Torsion sensitivity in NMR of aligned molecules: study on various substituted biphenyls
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To estimate the torsion sensitivity of dipolar coupling, biphenylic molecules were chosen as probes due to their relatively simple structure and the surprisingly high ambiguity of the only flexible parameter-the interring torsion angle. Solution structures of 4,4'-dibromobiphenyl and 4,4'-diiodobiphenyl are reported for the first time in two liquid crystals I52 and ZLI 1695. The comparison of NMR structures of various para-substituted biphenyls (BPs), calculated by the additive potential maximum entropy (APME) approach, shows that the small spread of torsion angle values in case of different solvents and para-substituents is in good agreement with theoretical expectations from hybrid density functional theory (DFT) methods. Furthermore, the real structural changes of interring torsion and the prevalence of solvent effects over para-halosubstitution can be correctly revealed from these small fluctuations.Keywords:
Dihedral angle
Proton NMR
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In the title molecule, C 22 H 18 O, the o -tolyl ring is connected through a conjugated double bond. The molecule adopts an E conformation and the C—C=C—C torsion angle is 178.77 (13)°. The overall conformation may be described by the values of dihedral angles between the different planes. The terminal rings are twisted by an angle of 54.75 (8)°, while the biphenyl part is not planar, the dihedral angle between the planes of the rings being 40.65 (8)°. The dihedral angle between the benzene rings is 14.10 (7)°. There are three weak C—H...π interactions found in the crystal structure. No classic hydrogen bonds are observed.
Dihedral angle
Biphenyl
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In principle the correct three-dimensional structure of a protein molecule can be reproduced by setting the dihedral angles of its backbone and side chains without the need for measuring coordinates. Dihedral angles ø, Ψ, and ω determine the conformation of a protein's backbone while angles ϰ1, ϰ2, etc., determine the dispositions of its side chains. In most cases ω is taken as 0° (Edsall et al., 1966) since peptide bonds are generally trans- and coplanar. The use of dihedral angles with C.P.K. models was initiated by Hauschka and Segal (1966) who described the use of paper dials in setting angles ø and Ψ. Their contribution led us to ask the question: Can an accurate space-filling model of a protein actually be constructed from C.P.K. models relying entirely on dihedral angles?
Dihedral angle
Side chain
Dihedral group
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Abstract The three dimensional native structure plays an important role in determining the function of a protein. However, structure determination is tedious and costly, so prediction of protein three dimensional structures is a very important as well as a challenging task in computational biophysics. Prediction of dihedral angle is particularly helpful for predicting tertiary structure of proteins as knowledge of backbone torsion angles significantly narrow down the conformational search space for tertiary structure prediction. Dihedral angles provide a detailed description of local conformation of a protein. With the advancement of machine learning and other relevant techniques, dihedral angle prediction may establish itself as a fascinating supplement to secondary structure prediction. Over the last two decades, research in this direction has led to development of several dihedral angle prediction methods. In this article we critically review available methods for protein dihedral angle prediction with an emphasis on deep learning based real value angle prediction methods. We believe this review will provide important insights into the state of the art of protein dihedral angle prediction.
Dihedral angle
Protein tertiary structure
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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.
Dihedral angle
Ultraviolet
Molecular geometry
Moiety
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Dihedral angle
Coupling constant
MINDO
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Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins. Proteins 2016; 84:501–514. © 2016 Wiley Periodicals, Inc.
Dihedral angle
Globular protein
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Abstract The synthesis of the 3‐azaphenoxathiin ring system and its molecular structure are reported. Based on 13 C‐nmr chemical shift additivities associated with the insertion of an annular nitrogen atom and the observed 13 C‐nmr shift of Cα, the title compound was predicted to have a dihedral angle θ = 160.2°. The observed dihedral angle from the crystal structure was found to be θ = 167.07° which is in reasonably good agreement with the predicted value. It is proposed that the position of the annular nitrogen atom is solely in‐control of the observed dihedral angle.
Dihedral angle
Nitrogen atom
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In the title compound, C12H6Cl5O2, the dihedral angle between the two rings is 37°. This dihedral angle is different from the calculated dihedral angle in aqueous solution (48°), a likely cause being the influence of crystal packing.
Dihedral angle
Crystal (programming language)
Benzoquinone
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Dihedral angle databases are protein databases that store all occurring dihedral angle (phi, psi) values of amino acids in proteins. None of the existing dihedral angle databases have classified their data based on an important bonding characteristic of proteins called disulfide bonds. In this paper, using statistical analysis, the need to classify values in a dihedral angle database based on disulfide bonds is shown. This paper discusses how our dihedral angle database (DAB) is classified into two; dihedral database (DABSS) having proteins with at least one disulfide bond and dihedral database (DABNSS) having proteins without any disulfide bonds. Statistical analysis is used to show that the dihedral values (and hence the structure) of sub-sequences of amino acids obtained from DABSS are significantly different from their corresponding values in DABNSS, thus justifying the need to classify data based on disulfide bonds. Using statistical analysis to show that the values in DAB are significantly different from the corresponding values in DABSS and DABNSS strengthens this justification. Using this analysis and by querying DAB, DABSS and DABNSS it is shown how the values obtained by a protein structure prediction program yields different results and how querying DAB gives mixed results as it contains dihedral values from proteins with and without disulfide bonds together.
Dihedral angle
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Because of the relatively low-resolution diffraction of typical protein crystals, structure refinement is usually carried out employing stereochemical restraints to increase the effective number of observations. Well defined values for bond lengths and angles are available from small-molecule crystal structures. Such values do not exist for dihedral angles because of the concern that the strong crystal contacts in small-molecule crystal structures could distort the dihedral angles. This paper examines the dihedral-angle distributions in ultra-high-resolution protein structures (1.2 Å or better) as a means of analysing the population frequencies of dihedral angles in proteins and compares these with the stereochemical restraints currently used in one of the more widely used molecular-dynamics refinement packages, X-PLOR , and its successor, CNS . Discrepancies between the restraints used in these programs and what is actually seen in high-resolution protein structures are examined and an improved set of dihedral-angle restraint parameters are derived from these inspections.
Dihedral angle
Crystal (programming language)
Molecular geometry
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