Showing papers on "Dihedral angle published in 1993"
TL;DR: Molecular dynamics simulation covering a wide range of hydration indicate that myoglobin is fully hydrated by 350 water molecules, in agreement with experiment, and anharmonic protein motion above 220 K is enhanced by protein hydration.
Abstract: Molecular dynamics (MD) simulation covering a wide range of hydration indicate that myoglobin is fully hydrated by 350 water molecules, in agreement with experiment. These waters, originally placed uniformly about the protein, form clusters that hydrate every charged group throughout the entire simulation. Some atoms in charged groups are hydrated by two water layers while 37% of the protein surface remains uncovered. The locations of the 350 waters are consistent with those of crystallographic waters resolved by x-ray and neutron diffraction. Hydration by 350 waters at 300 K stabilizes the conformation of carboxymyoglobin measured by x-ray diffraction throughout the entire protein, halves the rate of torsional transitions, and promotes alternative conformations for surface atoms. The glass transition observed experimentally in hydrated myoglobin near 220 K is also seen in the simulations and correlates with an increase in the number of dihedral angles undergoing transitions. The anharmonic protein motion above 220 K is enhanced by protein hydration.
230 citations
TL;DR: Application of the reduced representation model, which has been described in previous reports, to apamin, an 18‐residue polypeptide with two disulfide bonds, shows that it folds apamin to native‐like conformations with the correct disulfides formed.
Abstract: A reduced representation model, which has been described in previous reports, was used to predict the folded structures of proteins from their primary sequences and random starting conformations. The molecular structure of each protein has been reduced to its backbone atoms (with ideal fixed bond lengths and valence angles) and each side chain approximated by a single virtual united-atom. The coordinate variables were the backbone dihedral angles phi and psi. A statistical potential function, which included local and nonlocal interactions and was computed from known protein structures, was used in the structure minimization. A novel approach, employing the concepts of genetic algorithms, has been developed to simultaneously optimize a population of conformations. With the information of primary sequence and the radius of gyration of the crystal structure only, and starting from randomly generated initial conformations, I have been able to fold melittin, a protein of 26 residues, with high computational convergence. The computed structures have a root mean square error of 1.66 A (distance matrix error = 0.99 A) on average to the crystal structure. Similar results for avian pancreatic polypeptide inhibitor, a protein of 36 residues, are obtained. Application of the method to apamin, an 18-residue polypeptide with two disulfide bonds, shows that it folds apamin to native-like conformations with the correct disulfide bonds formed.
208 citations
TL;DR: In this article, density functional calculations with simulated annealing have been performed for clusters of aluminum Aln and gallium Gan up to n=10, with a rich variety of structures and spin multiplicities.
Abstract: Density functional calculations with simulated annealing have been performed for clusters of aluminum Aln and gallium Gan up to n=10. There are many local minima in the energy surfaces, with a rich variety of structures and spin multiplicities. With increasing cluster size we find transitions from planar to nonplanar structures at n=5, and to states with minimum spin degeneracy at n=6. Isomers (n≥5) with buckled planar structures reminiscent of the layers in crystalline α‐gallium are generally less stable than ‘‘three‐dimensional’’ isomers. All structures show regular patterns of bond and dihedral angles. Systematic differences between Al and Ga clusters—bonds in the latter are shorter and bond angles closer to 90°—can be understood in terms of atomic properties. Trends in binding and ionization energies are compared with experiment and with the predictions of other calculations.
183 citations
TL;DR: High-resolution three-dimensional structures of bovine pancreatic ribonuclease A in aqueous solution determined by nuclear magnetic resonance (NMR) spectroscopy combined with restrained molecular dynamics calculations are presented.
148 citations
TL;DR: Overall the structure of the bound ligand seems to be organized to protect the lipophilic palmitoyl part from the polar solvent.
142 citations
TL;DR: The structure of the 129-residue protein hen lysozyme has been determined in solution by two-dimensional 1H nuclear magnetic resonance methods, and many side-chains on the surface, however, are highly disordered amongst the set of solution structures.
140 citations
TL;DR: The dihedral angles of H2O CO2 fluids in quartz aggregates have been determined experimentally at 450-1080°C and 1-9.5 kbar.
128 citations
TL;DR: The high-resolution three-dimensional solution structure of recombinant human interleukin-4 (IL-4), a protein of approximately 15 kDa which plays a key role in the regulation of B and T lymphocytes, has been determined using three- and four-dimensional heteronuclear NMR spectroscopy.
Abstract: The high-resolution three-dimensional solution structure of recombinant human interleukin-4 (IL-4), a protein of - 15 kDa which plays a key role in the regulation of B and T lymphocytes, has been determined using three- and four-dimensional heteronuclear NMR spectroscopy. The structure is based on a total of 2973 experimental NMR restraints, comprising 25 15 approximate interproton distance restraints, 102 distance restraints for 51 backbone hydrogen bonds, and 356 torsion angle restraints. A total of 30 structures was calculated by means of hybrid distance geometry-simulated annealing, and the atomic rms distribution about the mean coordinate positions for residues 8-129 is 0.44 f 0.03 A for the backbone atoms, 0.83 f 0.03 A for all atoms, and 0.51 f 0.04 A for all atoms excluding disordered side chains. The N- and C-terminal residues (1-7 and 130-133, respectively) appear to be disordered. The structure of IL-4 is dominated by a left-handed four-helix bundle with an unusual topology comprising two overhand connections. The linker elements between the helices are formed by either long loops, small helical turns, or short strands. The latter include a mini anti-parallel P-sheet. A best fit superposition of the NMR structure of IL-4 with the 2.25 A resolution crystal structure (Wlodawer, A., Pavlovsky, A., & Gutschina, A. (1992) FEBS Lett. 309, 59-64) yields a backbone atomic rms difference of 1.37 A which can be mainly attributed to tighter packing of the helices in the crystal structure. This is indicated by an approximately 20% reduction in the axial separation of three pairs of helices (CYA-CYC, CYA-CYD, and CYCCYD) in the crystal structure relative to the NMR structure and may reflect the greater flexibility of the molecule in solution which is reduced in the crystal due to intermolecular contacts. Comparison of the NMR structure of IL-4 with the X-ray structures of two other related proteins, granulocyte-macrophage colony stimulating factor ( Diedrichs, K., Boone, T., & Karplus, P. A. (1992) Science 254,1779-17821 and human growth hormone (de Vos, A. M., Ultsch, M., & Kossiakoff, A. A. (1992) Science 255, 306-3121, that bind to the same hematopoietic superfamily of cell surface receptors reveals a remarkably similar topological fold, despite the absence of any significant overall sequence identity, and substantial differences in the relative lengths of the helices, the lengths and the nature of the various connecting elements, and the pattern and number of disulfide bridges. Indeed, the Ca atom coordinates of 72 and 79 residues of IL-4 can be superimposed on the Ca coordinates of granulocyte-macrophage colony stimulating factor and human growth hormone with rms differences of - 1.7 and 2.0 A, respectively.
123 citations
TL;DR: The patterns of disorder in this structure reveal important principles of protein structure and its dynamics, and suggests that co-ordinated motion extends in groups rather than simply as uncorrelated movement around an atom center.
120 citations
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TL;DR: The topography of the β-turn was investigated in this paper using 146 examples of βturns reported in the literature and common topographical features were observed across a wide variety of β turn types, including the spatial relationship between the entry and exit peptide bonds and the relative orientations of the intervening sidechains.
111 citations
TL;DR: A new penalty function for use in restrained molecular dynamics simulations which allows experimental J-coupling information to be enforced as a time-averaged, rather than instantaneous, quantity is described.
Abstract: We describe a new penalty function for use in restrained molecular dynamics simulations which allows experimental J-coupling information to be enforced as a time-averaged, rather than instantaneous, quantity. The pseudo-energy term has been formulated in terms of a calculated J value (a measured quantity) rather than the relevant dihedral angle (a derived quantity). This accounts for the distinct non-linearity of the coupling constant with respect to either Cartesian coordinates or dihedral angles. Example simulations of the cyclic decapeptide antamanide show the procedure's ability to enforce experimental restraints while exploring a large region of conformational space and producing a relatively small disturbance of the physical force field.
TL;DR: In this paper, the three-dimensional solution structure of calcium-loaded calbindin D 9k has been determined using experimental constraints obtained from nuclear magnetic resonance spectroscopy, including 1002 distance and 174 dihedral angle constraints.
TL;DR: In this article, the location of minima and transition states by eigenvector following using Cartesian coordinates and a projection operator was described, and compared with calculations employing standard internal coordinates are made for a wide variety of model clusters.
Abstract: Location of minima and transition states by eigenvector following using Cartesian coordinates and a projection operator is described. Comparisons with calculations employing standard internal coordinates are made for a wide variety of model clusters. The new method, suggested by Baker and Hehre, generally produces faster converagence and solves a number of problems that are inherent when using distance, bond angle, dihedral angle internal coordinates. In particiular, eigenvector-following calculations using analytic first and second energy derivatives should now be possible for much larger systems. Some example reaction paths are illustrated, including a new facetting rearrangement of 55- and 147-atom Mackay icosahedra. The basins of attraction of minima and transition states are also calculated, that is, the regions of the potential-energy surface for which stationary-point searches converge to a given structure. The superiority of the projection operator approach is again demonstrated, and the previous observation that initial geometrical contraction is helpful in transition-state searches is confirmed.
TL;DR: In this article, a wide variety of different rearrangements for both (H2O)8 and (H 2O)20 are illustrated, with barrier heights ranging over three orders of magnitude.
Abstract: We have calculated rearrangement mechanisms for (H2O)8 and (H2O)20 clusters by eigenvector following. For (H2O)8, two different parametrizations of a four‐site, rigid water effective pair potential were considered and found to give very similar results. Hence, only one of the potentials is applied to (H2O)20. 6N−6 internal coordinates are required to describe a (H2O)N cluster in these calculations, of which 3N−6 were chosen as center‐of‐mass distances, angles, and dihedral angles, the other 3N being Euler angles. A wide variety of different rearrangements for both (H2O)8 and (H2O)20 are illustrated, with barrier heights ranging over three orders of magnitude. The mechanisms range from almost imperceptible changes of geometry to folding processes that result in dramatic structural transformations.
TL;DR: In this article, the authors investigate the utility of reversible multiple time-step methods for determining the dynamics of n−alkanes as neat liquids and in aqueous solution, and show that stable integrations that yield agreement with standard dynamics can be achieved with a saving up to a factor of 5 in computer time.
Abstract: In molecular dynamics simulations of flexible molecules, the treatment of motions that take place on different time scales (e.g., bond stretching and bond angle bending vs dihedral angle librations and overall translation and rotation) or of forces that vary differently with distance (e.g., bonding forces vs electrostatic forces) is a major consideration. The most rapidly varying quantity limits the integration time step, while the most slowly varying quantity usually determines the simulation time required. The reversible multiple time‐step methods introduced by Tuckerman, Berne, and Martyna [J. Chem. Phys. 97, 1990 (1992)] allow one to use different integration time steps in the same simulation so as to treat the time development of the slow and fast motions most effectively. As a first step toward extending multiple time‐step methods to macromolecules, we investigate their utility for determining the dynamics of n‐alkanes as neat liquids and in aqueous solution. Because the dynamics is done in Cartesian rather than internal coordinates, the different time steps are implemented in terms of hard and soft forces acting on individual atoms; e.g., hard forces are contributed by bond stretching (and bond angle bending) terms and soft forces by the remaining intramolecular and intermolecular (van der Waals and electrostatic) terms in the additive empirical potential function used to describe these systems. Integrations with and without a Nose–Hoover thermostat are performed. Comparisons are made with ordinary single time step molecular dynamics and dynamics with constraints applied to the bonds. The stability of the integration methods and the dynamic properties are considered. It is shown that stable integrations that yield agreement with standard dynamics can be achieved with a saving of up to a factor of 5 in computer time.
TL;DR: In this paper, the rotational isomerization of a poly(alkylthiophene) oligomer, 3',4'-dibutyl-2,2':5',2''-terthyphene, was reported.
Abstract: We report on the crystal structure and rotational isomerization of a poly(alkylthiophene) oligomer, 3',4'-dibutyl-2,2':5',2''-terthiophene. The X-ray crystal structure of this polythiopheneoligomer shows an all-anti configuration with an ∼33 o mean dihedral angle between adjacent thiophene rings. Measurements of the torsional carrier to rotation between thiophene rings have been performed for both the ground and first excited singlet states of this oligomer. The S 0 barrier to rotation is measured to be 19.7 Kcal/mol using 1 H NMR and the S 1 barrier to rotation is determined to be 4.2 kcal/mol using fluorescence lifetime measurements. We discuss the significance of these results in the context of understanding structure/property relationships in poly(alkylthiophenes)
TL;DR: In this article, two types of experiment involving synthetic clinopyroxenites were performed at 900°-950°C and 1.5 GPa: (1) annealing of ferrosalite (CaMg 0.4 Fe 0.54 Mn 0.06 Si 2 O 6 ) or diopside (caMg0.6, 1.3, 2.7, 4.0 and 8.0 vol% H 2 O (at run P and T ) showed no Fe = Mg interdiffusion for all but the most
TL;DR: Fullerene polyhedra are realisable within exactly 28 point groups: I h, I, T d, T h, T, D n h,D n d, S 2 m, C m h, C m v, Cm (m = 2, 3), C s, C i, C 1, and isolated-pentagon fullerenes can be constructed for all 28 groups as discussed by the authors.
TL;DR: In this paper, the photophysical and photochemical properties of phenyldisilanes having a trifluoromethyl substituent on a benzene ring as one of the most suitable substituents for stabilization of the OICT (σπ * orthogonal intramolecular charge transfer) state were investigated in detail.
Abstract: Photophysical and photochemical properties of phenyldisilanes having a trifluoromethyl substituent on a benzene ring as one of the most suitable substituents for stabilization of the OICT (σπ * orthogonal intramolecular charge-transfer) state were investigated in detail. The OICT mechanism for CT fluorescence in nonpolar solvents was supported by the remarkable dependence of absorption and fluorescence spectra of trifluoromethyl-substituted phenyldisilanes on the dihedral angle between benzene pπ orbital and the SiSi a bond
TL;DR: In this article, three new heterodinuclear CuIIMnII complexes of formula [cu(salen)Mn(hfa)2] (1), [Cu(pdmg)mn(phen)2](ClO4)2·2.
TL;DR: Twenty structures were calculated based on 676 nontrivial distance restraints, 152 torsion angle restraints, and stereospecific assignments of 38 chiral centers, using distance geometry, simulated annealing, and restrained energy minimization and none of the distance restraints was violated by more than 0.5 A in any of the 20 structures.
Abstract: The solution structure of a 125-residue basic protein, barwin, has been determined using 1H nuclear magnetic resonance spectroscopy. This protein is closely related to domains in proteins encoded by wound-induced genes in plants. Analysis of the 1H nuclear Overhauser spectrum revealed the assignment of more than 1400 nuclear Overhauser effects. Twenty structures were calculated based on 676 nontrivial distance restraints, 152 torsion angle restraints (92 phi, 56 chi 1, and 4 omega for proline), and stereospecific assignments of 38 chiral centers, using distance geometry, simulated annealing, and restrained energy minimization. None of the distance restraints was violated by more than 0.5 A in any of the 20 structures, and none of the torsion angle restraints was violated by more than 1 degree in any of the structures. The RMS difference between the calculated and target interproton distance restraints is 0.033 A, and the average atomic RMS differences between the 20 structures and their geometric average are 1.23 A for backbone atoms and 1.73 A for all heavy atoms. The dominating structural feature of the protein is a well-defined four-stranded antiparallel beta-sheet, two parallel beta-sheets packed antiparallel to each other and four short alpha-helices. The binding site of barwin to the tetramer N-acetylglucosamine has been qualitatively investigated, and the dissociation constant of the complex has been determined using one-dimensional 1H nuclear magnetic resonance spectroscopy.
TL;DR: In this article, the authors present a method for the synthesis of (R)-3-hydroxybutanoate (3-HB) units from the hydroxy acid itself, its methyl ester, its lactone (monolide) or its polymer.
Abstract: Cyclic Oligomers of (R)-3-Hydroxybutanoic Acid: Preparation and Structural Aspects
The oligolides containing three to ten (R)-3-hydroxybutanoate (3-HB) units (12-through 40-membered rings 1–8) are prepared from the hydroxy acid itself, its methyl ester, its lactone (‘monolide’), or its polymer (poly(3-HB), mol. wt. ca. 106 Dalton) under three sets of conditions: (i) treatment of 3-HB (10) with 2,6-dichlorobenzoyl chloride/pyridine and macrolactonization under high dilution in toluene with 4-(dimethylamino)pyridine (Fig. 3); (ii) heating a solution (benzene, xylene) of the β-lactone 12 or of the methyl ester 13 from 3-HB with the tetraoxadistanna compound 11 as trans-esterification catalyst (Fig. 4); (iii) heating a mixture of poly(3-HB) and toluene-sulfonic acid in toluene/1,2-dichloroethane for prolonged periods of time at ca. 100° (Fig. 6). In all three cases, mixtures of oligolides are formed with the triolide 1 being the prevailing component (up to 50% yield) at higher temperatures and with longer reaction times (thermodynamic control, Figs. 3–6). Starting from rac-β-lactone rac-12, a separable 3:1 to 3:2 mixture of the l,u- and the l,l-triolide diasteroisomers rac-14 and rac-1, respectively, is obtained. An alternative method for the synthesis of the octolide 6 is also described: starting from the appropriate esters 15 and 17 and the benzyl ether 16 of 3-HB, linear dimer, tetramer, and octamer derivatives 18–23 are prepared, and the octamer 23 with free OH and CO2H group is cyclized (6) under typical macrolactonization conditions (see Scheme). This ‘exponential fragment coupling protocol’ can be used to make higher linear oligomers as well. The oligolides 1–8 are isolated in pure form by vacuum distillation, chromatography, and crystallization, an important analytical tool for determining the composition of mixtures being 13C-NMR spectroscopy (each oligolide has a unique and characteristic chemical shift of the carbonyl C-atom, with the triolide 1 at lowest, the decolide 8 at highest field). The previously published X-ray crystal structures of triolide 1, pentolide 3, and hexolide 4 (two forms), as well as those of the l,u-triolide rac-14, of tetrolide ent-2, of heptolide 5, and of two modifications of octolide 6 described herein for the first time are compared with each other (Figs. 7–10 and 12–15, Tables 2 and 5–7) and with recently modelled structures (Tables 3 and 4, Fig. 11). The preferred dihedral angles τ1 to τ4 found along the backbone of the nine oligolide structures (the hexamer and the larger ones all have folded rings!) are mapped and statistically evaluated (Fig. 16, Tables 5–7). Due to the occurrence of two conformational minima of the dihedral angle OCOCH2CH (τ3 = + 151 or −43°), it is possible to locate two types of building blocks for helices in the structures at hand: a right-handed 31 and a left-handed 21 helix; both have a ca. 6 A pitch, but very different shapes and dispositions of the carbonyl groups (Fig. 17). The 21 helix thus constructed from the oligolide single-crystal data is essentially superimposable with the helix derived for the crystalline domains of poly(3-HB) from stretched-fiber X-ray diffraction studies. The absence of the unfavorable (E)-type arrangements around the OCOR bond (‘cis-ester’) from all the structures of (3-HB) oligomers known so far suggests that the model proposed for a poly(3-HB)-containing ion channel (Fig. 2) must be modified.
TL;DR: In this paper, the effect of molecular steric properties on the melting of quasi-two-dimensional solids is investigated by comparing results of molecular dynamics simulations of the butane and hexane monolayers adsorbed on the basalplane surface of graphite.
Abstract: The effect of molecular steric properties on the melting of quasi‐two‐dimensional solids is investigated by comparing results of molecular dynamics simulations of the melting of butane and hexane monolayers adsorbed on the basal‐plane surface of graphite. These molecules differ only in their length, being members of the n‐alkane series [CH3(CH2)n−2CH3] where n=4 for butane and n=6 for hexane. The simulations employ a skeletal model, which does not include the hydrogen atoms explicitly, to represent the intermolecular and molecule–substrate interactions. Nearest‐neighbor intramolecular bonds are fixed in length, but the molecular flexibility is preserved by allowing the bend and dihedral torsion angles to vary. The simulations show a qualitatively different melting behavior for the butane and hexane monolayers consistent with neutron and x‐ray scattering experiments. The melting of the low‐temperature herringbone (HB) phase of the butane monolayer is abrupt and characterized by a simultaneous breakdown of ...
TL;DR: In this article, the title compound (1) was obtained as black diamagnetic crystals by reaction of CpLuCl 2 with sodium naphthalide in DME, and it was shown that the Lu atom is bent about the C(1)⋯C(4) plane (dihedral angle 148.5°).
TL;DR: The 3D structure of bovine recombinant acyl-coenzyme A binding protein has been determined using multidimensional heteronuclear magnetic resonance spectroscopy in a study that combines investigations of 15N-labeled and unlabeled protein.
Abstract: The 3D structure of bovine recombinant acyl-coenzyme A binding protein has been determined using multidimensional heteronuclear magnetic resonance spectroscopy in a study that combines investigations of 15N-labeled and unlabeled protein. The present structure determination is a refinement of the structure previously determined (Andersen, K.V. and Poulsen, F.M. (1992) J. Mol. Biol., 226, 1131–1141). It is based on 1096 distance restraints and 124 dihedral angle restraints of which 69 are for ϕ-angles and 8 for chiral centers and 47 for prochiral centers. The new experimental input for the structure determination has provided an increase of 263 distance restraints, 5 ϕ-angle restraints, and 32 χ-angle restraints in 2 chiral centers, and 31 prochiral centers restraining an additional 23 χ
1, 8 χ
2, and 1 χ
3 angles. The increase of 300 distance and dihedral angle restraints representing an additional 30% of input parameters for the structure determination has been shown to be in agreement with the first structure. A set of 29 structures has been calculated and each of the structures has been compared to a mean structure to give an atomic root mean square deviation of 0.44±0.12 A (1 A is 0.1 nm) for the backbone atoms C, Cα, and N in the four α-helices A1, residues 4–15, A2, residues 21–36, A3, residues 51–62 and A4, residues 65–84. The loop-region of residues Gly45-Lys50 could not be defined by the restraints obtained by NMR. The program PRONTO has been used for the spectrum analysis, assignment of the individual nuclear Overhauser effects, the integration of the cross peaks, and the measurement of the coupling constants. The programs DIANA, X-PLOR and INSIGHT have been used in the structure calculations and evaluations.
TL;DR: The use of dimethylsulfoxide and chloroform in molecular dynamics is described, with some advantages of the use of these solvents highlighted.
Abstract: In this article a few methods or modifications proven to be useful in the conformational examination of peptides and related molecules by molecular dynamics are illustrated. The first is the explicit use of organic solvents in the simulations. For many cases such solvents are appropriate since the nmr measurements (or other experimental observations) were carried out in the same solvent. Here, the use of dimethylsulfoxide and chloroform in molecular dynamics is described, with some advantages of the use of these solvents highlighted.
A constant allowing for the scaling of the nonbonded interactions of the force field, an idea previously employed in distance geometry and simulated annealing, has been implemented. The usefulness of this method is that when the nonbonded term is turned to zero, atoms can pass through each other, while the connectivity of the molecule is maintained. It will be shown that such simulations, if a sufficient driving force is present (i.e., nuclear Overhauser effects restraints), can produce the correct stereoconfiguration (i.e., chiral center) as well as configurational isomer (i.e., cis/trans isomers).
Lastly, a penalty term for coupling constants directly related to the Karplus curve has been plemented into the potential energy force field. The advantages of this method over the commonly used dihedral angle restraining are discussed. In particular, it is shown that with more than one coupling constant about a dihedral angle a great reduction of the allowed conformational space is obtained. © 1993 John Wiley & Sons, Inc.
TL;DR: In this paper, the conformation of the C5-C6 bond in β-gentiobiose was analyzed in terms of the maximum entropy probability density distribution of the dihedral angle, and two major conformations characterized by Ω=-68.9 o ± 6.3 o and Ω=79.0 o ± 3.4 o were found.
Abstract: The conformation about the C5-C6 bond in β-gentiobiose, (β-D-Glcp-(1→6)-β-D-Glcp), has been analyzed in terms of the maximum entropy probability density distribution of the dihedral angle Ω. This analysis used the information carried by proton-proton and carbon-proton vicinal coupling constants and proton-proton cross-relaxation rates. Two major conformations characterized by Ω=-68.9 o ±6.3 o and Ω=79.0 o ±3.4 o were found with populations of 0.34±0.06 and 0.66±0.06, respectively
TL;DR: The three-dimensional structure of the DNA-binding domain of the human retinoic acid receptor-β (hRAR-β) has been determined by nuclear magnetic resonance spectroscopy in conjunction with distance geometry, restrained molecular dynamics and iterative relaxation matrix calculations.
Abstract: The three-dimensional structure of the DNA-binding domain of the human retinoic acid receptor-β (hRAR-β) has been determined by nuclear magnetic resonance spectroscopy in conjunction with distance geometry, restrained molecular dynamics and iterative relaxation matrix calculations. A total of 1244 distance restraints were obtained from NOE intensities, of which 448 were intra-residue and 796 inter-residue restraints. In addition 23 χ and 30 ϕ dihedral angle restraints were obtained from J-coupling data. The two ‘zinc-finger’ regions of the 80-amino acid residue protein are followed by two α-helices that cross each other perpendicularly. There is a short stretch of b-sheet near the N-terminus. The α-helical core of the protein is well determined with a backbone root-mean-square deviation (r.m.s.d.) with respect to the average of 0.18 A and 0.37 A when the side chains of residues 31, 32, 36, 61, 62, 65 and 69 are included. The r.m.s.d. for the backbone of residues 5–80 is 0.76 A. For the first finger (residues 8–28), the r.m.s.d. of the backbone is 0.79 A. For the second finger (residues 44–62) the r.m.s.d. is 0.64 A. The overall structure is similar to that of the corresponding domain of the glucocorticoid receptor, although the C-terminal part of the protein is different. The second α-helix is two residues shorter and is followed by a well-defined region of extended backbone structure.
TL;DR: In this paper, the Re-O conformation maximizes overlap of the d orbital HOMO of the rhenium fragment with C[double bond]O [pi]* orbital lobes on oxygen.
Abstract: Reactions of [([eta][sup 5]-C[sub 5]H[sub 5])Re(NO)(PPh[sub 3])(ClCH[sub 2]Cl)][sup +]BF[sub 4][sup [minus]] and ArCHO (Ar = a, C[sub 6]F[sub 5]; b, 4-C[sub 6]H[sub 4]CF[sub 3]; c, 3-C[sub 6]H[sub 4]CF[sub 3]; d, 3-C[sub 6]H[sub 4]OCH[sub 3]; e, 2-C[sub 6]H[sub 4]OCH[sub 3]; f, 4-C[sub 6]H[sub 4]Cl; g, 4-C[sub 6]H[sub 4]F; h, 1-naphthyl; i, C[sub 6]H[sub 5]; j, 3,4,5-C[sub 6]H[sub 2](OCH[sub 3])[sub 3]; k, 4-C[sub 6]H[sub 4]C[sub 6]H[sub 5]; l, 4-C[sub 6]H[sub 4]CH[sub 3]; m, 2,4-C[sub 6]H[sub 3](OCH[sub 3])[sub 2]; n, 3,4-C[sub 6]H[sub 3](OCH[sub 3])[sub 2]; o, 4-C[sub 6]H[sub 4]OCH[sub 3]) give aromatic aldehyde complexes [([eta][sup 5]-C[sub 5]H[sub 5])Re(NO)(PPh[sub 3])(O[double bond]CHAr)][sup +]BF[sub 4][sup [minus]] (4a--o[sup +]BF[sub 4][sup [minus]], 80--97%). IR analyses (CH[sub 2]Cl[sub 2], 26[degrees]C) show 4a--o[sup +]BF[sub 4][sup [minus]] to be >96:<4 to 15:85 mixtures of [pi]/[sigma] isomers (v[sub NO] 1745--1733/1701--1692 cm[sup [minus]1]). Electron withdrawing substituents (which enhance aldehyde [pi] acidity and lower [sigma] basicity) favor the [pi] binding model. Electron donating substituents have an opposite effect. The [pi]/[sigma] ratios increase in more polar solvents and at lower temperatures. Van't Hoff plots give [Delta]H (4i,l,o[sup +]BF[sub 4][sup [minus]]; [pi] [yields] [sigma]) of 3.6, 2.8, and 1.8 kcal/mol and [Delta]S of 9.2, 9.5, and 9.1 eu. IR features unique to both binding modes, andmore » visible absorptions characteristic of [sigma] isomers, are identified. Complex 4o[sup +]PF[sub 6][sup [minus]] crystallizes as a [sigma] isomer, with a conjugated Ar/C[double bond]O linkage, a lengthened C[double bond]O bond (1.271 (8) [angstrom]), and a 0[degrees] N-Re-O-C torsion angle. This Re-O conformation maximizes overlap of the d orbital HOMO of the rhenium fragment with C[double bond]O [pi]* orbital lobes on oxygen. 60 refs., 8 figs., 5 tabs.« less
TL;DR: The three-dimensional structure in solution of the pheromone Er-10 from the ciliated protozoan Euplotes raikovi has been determined by nuclear magnetic resonance spectroscopy and shows an asymmetric charge distribution that results in a predominantly apolar surface on one side of the molecule.