scholarly journals Survey of ribose ring pucker of signaling nucleosides and nucleotides

2020 ◽  
Author(s):  
Veronica Salmaso ◽  
Kenneth Jacobson
Keyword(s):  
Ring Pucker

Calculating Ring Pucker Free Energy Surfaces From Reaction Coordinate Forces

2009 ◽  
Author(s):  
Christopher B. Barnett ◽  
Kevin J. Naidoo ◽  
Dong-Qing Wei ◽  
Xi-Jun Wang
Keyword(s):  
Free Energy ◽  
Reaction Coordinate ◽  
Energy Surfaces ◽  
Ring Pucker

scholarly journals Survey of ribose ring pucker of signaling nucleosides and nucleotides

2019 ◽  
Vol 39 (1-3) ◽  
pp. 322-341 ◽  
Author(s):  
Veronica Salmaso ◽  
Kenneth A. Jacobson
Keyword(s):  
Ring Pucker

Polysulfonylamine, CXL [1]. N-Cycloalkyldimesylamine C„H2n-1/N(SO2CH3)2: Synthesen (n = 3 -6 ), Festkörper-Molekülstrukturen (n = 4 -6 ) Und Rolle Schwacher Wasserstoffbrücken C-H···O In Den Kristallstrukturen

2001 ◽  
Vol 56 (8) ◽  
pp. 765-777
Author(s):  
Wiebke Schaper ◽  
Ilona Lange ◽  
Dagmar Henschel ◽  
Oliver Moers ◽  
Armand Blaschette ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Monoclinic Space Group ◽  
Equatorial Position ◽  
X Ray Diffraction ◽  
Step Procedure ◽  
One Step ◽  
Crystal Packings ◽  
Ring Pucker

The new disulfonylamines R -N (SO2Me)2, where R = cyclopropyl (1), cyclobutyl (2), cyclopentyl (3) or cyclohexyl (4), were prepared according to an established one-step procedure (condensation of RNH2 with two equivalents of MeSO2Cl, NaH as basic auxiliary). Whereas the structure determination for 1 was marred by severe disorder, compounds 2 -4 have been characterized by low-temperature X-ray diffraction (2: monoclinic, space group P21 Z ' = 2, pseudo-P21/c packing; 3: triclinic, P1̄, Z' - 1; 4: orthorhombic, Pbca, Z ' = 1). The four independent molecules display puckered carbocycles, whereby the electronegative (MeSO2)2N substituent occupies an equatorial position, leading to short intramolecular C - H···O contacts (2: angles of ring pucker φ ≈ 30-33°; 3: envelope conformation, φ ≈ 40°; 4: chair conformation, φ1 ≈ φ2 51°). In accordance with known congener structures, the C(sp3)-N (S)2 moieties feature trigonal-planar N configurations and unusually long C -N bonds (ranges for 2-4: C -N 148.8-150.8 pm, S -N 166.6-168.9 pm, S -N -S 118.3-119.3°). The three crystal packings are governed by a plethora of weak intermolecular hydrogen bonds C(sp3)-H···O , and a thorough survey of these interactions reveals that the inductively activated methyl groups are distinctly more efficient hydrogen bond donors than the methine and methylene ring groups. In each structure, the principal hydrogen bonds create layer substructures parallel to a unit cell face, which are cross-linked by the remaining C -H···O contacts to form three-dimensional networks

Ring pucker in dihydroaromatic epoxides: The molecular structure ofr-1-hydroxy-t-2-methyl-t,t-3,4-epoxy-1,2,3,4-tetrahydronaphthalene

1995 ◽  
Vol 6 (2) ◽  
pp. 89-97
Author(s):  
D. E. Zacharias ◽  
J. P. Glusker ◽  
D. L. Whalen ◽  
S. Friedman ◽  
T. M. Pohl
Keyword(s):  
Molecular Structure ◽  
Ring Pucker

Base dependent pyrrolidine ring pucker in aep-PNA monomers: NMR and PSEUROT analysis

Tetrahedron ◽  
2010 ◽  
Vol 66 (47) ◽  
pp. 9165-9170 ◽  
Author(s):  
Nagendra K. Sharma ◽  
Krishna N. Ganesh
Keyword(s):  
Pyrrolidine Ring ◽  
Ring Pucker

scholarly journals Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Irfan Alibay ◽  
Richard Bryce
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Biological Function ◽  
Enhanced Sampling ◽  
Energy Profiles ◽  
Ring Puckering ◽  
Dynamics Simulations ◽  
Ring Pucker ◽  
Free Energy Profiles

<p>The conformational flexibility of the glycosaminoglycans (GAGs) are known to be key in their binding and biological function, for example in regulating coagulation and cell growth. In this work, we employ enhanced sampling molecular dynamics simulations to probe the ring conformations of GAG-related monosaccharides, including a range of acetylated and sulfated GAG residues. We first perform unbiased MD simulations of glucose anomers and the epimers glucoronate and iduronate. These calculations indicate that in some cases, an excess of 15 microseconds are required for adequate sampling of ring pucker due to the high energy barriers between states. However, by applying our recently developed msesMD simulation method (multidimensional swarm enhanced sampling molecular dynamics), we were able to quantitatively and rapidly reproduce these ring pucker landscapes. From msesMD simulations, the puckering free energy profiles were then compared for eleven monosaccharides found in GAGs; this includes to our knowledge the first simulation study of sulfation effects on GalNAc ring puckering. For the force field employed, we find that in general the calculated pucker free energy profiles for sulfated sugars were similar to the corresponding unsulfated profiles. This accords with recent experimental studies suggesting that variation in ring pucker of sulfated GAG residues is primarily dictated by interactions with surrounding residues rather than by intrinsic conformational preference. As an exception to this, however, we predict that 4-O-sulfation of GalNAc leads to reduced ring rigidity, with a significant lowering in energy of the <sup>1</sup>C<sub>4</sub> ring conformation; this observation may have implications for understanding the structural basis of the biological function of GalNAc-containing glycosaminoglycans such as dermatan sulfate.</p>

Determinants of Substrate Specificity in APOBEC3B

2018 ◽  
Author(s):  
Jeffrey Wagner ◽  
Özlem Demir ◽  
Michael A. Carpenter ◽  
Hideki Aihara ◽  
Daniel A. Harki ◽  
...  
Keyword(s):  
Binding Site ◽  
Experimental Studies ◽  
Substrate Selectivity ◽  
Computational Tools ◽  
Substrate Protein ◽  
Native Sequence ◽  
Sugar Ring ◽  
Dynamics Simulations ◽  
Ring Pucker ◽  
State Experience

APOBEC3B (A3B) is a newly discovered driver of mutation in many cancers. We use computational tools to revert a recent crystal structure of an A3B construct to its native sequence, and run molecular dynamics simulations to study its underlying dynamics and substrate recognition mechanisms. The A3B-oligonucleotide substrate simulations show a series of dynamic substrate-protein contacts that correlate with previous work on A3B substrate selectivity. A second series of simulations in which the target cytosine nucleotide was computationally mutated from a deoxyribose to a ribose showed a change in sugar ring pucker, leading to a rearrangement of the binding site and revealing a potential intermediate in the binding pathway. Finally, apo simulations of A3B beginning in the open state experience a rapid and consistent closure of the binding site, reaching a conformation incompatible with substrate binding. These simulations agree with previous experimental studies, and we report the atomistic details of these events to further therapeutic studies on A3B.

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