Molecular structure and biological function.
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Acridines↗
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The molecular structure of cell adhesion molecules.
Considerable advances have been made in our knowledge of the molecular structure of cell adhesion molecules, their binding sites, and adhesion complexes. For the cadherins, protein zero, and CD2, additional experimental data support the insights obtained from structural analysis of their domains and molecular models of their adhesion complexes. For neural cell adhesion molecules, L1, fibronectin, tenascin-C, integrins, and vascular cell adhesion molecules, the molecular structure of domains, and in most cases their binding sites, have been elucidated. The substrate recognition sites in some of these molecules possess rate constants for association and dissociation that permit both rapid cell migration and, through avidity, high-affinity cell-cell interactions.
Animals↗
Effect of water on the molecular structure and arrangement of nitrile-functionalized ionic liquids.
Water changes the physical properties of ionic liquids (ILs). In this paper, the effect of water on ILs is investigated at the molecular level. The molecular structure and arrangement of 1-butyronitrile-3-methylimidazolium halide, in the presence and absence of the intruded water molecule, have been elucidated by single-crystal X-ray crystallography and near-infrared Raman spectroscopy. Water molecule is found to change the conformation of the n-butyronitrile chain of the cation. The hydrogen bonding interaction between the anion and water molecule, leading to loose molecular packing, is most likely to be responsible for the change. Distinct molecular structures and arrangements of ILs with and without water molecule have been presented here for the first time. As the unique properties of ILs are related to their structures and molecular arrangements, the presence of water, wanted or unwanted, must be carefully examined in any kind of IL research and applications.
Crystallography, X-Ray↗
Molecular structures from low angle X-ray and neutron scattering studies.
Molecular structures can be extracted from solution scattering analyses of multidomain or oligomeric proteins by a new method of constrained automated scattering curve fits. Scattering curves are calculated using a procedure tested by comparisons of crystal structures with experimental X-ray and neutron data. The domains or subunits in the protein of interest are all represented by atomic coordinates in order to provide initial constraints. From this starting model, hundreds or thousands of different possible structures are computed, from each of which a scattering curve is computed. Each model is assessed for steric overlap, radii of gyration and R-factors in order to leave a small family of good fit models that corresponds to the molecular structure of interest. This method avoids the tedium of curve fitting by hand and error limits on the ensuing models can be described. For single multidomain proteins, the key constraint is the correct stereochemical connections between the domains in all the models. Successful applications to determine structures are summarised for the Fab and Fc fragments in immunoglobulin G, the three domain pairs in the Fc subunit of immunoglobulin E and the seven, domains in carcinoembryonic antigen. For oligomeric proteins, the key constraint is provided by symmetry and successful analyses were performed for the association of the monomers of the bacterial amide sensor protein AmiC to form trimers and pentameric serum amyloid P component to form decameric structures. The successful analysis of the heterodimeric complex of tissue factor and factor VIIa required the use of constraints provided from biochemical data. The outcome of these analyses is critically appraised, in particular the biological significance of structures determined by these solution scattering curve fits.
Animals↗
Quantitative relationship between chromatographic retentions and molecular structures of polychlorinated dibenzo-p-dioxins (PCDDs).
A new approach to study the quantitative relationships between chromatographic retentions and molecular structures of polychlorinated dibenzo-p-dioxins (PCDDs) is described. The retention equations of PCDDs log k' = A + B/T in gas chromatography (GC) are used to evaluate the properties of the regression coefficients A and B, which have been widely accepted as highly reliable chromatographic retentions. The quantitative relationships between the A, B values and the molecular structures are found. The molecular descriptors given for the first time in this article are very effective. As a result, the regression equations are derived with correlation coefficients greater than 0.9995. The A, B values of PCDDs with no standards available have been predicted according to these relationships. They are very useful in chromatographic identification. The retention times of all PCDDs can be conveniently predicted at any temperature program. Compared with the data obtained from the relevant experiments, the results of prediction are very accurate.
Chromatography, Gas↗
Calculation of crystal and molecular structures of carbon disulfide CS2.
Crystal and molecular structures of carbon disulfide CS(2) were investigated by molecular packing analysis with a computed dynamical model. This model includes thermal motions, molecular deformations, and anisotropic atomic repulsive interactions. Several crystalline structures with orthorhombic symmetry Cmca have been found by the calculation. The lowest energy structure agrees with the experimental one. The temperature dependence of the crystal structure parameters reproduces the general features and the particular increase with decreasing temperature of the lattice parameter c (and orientational angle psi) as determined by x-ray diffraction or neutron scattering experiments. The pressure behavior of the crystal structure parameters up to 12 GPa at room temperature is also correctly reproduced.
Journal Article↗
The molecular structure of tetra-tert-butyldiphosphine: an extremely distorted, sterically crowded molecule.
The molecular structure of tetra-tert-butyldiphosphine has been determined in the gas phase by electron diffraction using the new DYNAMITE method and in the crystalline phase by X-ray diffraction. Ab initio methods were employed to gain a greater understanding of the structural preferences of this molecule in the gas phase, and to determine the intrinsic P-P bond energy, using recently described methods. Although the P-P bond is relatively long [GED 226.4(8) pm; X-ray 223.4(1) pm] and the dissociation energy is computed to be correspondingly small (150.6 kJ mol(-1)), the intrinsic energy of this bond (258.2 kJ mol(-1)) is normal for a diphosphine. The gaseous data were refined using the new Edinburgh structure refinement program ed@ed, which is described in detail. The molecular structure of gaseous P(2)Bu(t)(4) is compared to that of the isoelectronic 1,1,2,2-tetra-tert-butyldisilane. The molecules adopt a conformation with C(2) symmetry. The P-P-C angles returned from the gas electron diffraction refinement are 118.8(6) and 98.9(6) degrees, a difference of 20 degrees, whilst the C-P-C angle is 110.3(8) degrees. The corresponding parameters in the crystal are 120.9(1), 99.5(1) and 109.5(1) degrees. There are also large deformations within the tert-butyl groups, making the DYNAMITE analysis for this molecule extremely important.
Journal Article↗
Synthesis, structure and magnetic properties of tetrakis-mu-carboxylato-bis(dodecylnicotinato)dicopper(II) complexes; crystal and molecular structure of the decyl carboxylate derivative.
Dodecylnicotinate bis-adducts of binuclear copper carboxylates, of the general formula Cu2(O2CC(n-1)H(2n-1))4(C5H4NCOOC12H25)2, were synthesized for n = 10, 12, 14, 16, 18 and 20, and their crystal structure, thermal behavior and magnetic properties studied. The molecular structure of the decyl derivative has been determined from single-crystal X-ray diffraction data. The dimer is centrosymmetric with the CuII ions in a square-pyramidal coordination with four O-alkyl O atoms [average d(Cu-O) 1.960 (6) A] in the basal plane and the nicotine N atom at apical positions [d(Cu-N) 2.183 (3) A]. The copper ions, 2.615 (1) A apart, are bridged by four O-alkyl carboxylate groups. Both the n = 20 and n = 18 homologues exhibit lamellar phases, which can be related to the supramolecular arrangement found in the n = 10 derivative. The magnetic behavior of the decyl and octadecyl dimers was studied in the 2-300 K temperature range. They exhibit a strong intramolecular antiferromagnetic interaction (Cu-Cu superexchange coupling constant J = -347 cm(-1) for the decyl derivative), which can be attributed to a large overlap of the metal 3d orbitals and the oxygen lone pair orbitals of the linking carboxylate groups.
Carboxylic Acids↗
Imaging molecular structure and physiological function of gap junctions and hemijunctions by multimodal atomic force microscopy.
Gap junctions are specialized plasma membrane structures that join neighboring cells via specialized intercellular ion channels (hemichannels) and provide a direct pathway for cell-cell communication. They presumably mediate regulation of growth, transmission of developmental signals, coordination of muscle contraction, and maintenance of metabolic homeostasis. Hemichannels are also present in the non-junctional regions of the cell plasma membrane and they provide a direct pathway for communication between the cytoplasm and the extracellular region. Recent studies suggest that gap junctional communication is much more complex than previously anticipated, in terms of both its structure as well as its activity. While the mechanism of gap junction activity is being studied extensively, their quaternary structure, assembly, and conformational changes underlying gating of their activity as well as their physiological role are poorly understood because, due to their complex structure, these junctions are less amenable to existing techniques for high-resolution three-dimensional structure-function analyses. Atomic Force Microscopy (AFM) images molecular structure of biological specimens in an aqueous environment, allows on-line perturbations, and can be coupled with electrophysiological, biochemical, and other microscopic techniques. The present review examines the potential of AFM application for the study of the molecular structure of hydrated, native gap junctions and hemijunctions as well as their physiological functions. Special attention is paid to new, complementary, or provocative findings from AFM studies of both vertebrate and invertebrate gap junctions and hemijunctions.
Animals↗
Crystal and molecular structure of didemnin A, an antiviral depsipeptide.
The molecular structure of didemnin A, the parent compound of a series of antiviral cytotoxic depsipeptides extracted from a marine tunicate Trididemnum solidum of the family of Didemnidae, has been determined by single-crystal X-ray diffraction. In the crystal, didemnin A molecules form pseudo-symmetric dimeric pair. The two molecules in the dimer are held together by strong N--H center dot center dot center dot O and N--H center dot center dot center dot N hydrogen bonds. A chloride ion, placed almost symmetrically between the dimeric pair, forms N--H center dot center dot center dot Cl hydrogen bonds (3.19 and 3.23 Angstrom) with both the molecules. The two independent molecules in the structure have closely similar geometry. For each molecule, the 23-membered depsipeptide ring assumes a folded conformation in the shape of a 'bent figure-of-eight' similar to that observed in the didemnin B crystal structure. The major conformational differences in the macrocycle of didemnin A and didemnin B are around the Hip residue. The root mean-square (RMS) difference of 20 of the 23 endocyclic torsion angles for the two structures is less than 10 degrees, while the three bond torsions in the Hip residue vary by about 50 degrees. The macrocycle conformation is stabilized by a transannular N--H center dot center dot center dot O hydrogen bond linking the isostatine amide group with the leucine carbonyl group. The truncated linear chain is folded back toward the macrocyclic ring and is held by a N--H center dot center dot center dot O hydrogen bond between the leucine amide group and Me-Leu carbonyl group. The transannular hydrogen bond in the didemnin A structure (N4--H center dot center dot center dot O3 = 2.83 Angstrom in both molecule a and molecule b) is noticeably stronger than that observed in the didemnin B structure (3.02 Angstrom). The X-ray structure of didemnin A is generally consistent with that obtained by NMR studies. Within the crystal, the molecules are packed in zig-zag chains formed by intermolecular O--H center dot center dot center dot O hydrogen bonds. The crystal structure and packing of didemnin A are quite different from that of the didemnin B structure.
Antiviral Agents↗
The molecular structure of adrenal medulla kinesin.
The molecular structure of bovine adrenal kinesin was studied by electron microscopy using the low-angle rotary shadowing technique. Adrenal kinesin exhibited either a folded or an extended configuration; the ratio of the two is dependent on the salt concentration. Almost all adrenal kinesin molecules were folded in a low-ionic solution, and the ratio of extended molecules increased to 40-50% in a solution containing 1 M ammonium acetate. Kinesin in the extended configuration displayed a rod-shaped structure with a mean length of about 80 nm. The morphologies of the ends were different; one end was composed of two globular particles, similar to the two-headed structure of myosin, while the other end had a more ill-defined structure, appearing either as a globular particle, an aggregate of two to four small granules, or a frayed, fan-like structure. The folded kinesin molecule possessed a hinge region in the middle of the rod, at about 32 nm from the neck of the two heads. In our preparations, the majority of adrenal kinesin molecules were folded at physiological salt concentrations. Adrenal kinesin bound to microtubules in the presence of adenylyl imidodiphosphate (AMP-PNP) also displayed a folded morphology.
Acetates↗
Polypeptide multilayer films: role of molecular structure and charge.
The role of molecular structure, charge, and hydrophobicity in polyelectrolyte layer-by-layer assembly (LbL) of thin films has been studied using the model polypeptides poly-L-glutamatic acid (PLGA) and poly-L-lysine (PLL), quartz crystal microbalance (QCM), and circular dichroism spectroscopy (CD). The adsorption behavior of PLGA and PLL has been compared with the structure of these molecules in aqueous solution under the same conditions. The data show that the deposition of polypeptide per adsorption step scales with average secondary structure content, whether alpha helix or beta sheet. This is contrary to the expectation based on the view that hydrogen bonds are crucial to polypeptide film assembly, because secondary structure formation in a polypeptide reduces its intermolecular hydrogen-bonding potential. The data also show that polypeptide adsorption scales with ionic strength and chain length. Taken together, the results increase knowledge of polypeptide-based LbL thin film fabrication and will help to provide a firmer foundation for the use of natural or designed polypeptides in LbL.
Biopolymers↗
Crystal and molecular structures of 2-
The crystal and molecular structures of 2-[1-(2-aminoethyl)-2-imidazolidinylidene]-2-nitroacetonitrile [C(7)H(11)N(5)O(2); space group P2(1)/n; Z = 4; a = 7.4889 (8), b = 17.273 (2), c = 7.4073 (8) Å, beta = 111.937 (6) degrees ], (I), and 2,6-diamino-5-hydroxy-3-nitro-4H-pyrazolo[1,5-a]pyrimidin-7-one monohydrate [C(6)H(6)N(6)O(4).H(2)O; space group P2(1)/n; Z = 4; a = 17.576 (3), b = 10.900 (2), c = 4.6738 (6) Å, beta = 92.867 (8) degrees ], (II), have been determined from X-ray, synchrotron and neutron powder diffraction data using various methods. The structures were originally solved from Guinier photographs with a grid search procedure and the program MRIA using a priori information from NMR and mass spectra on the possible geometry of the molecules. Because the conformation of molecule (I) changed during the bond-restrained Rietveld refinement, solvent water was found in (II) and, moreover, as both Guinier patterns were corrupted by texture, high-resolution texture-free synchrotron data were collected at the BM16 beamline, ESRF, to confirm the original results. Using the set of |F|(2) values derived from the synchrotron patterns after full-pattern decomposition procedures, the structures of (I) and (II) were solved by direct methods via SHELXS96, SIRPOW.92 and POWSIM without any preliminary models of the molecules, and by Patterson search methods via DIRDIF96 and PATSEE with the use of rigid fragments from each of the molecules. The neutron patterns allowed (I) and (II) to be solved using the grid search procedure and correct initial models of the molecules including H atoms. The results obtained from powder patterns measured on different devices demonstrate the high level of reproducibility and reliability of various powder software and equipment, with a certain preference for synchrotron facilities.
Journal Article↗
NMR study of Galeorhinus japonicus myoglobin. 1H-NMR study of molecular structure of the heme cavity.
The molecular structure of the active site of myoglobin from the shark, Galeorhinus japonicus, has been studied by 1H-NMR. Some hyperfine-shifted amino acid proton resonances in the met-cyano form of G. japonicus myoglobin have been unambiguously assigned by the combined use of various two-dimensional NMR techniques; they were compared with the corresponding resonances in Physter catodon myoglobin. The orientations of ThrE10 and IleFG5 residues relative to the heme in G. japonicus met-cyano myoglobin were semiquantitatively estimated from the analysis of their shifts using the magnetic susceptibility tensor determined by a method called MATDUHM (magnetic anisotropy tensor determination utilizing heme methyls) [Yamamoto, Y., Nanai, N. & Chûjô, R. (1990) J. Chem. Soc., Chem. Commun., 1556-1557] and the results were compared with the crystal structure of P. catodon carbonmonoxy myoglobin [Hanson, J. C. & Schoenborn, B. P. (1981) J. Mol. Biol. 153, 117-124]. In spite of a substantial difference in shift between the corresponding amino acid proton resonances for the two proteins, the orientations of these amino acid residues relative to the heme in the active site of both myoglobins were found to be highly alike.
Amino Acid Sequence↗
Quantifying the molecular structure of behavior: separate effects of caffeine, cocaine, and adenosine agonists on interresponse times and lever-press durations.
One difficulty in analyzing the molecular structure of behavior lies in reducing the data to a manageable size so that they can be described concisely but without a loss of important information. An approach to quantifying and comparing distributions of interresponse times (IRTs) and lever-press durations is described and then used to examine the acute effects of caffeine (an adenosine antagonist), cocaine, and three adenosine agonists in rats chronically consuming either tap water or water containing 1.0 mg/ml caffeine. The adenosine agonists used were R(-)N6-(2-phenylisopropyl)adenosine [R-PIA (preferential A1 receptor agonist)], 5'-(N-cyclopropyl)-carboxamidoadenosine [CPCA (preferential A2 agonist)], and 5'-N-ethylcarboxamidoadenosine [NECA (about equal agonist activity at A1 and A2 receptors)]. The rats' behavior was maintained under a Multiple Fixed-Interval (FI) 120 s, Duration > 5 s schedule of reinforcement. Under the FI schedule, the first lever-press after 120 s resulted in pellet delivery. Under the Duration > 5 s schedule, all lever-press durations greater than 5 s were reinforced. Molecular analyses of distributions of true IRTs (exclusive of lever-press durations) and lever-press durations were conducted by regressing percentiles of the distribution obtained from drug conditions against percentiles obtained from control conditions, a technique called empirical percentile-percentile analysis (or quantile-quantile analysis). The pattern of effects on response durations differed from that seen in IRTs. After acute administration of adenosine agonists, the distributions of lever-press durations under the FI schedule and subcriterion durations under the Duration > 5 s schedule were shifted rightward by a constant proportion, indicative of a generalized slowing of responding by these drugs. The effects of adenosine agonists on IRTs could be described by a power-function relationship whereby long IRTs were increased more than shorter ones. A rate-increasing dose of caffeine (10 mg/kg) did nothing to the molecular structure of lever-press durations or of IRTs, indicating that rate increases seen after this dose were due to an earlier onset of responding in the fixed-interval and were unaccompanied by disruptions in the physical execution of the response. The molecular structure of interresponse time distributions seen at the rate-decreasing dose of caffeine (60 mg/kg) resembled that of a rate-decreasing dose of cocaine, but not of the adenosine agonists. Both caffeine and cocaine produced a curvilinear relationship between drug and control percentiles such that very short IRTs were unaffected, but long ones were lengthened five- to 10-fold. This same dose of caffeine lengthened lever-press durations in a manner that resembled adenosine agonists but not cocaine. Percentile-percentile analyses reveal details about drug effects on the temporal structure of behavior and its physical execution that are not visible in molar analyses.
Adenosine↗
From non-random molecular structure to life and mind.
The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.
Cell Membrane↗
Molecular structure of LSD.
The molecular configuration of lysergic acid diethylamide (LSD) in crystals of the iodobenzoate has been determined by using x-ray diffraction techniques. The configuration shows strain and steric hindrance and the conformation is fixed. Some of the implications of this for the hallucinogenic activity of LSD are discussed.
Lysergic Acid Diethylamide↗
Deterministic global optimization of molecular structures using interval analysis.
The search for the global minimum of a molecular potential energy surface is a challenging problem. The molecular structure corresponding to the global minimum is of particular importance because it usually dictates both the physical and chemical properties of the molecule. The existence of an extremely large number of local minima, the number of which may increase exponentially with the size of the molecule, makes this global minimization problem extremely difficult. A new strategy is described here for solving such global minimization problems deterministically. The methodology is based on interval analysis, and provides a mathematical and computational guarantee that the molecular structure with the global minimum potential energy will be found. The technique is demonstrated using two sets of example problems. The first set involves a relatively simple potential model, and problems with up to 40 atoms. The second set involves a more realistic potential energy function, representative of those in current use, and problems with up to 11 atoms.
Journal Article↗