Showing papers on "Dihedral angle published in 1985"

Aromatic-aromatic interaction: a mechanism of protein structure stabilization

Abstract: Analysis of neighboring aromatic groups in four biphenyl peptides or peptide analogs and 34 proteins reveals a specific aromatic-aromatic interaction. Aromatic pairs (less than 7 A between phenyl ring centroids) were analyzed for the frequency of pair type, their interaction geometry (separation and dihedral angle), their nonbonded interaction energy, the secondary structural locations of interacting residues, their environment, and their conservation in related molecules. The results indicate that on average about 60 percent of aromatic side chains in proteins are involved in aromatic pairs, 80 percent of which form networks of three or more interacting aromatic side chains. Phenyl ring centroids are separated by a preferential distance of between 4.5 and 7 A, and dihedral angles approaching 90 degrees are most common. Nonbonded potential energy calculations indicate that a typical aromatic-aromatic interaction has energy of between -1 and -2 kilocalories per mole. The free energy contribution of the interaction depends on the environment of the aromatic pair. Buried or partially buried pairs constitute 80 percent of the surveyed sample and contribute a free energy of between -0.6 and -1.3 kilocalories per mole to the stability of the protein's structure at physiologic temperature. Of the proteins surveyed, 80 percent of these energetically favorable interactions stabilize tertiary structure, and 20 percent stabilize quaternary structure. Conservation of the interaction in related molecules is particularly striking.

Organic polymers based on aromatic rings (polyparaphenylene, polypyrrole, polythiophene): Evolution of the electronic properties as a function of the torsion angle between adjacent rings

Abstract: We present ab initio Hartree–Fock and valence effective Hamiltonian (VEH) calculations on polyparaphenylene, polypyrrole, and polythiophene dimers and polymer chains. These polymeric materials are among the most studied compounds in the field of conducting polymers. We examine, as a function of the torsion angle between consecutive rings, the evolution of electronic properties such as ionization potential, bandgap and width of the highest occupied bands and of the carbon–carbon bond length between rings. This investigation is motivated by the fact that many derivatives of these compounds have substituents that lead to an increase of the torsion angle between adjacent rings, as a result of steric interactions. As expected, on going from a coplanar to a perpendicular conformation, the ionization potential and bandgap values increase and the width of the highest occupied bands decreases. This makes it more difficult to ionize or reduce the polymer chains and can result in achieving lower maximum conductivities on doping. However, since the evolution of the electronic properties is found to follow a cosine law (related to the decrease of the overlap between the π orbitals on adjacent rings), the modifications up to a ∼40° torsion angle are not very large. For instance, in all three polymers, the ionization potential value for a 40° torsion angle is about 0.4 eV larger than the coplanar conformation value. Therefore, substituents that lead to torsion angles between consecutive rings smaller than 40° are quite acceptable. Finally we discuss the importance, for the substituted compounds, of the possibility of achieving a coplanar conformation upon doping, in order to permit high intrachain mobilities of charge carriers such as bipolarons.

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme

Abstract: A method is presented for finding particular normal modes for large molecules such as proteins and nucleic acids. The method is based on an iterative approach that extracts eigenvectors of interest from the full second-derivative matrix. Application of the method to the interdomain (hinge-bending) motion of lysozyme yields a frequency of 3.6 cm-1. This is similar to the value obtained from earlier adiabatic-energy-minimization studies. Analysis of the mode shows that the relaxation associated with the hinge bending is highly delocalized; that is, the dihedral angle and energy changes are distributed over many residues, including some (e.g., Trp-28) that are distant from the cleft and hinge region.

Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin.

Abstract: A new methodology for theoretically predicting the native, three-dimensional structure of a polypeptide is presented. Based on equilibrium statistical mechanics, an algorithm has been designed to determine the probable conformation of a polypeptide by calculating conditional free-energy maps for each residue of the macromolecule. The conditional free-energy map of each residue is computed from a set of probability integrals, obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. By locating the region(s) of lowest free energy for each map, the probable conformation for each residue can be identified. The native structure of the polypeptide is assumed to be the combination of the probable conformations of the individual residues. All multidimensional probability integrals are evaluated by an adaptive Monte Carlo algorithm (SMAPPS—Statistical-Mechanical Algorithm for Predicting Protein Structure). The Monte Carlo algorithm searches the entire conformational space, adjusting itself automatically to concentrate its sampling in regions where the magnitude of the integrand is largest (“importance sampling”). No assumptions are made about the native conformation. The only prior knowledge necessary for the prediction of the native conformation is the amino acid sequence of the polypeptide. To test the effectiveness of the algorithm, SMAPPS was applied to the prediction of the native conformation of the backbone of Met-enkephalin, a pentapeptide. In the calculations, only the backbone dihedral angles (ϕ and ψ) were allowed to vary; all side-chain (χ) and peptide-bond (ω) dihedral angles were kept fixed at the values corresponding to the alleged global minimum energy previously determined by direct energy minimization. For each conformation generated randomly by the Monte Carlo algorithm, the total conformational energy of the polypeptide was obtained from established empirical potential energy functions. Solvent effects were not included in the computations. With this initial application of SMAPPS, three distinct low-free-energy β-bend structures of Met-enkephalin were found. In particular, one of the structures has a conformation remarkably similar to the one associated with the previously alleged global minimum energy. The two additional structures of the pentapeptide have conformational energies lower than the previously computed low-energy structure. However, the Monte Carlo results are in agreement with an improved energy-minimization procedure. These initial results on the backbone structure of Met-enkephalin indicate that an equilibrium statistical-mechanical procedure, coupled with an adaptive Monte Carlo algorithm, can overcome many of the problems associated with the standard methods of direct energy minimization.

UV irradiation of nucleic acids: formation, purification and solution conformational analysis of the ‘6-4 lesion’ of dTpdT

Abstract: Irradiation of dTpdT with 300 kJ/m2 of 254 nm produces numerous photo-products, one of which labeled dT6pd4T[1] was purified by HPLC. dT6pd4T has a UV spectrum (H20, pH 7) with lambda max = 326 nm and lambda min = 265 nm, and a P-31 NMR resonance at -3.46 ppm (normal dTpdT occurs at -4.01 ppm; TMP, 30 degrees C). 2-D COSY NMR spectra facilitated proton resonance assignments and 2-D NOESY spectra aided analysis of spatial orientation. Carbon-13 and proton-coupled P-31 NMR spectra of dT6pd4T were also obtained. These analyses indicate: C5=C6 of dT6p- is saturated and the -pd4T base is more aromatic; the dT6p- base possesses a configuration of 5R, 6S; dT6p- and -pd4T have anti-type glycosidic conformations; furanose conformation of dT6p- is mainly C3'-endo and that of -pd4T exists in a C3'-endo in equilibrium C3'-exo; exocyclic bonds gamma (C5'-C4'), beta (05'-C5') and epsilon (C3'-03') are non-classical rotamers; dihedral angle about epsilon (C3'-03') is smaller relative to dTpdT.

Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions

Abstract: We present the results of molecular dynamics simulations on d(C-G-C-G-A) X d(T-C-G-C-G) with fully charged phosphates with and without inclusion of counterions. The average structures found in the two simulations are similar, but the simulation with counterions does give an average helix repeat, tilt, and twist in better agreement with those found in the x-ray structure of d(C-G-C-G-A-A-T-T-C-G-C-G)2. The average sugar pucker phases and amplitudes are in qualitative agreement with those found in NMR studies of double-helical DNA, and a number of examples of sugar repuckering from C2' endo to C3' endo carbon conformations in the sugar ring are found. The hydrogen bond correlations as well as torsion correlations are analyzed, and some interesting long-range correlations between dihedral angles are found.

Effect of dihedral angle on the morphology of grains in a matrix phase

Abstract: Minimum interface energy configurations of a uniformly intermixed grain-matrix aggregate are determined for various dihedral angles and matrix contents by numerical analysis of a model which consists of a rhombic dodecahedron grain in contact with matrix at its curved surfaces along truncated edges and corners. For dihedral angles, Φ, greater than 90 deg, the total interface energy,E, increases monotonically with the matrix volume fraction,Vm. For Φ= 0 deg,E decreases withVm until the grains become spherical atVm = 26 pct. For 0 deg Φ ≤ 75 deg,E vs Vm curves show the minima which represent the stable configurations to be obtained whenVm can be freely varied. For Φ ≤ 60 deg, the matrix is always continuous along the grain edges. For Φ 75 deg, the matrix becomes separated at the grain corners below certain critical values ofVm. The contiguity decreases monotonically withVm. The slope ofE vs Vm curve is shown to be an effective pressure on the specimen surface, which represents the driving force for changing the grain configuration with a corresponding change ofVm while keeping the grain volume constant. The implications of these results on solid state sintering, liquid phase sintering, and the penetration of liquid into liquid phase sintered alloys are discussed. Finally, the results of a previous analysis by Beere are shown to disagree with the present work for systems with low dihedral angles apparently because of inaccuracy in his calculation.

Conformational behavior of α,α‐dialkylated peptides

Abstract: The preferred conformations of N-acetyl-N′-methyl amides of some dialkylglycines have been determined by empirical conformational-energy calculations; minimum-energy conformations were located by minimizing the energy with respect to all the dihedral angles of the molecules. The conformational space of these compounds is sterically restricted, and low-energy conformations are found only in the regions of fully extended and helical structures. Increasing the bulkiness of the substituents on the Cα, the fully extended conformation becomes gradually more stable than the helical structure preferred in the cases of dimethylglycine. This trend is, however, strongly dependent on the bond angles between the substituents on the Cα atom: In particular, helical structures are favored by standard values (111°) of the N-Cα-C′ angle, while fully extended conformations are favored by smaller values of the same angle, as experimentally observed, for instance, in the case of α,α-di-n-propylglycine.

An equation utilizing empirically derived substituent constants for the prediction of vicinal coupling constants in substituted ethanes

Abstract: A simple equation has been developed for the prediction of vicinal coupling constants in HCCH fragments: The equation is a cosine series in θ, the torsion angle between vicinal hydrogens. The feature which distinguishes this equation from similar equations is the inclusion of δSi terms, which describe the magnitude of each substituent's effect. These substituent constants have been defined from experimental data. An orientation effect which is dependent on the torsion angle(s) between substituent(s) and a vicinal hydrogen is included. Substituent constants have been defined for 39 groups, of which 15 have been experimentally determined herein. The parameters for the equation have been defined from 49 torsion angles in 19 conformationally rigid compounds. The torsion angles have been determined from x-ray crystal structure data and molecular mechanics calculations. The multiplicity of structures used to determine the substituent constants should allow for the application of this equation to a wide variety of structures.

Vicinal coupling constants and protein dynamics

Abstract: The effects of motional averaging on the analysis of vicinal spin-spin coupling constants derived from proton NMR studies of proteins have been examined. Trajectories obtained from molecular dynamics simulations of bovine pancreatic trypsin inhibitor and of hen egg white lysozyme were used in conjunction with an expression for the dependence of the coupling constant on the intervening dihedral angle to calculate the time-dependent behavior of the coupling constants. Despite large fluctuations, the time-average values of the coupling constants are not far from those computed for the average structure in the cases where fluctuations occur about a single potential well. The calculated differences show a high correlation with the variation in the magnitude of the fluctuations of individual dihedral angles. For the cases where fluctuations involve multiple sites, large differences are found between the time-average values and the average structure values for the coupling constants. Comparison of the simulation results with the experimental trends suggests that side chains with more than one position are more common in proteins than is inferred from X-ray results. It is concluded that for the main chain, motional effects do not introduce significant errors where vicinal coupling constants are used in structure determinations; however, for side chains, the motional average can alter deductions about the structure. Accurately measured coupling constants are shown to provide information concerning the magnitude of dihedral angle fluctuations.

Conformations of blood group H-active oligosaccharides of ovarian cyst mucins.

Abstract: Spectroscopic data and conformational energy calculations are reported for eight oligosaccharides from ovarian cyst mucins and from human milk, the nonreducing terminals of which have fucose (α1 2)galactose linked either (β1 3) (type I) or (β1 4)(type II) to N-acetylglucosamine or in (β1 3) linkage to galactosaminitol. The fully assigned proton nmr spectra are reported along with nuclear Overhauser enhancement (NOE) data. Amide proton coupling constants and vacuum-uv CD spectra provide information on the amide plane orientation and amide environment. Our results imply that the fucosidic dihedral angles are similar for all three cases and that the substantial differences in the chemical shifts of the fucosyl protons of type I, type II, and 3-ol chains result from different perturbations by the amide group of the residue to which the β-galactose is linked. Stereopair diagrams of conformational models for both type I and II H chains are presented that are consistent with NOE, coupling constants, conformational energy calculations, and the CD data. While the temperature dependence of the observed NOE of penta- and hexasaccharides indicates that their rotational correlation times are strongly temperature dependent, we conclude that the conformations are essentially independent of temperature.

An ab initio investigation of the torsional potential function of n-butane

Abstract: The rotational potential function of n-butane has been calculated as a function of the dihedral angle of the skeletal carbon–carbon bonds using a 4–31 Gaussian basis set. Relaxation of the central C—C bond by up to 0.03 A and of the CCC angles by 2.8° accompanies the rotation. Apart from a vertical displacement in energy, the potential curve, when all coordinates are released, is closely similar to that obtained when the HCC angles are held to tetrahedral values and the C—H bond lengths are fixed at as much as 0.1 A greater than their equilibrium values. This suggests that the potential curves of more complex systems may be adequately reproduced in this simplifying approximation of not releasing the hydrogen coordinates. The calculated potential curves reproduce the experimental anti to gauche energy differences as well as the optimum gauche dihedral angle of 67°. Significant differences exist between the ab initio curve and the frequently used Scott and Scheraga curves. In particular the energy of the eclipsed configuration over the anti form is reduced from 45 to 27 kJ mol–1.

Carbon-13 NMR in conformational analysis of nucleic acid fragments. 4. The torsion angle distribution about the C3′–O3′ bond in DNA constituents

Abstract: Carbon-13 and proton NMR spectra of a series of oligodeoxynucleotides (d(CT), d(CC), d(TA), d(AT), d(CG), d(GC), d(AG), d(AAA), d(TATA) and d(GGTAAT] were measured at various temperatures. The three coupling constants that are related to the magnitude of backbone angle epsilon (J(C4'-P), J(C2'-P) and J(H3'-P] are analyzed in terms of a three-state equilibrium about this bond. Two epsilon (trans) angles occur, which differ in magnitude depending on the conformation (N or S) of the adjoining deoxyribose ring. The S-type deoxyribose ring is associated with a smaller epsilon (trans) angle: epsilon (t,S) = 192 degrees. The N-type deoxyribose ring is associated with a larger epsilon (trans) angle epsilon (t,N) = 212 degrees. The third rotamer participating in the conformational equilibrium, is a gauche(-) (epsilon (-] conformer and occurs exclusively in combination with the S-type sugar ring (epsilon (-,S) = 266 degrees). Within the limits of experimental error, the magnitude of these three angles appears to be independent of the particular base sequence, except in the case of d(CG) where a slightly larger epsilon (t,S) angle (197 degrees) is indicated. A simple equation is proposed which may be used to calculate the population of epsilon (t,S) conformer in cases where only J(H3'-P) is known.

Syntheses and Properties of Oligo-L-leucines Containing α-Aminoisobutyric Acid Residues. The Novel Strategy for Solubility Improvement in Helical Oligopeptides Based on the Restriction of the Values of the Backbone Dihedral Angles φ and ψ of α-Aminoisobutyric Acid Residues

Abstract: In order to provide a succinct demonstration of the usefulness of a new strategy for solubility improvement in protected peptide fragments included in α-helical regions of proteins, model oligo(Leu)s containing Aib or Ala residues were prepared by stepwise elongation and fragment condensation methods. The peptides prepared were the following: Boc–(Leu3–Aib)n–OBzl, Boc–(Leu4–Aib)n–OBzl, and Boc–(leu3–Ala)nOBzl (n=1–3). Carboxyl component peptides having Aib residues at the C-terminals smoothly reacted with amino component peptides in high yields with no care of racemization due to the absence of chiral centers in Aib residues. As expected, peptides containing Aib residues have high solubility in moderate- and high-polar organic solvents and are easily purified by recrystallization from aqueous ethanol. This is in remarkable contrast with the result that the octa- and dodecapeptides containing Ala residues are barely soluble or insoluble in these solvents. Conformational analyses by IR spectroscopies indica...

A comparison of the structure and dynamics of avian pancreatic polypeptide hormone in solution and in the crystal.

Abstract: A molecular dynamics simulation was carried out with avian pancreatic polypeptide hormone (aPP) as an isolated monomer explicitly including the solvent (MDS). The simulation and the resulting mean structure are compared with the results of a corresponding crystal simulation (MDC) with 4 aPP molecules plus interstitial water in a periodic boundary unit cell and with the X-ray structure (van Gunsteren, Haneef et al., manuscript in preparation). Comparison is based on the time span 5 to 15 ps and considering cartesian coordinates, dihedral angles, H-bond length, and accessible surface area. While in the MDC simulation equilibration is fast and complete, it does occur in MDS for most but not all parts of the molecule; the turn region starts moving away from the X-ray structure after 9 ps. Only minor differences result when dimer-forming side chains, e.g. tyrosines 7 and 21, are exposed to solvent. The largest rms fluctuations are encountered in exposed polar side chains of Asp 11, Glu 15, Arg 19, and Arg 33, but also in the hydrophobic core residue Phe 20, the only phenylalanine residue present. The latter undergoes an abrupt reorientation suitable for verification by NMR spectroscopy, which is possibly related to the motion of the turn region. The main-chain dihedral angles of the alpha-helix are shifted from values generally found in crystal structures towards those of the ideal Pauling helix. There is concomitant H-bond elongation. The effects are most pronounced and consistent in the MDS simulation.

Conformational studies of nucleic acids. II. The conformational energetics of commonly occurring nucleosides.

Abstract: We have examined the conformational energetics of the eight most commonly occurring nucleosides—A, U, G, C, dA, dT, dG, dC—as monitored by a semi-empirical energy force field. These are the first reported calculations to completely explore the entire conformational spaces available to all eight major nucleosides using experimentally consistent furanose geometries and an appropriate force field. Central to our approach is the ability to model an experimentally reasonable furanose for each nucleoside directly from only one parameter, the phase angle of pseudorotation P, as described in the previous paper (D.A. Pearlman, and S.-H. Kim, preceeding paper in this issue). This allows us to specify the conformation of a nucleoside by three variables: torsion angle γ (05′—C5′—C4′—C3′); torsion angle χ (04′—C1′—N9/N1—C4/C2); and P. In our study each of these parameters was allowed to vary independently and in small increments over the range 0–360°. The empirically observed preferences for C3′-endo and C2′-...

Inter-ring dihedral angles in polychlorinated biphenyls from photoelectron spectroscopy

Abstract: A proposal that the physiological activity of a chlorinated biphenyl is related to its degree of molecular planarity is explored through experimental measurements of inter-ring dihedral angles in t...

A model for the distribution of bond angles in vitreous SiO2: PHIL. MAG. LETTERS

Abstract: Exact expressions for the distributions of the intertetrahedral (Si-O-Si) angles θ and the dihedral angles δ in vitreous SiO2 have been derived by assuming a minimum oxygen-oxygen distance between

Conformational preferences and internal rotation in toluene, o-xylene and hexamethylbenzene

Abstract: Barriers to methyl internal rotation have been investigated through ab initio MO calculations with geometry optimization on toluene (STO-3G and 4-31G), o -xylene (STO-3G), and hexamethylbenzene (STO-3G), and compared with experimental results. Toluene is found to prefer a conformation in which one methyl CH bond makes a dihedral angle of 90° with the ring plane. However, the sixfold barrier to internal rotation is only 17 J mol −1 at the 4-31G level. The potential energy surface for coupled methyl group rotation in o -xylene is displayed and the preferred conformer is that known from microwave spectroscopy. Neglect of coupling and the sixfold component are partially responsible for over-estimates of the barrier from experiments. The most stable conformer of hexamethylbenzene has D 3d symmetry with slight puckering of the ring and tilting of the methyl groups to reduce steric crowding. The barrier to geared internal rotation is 2.42 kJ mol −1 .

High‐field orientation effects in the high‐resolution proton NMR spectra of diverse porphyrins

Abstract: Dipolar splittings with a quadratic dependence on static magnetic field strength are reported for selected pairs of nuclei in several porphyrins. These splittings are detectable as a result of a slight molecular alignment caused by the interaction of the static magnetic field with the anisotropic magnetic susceptibilities of the porphyrin rings. The magnitude of the splitting yields an effective value for ΔX, the anisotropy of the susceptibility. This value includes association effects which may be estimated therefrom. Dipolar splittings between protons of attached vinyl groups can also be measured, and provide information about the average dihedral angle between the planes of the vinyl group and porphyrin ring.

Resonance assignment of the 500-MHz proton NMR spectrum of self-complementary dodecanucleotide d-GGATCCGGATCC: altered conformations at BamHI cleavage sites.

Abstract: Resonance assignments of nonexchangeable base and sugar protons of the self-complementary dodecanucleotide d-GGATCCGGATCC have been obtained by two-dimensional NMR methods and strategies derived from interproton distance calculations on different secondary structures of nucleic acids. Conformational details about the glycosidic dihedral angle and sugar pucker have been derived from the relative intensities of cross peaks in the two-dimensional J-correlated and nuclear Overhauser enhancement correlated spectra in D2O solution. It is observed that d-GGATCCGGATCC assumes a predominantly B-type conformation with sequence-dependent changes along the chain. The recognition site of BamHI shows a distinctly different geometrical environment. The sugar rings of G1 and G7 assume a C3'-endo geometry while the rest of the sugars possess C2'-endo geometry.

The structure of poly-2,5-benzoxazole (ABPBO) and poly-2,6-benzothiazole (ABPBT) fibers by X-ray diffraction

Abstract: The determination of the crystalline structure of oriented fibers of poly-2,5-benzoxazole (ABPBO) and poly-2,6-ben-zothiazole (ABPBT) is described. Both unit cells are metrically orthorhombic, with the parameters: a = 6.061 (17), b = 3.384 (13), c (fiber axis) = 11.575 (6) A for ABPBO; and a = 6.044 (6), b = 3.417 (7), c (fiber axis) = 12.194 (18) A for ABPBT. The fiber repeat consists in each structure of two fused ring groups arranged in a planar, zigzag conformation. The conformational torsion angle and orientation of chains within the unit cells are derived from a linked-atom least squares refinement technique. Polymer chains pack laterally through van der Waals interactions. A plausible disorder model which involves defects in chain direction is presented. Refinement of a static disorder model for ABPBO in which 50% of the chains have their chain directions reversed leads to a lower R residual and sum of constraints.

Determination of the Karplus relationships for the C-2, H-1' and C-6, H-1' vicinal coupling paths of uridine derivatives

Abstract: A number of uracil cyclo-nucleosides with known glycosidic bond conformations have been synthesized as model compounds for evaluating the Karplus parameters of vicinal carbon-proton coupling across the glycosidic bond. The magnitudes of 3J(C-2, H-1′) and 3J(C-6, H-1′) were determined from proton-coupled 13C NMR measurements, and both coupling constants showed an approximate Karplus dependence with dihedral angle. Careful analysis of the results on model compounds reveals that the C-2, H-1′ and C-6, H-1′ coupling paths are not equivalent, and so the magnitudes of Karplus parameters have been determined for each coupling path for the Karplus relationship in the form 3J=A cos2 θ + B cos θ + C, i.e. A6 = 6.2, B6 = −2.4 and C6 = 0.1 Hz and A2 = 5.0, B2 = 2.1 and C2 = 0.1 Hz. Comparison is made between proton-carbon coupling magnitudes in nucleoside and peptide coupling paths.