2003
Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search
FADRNÁ, Eva a Jaroslav KOČAZákladní 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
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10403 Physical chemistry
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Odkazy
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
Změněno: 14. 2. 2005 11:45, Mgr. Eva Fadrná, Ph.D.
V originále
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.
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
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