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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, Suhai et al. fit the set of dipolar couplings by systematically varying the flexible dihedral angles φ and ψ while freezing local geometric details from the electronic structure calculations.
Abstract: The proton NMR spectra of unlabeled alanine dipeptide (Ac-L-Ala-NHMe) at 300 MHz and of alanine dipeptide with a single 13C label at 500 MHz are obtained in the lyotropic liquid-crystalline solvent cesium pentadecafluorooctanoate in water (CsPFO/H2O). Simulations of the spectra yield 9 and 13 dipolar couplings Dij, respectively, many with absolute sign determined. We fit the set of dipolar couplings by systematically varying the flexible dihedral angles φ and ψ while freezing local geometric details from the electronic structure calculations of Suhai and co-workers (Han, W. G.; Jalkanen, K. J.; Elstner, M.; Suhai, S. J. Phys. Chem. B 1998, 102, 2587). The orientation tensor is optimized at each combination of dihedral angles. Remarkably, a single conformer PII (φ ≈ −85°, ψ ≈ +160°) fits both sets of couplings within experimental error. The orientation tensor can be understood in terms of a simple rocking motion that dips the central methyl group into the fluorocarbon core of the CsPFO bicelle while altern...

90 citations

Journal ArticleDOI
TL;DR: Molecular dynamics simulations performed on a set of hairpin loops, duplexes and tetramers with the new parameter set show improved modeling for the structures of tetramer CCCC, CAAU, and GACC, and an RNA internal loop of noncanonical pairs, as compared to the conventional parameters.
Abstract: The backbone dihedral parameters of the Amber RNA force field were improved by fitting using multiple linear regression to potential energies determined by quantum chemistry calculations. Five backbone and four glycosidic dihedral parameters were fit simultaneously to reproduce the potential energies determined by a high-level density functional theory calculation (B97D3 functional with the AUG-CC-PVTZ basis set). Umbrella sampling was used to determine conformational free energies along the dihedral angles, and these better agree with the population of conformations observed in the protein data bank for the new parameters than for the conventional parameters. Molecular dynamics simulations performed on a set of hairpin loops, duplexes and tetramers with the new parameter set show improved modeling for the structures of tetramers CCCC, CAAU, and GACC, and an RNA internal loop of noncanonical pairs, as compared to the conventional parameters. For the tetramers, the new parameters largely avoid the incorrec...

90 citations

Journal ArticleDOI
TL;DR: The relative spatial disposition of interacting side-chain planar groups (aromatic, guanidinium, amide, carboxyl, imidazole) is analyzed for 186 non-homologous well-resolved protein structures and indicates that edge-to-edge and edge- to-center spatial dispositions of residue planar sections are prevalent, while complete stacking configurations are uncommon.
Abstract: The relative spatial disposition of interacting side-chain planar groups (aromatic, guanidinium, amide, carboxyl, imidazole) is analyzed for 186 non-homologous well-resolved protein structures. The dihedral angle of amide or carboxyl planar groups with other planar groups accords with a random distribution of planes. By contrast, the dihedral angle of the planes between close aromatic rings or of the histidine ring interacting with aromatic residues is significantly nonrandom, showing an approximately uniform distribution. Our results indicate that edge-to-edge and edge-to-center spatial dispositions of residue planar sections are prevalent, while complete stacking configurations are uncommon. The hypothesis that electrostatic forces are a major determinant of the geometry of interactions between side-chain planar groups is discussed.

90 citations

Journal ArticleDOI
TL;DR: The three-dimensional structure in solution of the oxidized Clostridium pasteurianum ferredoxin has been solved by 1H-NMR by using a recently derived Karplus-type relationship for the hyperfine shifts of cysteine beta CH2 protons.
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.

90 citations

Journal ArticleDOI
TL;DR: A comparative molecular dynamics simulation study of the local structure of pure liquid ethylene glycol (EG), ethylenediamine (ED), and 2-aminoethanol (AE), which are three well-known representatives of 1,2-disubstituted ethanes is described in this article.
Abstract: This paper describes a comparative molecular dynamics (MD) simulation study of the local structure of pure liquid ethylene glycol (EG), ethylenediamine (ED), and 2-aminoethanol (AE), which are three well-known representatives of 1,2-disubstituted ethanes. As an essential component of this investigation, 12 molecular models were constructed and their gas-phase characteristics were determined. The results obtained for the molecular geometries were compared with the most reliable experimental estimates, to test different force fields and molecular representations. Liquid-phase simulations were then performed on the more successful (OPLS-based) models. The heats of vaporization and self-diffusion coefficients were used as criteria for the final selection of molecular models to be used in our subsequent detailed structural analysis. The dihedral angle distributions were calculated and relative populations of rotational isomers, with respect to the central dihedral angle, were determined. It was confirmed that,...

89 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2023203
2022473
2021160
2020195
2019193
2018216