Z-RNA: A Left-Handed Double Helix

Pili in Gram-positive bacteria are flexible rod proteins associated with the bacterial cell surface, and they play important roles in the initial adhesion to host tissues and colonization. The pilus shaft is formed by the covalent polymerization of major pilins, catalyzed by sortases, a family of cysteine transpeptidases. Here, X-ray structures of the major pilins from Clostridium perfringens strains 13 and SM101 and of sortase from strain SM101 are presented with biochemical analysis to detect the formation of pili in vivo. The major pilin from strain 13 adopts an elongated structure to form noncovalently linked polymeric chains in the crystal, yielding a practical model of the pilus fiber structure. The major pilin from strain SM101 adopts a novel bent structure and associates to form a left-handed twist like an antiparallel double helix in the crystal, which is likely to promote bacterial cell–cell interactions. A modeling study showed that pilin with a bent structure interacts favorably with sortase. The major pilin from strain SM101 was considered to be in an equilibrium state between an elongated and a bent structure through dynamic conformational change, which may be involved in pili-mediated colonization and sortase-mediated polymerization of pili.

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The Effect of Calcium and Halide Ions on the Gramicidin A Molecular State and Antimicrobial Activity

International Journal of Molecular Sciences ◽

10.3390/ijms21176177 ◽

2020 ◽

Vol 21 (17) ◽

pp. 6177

Author(s):

Kathleen D. Carillo ◽

Chi-Jen Lo ◽

Der-Lii M. Tzou ◽

Yi-Hung Lin ◽

Shang-Ting Fang ◽

...

Keyword(s):

Antimicrobial Activity ◽

Calcium Salt ◽

Double Helix ◽

Single Species ◽

Molecular State ◽

Vital Role ◽

Gramicidin A ◽

Halide Anion ◽

Left Handed ◽

State 1

Gramicidin A (gA) forms several convertible conformations in different environments. In this study, we investigated the effect of calcium halides on the molecular state and antimicrobial activity of gramicidin A. The molecular state of gramicidin A is highly affected by the concentration of calcium salt and the type of halide anion. Gramicidin A can exist in two states that can be characterized by circular dichroism (CD), mass, nuclear magnetic resonance (NMR) and fluorescence spectroscopy. In State 1, the main molecular state of gramicidin A is as a dimer, and the addition of calcium salt can convert a mixture of four species into a single species, which is possibly a left-handed parallel double helix. In State 2, the addition of calcium halides drives gramicidin A dissociation and denaturation from a structured dimer into a rapid equilibrium of structured/unstructured monomer. We found that the abilities of dissociation and denaturation were highly dependent on the type of halide anion. The dissociation ability of calcium halides may play a vital role in the antimicrobial activity, as the structured monomeric form had the highest antimicrobial activity. Herein, our study demonstrated that the molecular state was correlated with the antimicrobial activity.

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A critical analysis of a left-handed double helix model for B-DNA fibers

Nucleic Acids Research ◽

10.1093/nar/10.13.4027 ◽

1982 ◽

Vol 10 (13) ◽

pp. 4027-4034 ◽

Cited By ~ 6

Author(s):

G. Albiser ◽

S. Premilat

Keyword(s):

Critical Analysis ◽

Double Helix ◽

Left Handed

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The tetraribonucleotiderCpGpCpG forms a left-handed Z-RNA double-helix

Nucleic Acids Research ◽

10.1093/nar/14.3.1279 ◽

1986 ◽

Vol 14 (3) ◽

pp. 1279-1291 ◽

Cited By ~ 27

Author(s):

Peter W. Davis ◽

Kathleen Hall ◽

Phillip Cruz ◽

Ignacio Tinoco ◽

Thomas Neilson

Keyword(s):

Double Helix ◽

Left Handed

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Cryo-electron microscopy of chromosome fibers is consistent with the crossed-linker model for chromatin structure

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100127670 ◽

1987 ◽

Vol 45 ◽

pp. 648-649

Author(s):

B. Athey ◽

J. Langmore ◽

S. Williams ◽

M. Smith ◽

C.F. Chang ◽

...

Keyword(s):

Chromatin Structure ◽

Double Helix ◽

Histone Octamer ◽

Left Handed ◽

Variable Diameter ◽

Cryo Electron Microscopy ◽

Constant Diameter ◽

Constant Pitch ◽

Conserved Core ◽

Helical Parameters

Although there is general agreement that inactive chromosome fibers consist of helically packed nucleosomes, the pattern of packing is still disputed. The nucleosome itself is composed of a highly conserved “core” comprised of 146bp of DNA and a histone octamer, and a variable “linker” comprised of 20-100bp of DNA bound to histone H1. The models of chromatin structure can be distinguished by their dependence upon linker length. The solenoid model for chromatin structure is a single helix with constant pitch (11 nm) and constant diameter (25-30nm). The twisted-ribbon model is a double helix with variable pitch (26-40nm) and constant diameter (30nm). The crossed-linker model is a double helix with conserved pitch (26-28nm) and variable diameter (26-40nm). Measurements of the diameter and apparent helical parameters of negatively-stained chromatin from Thyone sperm (87bp linker) and Necturus erythrocytes (48bp linker) are in agreement with a left-handed crossed-linker model, and in disagreement with the solenoid and twisted-ribbon models.

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