Molecular dynamics simulations of sarcin-ricin rRNA motif

ŠPAČKOVÁ, Naděžda and Jiří ŠPONER. Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Research. Oxford University Press, 2006, vol. 34, No 2, p. 697-708. ISSN 0006-3465.

Basic information

• Original name: Molecular dynamics simulations of sarcin-ricin rRNA motif
• Name in Czech: Molecular dynamics simulations of sarcin-ricin rRNA motif
• Authors: ŠPAČKOVÁ, Naděžda (203 Czech Republic) and Jiří ŠPONER (203 Czech Republic, guarantor).
• Edition: Nucleic Acids Research, Oxford University Press, 2006, 0006-3465.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10403 Physical chemistry
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• RIV identification code: RIV/00216224:14310/06:00016779
• Organization unit: Faculty of Science
• UT WoS: 000235291300039
• Keywords in English: molecular dynamics;sarcin-ricin
• Tags: molecular dynamics, sarcin-ricin
• Tags: International impact, Reviewed

Abstract

Explicit solvent molecular dynamics (MD) simulations were carried out for sarcinricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other SRD features is presented. The SRD is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean square deviation (r.m.s.d.) values between averaged MD and high-resolution X-ray structures of 11.4 A . Modest dynamics is observed in the tetraloop, namely, rotation of adenine in its apex and subtle reversible shift of the tetraloop with respect to the adjacent base pair.The deformedflexible region in low-resolution rat X-ray structure is repaired by simulations. The simulations reveal few backbone flips, which do not affect positions of bases and do not indicate a force field imbalance. Non-Watson Crick base pairs are rigid and mediated by longresidency water molecules while there are several modest cation-binding sites around SRD. In summary, SRD is an unusually stiff rRNA building block. Its intrinsic structural and dynamical signatures seen in simulations are strikingly distinct from other rRNA motifs such as Loop E and Kink-turns.

Abstract (in Czech)

Explicit solvent molecular dynamics (MD) simulations were carried out for sarcinricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other SRD features is presented. The SRD is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean square deviation (r.m.s.d.) values between averaged MD and high-resolution X-ray structures of 11.4 A . Modest dynamics is observed in the tetraloop, namely, rotation of adenine in its apex and subtle reversible shift of the tetraloop with respect to the adjacent base pair.The deformedflexible region in low-resolution rat X-ray structure is repaired by simulations. The simulations reveal few backbone flips, which do not affect positions of bases and do not indicate a force field imbalance. Non-Watson Crick base pairs are rigid and mediated by longresidency water molecules while there are several modest cation-binding sites around SRD. In summary, SRD is an unusually stiff rRNA building block. Its intrinsic structural and dynamical signatures seen in simulations are strikingly distinct from other rRNA motifs such as Loop E and Kink-turns.

Links

• MSM0021622413, plan (intention): Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment