Crystal structure and conformational flexibility of 2-(acetylamino)prop-2-enoic acid (N-acetyldehydroalanine)

1979 ◽  
pp. 927-929 ◽  
Author(s):  
David Ajò ◽  
Gaetano Granozzi ◽  
Eugenio Tondello ◽  
Antonio Del Prà ◽  
Giuseppe Zanotti
Keyword(s):  
Crystal Structure ◽  
Conformational Flexibility ◽  
Enoic Acid

scholarly journals Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 532
Author(s):  
Jonathan H. Sheehan ◽  
Jarrod A. Smith ◽  
Pradeep S. Pallan ◽  
Terry P. Lybrand ◽  
Martin Egli
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Base Pair ◽  
Crystal Packing ◽  
Md Simulations ◽  
Conformational Flexibility ◽  
Dynamics Simulation ◽  
Dna Duplex ◽  
Solution Studies

The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed to a conformation that was nearly devoid of a twist and a stacking distance in excess of 4.5 Å. By contrast, the crystal structure of the homo-DNA octamer dd(CGAATTCG) revealed a right-handed duplex with average values for helical twist and rise of ca. 15° and 3.8 Å, respectively. Other key features of the structure were strongly inclined base-pair and backbone axes in the duplex with concomitant base-pair slide and cross-strand stacking, and the formation of a dimer across a crystallographic dyad with inter-duplex base swapping. To investigate the conformational flexibility of the homo-DNA duplex and a potential influence of lattice interactions on its geometry, we used molecular dynamics (MD) simulations of the crystallographically observed dimer of duplexes and an isolated duplex in the solution state. The dimer of duplexes showed limited conformational flexibility, and key parameters such as helical rise, twist, and base-pair slide exhibited only minor fluctuations. The single duplex was clearly more flexible by comparison and underwent partial unwinding, albeit without significant lengthening. Thus, base stacking was preserved in the isolated duplex and two adenosines extruded from the stack in the dimer of duplexes were reinserted into the duplex and pair with Ts in a Hoogsteen mode. Our results confirmed that efficient stacking in homo-DNA seen in the crystal structure of a dimer of duplexes was maintained in the separate duplex. Therefore, lattice interactions did not account for the different geometries of the homo-DNA duplex in the crystal and earlier models that resembled inclined ladders with large base-pair separations that precluded efficient stacking.

scholarly journals Crystal structure of (E)-hex-2-enoic acid

2015 ◽  
Vol 71 (5) ◽  
pp. o323-o323 ◽  
Author(s):  
Tim Peppel ◽  
Marcel Sonneck ◽  
Anke Spannenberg ◽  
Sebastian Wohlrab
Keyword(s):  
Crystal Structure ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Enoic Acid ◽  
Acid Molecule ◽  
Unsaturated Carboxylic Acid ◽  
Compound C

The crystal structure of the title compound, C6H10O2, an α,β-unsaturated carboxylic acid, displays carboxylic acid inversion dimers linked by pairs of O—H...O hydrogen bonds. The packing is characterized by layers of acid dimers. All the non-H atoms of the (E)-hex-2-enoic acid molecule lie almost in the same plane (r.m.s. deviation for the non-H atoms = 0.018 Å).

scholarly journals Crystal Structure of Prothrombin Reveals Conformational Flexibility and Mechanism of Activation

2013 ◽  
Vol 288 (31) ◽  
pp. 22734-22744 ◽  
Author(s):  
Nicola Pozzi ◽  
Zhiwei Chen ◽  
David W. Gohara ◽  
Weiling Niu ◽  
Tomasz Heyduk ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Flexibility
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