Guanine residues in d(T2AG3) and d(T2G4) form parallel-stranded potassium cation stabilized G-quadruplexes with anti glycosidic torsion angles in solution

Biochemistry ◽  
1992 ◽  
Vol 31 (35) ◽  
pp. 8112-8119 ◽  
Author(s):  
Yong Wang ◽  
Dinshaw J. Patel
Keyword(s):  
Potassium Cation ◽  
Torsion Angles

An Effective Cumulative Torsion Angles Model for Prediction of Protein Folding Rates

2020 ◽  
Vol 27 (4) ◽  
pp. 321-328 ◽  
Author(s):  
Yanru Li ◽  
Ying Zhang ◽  
Jun Lv
Keyword(s):  
Protein Folding ◽  
Size Structure ◽  
Conformational Space ◽  
Coefficient Of Determination ◽  
Folding Rate ◽  
Torsion Angles ◽  
Folding Rates ◽  
Protein Folding Rate ◽  
Optimal Set ◽  
Conformation Space

Background: Protein folding rate is mainly determined by the size of the conformational space to search, which in turn is dictated by factors such as size, structure and amino-acid sequence in a protein. It is important to integrate these factors effectively to form a more precisely description of conformation space. But there is no general paradigm to answer this question except some intuitions and empirical rules. Therefore, at the present stage, predictions of the folding rate can be improved through finding new factors, and some insights are given to the above question. Objective: Its purpose is to propose a new parameter that can describe the size of the conformational space to improve the prediction accuracy of protein folding rate. Method: Based on the optimal set of amino acids in a protein, an effective cumulative backbone torsion angles (CBTAeff) was proposed to describe the size of the conformational space. Linear regression model was used to predict protein folding rate with CBTAeff as a parameter. The degree of correlation was described by the coefficient of determination and the mean absolute error MAE between the predicted folding rates and experimental observations. Results: It achieved a high correlation (with the coefficient of determination of 0.70 and MAE of 1.88) between the logarithm of folding rates and the (CBTAeff)0.5 with experimental over 112 twoand multi-state folding proteins. Conclusion: The remarkable performance of our simplistic model demonstrates that CBTA based on optimal set was the major determinants of the conformation space of natural proteins.

Crystal Forms of Semisynthetic Ergot Alkaloid Terguride

2002 ◽  
Vol 67 (4) ◽  
pp. 479-489 ◽  
Author(s):  
Michal Hušák ◽  
Bohumil Kratochvíl ◽  
Ivana Císařová ◽  
Ladislav Cvak ◽  
Alexandr Jegorov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ergot Alkaloid ◽  
Simplified Model ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray Diffraction ◽  
Torsion Angles ◽  
Crystal Forms ◽  
X Ray ◽  
Independent Molecules

Two new structures of semisynthetic ergot alkaloid terguride created by unusual number of symmetry-independent molecules were determined by X-ray diffraction methods at 150 K. Form A (monoclinic, P212121, Z = 12) contains three symmetry-independent terguride molecules and two molecules of water in the asymmetric part of the unit cell. The form CA (monoclinic, P21, Z = 8) is an anhydrate remarkable by the presence of four symmetry-independent molecules in the crystal structure. Conformations of twelve symmetry-independent molecules that were found in four already described terguride structures are compared with torsion angles obtained by ab initio quantum-mechanical calculations for the simplified model of N-cyclohexyl-N'-diethylurea.

Crystal structure of tricyclo-DNA: an unusual compensatory change of two adjacent backbone torsion angles

2008 ◽  
pp. 883-885 ◽  
Author(s):  
Pradeep S. Pallan ◽  
Damian Ittig ◽  
Annie Héroux ◽  
Zdzislaw Wawrzak ◽  
Christian J. Leumann ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Torsion Angles ◽  
Compensatory Change

Molecular Origins of the Unique Conformational Properties of the Polysilanes: A Molecular Dynamics Study of Poly(Di-N-Hexylsilane)

1992 ◽  
Vol 278 ◽  
Author(s):  
William J. Welsh ◽  
Samuel H. Tersigni ◽  
Wangkan Lin
Keyword(s):  
Molecular Dynamics ◽  
Torsion Angle ◽  
Model Compound ◽  
Energy Surface ◽  
Conformational Dynamics ◽  
Conformational Transitions ◽  
Torsion Angles ◽  
Global Energy Minimum ◽  
Conformational Properties ◽  
Backbone Torsion Angle

AbstractThe conformational dynamics of a model compound for poly(di-n-hexylsilane) (PDHS) has been explored using the new molecular dynamics program MM3-MD. MM3-MD trajectories at variable temperatures reveal two abrupt conformational transitions, one near -182°C and another near -175°C, associated with two energy barriers on the potential-energy surface. The first transition near -182°C allows shifts in the backbone torsion angle from that defined by the global energy minimum designated off-trans to that corresponding to a statistical collection of torsion angles within the range trans ±30°. The second transition near -175°C allows the backbone torsion angle to explore the remainder of its torsional space. The sidechain dynamics follows a similar pattern. We suggest that the abrupt transition calculated here at -182°C for “gas.phase” PDHS corresponds to that observed for PDHS at -28°C in solution and at 42°C in the solid state.

4-(Piperidin-1-yl)pyridinium hexafluorophosphate at 150 K

2003 ◽  
Vol 59 (11) ◽  
pp. o622-o624 ◽  
Author(s):  
Bruce D. James ◽  
Siti Mutrofin ◽  
Brian W. Skelton ◽  
Allan H. White
Keyword(s):  
Hydrogen Bonds ◽  
Structural Characterization ◽  
Title Compound ◽  
Ion Pairs ◽  
Piperidine Ring ◽  
Torsion Angles ◽  
Compound C ◽  
Counter Ions

Structural characterization of the title compound, C10H15N2 +·PF6 −, shows it to be ionic, with the pyridine rather than the piperidine N atom being protonated and forming hydrogen bonds to the counter-ions, resulting in two independent ion pairs. A number of unusual features are noted, in particular the remarkably close inter-ring hydrogen contacts [1.97 (3)–2.00 (3) Å] and the considerable differences in the pair of cations, in respect of the torsion angles within the piperidine ring involving the bonds to either side of the N atom.

Conformational features of bisphenol-A polycarbonate

1985 ◽  
Vol 63 (1) ◽  
pp. 103-110 ◽  
Author(s):  
P. R. Sundararajan
Keyword(s):  
Bisphenol A ◽  
Repeat Unit ◽  
Methyl Groups ◽  
Bisphenol A Polycarbonate ◽  
Carbonate Group ◽  
Torsion Angles ◽  
Thermal Crystallization ◽  
Lennard Jones ◽  
Empirical Force Field ◽  
Conformational Energies

Conformational energies have been estimated for the segments of the bisphenol polycarbonate chain, using the Lennard–Jones and Hill's empirical force field type of functions. It is found that the conformation of the carbonate group, defined by the torsion angle ζ, is restricted to the range of 45° to 65°. The rotations χ and χ′ of the methyl groups also show similar limited flexibility. However, accessible conformations of the diphenyl propane (DPP) segment, defined by torsion angles [Formula: see text] and ψ, span a wide area of the [Formula: see text] surface, with the restriction that the rotations [Formula: see text] and ψ be synchronized such that [Formula: see text] or 270°. These features explain the slow thermal crystallization behaviour of the polycarbonate chains. The variability of the conformations of the repeat unit is illustrated with a series of figures.

Experimental and Theoretical Study on Cation–π Interaction of the Potassium Cation with [2.2.2]Paracyclophane

2017 ◽  
Vol 29 (1) ◽  
pp. 21-25 ◽  
Author(s):  
Emanuel Makrlík ◽  
David Sýkora ◽  
Stanislav Böhm ◽  
Petr Vaňura
Keyword(s):  
Theoretical Study ◽  
Potassium Cation

Chemical reasonableness in Rietveld analysis; organics

2007 ◽  
Vol 22 (1) ◽  
pp. 74-82 ◽  
Author(s):  
James A. Kaduk
Keyword(s):  
Rietveld Refinement ◽  
Normal Values ◽  
Solution Process ◽  
Molecular Geometry ◽  
Rietveld Analysis ◽  
Rigid Bodies ◽  
Torsion Angles ◽  
Structure Solution ◽  
Calcium Tartrate

We know a lot about normal values of bond distances, bond angles, torsion angles, and other molecular parameters. This knowledge can be incorporated into the structure solution process and into Rietveld refinement through the use of restraints and rigid bodies. An important measure of the quality of the refined model is the chemical reasonableness of molecular geometry. Refinement of the structures of calcium tartrate tetrahydrate and guaifenesin is used to illustrate the importance of chemical reasonableness in determining the quality of a Rietveld refinement.

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