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Dihedral angle
About: Dihedral angle is a research topic. Over the lifetime, 15718 publications have been published within this topic receiving 174904 citations.
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TL;DR: In this paper, a novel resolution enhancement technique which applies a sinusoidal half-wave window to the free induction decay combined with multiplication by an increasing exponential was used to extract resonances out of crowded spectral regions.
Abstract: The thus far unexplored aliphatic region of the proton magnetic resonance spectra of ferrichrome peptides was investigated at 360 MHz. Six isomorphic diamagnetic analogues of the ferric cyclohexapeptide differing in the coordinated cation (AL3+ or Ga3+) and the amino acid composition were studied in d6-DMSO solution. By use of a novel resolution enhancement technique which applies a sinusoidal half-wave window to the free induction decay combined with multiplication by an increasing exponential, the proton chemical shifts and spin-spin couplings were accurately measured. Homonuclear decoupling combined with Fourier difference spectroscopy was used to selectively extract resonances out of crowded spectral regions. The spectra revealed unique features of fine structure in the proton resonance lines. Thus, the conformation-dependent geminal coupling constants of glycyl α-protons were found to be constant throughout the suite of analogue peptides. A similar invariance was observed for the vicinal coupling constants between α-, β-, γ-, and δ-protons in the ornithyl side chains. Comparison of the proton spin–spin coupling constants with the crstallographic dihedral angles led to a unique stereochemical assignment of the side-chain resonances. The combined data sets of x-ray atomic coordinates and 1H-nmr spin-spin coupling parameters have been used to calibrate the coefficients for a Karplus curve related to the torsional x angles in amino acid side chains:
Structurial information was also obtained for the seryl residues, where the multiplet structures of the OH resonances indicate preferred spatial arrangements of the side chains.
154 citations
TL;DR: In this article, the additive all-atom CHARMM force field for acyclic polyalcohols, inositol, and carbonyls was optimized targeting quantum mechanical interaction data for solute−water pairs and pure solvent thermodynamic data.
Abstract: Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates, and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute−water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde, and glycerol. C−C−C−C, C−C−C−O, C−C−O−H, and O−C−C−O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential-energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed co...
153 citations
TL;DR: The results show that in the amide I region, β‐turn frequencies can overlap with those of the α‐helix and β‐sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region.
Abstract: modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide I1 modes. The results show that in the amide I region, P-turn frequencies can overlap with those of the cu-helix and @-sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide I11 modes of 0-turns are predicted at significantly higher frequencies than those of (?-helix and 0-sheet structures, and this region therefore provides the hest possibility of identifying 0-turn structures. Amide V frequencies of fl-turns may also he distinctive for such structures.
152 citations
TL;DR: The linear dependence of the S-S stretching frequency on dihedral angle leads to a dihedral angles for the plant hormone, malformin A, that is in excellent agreement with that estimated from the longest wavelength CS-SC ultraviolet absorption band.
Abstract: Raman spectra of several compounds containing the CS-SC moiety were obtained (in the solid phase) from 450-800 cm(-1) to investigate the S-S and C-S stretching behavior. The S-S stretching frequency varied linearly with the CS-SC dihedral angle (obtained from either x-ray or neutron diffraction or ultraviolet absorption) for compounds whose CC-SS dihedral angles were not very different. The ratio of the intensities of the S-S and C-S stretching bands exhibited no recognizable correlation with either the CS-SC dihedral angle or the CSS bond angle, probably because this ratio is sensitive to the crystalline environment. The linear dependence of the S-S stretching frequency on dihedral angle leads to a dihedral angle for the plant hormone, malformin A, that is in excellent agreement with that estimated from the longest wavelength CS-SC ultraviolet absorption band.
151 citations
TL;DR: In this article, a survey of the influence of the N-Ca-C′ angle in determining allowed helical conformations can be found, and the potential energy contour maps obtained in this manner are basically similar to the conformational maps calculated by the first method.
150 citations