Dihedral angle

About: Dihedral angle is a research topic. Over the lifetime, 15718 publications have been published within this topic receiving 174904 citations.

High-resolution solution structure of basic fibroblast growth factor determined by multidimensional heteronuclear magnetic resonance spectroscopy.

Abstract: The high-resolution solution structure of recombinant human basic fibroblast growth factor (FGF-2), a protein of 17.2 kDa that exhibits a variety of functions related to cell growth and differentiation, has been determined using three-dimensional heteronuclear NMR spectroscopy. A total of 30 structures were calculated by means of hybrid distance geometry--simulated annealing using a total of 2865 experimental NMR restraints, consisting of 2486 approximate inteproton distance restraints, 50 distance restraints for 25 backbone hydrogen bonds, and 329 torsion angle restraints. The atomic rms distribution about the mean coordinate positions for the 30 structures for residues 29-152 is 0.43 +/- 0.03 A for the backbone atoms, 0.83 +/- 0.05 A for all atoms, and 0.51 +/- 0.04 A for all atoms excluding disordered side chains. The overall structure of FGF-2 consists of 11 extended antiparallel beta-strands arranged in three groups of three or four strands connected by tight turns and loop regions creating a pseudo-3-fold symmetry. Two strands from each group come together to form a beta-sheet barrel of six antiparallel beta-strands. A helix-like structure was observed for residues 131-136, which is part of the heparin binding site (residues 128-138). The discovery of the helix-like region in the primary heparin binding site instead of the beta-strand conformation described in the X-ray structures may have important implications in understanding the nature of heparin--FGF-2 interactions. A total of seven tightly bound water molecules were found in the FGF-2 structure, two of which are located in the heparin binding site. The first 28 N-terminal residues appear to be disordered, which is consistent with previous X-ray structures. A best fit superposition of the NMR structure of FGF-2 with the 1.9 A resolution X-ray structure by Zhu et al. (1991) yields a backbone atomic rms difference of 0.94 A, indicative of a close similarity between the NMR and X-ray structures.

Signature of n→π* interactions in α-helices.

Abstract: The oxygen of a peptide bond has two lone pairs of electrons. One of these lone pairs is poised to interact with the electron-deficient carbon of the subsequent peptide bond in the chain. Any partial covalency that results from this n→π* interaction should induce pyramidalization of the carbon (C′i) toward the oxygen (Oi−1). We searched for such pyramidalization in 14 peptides that contain both α- and β-amino acid residues and that assume a helical structure. We found that the α-amino acid residues, which adopt the main chain dihedral angles of an α-helix, display dramatic pyramidalization but the β-amino acid residues do not. Thus, we conclude that Oi−1 and C′i are linked by a partial covalent bond in α-helices. This finding has important ramifications for the folding and conformational stability of α-helices in isolation and in proteins.

Molecular‐mechanics studies on d(CGCGAATTCGCG)2 and dA12·dT12: An illustration of the coupling between sugar repuckering and DNA twisting

Abstract: Molecular-mechanics calculations have been carried out on the base-paired deoxy dodecanucleoside undecaphosphates d(CGCGAATTCGCG)2 and d(A12)·d(T12). These refinements were carried out using the model-built Arnott B-DNA geometry as initial coordinates (with a helix repaeat of 10.0 residues/turn), as well as helix repeats ranging from 9 to 12 residues/turn. There was some variation in the optimum calculated helix repeat, depending on the dielectric model, the presence or absence of counterions, and the method used for inclusion for nonbonded interactions; the most interesting general result of these calculations was the coupling between furanose sugar puckering and twist. This coupling was observed for all models. With a helix repeat of 9.0 residues/turn, all sugars remain C(2′)endo after refinement; as the helix repear increases to 12.0 residues/turn, the number of sugars repuckering to O(1′)endo and C(3′)endo increases also. With our most rigorous model (i.e., a model with no cutoff distance for nonbonded interactions) and a helix repeat of 10.0 residues/turn, we find a greater tendency for pyrimidine than purine repuckering in d(CGCGAATTCGCG)2, in agreement with the x-ray structural data of Drew et al. [(1981) Proc. Natl. Acad. Sci. USA78, 2179–2185]. We also carried out a number of calculations in which we “forced” one of two deoxy sugars to repucker or one of the C3′-O3′-P-O5′ (ω) torsion angles to change from gauche− to trans using dihedral angle constraints. After the constraints were removed, some of these structures “reverted” to the sugar pucker of the initial structures, while others remained repuckered. In all cases, the energies for repuckered structures after refinement were very similar to energies of the initial structure. Experiments and theory suggest that local conformational fluctuations play an essential role in nmr relaxation of 31P and 13C atoms in double-helical DNA. The results of our previous calculations on hexanucleoside phosphates and the calculations presented there are consistent with an important contribution to nmr relaxation processes of conformational changes in the torsion angle ω′ from gauche− to trans and deoxy sugar repuckering from C(2′)endo to C(3′)endo. Specifically, the calculations presented here indicate a very flexible phosphate backbone in helixes having an intermediate helix repeat of 10 to 11 residues/turn. These helixes may accommodate sugars of variable pucker without significantly disrupting base–base hydrogen-bonding and stacking interactions. All of the variant structures are similar in energy, suggesting that conversion between them can occur on a nanosecond time scale, as observed in nmr relaxation experiments.

Structural Interpretation of Vicinal Proton-Proton Coupling Constants 3JHαHβ in the Basic Pancreatic Trypsin Inhibitor Measured by Two-Dimensional J-Resolved NMR Spectroscopy

Abstract: Two-dimensional J-resolved 1H NMR spectroscopy was used to measure the vicinal spin-spin coupling constants 3JHαHβ for numerous, previously individually assigned amino acid residues in the basic pancreatic trypsin inhibitor at various temperatures between 30 and 85° C. An analysis of this data is proposed which enables one to compare the spatial arrangements of individual amino acid side chains in solution and in single crystals of the protein, and which also provides information on the mobility of the side chains in the solution conformation. As a rule, the amino acid side chains in the interior of the protein were found to be locked into unique spatial orientations, with the mobility restricted to rapid rotational fluctuations about this unique value for the dihedral angle Z1. In most, but not all, instances the data for the interior amino acids indicate identical average conformations for the amino acid side chains in single crystals and in solution. For residues on the protein surface structural rearrangements between crystal and solution appear to be common, and the mobility in the solution conformation may include rapid averaging between two or several distinct, preferentially populated values of χ1, analogous to the gauche-trans-gauche isomerization in isolated amino acids.

Molecular dynamics simulation of liquid ethylene glycol and its aqueous solution

Abstract: Molecular dynamics simulations were used to study pure liquid ethylene glycol (EG) and EG-water binary mixtures as a function of the molar fraction. Calculations were performed in the isothermal and isobaric (NpT) ensemble. New improvement in the OPLSS-AA-SEI force field was obtained optimizing the Lennard-Jones parameters and charges taking part in 1–4 interactions. With the new force field density and heat of vaporization of pure liquid ethylene glycol were obtained in good agreement with experimental data. The value of the O-C-C-O dihedral was also monitored in the course of force field optimization process. The new optimized force field was named OPLSA-AA-SE-M. Concerning the pure liquid simulation, features observed on the radial distribution functions (RDF) show characteristics of intermolecular and intramolecular hydrogen bonding. The RDF integrations show that each EG molecule in the pure liquid has an average coordination number of five molecules in its first coordination shell. Therefore, the average oxygen-hydrogen contact number due to hydrogen bonding is seven: two of them arising from intramolecular and five from interactions with neighboring molecules. Dihedral angle distributions were calculated, showing the predominance of EG molecules with the O-C-C-O dihedral corresponding to gauche conformations. In the study of water-ethylene glycol binary mixtures, the average structural parameters observed for EG molecules are very similar to the ones found in the pure liquid simulation. RDF analyses also present characteristic features of hydrogen bonding. Particularly, no significant changes were observed on the dihedral angle distributions. The structures of EG-EG and EG-water dimers calculated with OPLS-AA-SEI-M force field and DFT at B3LYP 6-311 g (3df,3pd) level are in very good agreement.