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

FADRNÁ, Eva a 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, roč. 20, č. 5, s. 715-731. ISSN 0739-1102.

Základní údaje

• Originální název: Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search
• Název česky: Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search
• Autoři: FADRNÁ, Eva (203 Česká republika, garant) a Jaroslav KOČA (203 Česká republika).
• Vydání: Journal of Biomolecular Structure and Dynamics, USA, Adenine Press, 2003, 0739-1102.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Článek v odborném periodiku
• Obor: 10403 Physical chemistry
• Stát vydavatele: Spojené státy
• Utajení: není předmětem státního či obchodního tajemství
• WWW: URL
• Impakt faktor: Impact factor: 1.131
• Kód RIV: RIV/00216224:14310/03:00008713
• Organizační jednotka: Přírodovědecká fakulta
• UT WoS: 000182182000011
• Klíčová slova anglicky: Conformational search; RNA trimers; Molecular dynamics; AMBER; CICADA; Database Search
• Štítky: AMBER, CICADA, Conformational search, Database Search, molecular dynamics, RNA trimers

Anotace

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.

Anotace česky

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.

Návaznosti

• LN00A016, projekt VaV: Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum