PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Molecular Structure”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 181 records · Page 10Linked to original sources
PubMed2002

Molecular structures and associations of humic substances in the terrestrial environment.

Here we show, for the first time, evidence of the primary molecular structures in humic substances (HS), the most abundant naturally occurring organic molecules on Earth, and their associations as mixtures in terrestrial systems. Multi-dimensional nuclear magnetic resonance (NMR) experiments show us that the major molecular structural components in the mixtures operationally defined as HS are aliphatic acids, ethers, esters and alcohols; aromatic lignin derived fragments; polysaccharides and polypeptides. By means of diffusion ordered spectroscopy, distinct diffusion coefficients consistent with relatively low molecular weight molecules were observed for all the components in the mixtures, and saccharides were the largest single class of component present. Liquid chromatography NMR confirmed that HS components can be easily separated and nuclear Overhauser effect (NOE) enhancements support the finding that the components are of relatively low molecular weight <approximately 2,000 Da. The widely recognized properties of HS, i.e., characteristics indicative of crosslinked, macromolecular networks, can now be explained as aggregation of mixtures, most likely instigated by complexation with metal cations.

Animals↗
PubMed2005

An experimental and theoretical study of the molecular structure and vibrational spectra of iodotrimethylsilane (SiIMe3).

The gas-phase molecular structure of iodotrimethylsilane (ITMS) has been determined from electron diffraction data. Infrared and Raman spectra have been completely assigned. The experimental work is supported by ab initio HF and MP2 calculations for the gas-phase structure determination and DFT(B3LYP) calculations, combined with Pulay's SQM method, for the vibrational spectra data.

Computer Simulation↗
PubMed2006

Effects of metal-binding properties of human Kv channel-interacting proteins on their molecular structure and binding with Kv4.2 channel.

The goal of the present study is to explore whether Ca2+ and Mg2+-binding properties of isomeric Kv channel-interacting proteins (KChIPs) have different effects on their molecular structure and the binding with Kv channel. 8-Anilinonaphthalene- 1-sulfonate fluorescence measurement showed that KChIP4.1 and KChIP2.2 possessed one and two types of Ca2+-binding sites, respectively, and only one type of Mg2+-binding site was noted in the two KChIP proteins. Removal of EF-hand 4 (EF-4) caused a marked drop in their high affinities for Ca2+, but the binding affinity for Mg2+ remained mostly the same. Unlike KChIP4.1, the intact EF-4 was essential for the Kv channel-binding ability of KChIP2.2 in a metal-free buffer. Nevertheless, the interaction of wild-type KChIPs and EF-4-truncated mutants with Kv channel was enhanced by the addition of Mg2+ and Ca2+. In contrast to KChIP4.1, the thermal stability of KChIP2.2 was decreased by the binding of Mg2+ and Ca2+. These results suggest that the conformational change with metal-bound KChIP4.1 is crucial for its interaction with Kv channel but not for KChIP2.2, and that the Mg2+- and Ca2+-binding properties of KChIP2.2 and KChIP4.1 have different effects on their molecular structure.

Binding Sites↗
PubMed1993

Enzymic cleavage as a probe of the molecular structures of mammalian equilibrative nucleoside transporters.

We have used enzymic cleavage by trypsin in conjunction with glycosidase digestion to probe the transmembrane topologies and molecular structures of mammalian equilibrative, nitrobenzylthioinosine (NBMPR)-sensitive, nucleoside transport systems. Transporters from four species (human, pig, guinea pig, and rat) and three tissues (erythrocyte, liver, and lung), which differ from each other in size and in their sensitivity to inhibition by the vasodilator dipyridamole, were investigated. Broadly equivalent sites of [3H]NBMPR photolabeling, carbohydrate attachment, and trypsin cleavage were observed for all systems. Results from these experiments demonstrate that molecular weight differences between rat transporters and those from two other species (human and guinea pig) are due largely to oligosaccharide heterogeneity and that the low dipyridamole sensitivity of rat nucleoside transporters is probably a consequence of relatively minor differences in molecular structure. In marked contrast, carbohydrate removal increases the molecular weight difference between the pig erythrocyte transporter and, for example, that in human erythrocytes. This polypeptide difference is limited largely, if not completely, to one tryptic fragment of the protein. In the case of the human erythrocyte transporter, the site of N-linked glycosylation has been located very close to one end of the protein, and the site of NBMPR photolabeling to within 16 kDa of that site. Trypsin cleavage occurs endofacially. Our results provide evidence of substantial structural conservation among mammalian NBMPR-sensitive nucleoside transporters.

Affinity Labels↗
PubMed1991

The crystal and molecular structure of VH amylose by electron diffraction analysis.

The crystal and molecular structures of VH amylose were determined by a constrained linked-atom least-squares refinement, utilizing intensities measured from electron diffraction patterns and stereochemical restraints. Hexagonal platelet single crystals were grown from dilute aqueous ethanol solution and their electron diffraction diagrams analysed. These data indicated that the amylose chains were crystallized in a hexagonal lattice with a = b = 13.65 A, c (chain axis) = 8.05 A and space group P6(5)22. The best model obtained using the base plane data coupled with a stereochemical refinement yielded R = 0.24 (R'' = 0.25). It corresponded to a system of left-handed 6-fold helices packed on an hexagonal net but with statistically random up/down chain disorder. A column of six water molecules was present within each helical repeat. Additionally, the gap between each pair of adjacent helices was bridged by two water molecules positioned so as to allow hydrogen bonding with chains of either sense. This proposed crystal structure differs somewhat from previous reports which invoked orthorhombic lattices and requires a regularly alternating arrangement of up and down chains to account for the intensity. Suggestions are made to account for these differences.

Amylose↗
PubMed1991

Prediction of octanol/water partition coefficients using parameters derived from molecular structures.

A method is presented to estimate log P values using molecular surface area, electrostatic potentials and charge transfer interactions derived from three-dimensional molecular structures. Estimated logP values for 63 small organic molecules with a variety of structures gave a correlation coefficient of 0.983 with a standard deviation of 0.260. The method is applicable to rather complex and large molecules. A striking feature of the method is that it can estimate the logP values of novel compounds to which "fragment constant approaches" have not been applicable so far.

Chemical Phenomena↗
PubMed2005

Predicting physiological concentrations of metabolites from their molecular structure.

Physiological concentrations of metabolites can partly be explained by their molecular structure. We hypothesize that substances containing certain chemical groups show increased or decreased concentration in cells. We consider here, as chemical groups, local atomic configurations, describing an atom, its bonds, and its direct neighbor atoms. To test our hypothesis, we fitted a linear statistical model that relates experimentally determined logarithmic concentrations to feature vectors containing count numbers of the chemical groups. In order to determine chemical groups that have a clear effect on the concentration, we use a regularized (lasso) regression. In a dataset on 41 substances of central metabolism in different organisms, we found that the physical concentrations are increased by the occurrence of amino and hydroxyl groups, while aldehydes, ketones, and phosphates show decreased concentrations. The model explains about 22% of the variance of the logarithmic mean concentrations.

Animals↗
PubMed2025

Glutamate molecular structure and protein affect the inhibition of breast cancer cell metastasis: Cell-derived exosomes inhibitory effects through the MAPK signaling pathway.

The aim of this study was to investigate the inhibitory effect of glutamate molecular structure and protein on breast cancer cell metastasis and the potential inhibitory mechanism of cell-derived exosomes via MAPK signaling pathway. Breast cancer cell lines with high metastatic potential were selected by in vitro cell culture technique. The effects of specific inhibitors of glutamic acid on the proliferation and metastasis of breast cancer cells were studied. Changes in protein expression profiles were analyzed by proteomics techniques to identify key proteins associated with breast cancer metastasis. Breast cancer cells were treated with inhibitors of the MAPK signaling pathway to evaluate their effect on cell metastasis and compare with exosome treatment. The results showed that the specific inhibitors of glutamate molecular structure could significantly inhibit the proliferation and metastasis of breast cancer cells. Proteomic analysis revealed several down-regulated proteins that are closely related to breast cancer metastasis.

Humans↗
PubMed1987

Molecular structure of mammalian neuropeptide Y: analysis by molecular cloning and computer-aided comparison with crystal structure of avian homologue.

Identification and characterization of the cDNA encoding rat neuropeptide Y revealed the nucleotide sequence coding for a 98-amino acid precursor. The deduced amino acid sequence for rat neuropeptide Y is identical to the human peptide and is highly homologous to avian pancreatic polypeptide. The tertiary structure of avian pancreatic polypeptide has been previously derived from crystallographic data by Blundell and coworkers. The homology between neuropeptide Y and avian pancreatic polypeptide preserves all of the residues essential for the maintenance of the tertiary structure. Thus, it has been possible to compute a three-dimensional model of the mammalian neuropeptide, neuropeptide Y, based on the known structure of the avian homologue. This model suggest that neuropeptide preserves a compact tertiary structure characterized by extensive hydrophobic interactions between an N-terminal polyproline-II-like helix and a C-terminal alpha-helix. The model has been used to identify amino acids residing in key positions within this structure and, thereby, to direct future analysis of neuropeptide Y structure-function relationships.

Amino Acid Sequence↗
PubMed2005

Electron-donating alkoxy-group-driven synthesis of heteroleptic tris(phthalocyaninato) lanthanide(III) triple-deckers with symmetrical molecular structure.

Reaction of heteroleptic bis(phthalocyaninato) lanthanide compounds [(Pc)M{Pc(OC8H17)8}] [H2Pc=unsubstituted phthalocyanine; H2Pc(OC8H17)8 = 2,3,9,10,16,17,23,24-octakis(octyloxy)phthalocyanine] with monomeric complexes [(Pc)M(acac)] (Hacac=acetylacetone), both of which generated in situ, led to the isolation of heteroleptic phthalocyaninato-[2,3,9,10,16,17,23,24-octakis(octyloxy)phthalocyaninato] lanthainde(III) triple-decker complexes [(Pc)M{Pc(OC8H17)8}] (M=Gd-Lu) (1-8) as the sole product. Heterodinuclear analogues [(Pc)Lu{Pc(OC8H17)8}M(Pc)] (M=Gd-Yb) (9-15) were obtained in a similar manner from the reaction of [(Pc)M{Pc(OC8H17)8}] (M=Gd-Yb) and [(Pc)Lu(acac)]. The molecular structures of the herterodinuclear compound [(Pc)Lu{Pc(OC8H17)8}Er(Pc)] (13) and its homodinuclear counterparts [(Pc)M{Pc(OC8H17)8}M(Pc)] (M=Er, Lu) (5, 8) have been determined by X-ray diffraction analysis; these structures exhibit a symmetrical molecular structure with one inner planar Pc(OC8H17)8 ligand and two outer domed Pc ligands. In addition to various spectroscopic analyses, the electrochemistry of these compounds has also been studied by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) methods, revealing the gradually enhanced pi-pi interactions among the phthalocyanine rings in the triple-deckers along with the lanthanide contraction.

Journal Article↗
PubMed2002

Effect of molecular structures on the solubility enhancement of hydrophobic organic compounds by environmental amphiphiles.

Amphiphilic molecules, such as humic substances and surfactants, are known to increase the apparent aqueous solubility of hydrophobic organic compounds (HOCs) in the aqueous phase because of their molecular structures, which consist of hydrophilic and hydrophobic moieties. In this study, we examined the effect of the structures of humic acid and HOCs on the sorption of four polycyclic aromatic hydrocarbons (PAHs) and an organochlorine pesticide, p,p'-DDT, to humic acid. As the number of aromatic rings was increased, the extent of solubility enhancement of PAHs by humic acid was increased. Although p,p'-DDT was more hydrophobic than pyrene in this study, the extent of solubility enhancement of p,p'-DDT by humic acid was lower than that of pyrene because of the molecular structures of the solutes. Anionic surfactants with and without aromatic rings also were studied for comparison, and the dianionic surfactant with two benzene rings exhibited similar results with humic acid, unlike the surfactants without and with one benzene ring. The results from this study indicate that bulky molecules, such as p,p'-DDT sorbed with more difficulty to the aggregates of amphiphiles with larger molecules, such as humic substances and the dianionic surfactants.

Adsorption↗
PubMed2003

Quantitative relationships between molecular structures, environmental temperatures and octanol-air partition coefficients of polychlorinated biphenyls.

A quantitative model that incorporates information on both environmental temperatures (T) and molecular structures, for logarithm of octanol-air partition coefficient to base 10 (logK(OA)) of polychlorinated biphenyls (PCBs) was developed. Partial least squares (PLS) analysis together with 16 theoretical molecular structural descriptors was used to develop the Quantitative relationships between structures, environmental temperatures and properties (QRSETP) model. The cross-validated Q(cum)(2) value for the optimal QRSETP model is 0.976, indicating a good predictive ability for logK(OA) of PCBs at different environmental temperatures. T, E(LUMO) (the energy of the lowest unoccupied molecular orbital), molecular size or average molecular polarizability (alpha), and the net atomic charges on chlorine, hydrogen and carbon atoms of PCB molecules, are major factors governing logK(OA). The lower the E(LUMO), the greater the intermolecular interactions between octanol and PCB molecules, and thus the greater the logK(OA) values. Because of intermolecular dispersive forces, the more chlorine atoms in PCB molecules, the greater the molecular size or alpha, the greater the logK(OA). The largest negative net atomic charge on a carbon atom (q(C)(-)) and molecular size or average molecular polarizability (alpha) are major factors governing temperature dependence of logK(OA). PCB molecules with low q(C)(-) values and more chlorines (big size or alpha) tend to have strong temperature dependence, due to intermolecular electrostatic interactions and dispersive forces, respectively.

Journal Article↗
PubMed2004

Solution 1H NMR study of the active site molecular structure and magnetic properties of the cyanomet complex of the isolated, tetrameric beta-chain from human adult hemoglobin.

The solution molecular structure and the electronic and magnetic properties of the heme pocket of the cyanomet complex of the isolated beta-chain of human adult hemoglobin, HbA, have been investigated by homonuclear 2D (1)H NMR in order to assess the extent of assignments allowed by (1)H NMR of a homo-tetrameric 65-kDa protein, to guide the future assignments of the heterotetrameric complex of HbA, and to compare the structure of the beta-chain to the crystallographically characterized complexes that contains the beta-chain. The target residues are those that exhibit significant (>|0.2| ppm) dipolar shifts, as predicted by a "preliminary" set of magnetic axes determined from a small set of easily assigned active site residues. All 104 target residues ( approximately 70% of total) were assigned by taking advantage of the temperature dependence predicted by the "preliminary" magnetic axes for the polypeptide backbone; they include all residues proposed to play a significant role in modulating the ligand affinity in the tetramer HbA. Left unassigned are the A-helix, the end of the G-helix and the beginning of the H-helix where dipolar shifts are less than |0.2| ppm. These comprehensive assignments allow the determination of a robust set of orientation and anisotropies of the paramagnetic susceptibility tensor that leads to quantitative interpretation of the dipolar shifts of the beta-chain in terms of the crystal coordinates of the beta-subunit in ligated HbA which, in turn, confirms a largely conserved molecular structure of the isolated beta-chain relative to that in the intact R-state HbA. The major magnetic axis, which is correlated with the tilt of the Fe-CN unit, is tilted approximately 10 degrees from the heme normal so that the Fe-CN unit is tilted toward the beta-meso-H in a fashion remarkably similar to the Fe-CO tilt in the beta-subunit of HbCO. It is concluded that a set of "preliminary" magnetic axes and the use of variable temperature 2D NMR spectra are crucial to effective assignments in the tetrameric cyanomet beta-chain and that this approach should be similarly effective in HbA.

Catalytic Domain↗
PubMed2003

Solution 1H NMR study of the active site molecular structure and magnetic properties of the cyanomet complex of the isolated alpha-chain from human hemoglobin A.

The solution electronic and molecular structure for the heme pocket of the cyanomet complex of the isolated alpha-chain of human adult hemoglobin (HbA) has been investigated by homonuclear two-dimensional 1H NMR in order to establish an assignment protocol for the dimeric chain that will guide similar assignments in the intact, heterotetrameric HbA complex, and to compare the structures of the alpha-chain with its subunit in HbA. The target residues are those that exhibit significant (>0.2 ppm) dipolar shifts, as predicted by a "preliminary" set of magnetic axes determined from a small set of easily assigned active site residues. All 97 target residues (approximately 70% of total) were assigned by taking advantage of the temperature dependence predicted by the "preliminary" magnetic axes for the polypeptide backbone; they include all residues proposed to play a significant role in modulating the ligand affinity in the tetramer HbA. Left unassigned are the A-helix, the end of the G-helix and the beginning of the H-helix where dipolar shifts are less than 0.2 ppm. The complete assignments allow the determination of a robust set of orientation and anisotropies of the paramagnetic susceptibility tensor that leads to quantitative interpretation of the dipolar shifts of the alpha-chain in terms of the crystal coordinates of the alpha-subunit in ligated HbA which, in turn, confirms a largely conserved molecular structure of the isolated alpha-chain relative to that in the intact HbA. The major magnetic axis, which is correlated with the tilt of the Fe-CN unit, is tilted approximately 10 degrees from the heme normal so that the Fe-CN unit is tilted toward the beta-meso-H in a fashion remarkably similar to the Fe-CO tilt in HbACO. It is concluded that a set of "preliminary" magnetic axes and the use of variable temperature two-dimensional NMR spectra are crucial to effective assignments in the cyanomet alpha-chain and that this approach should be similarly effective in HbA.

Binding Sites↗
PubMed2000

The importance of molecular structure and conformation: learning with scanning probe microscopy.

Molecular structure holds a key to understanding Nature's intricate design mechanisms and blueprints. If we can understand her blueprints and basic materials, perhaps we can begin to mimic her beautiful products more cost effectively and with less detrimental environmental consequences. Higher resolution instrumentation has allowed us to study single molecules. Indeed, many stellar contributions to the field have come forth in the last couple of years. We can measure the forces required to unravel individual domains of biological molecules such as titin or DNA to a few picoNewtons resolution. This review will attempt to provide a general overview of the field of single molecule analysis using scanning force microscopy.

Adhesives↗
PubMed2005

Molecular structures and properties of the complete series of bromophenols: Density functional theory calculations.

The complete series of 19 bromophenols have been studied by density functional theory (DFT) calculations at the B3LYP/6-311G++(d,p) level. The molecular structures and properties of bromophenols are strongly influenced by intramolecular hydrogen bonding of ortho-bromine, steric and inductive effects of substituted bromine, and other intramolecular electrostatic interactions. Systematic trends in several structural parameters and molecular properties of bromophenols have been found with the increasing number of bromine substitutions, including increase in O-H bond length, decrease in C-O bond length, red shift in O-H stretching frequency, and blue shift in O-H torsional frequency. Correlations among several key molecular parameters as well as those with available aqueous pKa values are examined. Comparisons with chlorophenols have indicated that the inductive effect of substituted bromine appears larger and bromophenols are slightly stronger acids than chlorophenols.

Bromine↗
PubMed2006

Crystal and molecular structures of diglycosyl disulfide derivatives.

The crystal and molecular structures of S-(2,3,4,6-tetra-O-acetyl-beta-d-glucopyranosyl)-S'-(2,3,4,6-tetra-O-acetyl-beta-d-galactopyranosyl)disulfide (1) and the mono-sulfoxide (3) of bis(2,3,4,6-tetra-O-acetyl-beta-d-glucopyranosyl)disulfide (2) are described. Comparison of 2 and 3, containing -S-S- and -S-S(O)- bonds, respectively, allows to delineate structural differences brought about by the different oxidation states of one of the sulfur atoms in carbohydrate disulfides.

Crystallization↗