Showing papers on "Dihedral angle published in 1991"

Three-dimensional structure of interleukin 8 in solution.

Abstract: The solution structure of the interleukin 8 (IL-8) dimer has been solved by nuclear magnetic resonance (NMR) spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. The structure determination is based on a total of 1880 experimental distance restraints (of which 82 are intersubunit) and 362 torsion angle restraints (comprising phi, psi, and chi 1 torsion angles). A total of 30 simulated annealing structures were calculated, and the atomic rms distribution about the mean coordinate positions (excluding residues 1-5 of each subunit) is 0.41 +/- 0.08 A for the backbone atoms and 0.90 +/- 0.08 A for all atoms. The three-dimensional solution structure of the IL-8 dimer reveals a structural motif in which two symmetry-related antiparallel alpha-helices, approximately 24 A long and separated by about 14 A, lie on top of a six-stranded antiparallel beta-sheet platform derived from two three-stranded Greek keys, one from each monomer unit. The general architecture is similar to that of the alpha 1/alpha 2 domains of the human class I histocompatibility antigen HLA-A2. It is suggested that the two alpha-helices form the binding site for the cellular receptor and that the specificity of IL-8, as well as that of a number of related proteins involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response, is achieved by the distinct distribution of charged and polar residues at the surface of the helices.

Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints.

Abstract: A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985)J. Mol. Biol.,186, 611) is described, which makes use of redundant dihedral angle constraints (REDAC) derived from preliminary calculations of the complete structure. The REDAC approach reduces the computation time for obtaining a group of acceptable conformers with the program DIANA 5-100-fold, depending on the complexity of the protein structure, and retains good sampling of conformation space.

First-principles molecular-dynamics simulation of liquid and amorphous selenium.

Abstract: A molecular-dynamics simulation has been carried out for liquid and amorphous selenium in the temperature range 350\char21{}720 K. The simulation used 64 atoms in a constant-volume simple cubic cell, and the energy surfaces and forces were calculated using the density-functional formalism, with a local-density approximation for the exchange-correlation energy. The main focus is on the microscopic atomic structure, with the associated short- and intermediate-range ordering phenomena. Ring statistics, pair correlation functions g(r), structure factors S(Q), bond angle and dihedral angle distribution functions, phonon densities of states, and diffusion constants D were computed and compared with experimental and theoretical data where available. Several structural models proposed previously for Se are evaluated and their predictions compared with the results of the present simulation. Special emphasis is given to the concentration, structure, and stability of the dominant defects, and a new structure and defect model is presented.

Reaction path study of helix formation in tetrapeptides: Effect of side chains

Abstract: A computational protocol to calculate steepest descent paths in flexible molecules is discussed in detail The algorithm does not use second derivatives and related matrices, and is therefore suitable for large systems The shortest reaction coordinate from the helix to the extended chain conformation is calculated for a series of different tetrapeptides The formation of a helical turn is investigated as a function of side chain properties The known reaction coordinate for isobutyryl‐ala3 ‐NH‐methyl is employed as a starting guess in path calculations for six different tetrapeptides The main results are: (i) χ1 (the side chain orientation angle) does not change significantly along the reaction coordinate Alternative static values of χ1 (60,−60) significantly affect the size of the energy barrier (≊3 kcal/mol for valine) (ii) The mechanism for the transition is similar in all the peptides examined and is based on sequential flips of backbone torsions (Ψ dihedral angles) (iii) The energy barrier which

Crystal structure and electronic properties of tetrakis[µ3-bis(2-pyridyl)amido]dichlorotrinickel(II)–water–acetone (1/0.23/0.5)

Abstract: The crystal structure of [Ni3(bipyam–H)4Cl2]·023H2O·05(CH3)2CO 1[bipyam–H = bis(2-pyridyl)-amide] has been determined using X-ray diffractometer data; C415H355Cl2N12Ni3O075, monoclinic, space group C2/c, with a= 37525(7), b= 16237(3), c= 22550(6)A, β= 11012(2), Z= 12; 5778 measured and 5519 unique reflections gave a final R value of 0051 The structure involves two independent Ni3(bipyam–H)4Cl2 units, (1) and (2)[(1) occupies a general position and (2) is on a C2 axis], one non-co-ordinated water molecule [site occupation factor (sof) 023], and one acetone molecule (sof 05) The Ni3N12Cl2 chromophores of (1) and (2) involve a nearly linear Ni3 unit, mean Ni–Ni–Ni angle 1784(1)°, terminated by the two chloride anions The four separate bipyam–H ligands act as tridentate ligands, involving co-ordination to three separate nickel(II) ions with Ni–Ni distances 2443(1)(twice) and 2431(1)A for units (1) and (2), respectively If the Ni–Ni separations are ignored the central Ni atom in both units involves a four-co-ordinate rhombic coplanar NiN4 chromophore, generated by the four central amido nitrogens of the bipyam–H ligands The two terminal Ni atoms involve a square-based pyramidal NiN4Cl chromophore, involving the four pyridine nitrogens of the bipyam–H ligands and an axial Cl atom A dihedral angle of ca 54° is involved between the planes of the individual pyridine rings of each bipyam–H ligand and results in a spiral configuration in the Ni3(bipyam–H)4Cl2 unit The room-temperature magnetic moment µeff of compound 1 is 246, consistent with a diamagnetic central NiN4 chromophore and two paramagnetic terminal NiN4Cl chromophores The electronic spectrum involves a low-energy peak at 6500 cm–1, an intense peak at 17 700 cm–1, and a low-intensity shoulder at 10 800 cm–1, consistent with the two nickel(II) stereochemistries present

Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy

Abstract: The solution conformation of the ribonuclease barnase has been determined by using 1H nuclear magnetic resonance (NMR) spectroscopy. The 20 structures were calculated by using 853 interproton distance restraints obtained from analyses of two-dimensional nuclear Overhauser spectra, 72 phi and 53 chi 1 torsion angle restraints, and 17 hydrogen-bond distance restraints. The calculated structures contain two alpha-helices (residues 6-18 and 26-34) and a five-stranded antiparallel beta-sheet (residues 50-55, 70-75, 85-91, 94-101, and 105-108). The core of the protein is formed by the packing of one of the alpha-helices (residues 6-18) onto the beta-sheet. The average RMS deviation between the calculated structures and the mean structure is 1.11 A for the backbone atoms and 1.75 A for all atoms. The protein is least well-defined in the N-terminal region and in three large loops. When these regions are excluded, the average RMS deviation between the calculated structures and the mean structure for residues 5-34, 50-56, 71-76, 85-109 is 0.62 A for the backbone atoms and 1.0 A for all atoms. The NMR-derived structure has been compared with the crystal structure of barnase [Mauguen et al. (1982) Nature (London) 297, 162-164].

Protein secondary structure from FT-IR spectroscopy : correlation with dihedral angles from three-dimensional Ramachandran plots

Abstract: The frequency of the so-called "amide I" band (amide C=O stretching vibration, vC=O) of proteins is discussed in terms of the dihedral angles of the various secondary structures present within prot...

Equilibrium dihedral angles in the system H2O−CO2−NaCl-calcite, and implications for fluid flow during metamorphism

Abstract: Fluid-calcite-calcite dihedral angles have been measured for fluids in the system H2O−CO2−NaCl, between 1 and 2 kbar, and 550–750° C. It is found that the calcite-calcite-H2O dihedral angle decreases steadily with addition of NaCl from a value of about 80° (pure water) to 44° (60 wt% NaCl). The CO2−H2O system displays a well-defined minimum at \(X_{CO_2 } = 0.5\), with a dihedral angle of 50°, in contrast to those of pure CO2 and H2O which are 90° and 80° respectively. Experiments containing fluids which are immiscible at run conditions showed a bimodal distribution of dihedral angles in the CO2−H2O−NaCl system, which can be approximately correlated with the compositions of the two fluid phases. Such bimodality was only observed for immiscible fluids in the H2O−NaCl system if the quench rate exceeded about 200°C per min. This is probably due to the extremely rapid establishment of the single phase dihedral angle on quenching. The fluid phase topology in devolatilising marbles will only be a connected network for very saline brines and fluids with \(X_{CO_2 } \) close to 0.5. Fluids trapped in fluid inclusions in calcite grains in marbles may be predominantly H2O-rich or CO2-rich, and of low salinity. All other fluid compositions in the H2O−CO2−NaCl-calcite system will occupy isolated pores, the largest of which will grow at the expense of the smallest. Escape of fluid produced during devolatilisation reactions under such conditions will occur by fluid overpressuring and hydrofracture. In contrast, previous experimental studies of quartz-fluid dihedral angles between 950° and 1100° C (Watson and Brenan 1987) predict that quartz-dominated lithologies will permit pervasive flow of H2O−NaCl fluids, but not of H2O−CO2 fluids. Documented geological examples of differences in permeability and fluid flow mechanism between metamorphic argillites, psammites and limestones which support the results of the experimental studies are discussed.

α-Helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A

Abstract: Conformation of the C-peptide fragment of RNase A is calculated by Monte Carlo simulated annealing. We adopt the total potential energy as given by the sum of generic interatomic energies whose parameters are determined separately for each amino acid without referring to the empirical structure of the C-peptide. The simulation is carried out in a completely unrestricted way without imposing any weight towards given final destinations. Starting from completely random initial conformations and minimizing the total potential energy with respect to main-chain dihedral angles and side-chain torsion angles, we have obtained partial alpha-helix structure with a high probability (approximately 40%). The energetically most favourable structure exhibits a 2.5-turn alpha-helix at the location identical with that of the 3-turn alpha-helix in the native enzyme molecule. Classification of conformations obtained in the simulation into clusters of similar structure shows that our simulation indeed predicts the alpha-helix structure for the isolated C-peptide with specific charged residues. The results of simulation with various amino acid substitutions are also found to be consistent with the experimental implication for the importance of intramolecular ionic interactions for alpha-helix stability for this peptide.

Ab initio studies of polyenes. I. 1,3‐butadiene

Abstract: The potential energy function about the C–C single bond for the ground state 1,3‐butadiene has been derived from ab initio calculations at both the Hartree–Fock (HF) level with 6‐31G, 6‐31G*, and 6‐311G** basis sets and the second‐order Mo/ller–Plesset perturbation (MP2) level with 6‐31G* basis set with the complete geometry optimizations at each of 15 fixed CCCC dihedral angles; the total energies and optimized geometries for the s‐trans, gauche, and s‐cis conformers were also determined at MP2 level with 6‐311G* basis set and the third‐order Mo/ller–Plesset perturbation (MP3) level with 6‐31G* basis set. The second stable conformer of the butadiene is predicted to be a gauche structure from all the calculations with a CCCC dihedral angle between 35° and 40° and a barrier of 0.5–1.0 kcal/mol to the s‐cis transition state, and the theoretical torsional potentials are in good agreement with the experimental potential function of trans–gauche–gauche case derived by Durig et al.; by contrast, the theoretical...

A 175‐psec molecular dynamics simulation of camphor‐bound cytochrome P‐450cam

Abstract: The structure and internal motions of cytochrome P-450cam, a monooxygenase heme enzyme with 414 amino acid residues, with camphor bound at the active site have been evaluated on the basis of a 175-psec molecular dynamics simulation carried out at 300 K. All hydrogen atoms were explicitly modeled, and 204 crystallographic waters were included in the simulation. Based on an analysis of the time course of the trajectory versus potential energy, root mean square deviation, radius of gyration, and hydrogen bonding, the simulation was judged to be stable and representative of the average experimental structure. The averaged structural properties of the enzyme were evaluated from the final 135 psec of the simulation. The average atomic displacement from the X-ray structure was 1.39 A for all heavy atoms and 1.17 A for just C-α atoms. The average root-mean-square (rms) fluctuations of all heavy atoms and backbone atoms were 0.42 and 0.37 A, respectively. The computed rms fluctuations were in reasonable agreement with the experimentally determined temperature factors. All 13 segments of α-helix and 5 segments of β-sheet were well preserved with the exception of the N-terminal half of halix F which alternated between an α-helix and a 310-helix. In addition there were in general only small variations in the relative orientation of adjacent α-helices. The rms fluctuations of the backbone dihedral angles in the secondary structure elements were almost uniformly smaller, with the fluctuation in α-helices and β-sheets, 31 and 10% less, respectively, than those in nonsecondary structure regions. The reported crystal structure contains kinks in both helices C and I. In the simulation, both of these regions showed high mobility and large deviations from their starting positions. Since the kink in the I helix is at the oxygen binding site, these motions may have mechanistic implications.

Solid-liquid interfacial free energy

Abstract: The solid-liquid interfacial free energy has been estimated by a broken-bond model modified to take the entropy loss of the liquid in contact with the crystal into account. The predictions for f.c.c., h.c.p., b.c.c., diamond and s.c. structures are compared with experimental data from supercooling and dihedral angle measurements.

Restrained energy refinement with two different algorithms and force fields of the structure of the α‐amylase inhibitor tendamistat determined by nmr in solution

Abstract: The solution structure of an α-amylase inhibitor, tendamistat, calculated from nmr data with the distance geometry program DISMAN is subjected to restrained energy minimization. To study the influence of force field parametrizations and the convergence behavior of refinement algorithms, two different programs were used. AMBER is an established software package including a steepest descent and/or conjugent gradient optimizer in the Euclidian space; the name AMBER also represents a force field. The program FANTOM (fast Newton–Raphson torsion angle energy minimizer) is a new restrained energy refinement implementation of the Newton–Raphson algorithm, which uses second derivatives of the conformational energy in dihedral angle space with the ECEPP/2 force field. For both programs the normal energy force field was supplemented with an additional potential of the form ΣA(di − ui)6 (if di > ui), which enforces upper limits ui to selected distances di as measured by nmr. Improvements of the intramolecular interactions with a decrease of the internal energies of about 1000 kcal/mol could be achieved without increasing the distance constraint violations. The restrained energy refinements caused only small changes of the molecular geometries: The root mean square distance values for the backbone atoms between the initial DISMAN structure and the refined structures are about 0.5 A for AMBER and about 0.7 A for FANTOM. Local conformational changes during the restrained energy minimizations are analyzed with respect to hydrogen-bond formation, and with respect to comparisons of the solution structure and the crystal structure.

Conformational dynamics of polypeptides and proteins in dihedral angle space and in the cartesian coordinate space: normal mode analysis of deca-alanine

Abstract: Effects of different treatments of the degrees of freedom of bond length stretching and bond angle bending in computational analysis of conformational dynamics of proteins and polypeptides are assessed. More specifically, the normal mode analysis of conformational dynamics of α-helix of deca-alanine has been carried out both in the dihedral angle space (DAS) and in the Cartesian coordinate space (CCS). Almost perfect one-to-one correspondence has been found between normal modes in the CCS with frequencies less than 128 cm−1 and those in the DAS with frequencies less than 164 cm−1. Patterns of atomic displacements in the corresponding modes are very similar. This indicates that the effects of fixing degrees of freedom of bond length stretching and bond angle bending on the very-low-frequency normal modes in the CCS with frequencies less than 128 cm−1 are almost solely to increase the frequencies by about 20%. The conclusion indicates that the different treatment of these degree does not lead to qualitatively different results as long as low-frequency motions are concerned. Based on the results of calculation, mechanical property of the α-helix of deca-alanine is discussed.

A numerical analysis of void shrinkage processes controlled by coupled surface and interface diffusion

Abstract: The shrinkage behaviour of voids arrayed on a bond-interface (grain boundary) is analyzed by computer simulations. It is assumed that surface and interface self-diffusion operate in series. The junction between the void-surface and bond-interface is treated as a tip with a dihedral angle θ. Two numerical models are proposed to discuss the effect of interface and surface tensions on the void shrinkage. One of them always restricts θ to the value of the equilibrium balance (model 1). In the other (model 2), the equilibrium balance is ignored, i.e. the change in θ (free dihedral angle) is considered during the void shrinkage. For discussing the rate controlling step, model 2 is essentially the same as model 1. But, when the void shrinkage is controlled by the interface diffusion, they give void shapes quite different from each other, i.e. when the diffusivity ratio ƒ ⪢ 1 (ƒ = 2δsDs/δbDb, where δsDs and δbDb are produced by the thickness of the diffusion layer and the self-diffusion coefficient for the surface and interface, respectively), model 1 gives the equilibrium void shape but model 2 only exhibits the stationary void shape. The void morphology is not only influenced by the prescription of the equilibrium balance but also by the diffusivity ratio ƒ. The stress and temperature dependence of the void shrinkage can roughly be expressed by 2δsDsδbDb/[2δsDs + δbDb)Pn], where P is the bonding pressure and n the stress exponent. If θ is prescribed by the equilibrium balance, n increases from −1 to −0.3 with decreasing P. But, if θ changes, n is about −1. It is verified by experiments that the dihedral angle is not always constant and changes as increasing net stress is applied to the bond-interface. It is suggested that model 2 more exactly predicts the void-shrinkage process than model 1 as the pressure is increased.

Solution structure of neuronal bungarotoxin determined by two-dimensional NMR spectroscopy: sequence-specific assignments, secondary structure, and dimer formation

Abstract: The solution structure of neuronal bungarotoxin (nBgt) has been studied by using two-dimensional 1H NMR spectroscopy. Sequence-specific assignments for over 95% of the backbone resonances and 85% of the side-chain resonances have been made by using a series of two-dimensional spectra at four temperatures. From these assignments over 75% of the NOESY spectrum has been assigned, which has in turn provided 582 distance constraints. Twenty-seven coupling constants (NH-alpha CH) were determined from the COSY spectra, which have provided dihedral angle constraints. In addition, hydrogen exchange experiments have suggested the probable position of hydrogen bonds. The NOE constraints, dihedral angle constraints, and the rates of amide proton exchange suggest that a triple-stranded antiparallel beta sheet is the major component of secondary structure, which includes 25% of the amino acid residues. A number of NOE peaks were observed that were inconsistent with the antiparallel beta-sheet structure. Because we have confirmed by sedimentation equilibrium that nBgt exists as a dimer, we have reinterpreted these NOE constraints as intermolecular interactions. These constraints suggest that the dimer consists of a six-stranded antiparallel beta sheet (three from each monomer), with residues 55-59 forming the dimer interface.

A new calibration algorithm of wide-band polarimetric measurement system

Abstract: The principle and experimental results of a new self-consistent calibration algorithm for a wideband polarimetric scattering measurement system are presented. The calibration targets include a flat plate, a dihedral corner reflector, and a rotated dihedral corner reflector. The rotation angle of the third calibrator can be derived in the calibration process and used to verify the calibration performance. Experimental results show that the calculated rotation angle of the third calibrator over the operation bandwidth is in good agreement with its actual angle, hence it provides a self-consistent parameter of the calibration algorithm. Based on the signal-to-noise consideration, an optimal rotation angle for a dihedral corner reflector is found to be 22.5 degrees . This calibration technique is also useful in characterizing the frequency and polarization responses of dual-polarization antennas. >

Theoretical studies of stereoselectivities of nucleophilic 1,2-additions to cyclohexenones. Transition structures and force-field models for metal hydride and keteniminate additions to ketones

Abstract: The transition structures of the reaction of 2-cyclohexenone with lithium hydride have been located with the 3-21G basis set. The transition structure for axial addition is more stable than the transition structure for equatorial addition by 2.1 kcal/mol. The enone moiety is more nearly coplanar in the transition structure of axial addition than in that of equatorial addition, as indicated by the O=C−C=C dihedral angles of 162° and 146°, respectively. The axial transition structure is nearly perfectly staggered, while there is severe eclipsing in the equatorial transition structure. The high axial selectivity for the nucleophilic additions to cyclohexenones is caused mainly by torsional strain and poor orbital overlap in the equatorial transition structure. The transition structure for the reaction of lithium acetonitrile with acetone was located with ab initio molecular orbital calculations. It is a six-membered planar structure. The transition structure for the reaction of potassium acetonitrile has a nonplanar geometry

Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.

Abstract: A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways. Derivatives of the NOE intensities with respect to the dihedral angles are analytically calculated, and efficiently evaluated with the use of a filter technique for identifying the dominant terms of these derivatives. This new method was implemented in the distance geometry program DIANA. As an initial test, we refined 30 rigid distorted helical structures, using a simulated data set of NOE distance constraints for a rigid standard α-helix. The final root-mean-square deviations of the refined structures relative to the standard helix were less than 0.1 A, and the R-factors dropped from values between 7% and 32% to values of less than 0.5% in all cases, which compares favorably with the results from distance geometry calculations. In particular, because spin diffusion was not explicitly considered in the evaluation of ‘exact’1H−1H distances corresponding to the simulated NOE intensities, a group of nearly identical distance geometry structures was obtained which had about 0.5 A root-mean-square deviation from the standard α-helix. Further test calculations using an experimental NOE data set recorded for the protein trypsin inhibitor K showed that the complete relaxation matrix refinement procedure in the DIANA program is functional also with systems of practical interest.

Stereoselectivity in Diastereomeric Tetrahedral Metal(II) Complexes of Chiral Salicylideneamines: Crystal Structure and Molecular Mechanics Calculation of Bis[N-(l-menthyl)salicylideneaminato]cobalt(II)

Abstract: Stereoselectivity of bis[N-(l-menthyl)salicylideneaminato]cobalt(II) [Co(sal-ment)2] has been studied by single crystal X-ray analysis and molecular mechanics calculations. The X-ray analysis has revealed a nearly tetrahedral surrounding (dihedral angle of 82.5°) and Δ configuration about the metal ion. Molecular mechanics calculations were made based on MM2 program, assuming a tetrahedral surrounding about the metal ion and fixing the four donor atoms and six atoms adjacent to the donor atoms at the positions as determined by the single crystal X-ray analysis. The most stable structure obtained from the MM2 calculation coincides well with that from the crystal structure analysis. Together with the X-ray structural results for [Cu(sal-ment)2] and bis[N-[(R)-1-phenylethyl]salicylideneaminato]cobalt(II) [Co(sal-Rmb)2] studied in this study and for related [Zn(sal-Rmb)2] and [Cu(sal-Rmb)2] studied previously, the factors responsible for the stereoselectivities of those bis(salicylideneaminato)metal(II) compl...

Bipyridylacetylenes 1: the synthesis of some bipyridylacetylenes via the palladium-catalyzed coupling of acetylenes with 2,2′-dibromobipyridyl, and the single crystal X-ray structure of 6,6′-bisphenylethynyl-2,2′-bipyridine

Abstract: The synthesis of a series of 6,6′-diethynyl-2,2′-bipyridyls from the palladium-catalyzed coupling of 6,6′-dibromo-2,2′-bipyridine with a series of arylacetylenes is reported. The single crystal X-ray structure of 6,6′-phenylethynyl-2,2′-bipyridyl was determined. Crystal data: monoclinic, A2/a, with cell constants a = 10.0385(4), b = 9.2166(4), c = 21.4130(8) A, and β = 102.981(3)°; Dcalc. = 1.226 g cm−3, Z = 4, Rf = 0.045, S = 1.22, using 886 reflections of the 1443 unique reflections. The packing diagram indicates essentially that the molecules pack in a layered assembly with the nitrogen atoms of the dipyridyl groups on opposite sides and with a dihedral angle of 59.85(16)° between the pyridyl and phenyl groups. The acetylenic bond distances are normal. Key words: acetylene, palladium, catalysis, coupling, monomers, crystal structure.