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At least 19 recordsLinked to original sources
PubMed1977

Mathematical description of molecular structure: Molecular topology.

The concepts of the topology of finite point sets are applied to a mathematical description of molecular structure. The combinatorial properties of the "bond topology," which arises naturally from atomic adjacency relationships within a molecule, are investigated in detail. The collection of closed sets, the cotopology, is found to be related to bonding. Combinatorial weights of bonds over the cotopology are defined and explicit expressions for a general molecule are derived. The bond weights are found to parallel molecular orbital bond orders. It is concluded that much of the variation in pi bond orders is topological in origin.

Journal Article↗
PubMed1994

The c-erbB-2 protein in oncogenesis: molecular structure to molecular epidemiology.

The c-erbB-2 (HER-2, neu) oncogene has been implicated frequently in many human tumors. This oncogene codes for a 185-kDa protein that functions as a transmembrane growth factor receptor. Overexpression of the normal protein or point mutations in the transmembrane domain of the protein have been shown to have a transforming effect. Molecular structure studies of the transmembrane domain provide a plausible explanation for this transforming effect in both cases and relate this to the process of receptor dimerization in the membrane, degradation of the protein with release of the extracellular domain (ECD) into the extracellular environment, and aberrant signal transduction. The release of the ECD into the extracellular environment provides a potential biomarker for the study of signal transduction at the molecular level in vivo. The ECD can be quantitated immunologically in the serum of individuals with cancers associated with p185 overexpression and in individuals at risk for the development of such cancers and can be used to distinguish these individuals from normal, healthy controls. Identification of such individuals by their serum ECD levels combined with specific chemotherapeutic/chemoprophylactic interventions could allow for improvement treatment and prevention of c-erbB-2-related cancers.

Amino Acid Sequence↗
PubMed2005

Calculation of the tau dependence of the vibration-internal rotation-overall rotation interactions in CH3OH from molecular structure and molecular dynamics.

The Guan and Quade theory for vibration-large-amplitude internal-motion-rotation interactions has been applied to the internal rotation problem in CH(3)OH. Through the molecular dynamics, the cos 3tau and sin 3tau dependence of the torsional-rotational coefficients in the effective Hamiltonian have been calculated from molecular structure. The internal rotation coordinate tau(') for the vibrationally distorted molecule is shown to have the necessary threefold symmetry for all values of tau('). For the methyl deformation modes, the vibrational dependence of the internal rotation potential energy is shown to have a threefold symmetry. The S(t) and S(t)S(t) dependence of the inertia tensor and Coriolis coupling coefficients has been developed in terms of curvilinear internal coordinates. The T transformation separating rotation from vibrations in zeroth order is then applied, the kinetic-energy tensor inverted to momentum space, and finally the effective torsion-rotation coefficients are calculated by Van Vleck perturbation theory. When compared to the empirical results, the kinetic-energy contributions to the cos 3tau and sin 3tau dependence of the coefficients are as follows: 54% of P(a)(2) is accounted for, 28% of P(a)P(b), 16% of P(a)P(c), and 91% of the asymmetry. The calculation is inadequate to account for the P(b)(2),P(c)(2), and P(b)P(c) coefficients, ranging from factors of 20-70, even with the incorrect sign for some of the terms. Anharmonic force contributions from the vibrations have not been used in the calculation since these forces are not known at this time.

Journal Article↗
PubMed1991

Crystal structure and molecular structure of mefloquine methylsulfonate monohydrate: implications for a malaria receptor.

The crystal structure of (+/-)-mefloquine methylsulfonate monohydrate was determined by X-ray diffraction and was compared with the crystal structures of mefloquine hydrochloride and mefloquine free base. The conformation of mefloquine was essentially the same in all three crystalline environments and was not dependent on whether mefloquine was a salt or a free base. In mefloquine methylsulfonate monohydrate, the angle between the average plane of the quinoline ring and the average plane of the piperidine ring was 76.9 degrees. The intramolecular aliphatic N-13...O-1 distance was 2.730 +/- 0.008 A (1 A = 0.1 nm), which is close to the aliphatic N...O distance found in the antimalarial cinchona alkaloids. The hydroxyl group formed a hydrogen bond with the water molecule, and the amine group formed hydrogen bonds with two different methylsulfonate ions. The crystallographic parameters for (+/-)-mefloquine methylsulfonate monohydrate were as follows: C17H17F6N2O(+).CH3SO3(-).H2O; Mr = 492.4; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell, a was 8.678 +/- 0.001 A, b was 28.330 +/- 0.003 A, c was 8.804 +/- 0.001 A, beta was 97.50 +/- 0.01 degrees; the volume of the unit cell was 2145.9 A3; the number of molecules per unit cell was 4; the calculated density was 1.52 g cm(-3); the source of radiation was Cu K alpha (lambda = 1.54178 A); mu (absorption coefficient) was 20.46 cm(-1); F(000) (sum of atomic scattering factors at zero scattering angle) was 1,016; room temperature was used; and the final R (residual index) was 6.58% for 1,740 reflections with magnitude of Fo greater than 3 sigma (F). Since the mechanism of antimalarial action and the mechanism of mefloquine resistance may involve hydrogen bond formation between mefloquine and a cellular effector or transport proteins, the common conformation of mefloquine found in each crystalline environment may define the orientation in which mefloquine forms these potentially critical hydrogen bonds with cellular constituents.

Crystallization↗
PubMed2001

Effect of pH and salt bridges on structural assembly: molecular structures of the monomer and intertwined dimer of the Eps8 SH3 domain.

The SH3 domain of Eps8 was previously found to form an intertwined, domain-swapped dimer. We report here a monomeric structure of the EPS8 SH3 domain obtained from crystals grown at low pH, as well as an improved domain-swapped dimer structure at 1.8 A resolution. In the domain-swapped dimer the asymmetric unit contains two "hybrid-monomers." In the low pH form there are two independently folded SH3 molecules per asymmetric unit. The formation of intermolecular salt bridges is thought to be the reason for the formation of the dimer. On the basis of the monomer SH3 structure, it is argued that Eps8 SH3 should, in principle, bind to peptides containing a PxxP motif. Recently it was reported that Eps8 SH3 binds to a peptide with a PxxDY motif. Because the "SH3 fold" is conserved, alternate binding sites may be possible for the PxxDY motif to bind. The strand exchange or domain swap occurs at the n-src loops because the n-src loops are flexible. The thermal b-factors also indicate the flexible nature of n-src loops and a possible handle for domain swap initiation. Despite the loop swapping, the typical SH3 fold in both forms is conserved structurally. The interface of the acidic form of SH3 is stabilized by a tetragonal network of water molecules above hydrophobic residues. The intertwined dimer interface is stabilized by hydrophobic and aromatic stacking interactions in the core and by hydrophilic interactions on the surface.

Adaptor Proteins, Signal Transducing↗
PubMed1988

Thyroid hormone structure-activity relationships: molecular structure of 3,5,3'-triiodothyropropionic acid.

The crystal and molecular structures of 3,5,3'-triiodothyropropionic acid (T3P), determined as an N-diethanolamine salt, were carried out and the results are compared with those of other thyroid hormone structures. These data show that T3P has an unusual conformation with the diphenyl ether bridge outside the range normally observed for other thyroactive acid structures and has the largest deviations from the ideal skewed conformation predicted for 3,5-diiodothyroactive compounds. These conformational properties are not observed in the structures of thyroformic or acetic acid analogues. Biochemical data indicate that thyropropionic acid analogue activity differs from that other acid analogues which could imply that their metabolism and activity can be controlled differently from that of other hormone metabolites.

Crystallography↗
PubMed1994

Refined 2.0 A X-ray crystal structure of the snake venom zinc-endopeptidase adamalysin II. Primary and tertiary structure determination, refinement, molecular structure and comparison with astacin, collagenase and thermolysin.

Adamalysin II, alias proteinase II, a 24 kDa zinc-endopeptidase isolated from the snake venom of the Eastern diamondback rattlesnake Crotalus adamanteus, is a prototype of the proteolytic domain of snake venom metalloproteinases and of domains found in mammalian reproductive tract proteins. Its 2.0 A crystal and molecular structure was solved by multiple isomorphous replacement using six heavy-atom derivatives, and was refined to a crystallographic R-value of 0.172. 201 of the 203 amino acid residues of adamalysin II are defined by electron density; only the first two residues are disordered and crystallographically undefined in the crystal structure. Three-quarters of these crystallographic amino acid residue assignments were confirmed by chemical sequencing. In addition, the active-site zinc-ion, a hepta-coordinated calcium ion, a fixed sulphate anion and 173 solvent molecules were localized in the structure. Adamalysin II is an ellipsoidal molecule with a relatively flat active-site cleft separating the "upper" main body from a small "lower" subdomain. The regularly folded N-terminal upper domain consists essentially of a central, highly twisted five-stranded beta-pleated sheet flanked by a long and a short surface located helix on its convex side, and by two long helices, one of which represents the central "active site helix", on its concave side. The lower subdomain, comprising the last 50 residues, is organized in multiple turns, with the chain ending in a long C-terminal helix and an extended segment clamped to the upper domain via a disulphide bridge. The catalytic zinc-ion, located at the bottom of the active-site cleft, is almost tetrahedrally co-ordinated by His142, His146 and His152, and a water molecule anchored to an intermediate glutamic acid residue (Glu143), with the three imidazole N epsilon 2 nitrogen atoms 2.1 A and the solvent oxygen atom 2.4 A away from the zinc ion. His142, Glu143 and His146 are part of the long active-site helix, which extends up to Gly149, where it turns sharply away towards His152. The importance of these residues for structure and activity of adamalysin II explains their occurrence in the HEXXHXXGXXH consensus sequence. Asp153, which is strictly conserved in these snake venom and reproductive tract metalloproteinases, is buried in the subdomain and seems to stabilize the hydrophobic active-site basement. Some residues behind, the adamalysin peptide chain folds into a characteristic 1,4-turn (the "Met-turn") containing the conserved Met166, which forms a hydrophobic basement for the three zinc-binding imidazoles.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2001

Issues in representation of molecular structure the development of molecular connectivity.

Significant issues in the representation of molecular structure and the development of the molecular connectivity paradigm are presented. In the molecular connectivity paradigm, molecular structure is represented directly. Kier and Hall developed the method by creating ways to encode electronic information based on the paradigm developed from the Randić branching index. The simple and valence delta values were created to encode atomic and valence-state electronic information through counts of sigma, pi, and lone pair electrons. A family of indices was created to provide a wide range of structure information. The key aspects of the development are presented and discussed in such a way as to reveal, at least in part, the imaginative thinking involved in the process. Possible future roles for molecular connectivity chi indices are discussed.

Algorithms↗
PubMed1992

Molecular structure and dynamics of the four 10-hydroxynortriptyline isomers.

The three-dimensional structures, molecular conformations, and electrostatic potentials of the R-E-, S-E-, R-Z-, and S-Z-isomers of 10-hydroxynortriptyline were examined by computer graphics, molecular mechanical energy calculations, and molecular dynamics simulations in vacuo and in aqueous solution. Molecular models of the isomers, based on the structure of nortriptyline, were refined by energy minimization and used as starting points in the simulations. R-E- and S-Z-10-hydroxynortriptyline formed intramolecular hydrogen bonds between the side-chain nitrogen atom and the hydroxyl group during the simulations in vacuo, and had the side chain folded over the ring system in the minimum energy conformations. Intramolecular hydrogen bonding was not observed for R-Z- and S-E-10-hydroxynortriptyline, which had extended side chains in the minimum energy conformations and stronger negative molecular electrostatic potentials around the hydroxyl group than the R-E- and S-Z-isomers.

Models, Molecular↗
PubMedDate not supplied

Nuragic bone collagen retains its molecular structure.

The molecular structure of bone collagen was found to be preserved in Nuragic bone samples several centuries after burial. Enhanced birefringence of bone and dentin collagen fibres observed in polarized light after Sirus red staining was used to demonstrate this fact.

Anthropology, Physical↗
PubMed1992

Alpha-beta-dehydro-amino acid residues in the design of peptide structures. Molecular and crystal structures of two folded dehydro peptides.

The molecular and crystal structures of two N alpha-protected tripeptide amides, containing in the central position the alpha-beta-dehydro-amino acid residue delta Phe (Z-configurational isomer), were determined by X-ray diffraction. While Z-Gly-delta Phez-L-Pro-NH2 is characterized in the crystal state by the presence of a type I beta-bend conformation (at the delta Phez-L-Pro sequence), Z-D-Ala-delta Phez-Gly-NH2 is folded into two consecutive beta-bends (type II' followed by type I), at the D-Ala-delta Phez and delta Phez-Gly sequences, respectively. In both cases the achiral delta Phez residue adopts a set of phi, psi angles typical of the right-handed helical conformation. The delta Phe residue may be exploited to design aromatic peptides with preferred secondary structures.

Amino Acid Sequence↗
PubMed2001

Effects of molecular structure on the stability of a thermotropic liquid crystal. Gas electron diffraction study of the molecular structure of phenyl benzoate.

As a model of the core of molecules forming liquid crystals, the molecular structure of phenyl benzoate (Ph-C(=O)-O-Ph) at 409 K was determined by gas electron diffraction, and the relationship between the gas-phase structures of model compounds and the nematic-to-liquid transition temperatures was studied. Structural constraints were obtained from RHF/6-31G ab initio calculations. Vibrational mean amplitudes and shrinkage corrections were calculated from the harmonic force constants given by normal coordinate analysis. Thermal vibrations were treated as small-amplitude motions, except for the phenyl torsion, which was treated as a large-amplitude motion. The potential function for torsion was assumed to be V(phi(1),phi(2)) = V(12)(1 - cos 2phi(1))/2 + V(14)(1 - cos 4phi(1))/2 + V(22)(1 - cos 2phi(2))/2, where phi(1) and phi(2) denote the torsional angles around the C-Ph and O-Ph bonds, respectively. The potential constants (V(ij)()/kcal mol(-)(1)) and the principal structure parameters (r(g)/A, angle(alpha)/deg) with the estimated limits of error (3sigma) are as follows: V(12) = -1.3 (assumed); V(14) = -0.5(9); V(22) = 3.5(15); r(C=O) = 1.208(4); r(C(=O)-O) = 1.362(6); r(C(=O)-O) - r(O-C) = -0.044 (assumed); r(C(=O)-C) = 1.478(10); = 1.396(1); angleOCO = 124.2(13); angleO=CC = 127.3(12); angleCOC = 121.4(22); ( angleOCC(cis) - angleOCC(trans))/2 = 3.0(15); ( angleC(=O)CC(cis) - angleC(=O)CC(trans))/2 = 4.8(17), where < > means an average value and C-C(cis) and C-C(trans) bonds are cis and trans to the C(=O)-O bond, respectively. The torsional angle around the O-Ph bond was determined to be 64(+26,-12) degrees. An apparent correlation was found between the contributions of the cores to the clearing point of liquid crystals and the gas-phase structures of model compounds of the cores of mesogens, i.e., phenyl benzoate, trans-azobenzene (t-AB), N-benzylideneaniline, N-benzylideneaniline N-oxide (NBANO), trans-azoxybenzene (t-AXB), and trans-stilbene. The structures of t-AB, NBANO, and t-AXB have been obtained by our research group.

Journal Article↗