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Structural investigation of helices II, III, and IV of B. megaterium 5S ribosomal RNA by molecular dynamics calculations.
Biopolymers. 1992 Sep; 32(9):1263-70.B

Abstract

The structures of the helices II-III region and the helix IV region of B. megaterium 5S rRNA have been examined by means of energy minimization and molecular dynamics calculations. Calculated distances between neighboring hydrogen-bonded imino protons in helices II, III, and IV were between 3.5 and 4.5 A. The overall axis for the helices II-III region is warped rather than straight. Formation of additional Watson-Crick base pairs in loop B and loop C was not evident from the atomic positions calculated by molecular dynamics. Bases in loop C are well stacked, showing no significant change during dynamics. Bulge migration in helix III does not seem to be possible; the helices II-III region prefers one conformation. Helix II is more stable than helix III. Five base pairs in helix IV were sufficiently stable to establish that helix IV is terminated by a hairpin loop of three nucleotides. U87 protrudes from loop D. Structures of the helices II-III segment and the helix IV segment of B. megaterium 5S rRNA obtained by molecular dynamics were generally consistent with the solution structure inferred from high-field proton nmr spectroscopy.

Authors+Show Affiliations

Kim JH
Department of Chemistry, Ohio State University, Columbus 43210.
Marshall AG
No affiliation info available

MeSH

Bacillus megateriumBase SequenceModels, MolecularMolecular Sequence DataNucleic Acid ConformationRNA, BacterialRNA, Ribosomal, 5S

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

1384750

Citation

Kim, J H., and A G. Marshall. "Structural Investigation of Helices II, III, and IV of B. Megaterium 5S Ribosomal RNA By Molecular Dynamics Calculations." Biopolymers, vol. 32, no. 9, 1992, pp. 1263-70.
Kim JH, Marshall AG. Structural investigation of helices II, III, and IV of B. megaterium 5S ribosomal RNA by molecular dynamics calculations. Biopolymers. 1992;32(9):1263-70.
Kim, J. H., & Marshall, A. G. (1992). Structural investigation of helices II, III, and IV of B. megaterium 5S ribosomal RNA by molecular dynamics calculations. Biopolymers, 32(9), 1263-70.
Kim JH, Marshall AG. Structural Investigation of Helices II, III, and IV of B. Megaterium 5S Ribosomal RNA By Molecular Dynamics Calculations. Biopolymers. 1992;32(9):1263-70. PubMed PMID: 1384750.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Structural investigation of helices II, III, and IV of B. megaterium 5S ribosomal RNA by molecular dynamics calculations. AU - Kim,J H, AU - Marshall,A G, PY - 1992/9/1/pubmed PY - 1992/9/1/medline PY - 1992/9/1/entrez SP - 1263 EP - 70 JF - Biopolymers JO - Biopolymers VL - 32 IS - 9 N2 - The structures of the helices II-III region and the helix IV region of B. megaterium 5S rRNA have been examined by means of energy minimization and molecular dynamics calculations. Calculated distances between neighboring hydrogen-bonded imino protons in helices II, III, and IV were between 3.5 and 4.5 A. The overall axis for the helices II-III region is warped rather than straight. Formation of additional Watson-Crick base pairs in loop B and loop C was not evident from the atomic positions calculated by molecular dynamics. Bases in loop C are well stacked, showing no significant change during dynamics. Bulge migration in helix III does not seem to be possible; the helices II-III region prefers one conformation. Helix II is more stable than helix III. Five base pairs in helix IV were sufficiently stable to establish that helix IV is terminated by a hairpin loop of three nucleotides. U87 protrudes from loop D. Structures of the helices II-III segment and the helix IV segment of B. megaterium 5S rRNA obtained by molecular dynamics were generally consistent with the solution structure inferred from high-field proton nmr spectroscopy. SN - 0006-3525 UR - https://www.unboundmedicine.com/medline/citation/1384750/Structural_investigation_of_helices_II_III_and_IV_of_B__megaterium_5S_ribosomal_RNA_by_molecular_dynamics_calculations_ DB - PRIME DP - Unbound Medicine ER -