2008
In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies
ADAM, Jan, Zdeněk KŘÍŽ, Martin PROKOP, Michaela WIMMEROVÁ, Jaroslav KOČA et. al.Základní údaje
Originální název
In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies
Název česky
In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies
Autoři
ADAM, Jan (203 Česká republika), Zdeněk KŘÍŽ (203 Česká republika), Martin PROKOP (203 Česká republika), Michaela WIMMEROVÁ (203 Česká republika) a Jaroslav KOČA (203 Česká republika, garant)
Vydání
Journal of Chemical Information and Modeling, 2008, 1549-9596
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10600 1.6 Biological sciences
Stát vydavatele
Česká republika
Utajení
není předmětem státního či obchodního tajemství
Impakt faktor
Impact factor: 3.643
Kód RIV
RIV/00216224:14310/08:00024957
Organizační jednotka
Přírodovědecká fakulta
UT WoS
000261103700013
Klíčová slova anglicky
lectins; molecular modeling; computational chemistry; in silico prediction; docking
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 24. 6. 2009 12:53, prof. RNDr. Michaela Wimmerová, Ph.D.
V originále
This article is focused on the application of two types of AutoDock and DOCK docking software, and aimed at studying the interaction of a calcium-dependent bacterial lectin PA-IIL from Pseudomonas aeruginosa as well as its mutants with saccharide ligands. The effect of different partial charges assigned to the calcium ions was tested and evaluated in terms of the best agreement with the crystal structure. The results of DOCK were further optimized by molecular dynamics and rescored using AMBER. For both software, the agreement of the docked structures and the provided binding energies were evaluated in terms of prediction accuracy. This was carried out by comparing the computed results to the crystal structures and experimentally determined binding energies, respectively. The performance of the both docking software applied on studied problem was evaluated as well. The molecular docking methods proved efficient in identifying the correct binding modes in terms of geometry, and partially also in predicting the preference changes caused by mutation. Obtaining a reasonable in silico method for the prediction of lectin-saccharide interactions may be possible in the future.
Česky
This article is focused on the application of two types of AutoDock and DOCK docking software, and aimed at studying the interaction of a calcium-dependent bacterial lectin PA-IIL from Pseudomonas aeruginosa as well as its mutants with saccharide ligands. The effect of different partial charges assigned to the calcium ions was tested and evaluated in terms of the best agreement with the crystal structure. The results of DOCK were further optimized by molecular dynamics and rescored using AMBER. For both software, the agreement of the docked structures and the provided binding energies were evaluated in terms of prediction accuracy. This was carried out by comparing the computed results to the crystal structures and experimentally determined binding energies, respectively. The performance of the both docking software applied on studied problem was evaluated as well. The molecular docking methods proved efficient in identifying the correct binding modes in terms of geometry, and partially also in predicting the preference changes caused by mutation. Obtaining a reasonable in silico method for the prediction of lectin-saccharide interactions may be possible in the future.
Návaznosti
| GA303/06/0570, projekt VaV |
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| LC06030, projekt VaV |
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| MSM0021622413, záměr |
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