Showing papers on "Dihedral angle published in 1995"

NMR solution structure of calcium-saturated skeletal muscle troponin C.

Abstract: Troponin C (TnC) is an 18 kDa (162-residue) thin-filament calcium-binding protein responsible for triggering muscle contraction upon the release of calcium from the sarcoplasmic reticulum. The structure of TnC with two calcium ions bound has previously been solved by X-ray methods. Shown here is the solution structure of TnC which has been solved using 3D and 4D heteronuclear nuclear magnetic resonance (NMR) spectroscopic techniques. The 1H, 13C, and 15N backbone chemical shifts have already been published [Slupsky, C. M., Reinach, F. C., Smillie, L. B., & Sykes, B. D. (1995) Protein Sci. 4, 1279-1290]. Presented herein are the 1H, 13C, and 15N side-chain chemical shifts which are 80% complete. The structure of calcium-saturated TnC was determined on the basis of 2106 NOE-derived distance restraints, 121 phi dihedral angle restraints, and 76 psi dihedral angle restraints. The appearance of calcium-saturated TnC reveals a dumbbell-shaped molecule with two globular domains connected by a linker. The structures of the N-terminal and C-terminal domains are highly converged [backbone atomic root mean square deviations (rmsd) about the mean atomic coordinate position for residues 10-80 and 98-155 are 0.66 +/- 0.17 and 0.69 +/- 0.18 A, respectively]; however, the orientation of one domain with respect to the other is not well-defined, and thus each domain appears to be structurally independent. Comparison of the calcium-saturated form of TnC determined herein with the half-saturated form determined by X-ray methods reveals two major differences. First, there is a major structural change which occurs in the N-terminal domain resulting in the opening of a hydrophobic pocket presumably to present itself to its target protein troponin I. This structural change appears to involve only helices B and C which move away from helices N/A/D by the alteration of the backbone phi, psi angles of glutamic acid 41 from irregular in the crystal structure (-97 degrees, -7 degrees) to helical in the NMR calcium-saturated structure (-60 degrees, -34 degrees). The other difference between the two structures is the presence of a flexible linker between the two domains in the NMR structure. This flexible linker allows the two domains of TnC to adopt any orientation with respect to one another such that they can interact with a variety of targets.

Collective protein dynamics and nuclear spin relaxation

Abstract: Theoretical methods are developed and applied to the protein crambin as a model system to characterize collective normal mode dynamics and their effects on correlations between torsion angle fluctuations and heteronuclear NMR relaxation parameters. Backbone N–H NMR S2 order parameters are found to be predominantly determined by local φ and ψ torsion angle fluctuations induced by collective protein modes. The ratio between Cβ–Hβ and Cα–Hα order parameters directly yields fluctuation amplitudes of the sidechain χ1 torsion angles. The results allow a more direct interpretation of motional effects monitored by nuclear spin relaxation.

The sintering of two particles by surface and grain boundary diffusion -- A two-dimensional numerical study

Abstract: We investigate the sintering of two touching circular particles by surface and grain boundary diffusion. Typical examples for the evolution of the shape of the particles, their surface curvatures, and their surface fluxes are given. The sintering kinetics are evaluated as a function of the dihedral angle at the grain boundary-surface junctions and the grain boundary to surface diffusivity ratio. In particular, the growth rates of the neck between the two particles, the growth rate exponents, and the changes in the lengths of the particle pairs are monitored. The times needed to reach certain fractions of the final equilibrium neck sizes are tabulated for typical experimental dihedral angles and diffusivity ratios. Our simulation is based on a rigorous mathematical system modeling the sintering of the two particles, and a rigorous numerical method for solving this system is adopted.

Solution structure of the oxidized 2[4Fe-4S] ferredoxin from Clostridium pasteurianum.

Abstract: Following the recently developed approach to the solution structure of paramagnetic high-potential iron-sulfur proteins, the three-dimensional structure in solution of the oxidized Clostridium pasteurianum ferredoxin has been solved by 1H-NMR. The X-ray structure is not available. The protein contains 55 amino acids and two [4Fe-4S] clusters. In the oxidized state, the clusters have S = 0 ground states, but are paramagnetic because of thermal population of excited states. Due to the somewhat small size of the protein and to the presence of two clusters, approximately 55% of the residues have at least one proton with a non-selective T1 smaller than 25 ms. The protein has thus been used as a test system to challenge the present paramagnetic NMR methodology both in achieving an extended assignment and in obtaining a suitable number of constraints. 79% of protein protons have been assigned. Analogy with other ferredoxins of known structure has been of help to speed up the final stages of the assignment, although we have shown that this independent information is not necessary. In addition to dipolar connectivities, partially detected through tailored experiments, 3JHN-H alpha, H-bond constraints and dihedral angle constraints on the Cys chi 2 angles have been generated by using a recently derived Karplus-type relationship for the hyperfine shifts of cysteine beta CH2 protons. In total, 456 constraints have been used in distance geometry calculations. The final quality of the structures is satisfactory, with root-mean-square deviation values of 66 pm and 108 pm for backbone and heavy atoms, respectively. The resulting structure is compared with that of Clostridium acidi urici ferredoxin [Duee, E. D., Fanchon, E., Vicat, J., Sieker, L. C., Meyer, J. & Moulis, J.-M. (1994) J. Mol. Biol. 243, 683-695]. The two proteins are very similar in the overall folding, secondary structure elements and side-chain orientations. The C alpha root-mean-square deviation values between the X-ray-determined C. acidi urici ferredoxin structure and the conformer with lowest energy of the C. pasteurianum ferredoxin family is 78 pm (residues 3-53). Discrepancies in residues 26-28 may arise from the disorder observed in the X-ray structure in that region.

Ab initio studies of critical conformations in ethane, methylamine, methanol, hydrazine, hydroxylamine, and hydrogen peroxide

Abstract: Ab initio calculations on conformations corresponding to the torsional energy minima and maxima of ethane, methylamine, methanol, hydrazine, hydroxylamine, and hydrogen peroxide were carried out with geometry optimizations using second‐order Mo/ller–Plesset perturbation theory (MP2) in the 6–311+G(3df,2p) basis. Compared with experiments the MP2/6–311+G(3df,2p) calculations yield absolute average deviations of 0.128 kcal/mol for 6 rotational barriers, 0.009 A for 18 bond lengths, 0.7° for 16 bond angles, 0.5° for 2 dihedral angles, and 0.17 D for 5 dipole moments. Three smaller basis sets, 6–31G(d), 6–31+G(d,p), and 6–311G(d,p), were also used to study variations in the total energies and barrier heights as a result of basis set expansions. Several single‐point calculations were performed to estimate effects of electron correlation enhancement from MP2 to quadratic configuration interaction [QCISD(T)]. Simulating a high level calculation with lower level calculations in a procedure similar to the recent G2(MP2) theory was found very successful.

A comprehensive study of the rotational energy profiles of organic systems by ab initio MO theory, forming a basis for peptide torsional parameters

Abstract: Ab initio molecular orbital calculations have been carried out on over 50 model organic molecules and ions to provide the data necessary in the determination of torsional parameters for a force field involving polypeptides. The rotational energy profiles were obtained at the HF/6-31G*//HF/6-31G* level. The results were supported, in many cases, by full geometry optimizations and with consideration of correlation corrections at the MP2 level. With the exception of the dihedral angle being studied, all of the molecules were fully optimized with C1 symmetry. © 1995 by John Wiley & Sons, Inc.

Rotational isomerism in acrylic acid. A combined matrix-isolated IR, Raman and ab initio molecular orbital study

Abstract: The results of a combined vibrational and structural study of the acrylic acid monomer undertaken by matrix-isolated low-temperature IR spectroscopy and ab initio SCF-HF and MP2 MO calculations are presented. In addition, both Raman and IR spectra of liquid acrylic acid and the Raman spectrum of the crystal are also reported and interpreted. It is shown that in both argon and krypton matrices acrylic acid monomer exists as a mixture of two conformers of similar energies, differing by the relative orientation of the CC—CO axis. Upon irradiation at λ= 243 nm by a xenon lamp, the s-cis form (CC—CO dihedral angle equal to 0 °), corresponding to the conformational ground state, converts to the s-trans form (CC—CO dihedral angle equal to 180 °). In the liquid phase, dimeric structures strongly predominate, but the existence in this phase of the two conformational states referred to above can also be inferred from the corresponding vibrational spectra. In turn, in the crystal only the thermodynamically most stable form (s-cis) exists. Results of ab initio SCF-HF and MP2 molecular orbital (MO) calculations, in particular optimised geometries, relative stabilities, dipole moments and harmonic force fields, for the relevant conformational states of acrylic acid are also presented and the conformational dependence of some relevant structural parameters is used to characterise the most important intramolecular interactions present in the studied conformers. Finally, the calculated vibrational spectra and both the results of a normal-mode analysis based on the theoretical harmonic force fields and of IR intensity studies based on the charge–charge flux–overlap (CCFO) model were used to help interpret the experimental vibrational data, enabling a detailed assignment of the acrylic acid spectra obtained in the different conditions considered.

Attempted prediction of the crystal structures of six monosaccharides

Abstract: A method is reported to generate possible crystal structures of the six hexopyranoses where comparison with an X-ray determination is possible. In these molecules, internal degrees of freedom are all-important. Using essentially only the information that the space group is P2 1 2 1 2 1 with one molecule in the asymmetric unit, a systematic search was made for all low-energy crystal structures of these substances. The energies were minimized with respect to nine lattice and rigid-body parameters and six intramolecular dihedral angles. The number of possible structures within the range 10 kcal mol −1 is of the order 1000. In all cases, the experimental structure was among them, and in four cases this was either the structure with the lowest energy or only a few tenths of a kcal mol −1 higher. However, in the two other cases the relative energy of the experimental structure was over 5 kcal mol −1 . Such calculations can provide a sensitive test for force fields

Dihedral bounds for mesh generation in high dimensions

Abstract: We show that any set of n points in IR has a Steiner Delaunay triangulation with O(ndd/2e) simplices, none of which has an obtuse dihedral angle. This result improves a naive bound of O(n). No bound depending only on n is possible if we require the maximum dihedral angle to measure at most 90◦−2 or the minimum dihedral to measure

P-T-X effects on equilibrium carbonate-H 2 O-CO 2 -NaCl dihedral angles: constraints on carbonate permeability and the role of deformation during fluid infiltration

Abstract: Fluid-solid-solid dihedral angles in the NaCl-H2O-CO2-calcite-dolomite-magnesite system have been determined at pressures ranging from 0.5 to 7 kbar and temperatures from 450°C to 750°C. At 1 kbar and 650°C, both dolomite and magnesite exhibit a dihedral angle minimum for intermediate H2O-CO2 fluids similar to that previously determined by the present authors for calcite, but the depth of the minimum is smaller, being above the critical value of 60° for both dolomite and magnesite for all fluid compositions. Calcite-calcite-brine dihedral angles at 650°C have been determined in the pressure range 1–5 kbar. Angles decrease with increasing salt content of the fluid, tending towards a constant value of about 65° for strong brines at pressures above 2 kbar. There is a general increase of angle with increasing pressure which is most marked for strong brines. A positive correlation of angle with pressure is also observed in calcite-H2O-CO2 fluids, the position of the minimum moving towards higher angles and towards H2O-rich fluids with increasing pressure. The permeability window previously observed by the present authors at 1 kbar and intermediate fluid compositions closes at about 1.5 kbar. The results demonstrate that the permeability of carbonates to grain edge fluid flow is only possible at low pressures and for fluids of restricted H2O-CO2-NaCl compositions. However, geochemical evidence from metamorphic terrains suggests that pervasive infiltration does occur under conditions where impermeability is predicted. From examination of published studies of infiltrated carbonates we conclude that deformation plays a critical role in enhancing carbonate permeability. Possible mechanisms for this include shear-enhanced dilatancy (micro-cracking), fluid inclusion drag by deformation-controlled grain boundary migration, and dynamically maintained transient grain boundary fluid films.

Conformational analysis of molecular chains using nano-kinematics.

Abstract: We present algorithms for 3-D manipulation and conformational analysis of molecular chains, when bond lengths, bond angles and related dihedral angles remain fixed. These algorithms are useful for local deformations of linear molecules, exact ring closure in cyclic molecules and molecular embedding for short chains. Other possible applications include structure prediction, protein folding, conformation energy analysis and 3D molecular matching and docking. The algorithms are applicable to all serial molecular chains and make no assumptions about their geometry. We make use of results on direct and inverse kinematics from robotics and mechanics literature and show the correspondence between kinematics and conformational analysis of molecules. In particular, we pose these problems algebraically and compute all the solutions making use of the structure of these equations and matrix computations. The algorithms have been implemented and perform well in practice. In particular, they take tens of milliseconds on current workstations for local deformations and chain closures on molecular chains consisting of six or fewer rotatable dihedral angles.

Metal search: a computer program that helps design tetrahedral metal-binding sites.

Abstract: We describe a computer program (Metal Search) that helps design tetrahedrally coordinated metal binding sites in proteins of known structure. The program takes as input the backbone coordinates of a protein and outputs lists of four residues that might form tetrahedral sites if wild-type amino acids were replaced by cysteine or histidine. The program also outputs the side chain dihedral angles of the amino acids and the coordinates of the predicted metal ion. The only function evaluated by Metal Search is the ability of side chains to meet simple geometric criteria for formation of a tetrahedral site, but these criteria are sufficient to produce a manageably small list that can then be evaluated by other means. The program has been used in the introduction of zinc binding sites in the designed four-helix bundle protein α 4 and in the B1 domain of streptococcal protein G, and in both cases the tetrahedral coordination of a bound metal ion has been confirmed1 (Klemba, M., Gardner, K. H., Marino, S., Clarke, N. D., and Regan, L., Nature: Structural Biology 2:368–373, 1995). © 1995 Wiley-Liss, Inc.

1H and 15N resonance assignments and structure of the N-terminal domain of Escherichia coli initiation factor 3.

Abstract: Initiation factor IF3 from Escherichia coli is composed of two domains connected by a hydrophilic peptide. In this study, the N-terminal domain (residues 7–83) has been overexpiessed, 15N labelled and purified. NMR assignments for this domain have been obtained by two-dimensional and three-dimensional heteronuclear and homonuclear spectroscopy. Using distance geometry and simulated annealing, a three-dimensional solution structure was calculated using 506 NOE and 56 dihedral angle restraints. The resulting structure is composed of a five-stranded antiparallel β sheet surrounded by two α helices. Since the heteronuclear 1H-15N correlation spectrum of the N-terminal domain of IF3 is an almost exact subset of that of the native protein, the assignments obtained and the structure calculated should be directly transposable to the full-length protein.

Solution conformation of cobrotoxin: a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study.

Abstract: The solution conformation of cobrotoxin has been determined by using proton nuclear magnetic resonance spectroscopy. With the combination of various two-dimensional NMR techniques, the 1H-NMR spectrum of cobrotoxin was completely assigned (Yu et al., 1990). A set of 435 approximate interproton distance restraints was derived from nuclear Overhauser enhancement (NOE) measurements. These NOE constraints, in addition to the 29 dihedral angle constraints (from coupling constant measurements) and 26 hydrogen bonding restraints (from the pattern of short-range NOEs), form the basis of 3-D structure determination by the hybrid distance geometry-dynamical simulated annealing method. The 23 structures that were obtained satisfy the experimental restraints, display small deviation from idealized covalent geometry, and possess good nonbonded contacts. Analysis of converged structures indicated that there are two antiparallel beta sheets (double and triple stranded), duly confirming our earlier observations. These are well defined in terms of both atomic root mean square (RMS) differences and backbone torsional angles. The average backbone RMS deviation between the calculated structures and the mean structure, for the beta-sheet regions, is 0.92 A. The mean solution structure was compared with the X-ray crystal structure of erabutoxin b, the homologous protein. This yielded information that both structures resemble each other except at the exposed loop/surface regions, where the solution structure seems to possess more flexibility.

Solution structure of porcine pancreatic phospholipase A2 complexed with micelles and a competitive inhibitor

Abstract: The three-dimensional structure of porcine pancreatic PLA2 (PLA2), present in a 40 kDa ternary complex with micelles and a competitive inhibitor, has been determined using multidimensional heteronuclear NMR spectroscopy. The structure of the protein (124 residues) is based on 1854 constraints, comprising 1792 distance and 62 ϕ torsion angle constraints. A total of 18 structures was calculated using a combined approach of distance geometry and restrained molecular dynamics. The atomic rms distribution about the mean coordinate positions for residues 1–62 and 72–124 is 0.75±0.09 A for the backbone atoms and 1.14±0.10 A for all atoms. The rms difference between the averaged minimized NMR structures of the free PLA2 and PLA2 in the ternary complex is 3.5 A for the backbone atoms and 4.0 A for all atoms. Large differences occur for the calcium-binding loop and the surface loop from residues 62 through 72. The most important difference is found for the first three residues of the N-terminal α-helix. Whereas free in solution Ala1, Leu2 and Trp3 are disordered, with the α-amino group of Ala1 pointing out into the solvent, in the ternary complex these residues have an α-helical conformation with the α-amino group buried inside the protein. As a consequence, the important conserved hydrogen bonding network which is also seen in the crystal structures is present only in the ternary complex, but not in free PLA2. Thus, the NMR structure of the N-terminal region (as well as the calcium-binding loop and the surface loop) of PLA2 in the ternary complex resembles that of the crystal structure. Comparison of the NMR structures of the free enzyme and the enzyme in the ternary complex indicates that conformational changes play a role in the interfacial activation of PLA2.

Three-dimensional structure in solution of the polypeptide cardiac stimulant anthopleurin-A.

Abstract: The three-dimensional structure in aqueous solution of the 49-residue polypeptide anthopleurin-A (AP-A), from the sea anemone Anthopleura xanthogrammica, has been determined from 1H NMR data. A restraint set consisting of 411 interproton distance restraints inferred from NOEs and 19 backbone and 13 side chain dihedral angle restraints from spin-spin coupling constants, as well as 15 lower bound restraints based on the absence of NOEs in the spectra, was used as input for distance geometry calculations in DIANA and simulated annealing and restrained energy minimization in X-PLOR. Stereospecific assignments for 12 beta-methylene pairs were also included. The final set of 20 structures had mean pairwise rms differences over the whole molecule of 2.04 A for the backbone heavy atoms (N, C alpha, and C) and 2.59 A for all heavy atoms. For the well-defined region encompassing residues 2-7 and 17-49, the corresponding values were 0.82 and 1.27 A, respectively. AP-A adopts a compact structure consisting of four short strands of antiparallel beta-sheet (residues 2-4, 20-23, 34-37, and 45-48) connected by three loops. The first loop commences with a type I beta-turn which includes two important Asp residues; this loop is the least well-defined region of the protein, although a beta-turn involving residues 13-16 is observed in nearly half the structures. The loop linking the second and third strands is constrained by the 29-47 disulfide bond and contains two well-defined beta-turns, while the third loop contains the Gly40-Pro41 sequence, which has been identified previously as the site of cis-trans isomerism. The carboxylate group of Asp7 is close to the epsilon-ammonium group of Lys37, suggesting that they may form a salt bridge. A pH titration monitored by 2D NMR supports this by showing that Asp7 has a low pKa. It is proposed that this region of the molecule and the nearby residues Asp9 and His39 form part of the molecular surface which interacts with the mammalian cardiac sodium channel.

29Si superhyperfine interactions of the E′ center: a potential probe of range-II order in silica glass

Abstract: An electron spin resonance study has been carried out on E′ γ centers in γ-irradiated silica glasses of various 29 Si enrichments, with the object of measuring superhyperfine splittings due to 29 Si nuclei at the three closest silicon neighbors to the silicon of the unpaired spin. Experimental spectra obtained at X band (9.1 GHz) in the absorption mode and at Ka band (35.0 GHz) in the rapid-passage dispersion mode are compared with computer lineshape simulations based on a simple tight-binding model anchored to literature values of the so-called ‘weak’ 29 Si hyperfine splittings of the E′ 1 center in α-quartz. Surprisingly few E′ γ sites are found in the glasses to exhibit such ‘weak’ splittings. To reconcile this result with the model assumption made by Mozzi and Warren and the supporting analyses of Galeener, it is suppose that dihedral angles in glassy silica might be relatively uniformly distributed and uncorrelated with the SiOSi angle distribution in the undamaged glass but that backward puckering relaxations (similar to that calculated by Rudra et al. for the E′ 2 center in quartz) may be pervasive at E′ γ (oxygen vacancy) sites in glassy silica, causing dihedral angles in the range 100 ≲ α 1 ≲ 140° to be ‘read out’ in the present experiment as falling in the range 80 ≳ α 1 ≳ 40°

The effect of feldspar on quartz-H2O−CO2 dihedral angles at 4 kbar, with consequences for the behaviour of aqueous fluids in migmatites

Abstract: An investigation was made of the effect of trace amounts of feldspar (Na and/or K) on dihedral angles in the quartz-H2O−CO2 system at 4 kbar and 450–1050°C. Quartz-quartz-H2O dihedral angles in feldspar-bearing quartz aggregates are observed to be the same as those in pure quartz aggregates at temperatures below 500°C. Above this temperature, they decrease with increasing temperature until the solidus. The final angle at the inception of melting is about 65° for microcline-quartz-H2O and microcline-albite-quartz-H2O, and much less than 60° (the critical value for formation of grain-edge fluid channels in an isotropic system) for the albite-quartz-H2O system. CO2 was observed to produce a constant quartz-quartz-fluid dihedral angle of 97° in feldspar-bearing quartz aggregates at all temperatures studied. Also examined were the dihedral angles for the two co-existing supersolidus fluids in quartz aggregates. In all systems the quartz-volatile fluid angle is greater than 60°, whereas the quartz-melt angle is lower than 60°. Both supersolidus angles decrease with increasing temperature. The transition from nonconnected to connected porosity with increasing temperature observed in the quartz-albite-H2O system some tens of degrees below the solidus (termed a permeability transition), if a common feature of rocks near their melting points, will play an important role in controlling the permeability of high-grade rocks to aqueous fluids.

Three-dimensional structure of gurmarin, a sweet taste-suppressing polypeptide.

Abstract: The solution structure of gurmarin was studied by two-dimensional proton NMR spectroscopy at 600 MHz. Gurmarin, a 35-amino acid residue polypeptide recently discovered in an Indian-originated tree Gymnema sylvestre, selectively suppresses the neural responses of rat to sweet taste stimuli. Sequence-specific resonance assignments were obtained for all backbone protons and for most of the side-chain protons. The three-dimensional solution structure was determined by simulated-annealing calculations on the basis of 135 interproton distance constraints derived from NOEs, six distance constraints for three hydrogen bonds and 16 dihedral angle constraints derived from coupling constants. A total of 10 structures folded into a well-defined structure with a triple-stranded antiparallel beta-sheet. The average rmsd values between any two structures were 1.65 +/- 0.39 A for the backbone atoms (N, C alpha, C) and 2.95 +/- 0.27 A for all heavy atoms. The positions of the three disulfide bridges, which could not be determined chemically, were estimated to be Cys3-Cys18, Cys10-Cys23 and Cys17-Cys33 on the basis of the NMR distance constraints. This disulfide bridge pattern in gurmarin turned out to be analogous to that in omega-conotoxin and Momordica charantia trypsin inhibitor-II, and the topology of folding was the same as that in omega-conotoxin.