2008
Molecular dynamics study of Pseudomonas eruginosa lectin-II complexed with monosaccharides
MISHRA, Navnit Kumar, Petr KULHÁNEK, Lenka ŠNAJDROVÁ, Martin PETŘEK, Anne IMBERTY et. al.Základní údaje
Originální název
Molecular dynamics study of Pseudomonas eruginosa lectin-II complexed with monosaccharides
Název česky
Molecular dynamics study of Pseudomonas eruginosa lectin-II complexed with monosaccharides
Autoři
MISHRA, Navnit Kumar (356 Indie), Petr KULHÁNEK (203 Česká republika), Lenka ŠNAJDROVÁ (203 Česká republika), Martin PETŘEK (203 Česká republika), Anne IMBERTY (250 Francie) a Jaroslav KOČA (203 Česká republika, garant)
Vydání
Proteins: Structure, Function, and Bioinformatics, Wiley, 2008, 0887-3585
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10600 1.6 Biological sciences
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Impakt faktor
Impact factor: 3.419
Kód RIV
RIV/00216224:14310/08:00025688
Organizační jednotka
Přírodovědecká fakulta
UT WoS
000256609800033
Klíčová slova anglicky
PA-IIL lectin; molecular dynamics; calcium ions; binding affinity; water density map; sodium ions; monosaccharide
Štítky
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 28. 6. 2009 19:52, prof. RNDr. Jaroslav Koča, DrSc.
V originále
We present the results of a series of 10-ns molecular dynamics simulations on Pseudomonas aeruginosa lectin-II (PA-IIL) and its complexes with four different monosaccharides. We compare the saccharide-free, saccharideoccupied, and saccharide- and ion-free forms of the lectin. The results are coupled with analysis of the water density map and calcium coordination. The water density pattern around the binding site in the free lectin molecular dynamics was fitted with that in the X-ray and with the hydroxyl groups of the monosaccharide within the lectin/monosaccharide complexes and the best ligand was predicted based on the best fit. Interestingly, the water density pattern around the binding site in the uncomplexed lectin exactly fitted the O2, O3, and O4 hydroxyl groups of the fucose complex with the lectin. This observation could lead to a hypothesis that the replacement of these three water molecules from the binding site by the monosaccharide decreases the entropy of the complex and increases the entropy of the water molecules, which favors the binding. It suggests that the high density peaks of the solvent around the binding site in the free protein could be the tool to predict hydroxyl group orientation of the sugar in the protein/sugar complexes. The high affinity of PA-IIL binding site is also attributed to the presence of two calcium ions, each of them making five to six coordinations with the protein part and two coordinations with either water or the monosaccharide. When the calcium ions are removed from the simulated system, they are replaced by sodium ions from the solvent. These observations rationalize the high binding affinity of PA-IIL towards fucose.
Česky
We present the results of a series of 10-ns molecular dynamics simulations on Pseudomonas aeruginosa lectin-II (PA-IIL) and its complexes with four different monosaccharides. We compare the saccharide-free, saccharideoccupied, and saccharide- and ion-free forms of the lectin. The results are coupled with analysis of the water density map and calcium coordination. The water density pattern around the binding site in the free lectin molecular dynamics was fitted with that in the X-ray and with the hydroxyl groups of the monosaccharide within the lectin/monosaccharide complexes and the best ligand was predicted based on the best fit. Interestingly, the water density pattern around the binding site in the uncomplexed lectin exactly fitted the O2, O3, and O4 hydroxyl groups of the fucose complex with the lectin. This observation could lead to a hypothesis that the replacement of these three water molecules from the binding site by the monosaccharide decreases the entropy of the complex and increases the entropy of the water molecules, which favors the binding. It suggests that the high density peaks of the solvent around the binding site in the free protein could be the tool to predict hydroxyl group orientation of the sugar in the protein/sugar complexes. The high affinity of PA-IIL binding site is also attributed to the presence of two calcium ions, each of them making five to six coordinations with the protein part and two coordinations with either water or the monosaccharide. When the calcium ions are removed from the simulated system, they are replaced by sodium ions from the solvent. These observations rationalize the high binding affinity of PA-IIL towards fucose.
Návaznosti
| LC06030, projekt VaV |
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| MSM0021622413, záměr |
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