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Showing papers on "Dihedral angle published in 1997"


Journal ArticleDOI
TL;DR: Test calculations starting from conformers with random torsion angle values showed that DYANA is capable of efficient calculation of high-quality protein structures with up to 400 amino acid residues, and of nucleic acid structures.

2,768 citations


Journal ArticleDOI
TL;DR: In this article, the authors explored the topological characteristics of multidimensional potential energy surfaces and mapped the full conformation space on the set of local minima, which is used to express the temporal behavior of the system in terms of basin-to-basin kinetics.
Abstract: Topological characteristics of multidimensional potential energy surfaces are explored and the full conformation space is mapped on the set of local minima. This map partitions conformation space into energy-dependent or temperature-dependent “attraction basins’’ and generates a “disconnectivity’’ graph that reflects the basin connectivity and characterizes the shape of the multidimensional surface. The partitioning of the conformation space is used to express the temporal behavior of the system in terms of basin-to-basin kinetics instead of the usual state-to-state transitions. For this purpose the transition matrix of the system is expressed in terms of basin-to-basin transitions and the corresponding master equation is solved. As an example, the approach is applied to the tetrapeptide, isobutyryl-(ala)3-NH-methyl (IAN), which is the shortest peptide that can form a full helical turn. A nearly complete list of minima and barriers is available for this system from the work of Czerminiski and Elber. The multidimensional potential energy surface of the peptide is shown to exhibit an overall “funnel’’ shape. The relation between connectivity and spatial proximity in dihedral angle space is examined. It is found that, although the two are similar, closeness in one does not always imply closeness in the other. The basin to basin kinetics is examined using a master equation and the results are interpreted in terms of kinetic connectivity. The conformation space of the peptide is divided up in terms of the surface topography to model its “folding’’ behavior. Even in this very simple system, the kinetics exhibit a “trapping’’ state which appears as a “kinetic intermediate,’’ as in the folding of proteins. The approach described here can be used more generally to classify multidimensional potential energy surfaces and the time development of complex systems.

753 citations


Journal ArticleDOI
TL;DR: Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances and J-coupling-constant-derived dihedral angle restraints to show increased computational efficiency and success rate for large proteins and a dramatically increased radius of convergence for DNA.

321 citations


Journal ArticleDOI
TL;DR: A new and-simple method is presented for judging the quality of a protein structure based on the distribution of backbone dihedral angles, resulting in a Ramachandran Z-score, expressing thequality of the Ramach andran plot relative to current state-of-the-art structures.
Abstract: Motivation: Statistical methods that compare observed and expected distributions of experimental observables provide powerful tools for the quality control of protein structures. The distribution of backbone dihedral angles ('Ramachandran plot') has often been used for such quality control, but without a firm statistical foundation. Results: A new and simple method is presented for judging the quality of a protein structure based on the distribution of backbone dihedral angles. Inputs to the method are 60 torsion angle distributions extracted from protein structures solved at high resolution; one for each combination of residue type and tri-state secondary structure. Output for a protein is a Ramachandran Z-score, expressing the quality of the Ramachandran plot relative to current state-of-the-art structures.

230 citations


Journal ArticleDOI
TL;DR: In this paper, a rotational sideband spectrum of the sum and difference of the two corresponding dipolar couplings is used to determine the torsion angle φ in peptides.
Abstract: We describe a method for determining the torsion angle φ in peptides. The technique is based on the measurement of the relative orientation of the N−HN and Cα−Hα bonds, which is manifested in the rotational sideband spectrum of the sum and difference of the two corresponding dipolar couplings. The method exploits 15N−13C double-quantum and zero-quantum coherences, which evolve simultaneously under the N−H and C−H dipolar interactions. The magnitudes of these dipolar couplings scaled by the proton homonuclear decoupling sequence are directly extracted from control experiments that correlate the dipolar interactions with the isotropic chemical shifts. Applied to 15N-labeled N-acetyl-d,l-valine, the experiment yielded φ = −135°, which agrees well with the X-ray crystal structure. Simulations indicate that the accuracy of the measured angle φ is within ±10° when the N−HN and Cα−Hα bonds are approximately antiparallel and ±20° when they are roughly parallel. The technique is sufficiently sensitive to be applie...

196 citations


Journal ArticleDOI
TL;DR: The side-chain torsion angle correlations are extended and improved, and the protein conformational were limited to one-dimensional potential energy surfaces database potential by employing a new database of 70 diverse for the x1, x3, and x4 angles, two- dimensional potential X-ray structures refined at 1.75 A or better.

184 citations


Journal ArticleDOI
TL;DR: The interpretation of heteronuclear 15N-¿1H¿ NOE data shows the co-existence of flexible regions within an otherwise rigid framework of the protein, which seems to be important in receptor interactions.

184 citations


Journal ArticleDOI
TL;DR: In this paper, the crystal structures of three porphyrin diacid species, [H4OEP]-ClO4)2,[H4TMP]-CLO4]2 and [H 4TMP]2+ have been determined from low-temperature X-ray diffraction data to delineate how the peripheral substituents of the porphrin affect the overall molecular flexibility.
Abstract: The crystal structures of three porphyrin diacid species, [H4OEP](ClO4)2, [H4TPP](ClO4)2, and [H4TMP](ClO4)2, have been determined from low-temperature X-ray diffraction data to delineate how the peripheral substituents of the porphyrin affect the overall molecular flexibility. [H4OEP](ClO4)2 (|Cb| = 0.46 A), [H4TMP](ClO4)2 (|Cb| = 0.67 A, molecule 1), and [H4TPP](ClO4)2 (|Cb| = 0.93 A) show increasingly saddled core conformations with effective D2d symmetry. The mean porphyrin−aryl group dihedral angles in [H4TPP](ClO4)2 and [H4TMP](ClO4)2 (molecule 1) are 27(2)° and 63(13)°, respectively. The steric bulk of the mesityl substituents in [H4TMP]2+ limits the range of observed porphyrin−aryl group dihedral angles to >50° and, consequently, the magnitude of the core distortion. [H4TMP]2+ is therefore less flexible than [H4TPP]2+. Molecular mechanics calculations, using a modified version of MM2(87) and a newly developed force field for porphyrin diacids, correctly predict that the flexibility of meso-tetraar...

147 citations


Journal ArticleDOI
TL;DR: A new formulation for a dihedral angle autocorrelation function is introduced and applied to study side-chain dynamics in L-Enk, finding that the side- chain dynamics of the large Tyr and Phe residues cannot be adequately sampled in 2.0-ns simulations, while this does seem to be possible for the smaller Leu side chain.

122 citations


Journal ArticleDOI
TL;DR: In this article, the authors used 15N relaxation measurements (T1, T2, heteronuclear nuclear Overhauser enhancement (NOE)) fitted with the Lipari-Szabo model-free formalism adapted for the trans-membrane and in-plane helices of a membrane protein.

109 citations


Journal ArticleDOI
TL;DR: In this article, the structural parameters treated contain internuclear distances between directly bonded or remote nuclei including nonproton pairs in a molecule and bond and dihedral angles, in addition to the normal mode vibrations, the libration of the whole molecule is considered in the theory.
Abstract: Vibrational effects on structural parameters obtained by solid-state NMR are studied by theoretical calculations and molecular-dynamics simulations. The structural parameters treated contain internuclear distances between directly bonded or remote nuclei including nonproton pairs in a molecule and bond and dihedral angles. In addition to the intramolecular normal mode vibrations, the libration of the whole molecule is considered in the theory. It is shown that the molecular libration as well as the intramolecular vibrations reduce dipolar interactions, and consequently lengthen the internuclear distances obtained from the dipolar interactions (RNMR). In contrast, the internuclear distances obtained by single crystal x-ray or neutron diffraction (Rcor) are proved to be shortened by the molecular libration. Molecular-dynamics simulations for glycine molecules in the crystal at room temperature reveal that RNMR are 1%–4% longer than Rcor, confirming the theoretical results. It is also demonstrated that the e...

Proceedings ArticleDOI
TL;DR: In this article, the influence of two stacking lines, namely sweep and dihedral, has been investigated in a linear compressor cascade and the results showed that dihedral is advantageous when the angle between the suction surface and the endwall is obtuse.
Abstract: The influence of two stacking lines, namely sweep and dihedral, has been investigated in a linear compressor cascade. Both types of blade considered are symmetric about midspan and consist of a straight central section with either swept or dihedral sections toward the endwalls. Two types of experiment have been carried out. First, a parametric study was performed by changing both the magnitude and the extent of the sweep or dihedral. In the case of swept blades, those with forward sweep (SWF), for which the stacking line is swept in the upstream direction toward the endwall, were found to have better performance than backward-swept blades. Subsequently, four sets of SWFs were compared. In the case of dihedral blades, it is well known that the dihedral is advantageous when the angle between the suction surface and the endwall is obtuse, i.e., positive dihedral. Thus, four sets of positive dihedral blades (DHP) were compared. In both SWF and DHP blades, those configurations that have better efficiency than straight blades were determined. Second, detailed three-dimensional measurements inside the blade passage were performed in the cases that showed the best performance in the parametric study. Both SWF and DHP showed significant effects on the flowfield.more » In the SWF case, a vortex, which has the opposite sense to the passage vortex, was observed in the forward portion inside the blade passage. This vortex supplies high-energy fluid to the endwall region and reduces the corner stall. The secondary flow is greatly reduced. In the DHP, the blade loading was reduced at the endwall and increased at the midspan. Reduction of the corner stall and the secondary flow was also observed.« less

Journal ArticleDOI
TL;DR: In this article, the synthesis, characterization and X-ray crystallographic structure determination are described for a "phosphaalkene" formally derived from 1,3,4,5-tetramethylimidazol-2-ylidene and phenylphosphinidene.
Abstract: The synthesis, characterization and X-ray crystallographic structure determination are described for a “phosphaalkene” formally derived from 1,3,4,5-tetramethylimidazol-2-ylidene and phenylphosphinidene. This carbene•phosphinidene adduct has a central P-C bond length of 179.4 pm and a dihedral twist of 46° which indicates a very weak C-P pπ-pπ interaction. The valence angle at phosphorus in 102.3°.

Journal ArticleDOI
TL;DR: The nuclear magnetic resonance (NMR) solution structure of free, unligated cyclophilin A (CypA), which is an 18 kDa protein from human T-lymphocytes that was expressed in Escherichia coli for the present study, was determined using multidimensional heteronuclear NMR techniques.

Journal ArticleDOI
TL;DR: In this paper, the chemical shift anisotropies (CSA) of the central alanine α-carbon in powdered crystalline tripeptides, whose structures have been determined previously by X-ray crystallography, were measured by crosspolarization magic-angle-spinning nuclear magnetic resonance.
Abstract: A simple method for the determination of backbone dihedral angles in peptides and proteins is presented. The chemical-shift anisotropies (CSA) of the central alanine α-carbon in powdered crystalline tripeptides, whose structures have been determined previously by X-ray crystallography, were measured by cross-polarization magic-angle-spinning nuclear magnetic resonance. The experimental CSA values were correlated with ab initio chemical-shielding calculations over Ramanchandran φ/ψ space on an N-formyl-l-alanine amide fragment. Using this correlation, φ/ψ probability surfaces for one of the tripeptides were calculated based only on the α-carbon CSA, allowing a prediction of backbone angles. Dihedral angles predicted by these calculations fall within ±12° of the values determined by crystallography. This approach should be useful in the determination of solid-state protein structure.

Journal ArticleDOI
TL;DR: In this article, a high-resolution triple-resonance NMR method is presented for the measurement of the protein backbone dihedral angle ψ based on cross-correlated relaxation between 1Hα−13Cα dipolar and 13C‘ (carbo...
Abstract: A high-resolution triple-resonance NMR method is presented for the measurement of the protein backbone dihedral angle ψ based on cross-correlated relaxation between 1Hα−13Cα dipolar and 13C‘ (carbo...

Journal ArticleDOI
TL;DR: In this article, the high-yield preparation, by double oxidative addition, of nine novel platinum and palladium bis(trans-M(PR3)2X)aryl (M = Pt or Pd; R = PPh3 or PEt3; X = Br or I; aryl = 1,4-benzene, 4,4‘-biphenyl.

Journal ArticleDOI
TL;DR: In this article, the global conformational potentials of 1,2-ethanediol, 2-aminoethanol, and 2-acetylbenzene were obtained at the MP2/6-311+G(2d,p) level by scanning through the dihedral angles of the two functional groups and the carbon−carbon bond with the remaining nuclear coordinates being energy-minimized.
Abstract: The global conformational potentials of 1,2-ethanediol, 1,2-ethanediamine, and 2-aminoethanol (X−CH2−CH2−Y; X, Y = OH or NH2) were obtained at the MP2/6-311+G(2d,p) level by scanning through the dihedral angles of the two functional groups and the carbon−carbon bond with the remaining nuclear coordinates being energy-minimized. It was found that the potentials could be represented by the direct-bond potentials between the adjacent molecular fragments and by the through-space electrostatic potentials between the vicinal and geminal fragments. Here, the through-direct-bond potentials are represented by the conventional three Fourier terms of the internal rotation angles, and the through-space potentials, which include the intramolecular hydrogen bonding between X and Y, are represented by the general functional forms of the electric dipole−dipole, dipole−quadrupole, and quadrupole−quadrupole interaction terms. The fitted electrostatic interaction strengths between the X and Y fragments are in good agreement...

Journal ArticleDOI
TL;DR: In this paper, the structure of poly (e-caprolactam) (nylon 6) in the β mesomorphic form is examined and the comparison of the diffraction intensity, calculated on modeled structures, with the experimental profiles, collected by an automatic diffractometer, is presented.
Abstract: The structure of poly (e-caprolactam) (nylon 6) in the β mesomorphic form is here examined. The comparison of the diffraction intensity, calculated on modeled structures, with the experimental profiles, collected by us through an automatic diffractometer, is presented. This analysis has put into evidence the following limiting structural features. (a) The β form of nylon 6 is made of small mesomorphic aggregates of chains (where the matter scatters coherently) with axes arranged in a hexagonal lattice (a = b = 0.48 nm; γ = 120°). (b) The chains have disordered conformations (and do not have a definite chirality, as it is the case for the 21 helices in the α and γ forms) with the −CH2− chains close to nearly all-trans (antiperiplanar) and the two dihedral angles adjacent to the amide bond, ±120°) to antiperiplanar (180°). This notwithstanding, the chains are straight and extended. As a result, the mean chain periodicity is close to 0.835 nm. (c) The H-bonds are formed along lines in the [100], [010], and [...

Journal ArticleDOI
TL;DR: A molecular dynamics simulation of a simple model membrane system composed of a single amphiphilic helical peptide in a fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayer indicated that residues 6 through 15 remain in a stable right-handed alpha-helical conformation, whereas both termini exhibit substantial fluctuations.

Journal ArticleDOI
TL;DR: Comparison of Spo0F structural features to those of other response regulators reveals subtle differences in the orientations of secondary structure in the putative recognition surfaces and the relative charge distribution of residues surrounding the site of phosphorylation.
Abstract: NMR has been employed for structural and dynamic studies of the bacterial response regulator, Spo0F This 124-residue protein is an essential component of the sporulation phosphorelay signal transduction pathway in Bacillus subtilis Three-dimensional 1H, 15N, and 13C experiments have been used to obtain full side chain assignments and the 1511 distance, 121 dihedral angle, and 80 hydrogen bonding restraints required for generating a family of structures (14 restraints per residue) The structures give a well-defined (α/β)5 fold for residues 4−120 with average rms deviations of 059 A for backbone heavy atoms and 102 A for all heavy atoms Analyses of backbone 15N relaxation measurements demonstrate relative rigidity in most regions of regular secondary structure with a generalized order parameter (S2) of 09 ± 005 and a rotational correlation time (τm) of 70 ± 05 ns Loop regions near the site of phosphorylation have higher than average rms deviation values and T1/T2 ratios suggesting significant int

Journal ArticleDOI
TL;DR: In this article, the X-ray structure of the 2,6-bis(trimethylsilyl)-3,5-bis (ferrocenyl)phosphinine 9 has been determined.

Journal ArticleDOI
TL;DR: In this paper, a new third transition is found between the two previously known singlet transitions, and the transition energies are nearly independent of the dihedral angle, while intensities vary widely.

Journal ArticleDOI
TL;DR: The three-dimensional structure in aqueous solution of native huwentoxin-I, a neurotoxin from the venom of the spider Selenocosmia huwena, has been determined from two-dimensional 1H NMR data recorded at 500 and 600 MHz.
Abstract: The three-dimensional structure in aqueous solution of native huwentoxin-I, a neurotoxin from the venom of the spider Selenocosmia huwena, has been determined from two-dimensional H NMR data recorded at 500 and 600 MHz. Structural constraints consisting of interproton distances inferred from NOEs and dihedral angles from spin-spin coupling constants were used as input for distance geometry calculation with the program XPLOR 3.1. The best 10 structures have NOE violations < 0.3 A, dihedral violations < 2 degrees, and pairwise root-mean-square differences of 1.08 (+/- 0.20) A over backbone atoms (N, C alpha, C). The molecule adopts a compact structure consisting of a small triple-stranded antiparallel beta-sheet and five beta-turns. A small hydrophobic patch consisting of Phe 6, Trp 28, and Trp 31 is located on one side of the molecule. All six lysine residues are distributed on the molecular surface. The three disulfide bridges are buried within the molecule. The structure contains an "inhibitor cystine knot motif" which is adopted by several other small proteins, such as omega-conotoxin, agatoxin IVA, and gurmarin.

Journal ArticleDOI
TL;DR: The trisaccharide β-d-glcp-(1→2)-β-dglcp(1→3)-α-dGlcp-OMe has been studied by Langevin dynamics simulations and NMR spectroscopy including measurement of transglycosidic 3JC,H coupling cons...
Abstract: The trisaccharide β-d-Glcp-(1→2)-β-d-Glcp-(1→3)-α-d-Glcp-OMe has been studied by Langevin dynamics (LD) simulations and NMR spectroscopy including measurement of transglycosidic 3JC,H coupling cons...

Journal ArticleDOI
TL;DR: A set of solution structures has been determined from distance and dihedral angle restraints, which provide a reasonable representation of the protein structure insolution, as evaluated by a principal component analysis of the globalpairwise root-mean-square deviation (rmsd) in a large set of structures.
Abstract: The assignment of the 1H and 15N nuclear magnetic resonance spectra of the Src-homology region 3 domain of chicken brain alpha-spectrin has been obtained. A set of solution structures has been determined from distance and dihedral angle restraints, which provide a reasonable representation of the protein structure in solution, as evaluated by a principal component analysis of the global pairwise root-mean-square deviation (rmsd) in a large set of structures consisting of the refined and unrefined solution structures and the crystal structure. The solution structure is well defined, with a lower degree of convergence between the structures in the loop regions than in the secondary structure elements. The average pairwise rmsd between the 15 refined solution structures is 0.71 +/- 0.13 A for the backbone atoms and 1.43 +/- 0.14 A for all heavy atoms. The solution structure is basically the same as the crystal structure. The average rmsd between the 15 refined solution structures and the crystal structure is 0.76 A for the backbone atoms and 1.45 +/- 0.09 A for all heavy atoms. There are, however, small differences probably caused by intermolecular contacts in the crystal structure.

Journal ArticleDOI
TL;DR: Normal mode calculations for two alternating sequence dodecamers in A, B, and Z conformations have been performed in dihedral angle space extended to endocyclic valence angles to account for sugar ring flexibility as mentioned in this paper.
Abstract: Normal mode calculations for two alternating sequence dodecamers in A, B, and Z conformations have been performed in dihedral angle space extended to endocyclic valence angles to account for sugar ring flexibility. Normal modes are analyzed in terms of helicoidal and backbone parameter variations with special attention being paid to global deformations of the double helix such as bending, twisting, or stretching. Results show that the allomorphic form of DNA has the largest influence on the flexibility of the sugar-phosphate backbone. Amplitudes of these vibrations follow the order: B > Z > A. In contrast, the amplitudes of helicoidal parameter variations are much more dependent on the base sequence. Global deformations of the double helix occur with characteristic times in the range of 1 to 10 ps and can be of mixed character, the strongest bending mode being at the same the time strongest stretching mode. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 796–811, 1997

Journal ArticleDOI
TL;DR: In this paper, the authors employed density functional theory and used ab initio pseudopotentials for the interaction between valence electrons and ions and the generalized gradient approximation to account for the many-body effects of exchange and correlation.
Abstract: We determine accurate molecular dipole moments for mesogenic fragments and liquid crystal molecules from quantum mechanical computer simulations adapted from large-scale electronic structure calculations on periodic solids. We employ density functional theory and use ab initio pseudopotentials for the interaction between valence electrons and ions and the generalized gradient approximation to account for the many-body effects of exchange and correlation. Periodic boundary conditions are enforced so that the molecular electronic wave function can be expanded in terms of a plane wave basis set. We test our method on several small molecules and then apply it to determine the direction, position and dipole moment magnitude for 4-4' pentyl-cyanobiphenyl (5CB) (and related fragments), phenyl benzoate, and 2-2'difluorobiphenyl. For the latter compound, we parametrize a torsional potential for rotation about the dihedral bond. We perform full structural optimization, and find that the torsional barrier heights for fully relaxed molecular structures are substantially reduced relative to nonoptimized geometries. We then demonstrate the influence of conformation and temperature on the molecular dipole moment. We also find that simple vector addition of dipole moments of fragments provides a good estimate of the total dipole moment of the complete molecule. We compare our results to experiment and to conventional quantum chemistry methods where data is available.

Journal ArticleDOI
TL;DR: In this article, the fluorescence of six secondary arenedicarboxamides has been investigated in single crystals, powders, melts, and ethanol solution, and the frequency shift between monomer and dimer fluorescence and the intensity and vibronic structure of the dimer emission are dependent upon the ground-state geometry.
Abstract: The fluorescence of six secondary arenedicarboxamides has been investigated in single crystals, powders, melts, and ethanol solution. Single crystals of four rodlike arenedicarboxamides which pack in one-dimensional tapes display dual emission attributed to excited-state monomers and dimers. These tapes have a constant 5-A separation between the long axes of neighboring arenes but differ in the arene−arene dihedral angle. The frequency shift between monomer and dimer fluorescence and the intensity and vibronic structure of the dimer emission are dependent upon the ground-state geometry. Single crystals of two naphthalenedicarboxamides which pack in two-dimensional sheets and have no close contacts between neighboring arenes within the same sheet display only monomer emission. Melted and resolidified samples display broad structureless emission attributed to fluorescence from a mixture of excited monomers and dimers with different ground-state geometries.

Journal ArticleDOI
01 Apr 1997-Geology
TL;DR: In this paper, the distribution of apparent dihedral angles expected in unequilibrated, fully crystallized monomineralic rocks is investigated for comparison with those expected in equilibrate textures.
Abstract: Three-dimensional numerical simulations have been constructed to investigate the distributions of apparent dihedral angles expected in unequilibrated rock textures for comparison with those expected in equilibrated rock textures. For unequilibrated, fully crystallized monomineralic rocks, the simulation shows that the distribution of apparent dihedral angles is nonrandom and similar to that expected from an equilibrated rock, and is largely independent of crystal shape and crystal nuclei distribution. This new distribution, together with the one previously derived for an equilibrated texture, defines a pair of apparent dihedral angle curves which encompass curves corresponding to any degree of textural equilibrium within a monomineralic rock. The location of a measured curve within this range allows a quantitative assessment of the degree of textural equilibrium within that rock. The simulations also show that unequilibrated, partially crystallized rocks generate apparent dihedral angle distributions for closed triangular pores that, depending on crystal shape, may mimic equilibrated dihedral angle distributions. They also indicate that unless a rock is in complete equilibrium, different dihedral angle distributions are produced by measuring the apparent dihedral angles of closed triangular or open nontriangular pores. An important conclusion of this work is that apparent dihedral angle curves for unequilibrated textures are similar to those for equilibrated textures. Therefore care must be taken when interpreting textural equilibrium from apparent dihedral angle curves.