Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search

FADRNÁ, Eva and Jaroslav KOČA. Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 2003, vol. 20, No 5, p. 715-731. ISSN 0739-1102.

Basic information

• Original name: Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search
• Name in Czech: Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search
• Authors: FADRNÁ, Eva (203 Czech Republic, guarantor) and Jaroslav KOČA (203 Czech Republic).
• Edition: Journal of Biomolecular Structure and Dynamics, USA, Adenine Press, 2003, 0739-1102.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10403 Physical chemistry
• Country of publisher: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 1.131
• RIV identification code: RIV/00216224:14310/03:00008713
• Organization unit: Faculty of Science
• UT WoS: 000182182000011
• Keywords in English: Conformational search; RNA trimers; Molecular dynamics; AMBER; CICADA; Database Search
• Tags: AMBER, CICADA, Conformational search, Database Search, molecular dynamics, RNA trimers

Abstract

Two RNA sequences, AAA and AUG, were studied by the conformational search program CICADA and by molecular dynamics (MD) in the framework of the AMBER force field, and also via thorough PDB database search. CICADA was used to provide detailed information about conformers and conformational interconversions on the energy surfaces of the above molecules. Several conformational families were found for both sequences. Analysis of the results shows differences, especially between the energy of the single families, and also in flexibility and concerted conformational movement. Therefore, several MD trajectories (altogether 16 ns) were run to obtain more details about both the stability of conformers belonging to different conformational families and about the dynamics of the two systems. Results show that the trajectories strongly depend on the starting structure. When the MD start from the global minimum found by CICADA, they provide a stable run, while MD starting from another conformational family generates a trajectory where several different conformational families are visited. The results obtained by theoretical methods are compared with the thorough database search data. It is concluded that all except for the highest energy conformational families found in theoretical result also appear in experimental data.

Abstract (in Czech)

Two RNA sequences, AAA and AUG, were studied by the conformational search program CICADA and by molecular dynamics (MD) in the framework of the AMBER force field, and also via thorough PDB database search. CICADA was used to provide detailed information about conformers and conformational interconversions on the energy surfaces of the above molecules. Several conformational families were found for both sequences. Analysis of the results shows differences, especially between the energy of the single families, and also in flexibility and concerted conformational movement. Therefore, several MD trajectories (altogether 16 ns) were run to obtain more details about both the stability of conformers belonging to different conformational families and about the dynamics of the two systems. Results show that the trajectories strongly depend on the starting structure. When the MD start from the global minimum found by CICADA, they provide a stable run, while MD starting from another conformational family generates a trajectory where several different conformational families are visited. The results obtained by theoretical methods are compared with the thorough database search data. It is concluded that all except for the highest energy conformational families found in theoretical result also appear in experimental data.

Links

• LN00A016, research and development project: Name: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Center