Lattice Conformation Research Articles

The transfer matrix method for lattice proteins—an application with cooperative interactions

The transfer matrix method for generating lattice conformations of proteins is explained and applied to lattice proteins having high-level cooperativity to represent hydrophobic interactions. The main advantage of the method is the extremely efficient attrition-free generation and enumeration of compact conformations. We review the application of the method for the generation and complete, exact enumeration of all conformation for linear and cyclic chains in 2D on the square lattice and in 3D on the cubic lattice. We show for compact conformations that the growth of the chain in a piecewise way, cross-section by cross-section, is much more efficient than the traditional linear chain growth. We discuss an extension of the method by including information about the amino acid sequence. We develop a Zimm–Bragg [J Chem Phys 31 (1959) 476–85]-like theory of hydrophobic cluster formation by using the transfer matrix method. We show that the transfer matrix approach to the generation and averaging over chain conformations can be formulated as an algebraic problem. We show also how the transfer matrix method can be extended to off-lattice proteins.

A combined approach for ab initio construction of low resolution protein tertiary structures from sequence.

An approach to construct low resolution models of protein structure from sequence information using a combination of different methodologies is described. All possible compact self-avoiding C alpha conformations (approximately 10 million) of a small protein chain were exhaustively enumerated on a tetrahedral lattice. The best scoring 10,000 conformations were selected using a lattice-based scoring function. All-atom structures were then generated by fitting an off-lattice four-state phi/psi model to the lattice conformations, using idealised helix and sheet values based on predicted secondary structure. The all-atom conformations were minimised using ENCAD and scored using a second hybrid scoring function. The best scoring 50, 100, and 500 conformations were input to a consensus-based distance geometry routine that used constraints from each the conformation sets and produced a single structure for each set (total of three). Secondary structures were again fitted to the three structures, and the resulting structures were minimised and scored. The lowest scoring conformation was taken to be the "correct" answer. The results of application of this method to twelve proteins are presented.

Efficient Method To Count and Generate Compact Protein Lattice Conformations

Efficient Method To Count and Generate Compact Protein Lattice Conformations

Global Optima of Lennard-Jones Clusters

This paper summarizes the current state of knowledge concerning putative global minima of the potential energy function for Lennard-Jones clusters, an intensely studied molecular conformation problem. Almost all known exceptions to global optimality of the well-known Northby multilayer icosahedral conformations for microclusters are shown to be minor variants of that geometry. The truly exceptional case of face-centered cubic lattice conformations is examined and connections are made with the macrocluster problem. Several types of algorithms and their limitations are explored, and a new variation on the growth sequence idea is presented and shown to be effective for both small and large clusters.

An atomistic simulation investigation of the inter-ring torsion in crystalline biphenyl

An atomistic simulation of solid-phase biphenyl describes the π character of the interphenyl bond by a torsional potential which predicts the observed torsional angle of the molecule in the vapour phase. In the crystal lattice the unit cell is defined by a doubling of the b axis vector of the early diffraction studies to allow for an alternation of torsional angles. The results predict a non-planar molecular conformation, with a dihedral angle of 15 ° between the rings and a torsional barrier of 1.65 kJ mol −1. Comparison with calculations conducted on the simple cell (in which no doubling of the b axis has been imposed) shows the stabilising effect of the alternation of the torsional angles. Thermal averaging would be expected to result in rapid interconversion of the two degenerate conformers at room temperature. The sensitivity found for the lattice conformation to small changes in the volume of the unit cell is discussed.

Electronic structure of highly conducting conjugated polymers: evolution upon doping of polyacetylene, polythiophene, and polyemeraldine

The electronic properties of three types of conducting polymers: trans-polyacetylene (proto-typical of systems with a degenerate ground state), polythiophene (as an example of compounds with a nondegenerate ground state), and polyemeraldine (which can be doped via protonation) are reviewed. The structural and electronic band structure properties of these systems are studied at various defect concentrations corresponding to undoped, lightly doped, and highly doped polymers. Geometry optimizations of oligomeric equivalents to the undoped and doped polymers are performed using the semi-empirical MNDO and AM1 methods. The electronic band structures are calculated using the VEH method. The interpretation of the optical absorption data is discussed in terms of interband transitions; for doped trans-polyacetylene including soliton defects and for doped polythiophene including bipolaron defects. For highly doped trans-polyacetylene and polythiophene as well as for protonated polyemeraldine, the electronic structure of a polaron lattice conformation is discussed and shown to be in agreement with existing optical and magnetic data on these polymers.

Statistical thermodynamics of flexible-chain surfactants in monolayer films. II. Calculations for a modified cubic lattice model

A modified cubic lattice model of chain conformations is incorporated within the general theory developed in the preceding article, and used to predict pressure-area isotherms for monolayers at the interface between water and a hydrophobic ‘‘solvent.’’ The statistical weight of each cubic lattice conformation is determined by enumerating all rotational isomeric states, and then performing a Boltzmann sum over the set of RIS conformers best described by that cubic lattice state. The isotherms are predicted to depend strongly on both chain length and on the energy of chain-solvent mixing, but only weakly on the energy difference between chain–water and solvent–water contact. In particular, with only a slight positive energy of chain–solvent mixing, two phase transitions are predicted. Both transitions are characterized by a critical point and involve only fluid phases. One extends to very low surface densities and resembles a liquid/gas transition. The other appears at high densities, and, by comparison with predictions of structural properties, is shown to result from the independence, in part, of conformational and translational degrees of freedom of the surfactant molecules.

Evolution of the electronic structure of polyacetylene and polythiophene as a function of doping level and lattice conformation

Band-structure calculations are presented for different lattice conformations of doped polyacetylene and polythiophene. At intermediate doping levels, the intraband transition energies are found to be in good agreement with experimental optical-absorption data for a soliton lattice conformation in polyacetylene and a bipolaron lattice conformation in polythiophene. At high doping levels, where both polymers exhibit a metalliclike behavior, we find the best agreement with observed optical-absorption and magnetic data to occur for a polaron lattice conformation. Important qualitative differences are found between the polaron lattice conformations obtained in this work and those reported previously. The polaron lattice band structures for polyacetylene and polythiophene are calculated to be very similar to one another, which is also consistent with the experimental trends. The evolutions of the \ensuremath{\pi}-${\ensuremath{\pi}}^{\mathrm{*}}$ and the \ensuremath{\pi}-to-soliton band energy gaps for polyacetylene are studied and compared with results of the Takayama, Lin-Liu, and Maki (TLM) model. We find that, in comparison with optical data probing these transitions, the valence effective Hamiltonian results are superior to the results of the TLM model. We stress that our results do not constitute a proof of the existence of polaron lattice conformation at high doping levels but indicate that the presence of such a conformation is in agreement with a large number of experimental (ir, optical conductivity, magnetic, electron-energy-loss spectroscopy) data.

Band Structure Calculations for the Polaron Lattice in the Highly Doped Regime of Polyacetylene, Polythiophene, and Polyaniline

Abstract Band structure calculations are presented for the polaron lattice conformation in the highly doped regime of polyacetylene, polythiophene, and polyemeraldine. We have also performed calculations for the soliton lattice in polyacetylene and for the bipolaron lattice in polythiophene and polyemeraldine. The polaron lattice band structures are found to be in good agreement with the observed optical absorption and magnetic data for the three polymers which all exhibit a metallic-like behavior in their highly doped state. The polaron lattice band structures for polyacetylene and polythiophene are calculated to be very similar, which is consistent with the experimental trends. The polyemeraldine salt bipolaron and polaron band structures present a single defect band deep in the gap, instead of the two defect bands usually found in other conjugated systems. This peculiarity is related to the lack of electron-hole symmetry in polyaniline and leads to a modified picture for the electronic transitions appe...

Interaction between major outer membrane protein (O-8) and lipopolysaccharide in Escherichia coli K12.

An ordered hexagonal lattice structure with a lattice constant of about 7nm was reconstituted from outer membrane protein O‐8 and/or O‐9 and lipopolysaccharide [H. Yamada and S. Mizushima, J. Bacteriol. 135, 1024–1031 (1978)]. Using this reconstitution system, the interaction between O‐8 and lipopolysaccharide was studied and the following results were obtained.At least one lipopolysaccharide molecule per one O‐8 trimer was required for the hexagonal lattice formation. The lattice constant of the hexagonal lattice formed under the conditions was about 6.5 nm. In the presence of a larger amount of lipopolysaccharide, the lattice constant increased to 7.5 nm, being almost the same as that observed in the dodecylsulfate‐treated cell envelope.The lattice constant observed with the heptoseless lipopolysaccharide was also 6.5 nm when the lipopolysaccharide/O‐8 ratio was low. Although the increase of the lattice constant was observed upon further addition of the lipopolysaccharide, it was appreciably smaller than that with the wild‐type lipopolysaccharide.A hexagonal lattice was also formed when lipopolysaccharide was replaced by an equivalent amount of lipid A or even fatty acids. The lattice constant was the same as that with the wild‐type lipopolysaccharide when the lipid/protein ratio was low. However, contrary to the case of lipopolysaccharide, the lattice constant remained almost unchanged even when a larger amount of either lipid A or fatty acid was added to the reconstitution system. A slight increase in the lattice constant was observed only when an extremely large amount of lipid A was added to the reconstitution system.These results suggest that (1) both the lipid A moiety and the polysaccharide moiety of lipopolysaccharide participate in the interaction with the O‐8 trimer, (2) in the lipid A moiety the fatty acid region primarily participates in the hexagonal arrangement of the O‐8 trimer and the minimum requirement of lipopolysaccharide for the lattice formation is most probably one lipopolysaccharide molecule per O‐8 trimer and (3) the polysaccharide moiety, probably both the 3‐deoxy‐d‐manno‐octulosonate region and the distal end region including heptose, are involved in an interaction of lipopolysaccharide with the O‐8 trimer to give a proper lattice conformation.

The primary structure of the coat protein of alfalfa mosaic virus strain VRU. A hypothesis on the occurrence of two conformations in the assembly of the protein shell.

The complete primary structure of the coat protein of strain VRU of alfalfa mosaic virus (AMV) is reported. The strain is morphologically different from all other AMV strains as it contains large amounts of unusually long virus particles. This is caused by structural differences in the coat protein chain. The amino acid sequence has mainly been established by the characterization of peptides obtained after cleavage with cyanogen bromide and digestion with trypsin, chymotrypsin, thermolysin or Staphylococcus aureus protease. The major sequencing technique used was the dansyl-Edman procedure. The VRU coat protein consists of 219 amino acid residues corresponding to a molecular weight of 24056. Compared to the coat protein of strain 425 [Van Beynum et al. (1977) Eur. J. Biochem. 72, 63-78], 15 amino acid substitutions were localized. Most of them have a conservative character and may be explained by single-point mutations. A correction is given for the AMV 425 coat protein: Asn-216 was shown to be Asp-216. The prediction of the secondary structure for the two viral coat proteins was not significantly influenced by the various amino acid substitutions except for the region containing residues 65-100. This led us to the hypothesis that the AMV coat protein may occur in two different conformations favouring its incorporation into either a pentagonal or hexagonal quasi-equivalent position in the lattice of the protein shell. The substitutions in the above-mentioned region of the VRU coat protein may have caused a strong preference for the hexagonal lattice conformation. The model is supported by preliminary sequence data of the same coat protein region in AMV 15/64, a strain morphologically intermediate between 425 and VRU.

CYCLIZATION OF POLYENES XXV. CONFORMATIONAL STUDY OF CEMBRENE TYPE DITERPENES BY X-RAY ANALYSIS

Abstract An X-ray crystallographic analysis of 15,16-dehydro epimukulol acetate has revealed that the exact stereostructure is indicated in figure 1, which can be depicted on the modified diamond lattice conformation model as shown in figure 2.

Infrared spectra and structure of 1,4,8,11-tetra-azacycotetradecanes

Infrared spectra of the title compounds were studied in the 1500–4000 cm −1 region. N-H — N hydrogen bonding was found to occur in crystalline 1,4,8,11-tetra- azacyclotetradecane (I) and in its 5,12-dimethyl derivatives (IIA and IIB), whereas no association was detected in saturated solutions of all compounds in molten amine I and in its crystalline 5,7,7,12, 14,14-hexamethyl derivative (IIIA). These facts are interpreted as induction of hydrogen bonding by crystal-lattice forces. It proved impossible to establish either the intra- or the intermolecular character of the observed hydrogen bonding. A group of bands in the 2600–2800 cm −1 region is assigned to the trans-CH. bands and their origin is interpreted on the basis of a diamond lattice conformation I (c) proposed for the tetra- azacyclotetradecane ring.