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Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations
Author(s) -
Réblová Kamila,
Lankas̆ Filip,
Rázga Filip,
Krasovska Maryna V.,
Koc̆a Jaroslav,
S̆poner Jir̆í
Publication year - 2006
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20503
Subject(s) - helix (gastropod) , thermus thermophilus , molecular dynamics , chemistry , crystallography , twist , base pair , bent molecular geometry , helix angle , chemical physics , geometry , dna , computational chemistry , materials science , ecology , biochemistry , mathematics , organic chemistry , escherichia coli , biology , snail , composite material , gene
Molecular dynamics (MD) simulations were employed to investigate the structure, dynamics, and local base‐pair step deformability of the free 16S ribosomal helix 44 from Thermus thermophilus and of a canonical A‐RNA double helix. While helix 44 is bent in the crystal structure of the small ribosomal subunit, the simulated helix 44 is intrinsically straight. It shows, however, substantial instantaneous bends that are isotropic. The spontaneous motions seen in simulations achieve large degrees of bending seen in the X‐ray structure and would be entirely sufficient to allow the dynamics of the upper part of helix 44 evidenced by cryo‐electron microscopic studies. Analysis of local base‐pair step deformability reveals a patch of flexible steps in the upper part of helix 44 and in the area proximal to the bulge bases, suggesting that the upper part of helix 44 has enhanced flexibility. The simulations identify two conformational substates of the second bulge area (bottom part of the helix) with distinct base pairing. In agreement with nuclear magnetic resonance (NMR) and X‐ray studies, a flipped out conformational substate of conserved 1492A is seen in the first bulge area. Molecular dynamics (MD) simulations reveal a number of reversible α‐γ backbone flips that correspond to transitions between two known A‐RNA backbone families. The flipped substates do not cumulate along the trajectory and lead to a modest transient reduction of helical twist with no significant influence on the overall geometry of the duplexes. Despite their considerable flexibility, the simulated structures are very stable with no indication of substantial force field inaccuracies. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 504–520, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com