models were built using multiple linear regression (MLR) and computational neural networks (CNNs). The best MLR model found contains six descriptors and predicts 94 of 113 peptides (83%) to within 2% of their experimentally determined values. The best CNN model using the same six descriptors predicts 105 of the 113 peptides (93%) to within 2% of their experimentally determined values. The best overall CNN model, using a different set of six descriptors, predicts 109 of the 113 peptides (96%) to within 2% of their experimentally determined values. In addition, this model can discriminate among peptides having identical amino acid composition, but differing in primary amino acid sequence. This represents a capability not found in previously described models. The descriptors used in the models presented may provide some insight into the nature of peptide ion folding in the gas phase.

Amino Acid Sequence↗
PubMed2007

Effects of molecular structure and interfacial ligation on the precision of Cu-bound alpha,omega-mercaptoalkanoic acid "molecular ruler" stacks.

Nanolithography processes based on designed, precision thickness multilayer thin films (molecular rulers) have been reported that enable patterning of features on surfaces from a few to the hundred nanometer range. These strategies are unique in their potential ability to enable wafer scale patterning of features of just a few nanometers. If these techniques could be developed to be sufficiently precise and generally applicable, they would fill a long-standing need in nanoscience. In this study a systematic and detailed analysis of the growth mechanisms and molecular layer structures has been carried out for the mercaptoalkanoic acid-copper ion multilayer thin film system currently used as the standard nanolithography resist. Our results show these films form via a redox reaction of thiol groups with surface-ligated Cu(II) ions to form adlayers at only approximately 50% coverage with islanding of the alkyl chains, thereby leading to rough topographies and less than theoretical thicknesses based on a 1:1 ideal adlayer. Strategies are suggested to help overcome these issues for molecular resist applications in nanolithographic processing.

Journal Article↗