Showing papers on "Dihedral angle published in 1992"

Large-amplitude nonlinear motions in proteins

Abstract: A molecular-dynamics calculation on a hydrated protein, crambin, demonstrates that (i) neighboring dihedral angles are correlated to local transitions in the protein backbone, and that (ii) the amplitude of collective excitations, representing correlated global motions in the protein, samples multicentered distributions. The time dependence of the multicentered dihedral and collective excitations show rapid transitions from the center of one distribution to another, followed for some time by damped, low-amplitude motions around one center. The global nonlinear collective excitations are responsible for most of the atomic fluctuations of the molecule. An analysis appropriate to multimodal conformations is reported.

Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.

Abstract: The three-dimensional solution structure of the recombinant B domain (FB) of staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G, was determined by NMR spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. On the basis of 692 experimental constraints including 587 distance constraints obtained from the nuclear Overhauser effect (NOE), 57 torsion angle (phi, chi 1) constraints, and 48 constraints associated with 24 hydrogen bonds, a total of 10 converged structures of FB were obtained. The atomic root mean square difference among the 10 converged structures is 0.52 +/- 0.10 A for the backbone atoms and 0.98 +/- 0.08 A for all heavy atoms (excluding the N-terminal segment from Thr1 to Glu9 and the C-terminal segment from Gln56 to Ala60, which are partially disordered). FB is composed of a bundle of three alpha-helices, i.e., helix I (Gln10-His19), helix II (Glu25-Asp37), and helix III (Ser42-Ala55). Helix II and helix III are antiparallel to each other, whereas the long axis of helix I is tilted at an angle of about 30 degrees with respect to those of helix II and helix III. Most of the hydrophobic residues of FB are buried in the interior of the bundle of the three helices. It is suggested that the buried hydrophobic residues form a hydrophobic core, contributing to the stability of FB.(ABSTRACT TRUNCATED AT 250 WORDS)

The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures.

Abstract: A high-precision solution structure of the elastase inhibitor eglin c was determined by NMR and distance geometry calculations. A large set of 947 nuclear Overhauser (NOE) distance constraints was identified, 417 of which were quantified from two-dimensional NOE spectra at short mixing times. In addition, a large number of homonuclear 1H-1H and heteronuclear 1H-15N vicinal coupling constants were used, and constraints on 42 chi 1 and 38 phi angles were obtained. Structure calculations were carried out using the distance geometry program DG-II. These calculations had a high convergence rate, in that 66 out of 75 calculations converged with maximum residual NOE violations ranging from 0.17 A to 0.47 A. The spread of the structures was characterized with average root mean square deviations ( ) between the structures and a mean structure. To calculate the unbiased toward any single structure, a new procedure was used for structure alignment. A canonical structure was calculated from the mean distances, and all structures were aligned relative to that. Furthermore, an angular order parameter S was defined and used to characterize the spread of structures in torsion angle space. To obtain an accurate estimate of the precision of the structure, the number of calculations was increased until the and the angular order parameters stabilized. This was achieved after approximately 40 calculations. The structure consists of a well-defined core whose backbone deviates from the canonical structure ca. 0.4 A, a disordered N-terminal heptapeptide whose backbone deviates by 0.8-12 A, and a proteinase-binding loop whose backbone deviates up to 3.0 A. Analysis of the angular order parameters and inspection of the structures indicates that a hinge-bending motion of the binding loop may occur in solution. Secondary structures were analyzed by comparison of dihedral angle patterns. The high precision of the structure allows one to identify subtle differences with four crystal structures of eglin c determined in complexes with proteinases.

Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution : a comparison of theoretical results

Abstract: The acetyl and methyl amide blocked alanine amino acid, commonly referred to as the alanine dipeptide, has often been used as a model in theoretical studies of backbone conformational equilibria in proteins. In order to evaluate the solvent effects on the conformational equilibrium of the dipeptide, we have used molecular dynamics simulations with holonomic backbone dihedral angle constraints and thermodynamic perturbation theory to calculate free energy profiles along paths connecting four important conformations of the dipeptide in the gas phase and in water. We found that the extended β conformation is the most stable both in the gas phase and in water

Effects of layering and anisotropy on fault geometry

Abstract: The geometry and orientation of faults are examined using several field examples of small-scale ( 1 ), with dihedral angles usually of about 50°, as predicted by the Coulomb theory of failure In layered rocks, the geometry of faults varies with the orientation of layering with respect to the stress field Where σ 1 , is approximately normal to layering or anisotropy, conjugate faults also develop symmetrically about σ 1 Where rocks have interbedded layers with different mechanical behaviours, however, faults tend to initiate orthogonal to the more brittle layers (ie originate as extension fractures sub-parallel to σ 1 ) , but oblique to the less brittle layers As the fault steps through the layering, pull-aparts are developed which may reduce the dihedral angle Where σ 1 is oblique ( c 25–75°) to anisotropy, one set of faults is developed at a high angle to layering, with another at a low angle, usually showing a ramp-flat geometry Large dihedral angles (up to 90°) may result and σ 1 , does not bisect this angle Where σ 1 is approximately parallel to layering, two cases can be recognized Where σ 3 is approximately normal to layering, faults with layer-parallel flats and contractional ramps develop Where σ 2 is approximately normal to layering, conjugate faults develop which are symmetrical about σ 1 , the geometry resembling that in isotropic rocks These observations are in agreement with rock deformation experiments which show the strong effect of anisotropy on fault orientation, but the observations incorporate the effects of layering of materials with different deformation characteristics

Observations of the water-vein system in polycrystalline ice.

Abstract: The geometry of the vein system in ice has been investigated using photographs of enlarged veins in ice samples that were grown in the laboratory. The veins, which are non-uniform, act as tiny triangular-shaped, water-filled prisms that refract the light passing through them. The three vein widths in the cross-section of a vein can be deduced from two photographs taken from different directions. The dihedral angle along a given vein edge can be observed directly by viewing it at a node, where four veins meet, from a particular direction. The dihedral angles range from 25° ± 1° to 105° ± 1°. It is shown that the vein cross-section can be constructed, given the three widths of a vein and one of the dihedral angles, providing that the radius of curvature around the vein wallsr v is a constant. This assumption can be checked if the values of at least two of the dihedral angles associated with the vein cross-section are known. Ifr v is a constant, then the solid-liquid interfacial energy ϒ sl must be isotropic for the veins in question and any deviations from uniform equilibrium geometry must derive primarily from anisotropy in the grain-boundary energy ϒ ss. The cross-sections of three veins that meet in a particular node are constructed. The assumption of isotropic ϒ sl is found to hold for this node.

XANES spectra of copper(II) complexes: correlation of the intensity of the 1s .fwdarw. 3d transition and the shape of the complex

Abstract: X-ray absorption spectra are measured for several copper complexes with four identical ligands, [CuL 4 ] 2- (L=chloro, succinimidato), whose geometry ranges from tetrahedral to square planar. Although the main features change complicatedly, the intensity of the 1s→3d peak increases with the increase in the dihedral angle between the two L-Cu-L planes. The relation between the intensity and the dihedral angle is explained by correlating the intensity with the mixing of the Cu 3d and 4p orbitals through the perturbation of the ligand field

Hydrogen bonding in the symmetry‐equivalent C2h dimer of 2‐pyridone in its S0 and S2 electronic states. Effect of deuterium substitution

Abstract: The properties of the two intermolecular N–H⋅⋅⋅O bonds that are responsible for the formation of the cis‐peptide‐like dimer of 2‐pyridone (2PY) have been examined using deuterium substitution of the bridging hydrogen atoms as a probe. Studies of the fully resolved S2←S0 electronic spectrum of (2PY)2 in a molecular beam show that the protonated dimer has a symmetry‐equivalent planar C2h structure in its S0(1Ag) and S2(1Bu) states. Analogous studies of (2PY)2–d1 and (2PY)2–d2 show that (2PY)2 and (2PY)2–d2 are energy delocalized dimers in their S2 states, with an exciton splitting of less than 20 cm−1. Effective structures of the symmetric dimers in both states are derived from the measured rotational constants. A comparison of these structures shows that there is a distortion of the hydrogen‐bonding geometry when hydrogen is replaced by deuterium, along both in‐plane and out‐of‐plane coordinates. ΔR(N–H⋅⋅⋅O)=0.008 A, Δθ[C=O⋅⋅⋅(H)–N]=0°, and Δφ (the dihedral angle)=0.96° in S0 (2PY)2–d2 and ΔR=0.003 A, Δθ=0...

Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two-dimensional NMR spectroscopy.

Abstract: The solution structure of the phosphocarrier protein, HPr, from Bacillus subtilis has been determined by analysis of two-dimensional (2D) NMR spectra acquired for the unphosphorylated form of the protein. Inverse-detected 2D (1H-15N) heteronuclear multiple quantum correlation nuclear Overhauser effect (HMQC NOESY) and homonuclear Hartmann-Hahn (HOHAHA) spectra utilizing 15N assignments (reported here) as well as previously published 1H assignments were used to identify cross-peaks that are not resolved in 2D homonuclear 1H spectra. Distance constraints derived from NOESY cross-peaks, hydrogen-bonding patterns derived from 1H-2H exchange experiments, and dihedral angle constraints derived from analysis of coupling constants were used for structure calculations using the variable target function algorithm, DIANA. The calculated models were refined by dynamical simulated annealing using the program X-PLOR. The resulting family of structures has a mean backbone rmsd of 0.63 A (N, C alpha, C', O atoms), excluding the segments containing residues 45-59 and 84-88. The structure is comprised of a four-stranded antiparallel beta-sheet with two antiparallel alpha-helices on one side of the sheet. The active-site His 15 residue serves as the N-cap of alpha-helix A, with its N delta 1 atom pointed toward the solvent to accept the phosphoryl group during the phosphotransfer reaction with enzyme I. The existence of a hydrogen bond between the side-chain oxygen atom of Tyr 37 and the amide proton of Ala 56 is suggested, which may account for the observed stabilization of the region that includes the beta-turn comprised of residues 37-40. If the beta alpha beta beta alpha beta (alpha) folding topology of HPr is considered with the peptide chain polarity reversed, the protein fold is identical to that described for another group of beta alpha beta beta alpha beta proteins that include acylphosphatase and the RNA-binding domains of the U1 snRNP A and hnRNP C proteins.

Atom-based modeling of amorphous 1,4-cis-polybutadiene

Abstract: The structure of amorphous 1,4-cis-polybutadiene is simulated with molecular mechanics and molecular dynamics subjected to periodic boundary conditions. All hydrogen atoms are explicitly taken into account. By means of the relaxation strategy which has been developed in this work, the low-energy states of relatively large systems can be reached within an acceptable computational time. With the five simulated structures, the distribution of bond angles, distribution of dihedral angles, and correlated distribution of pairs of neighbor dihedral angles, as well as cohesive energy, solubility parameter, and atom pair radial distribution functions, are evaluated and discussed

Detailed Chemical Kinetic Modeling: Chemical Reaction Engineering of the Future

Abstract: Publisher Summary A chemical reaction can be viewed as occurring via the formation of an excited state that can be any one of the degrees of freedom of the collection of N atoms. That is, translational, rotational, vibrational, and electronic excitation can lead to a chemical reaction. Most elementary chemical reactions can be categorized as unimolecular or bimolecular events. However, further phenomenological classification is useful for the development of detailed chemical kinetic models to estimate rate parameters for new reactions by analogy to similar reactions in the same phenomenological class. The transition state would be stable to all geometric deformations except the reaction coordinate, which may be a bond distance, bond angle, or dihedral angle, depending on the nature of the reaction for simple molecules. However, when large molecules are involved, such as those observed in biochemical reactions, complex reaction coordinates are possible. That is, the minimum energy path between the reactants and the products may not be represented by a simple reaction coordinate, but may involve a concerted deformation of bonds, bond angles, and dihedral angles.

Flexible-geometry conformational energy maps for the amino acid residue preceding a proline.

Abstract: Previously calculated Conformational energy maps suggest that the α-helical conformation for the residue preceding a proline is disfavored relative to the extended conformation by more than 7 kcal/mol. In known protein structures this conformation is observed, however, to occur for about 9% of all prolines. In addition, introduction or removal of prolines at theoretically unfavorable positions in proteins and peptides can have modest effects on stability and structure. To investigate the discrepancy between calculation and experiment, we have determined how the conformation of the proline affects the calculated energy. We have also explored the effect of bond length and bond angle relaxation on the Conformational energy map. The Conformational energy of the preceding residue is found to be unaffected by the conformation of the proline, but the effect of allowing covalent bond relaxation is dramatic. If bond lengths and angles, and dihedral angles within the pyrrolidine ring, are allowed to relax, a calculated energy difference between the α and β conformations of 1.1 kcal/mol is obtained, in reasonable agreement with experiment. The detailed shape of the calculated energy surface is also in excellent agreement with the observed Conformational distributions in known protein structures. © 1992 John Wiley & Sons, Inc.

Mean field theory as a tool for intramolecular conformational optimization. 1. Tests on terminally-blocked alanine and met-enkephalin

Abstract: A self-consistent multitorsional field (SCMTF) method of global optimization of the conformational energy of an oligopeptide is proposed. The method is based on the idea that the maximum of the square of the ground-state wave function is very often close to the global minimum of the potential energy and may be relatively unaffected by the complexity of the potential, e.g., its many minima. Using a mean field approximation, a set of coupled Schroinger equations for the motion of the nuclei is solved iteratively in a dihedral-angle space, each equation depending on a single dihedral angle

Capillary bridges between parallel and non-parallel surfaces and their stability

Abstract: Equilibrium shapes and the stability of capillary bridges between parallel and nonparallel solid surfaces are determined. Asymptotic and computer-aided techniques from bifurcation theory are used to determine the limits of stability in terms of the minimum volume of fluid in the bridge. These critical values depend on the contact angle, θc, its hysteresis range, and the dihedral angle between the plates, 2β. If gravity is present and acts away from the apex of the dihedral angle, then it is possible to balance the net surface tension force on the bridge even when the contact angle around the perimeter exhibits no hysterisis. Different shapes are grouped together into families of like symmetry, and values of volume are calculated for which no solution, or multiple solutions, exist. The relation of this problem to Rayleigh's stability of a liquid jet is discussed.

Molecular dynamics simulations of the conformational dynamics of tryptophan

Abstract: Molecular dynamics simulations of a single tryptophan molecule were performed using CHARMm-parametrized potential functions, where both explicit molecular and dielectric continuum models were used for the solvent. When all hydrogens were modeled explicitly, rotations about the χ 2 dihedral were more frequent than about the χ 1 dihedral. The presence or a molecular solvent damped librational motion about both dihedral angles. Conversely, when a united atom representation for hydrogen was used, rotations about the χ 2 dihedral were more frequent than about the χ 1 dihedral

Measurement of two-bond JCOH alpha coupling constants in proteins uniformly enriched with 13C.

Abstract: A simple E.COSY type technique is described for measurement of two-bond JCOHα coupling constants in proteins that are uniformly enriched with13C. The method has been used to measure2JCOHα for 132 residues in the proteins calmodulin and staphylococcal nuclease having non-overlapping Hα−Cα correlations. Measured2JCOHα coupling constants fall in the 0 to −9.5 Hz range. A separate experiment, measuring the accuracy of these values, indicates a root-mean-square error of 1 Hz. Comparison of the J couplings with the dihedral back bone angles from crystallographic studies confirms a weak but statistically significant correlation between the dihedral angle ψ and the magnitude of2JCOHα, but also indicates that parameters other than ψ have a significant effect on the value of the coupling.

The "CUPID" method for calculating the continuous probability distribution of rotamers from NMR data

Abstract: We present a new method, ContinUous ProbabIlity Distribution of rotamers (CUPID), for determining the distribution of rotamer probability p(X) about a dihedral angle χ. This method utilizes measured vicinal homonuclear and heteronuclear spin-spin coupling constants (J) and nuclear Overhauser enhancements (NOEs) from NMR spectra and demands no prior assumption about the conformations or the degree of flexibility across the bond

Three-dimensional solution structure of Ca(2+)-loaded porcine calbindin D9k determined by nuclear magnetic resonance spectroscopy.

Abstract: The three-dimensional solution structure of native, intact porcine calbindin D9k has been determined by distance geometry and restrained molecular dynamics calculations using distance and dihedral angle constraints obtained from 1H NMR spectroscopy. The protein has a well-defined global fold consisting of four helices oriented in a pairwise antiparallel manner such that two pairs of helix-loop-helix motifs (EF-hands) are joined by a linker segment. The two EF-hands are further coupled through a short beta-type interaction between the two Ca(2+)-binding loops. Overall, the structure is very similar to that of the highly homologous native, minor A form of bovine calbindin D9k determined by X-ray crystallography [Szebenyi, D. M. E., & Moffat, K. (1986) J. Biol. Chem. 261, 8761-8776]. A model structure built from the bovine calbindin D9k crystal structure shows several deviations larger than 2 A from the experimental distance constraints for the porcine protein. These structural differences are efficiently removed by subjecting the model structure to the experimental distance and dihedral angle constraints in a restrained molecular dynamics protocol, thereby generating a model that is very similar to the refined distance geometry derived structures. The N-terminal residues of the intact protein that are absent in the minor A form appear to be highly flexible and do not influence the structure of other regions of the protein. This result is important because it validates the conclusions drawn from the wide range of studies that have been carried out on minor A forms rather than the intact calbindin D9k.

Conformation dependence of the SH and CS stretch frequencies of the cysteine residue

Abstract: SYNOPSIS In order to relate the observed SH and CS stretch frequencies of the cysteine residue in proteins more closely to its conformation, we have done normal mode calculations on a model for this structure, viz., (CCONH) (CNHCO)CHCH2SH. A range of x' and x2 were studied, combined with the $,$ of the a-helix, P-sheet, glutathione, and extended-helix conformations. The force field was a combination of a scaled ab initio force field of the -CH2SH group, obtained from ethanethiol and tested on 1-propanethiol and 3-thiol-Nmethylpropionamide, and our empirical force field for the peptide group. The results provide more detailed structure-spectra correlations than are possible from experimental studies of model compounds. 0 1992 John Wiley & Sons, Inc. I NTRODU CTl ON The cysteine residue side chain, -CH2SH, is an important one in proteins, both because of its inherent properties as well as its ability to react with similar groups to form a disulfide bridge, -CH2SSCH2-, between polypeptide chains. It is therefore important to develop detailed spectroscopic correlations for characterizing its conformation. It has long been known that the SH stretch (s) mode, v(SH), is generally found in the range of 2500-2600 cm-' , being weak in the ir and strong in the Raman spectrum. Since v(SH) is sensitive to the presence of SH groups and to their environment, particularly hydrogen bonding, it has been studied in various proteins, such as hemoglobin, 122 eye lens proteins, 3-5 0-lactoglobulin, and virus protein^.^,' Conformational information with respect to the C"Cs-S-H dihedral angle ( x2) has been sought through experimental studies of model alkanethiolsg-" as well as normal mode calculations on such molecule~.'~~~~ Low-frequency torsional modes have also been studied14-16 in order to obtain information on rotational barriers. The v(CS) mode has been known to give rise to Raman bands in the 600-800-cm-' region. Confor

Three-dimensional structure of the apo form of the N-terminal EGF-like module of blood coagulation factor X as determined by NMR spectroscopy and simulated folding.

Abstract: The three-dimensional structure of a 42-residue fragment containing the N-terminal EGF-like module of blood coagulation factor X was determined by means of 2D NMR spectroscopy and computer simulation. The spectroscopic data consisted of 370 NOE distances and 27 dihedral angle constraints. These were used to generate peptide conformations by molecular dynamics simulation. The simulations used a novel functional form for the constraint potentials and were performed with two time steps to ensure rapid execution. Apart from preliminary runs to aid assignment of NOEs, 60 runs resulted in 13 accepted structures, which have two antiparallel β sheets, no α helices, and five tight turns. There is no hydrophobic cluster. The root mean square deviation for the backbone of the 13 conformations is 0.65 ± 0.11 A against their mean conformation. About half of the side chains have well-defined structure. The overall conformation is similar to that of murine EGF. (Less)

Conformations, spectroscopy, and photochemistry of methyl phenanthrene-9-carboxylate, phenanthrene-9-carboxamides, and their Lewis acid complexes

Abstract: The spectroscopic properties and photochemical behavior of methyl phenanthrene-9-carboxylate and of a primary, secondary, and tertiary phenanthrene-9-carboxamides have been investigated in the absence and presence of strong Lewis acids. The ground-state conformations of the free and complexed molecules have been investigated by means of NMR and Gaussian 88 calculations. The dihedral angle between the phenanthrene and the carbonylgroup is found to be dependent upon the bulk of the 9-substituent and upon Lewis acid complexation. Complexation alsochanges the secondary amide conformation from syn to anti