2007
Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation
MACEK, Pavel, Petr NOVÁK, Lukáš ŽÍDEK a Vladimír SKLENÁŘZákladní údaje
Originální název
Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation
Název česky
Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation
Autoři
MACEK, Pavel (203 Česká republika), Petr NOVÁK (203 Česká republika), Lukáš ŽÍDEK (203 Česká republika) a Vladimír SKLENÁŘ (203 Česká republika, garant)
Vydání
Journal of Physical Chemistry B, USA, The American Chemical Society, 2007, 1089-5639
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10610 Biophysics
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Impakt faktor
Impact factor: 2.918
Kód RIV
RIV/00216224:14310/07:00022171
Organizační jednotka
Přírodovědecká fakulta
UT WoS
000246569400028
Klíčová slova anglicky
Molecular dynamics; order parameter; NMR relaxation; motional analysis
Změněno: 11. 6. 2007 15:46, prof. Mgr. Lukáš Žídek, Ph.D.
V originále
Molecular motions of free and pheromone-bound mouse major urinary protein~I, previously investigated by NMR relaxation, were simulated in 30-ns molecular dynamics (MD) runs. The backbone flexibility was described in terms of order parameters and correlation times, commonly used in the NMR relaxation analysis. A special attention was paid to the effect of conformational changes on the nanosecond time scale. Time-dependent order parameters were determined in order to separate motions occurring on different time scales. As an alternative approach, slow conformational changes were identified from the backbone torsion angle variances and a "conformationally filtered" order parameters were calculated for well-defined conformation states. A comparison of the data obtained for the free and pheromone-bound protein showed that some residues are more rigid in the bound form, but larger portion of the protein becomes more flexible upon the pheromone binding. This finding is in a general agreement with the NMR results. The higher flexibility observed on the fast (fs--ps) time scale was typically observed for the residues exhibiting higher conformational freedom on the ns time scale. An inspection of the hydrogen bond network provided a structural explanation for the flexibility differences between the free and pheromone-bound proteins in the simulations.
Česky
Molecular motions of free and pheromone-bound mouse major urinary protein~I, previously investigated by NMR relaxation, were simulated in 30-ns molecular dynamics (MD) runs. The backbone flexibility was described in terms of order parameters and correlation times, commonly used in the NMR relaxation analysis. A special attention was paid to the effect of conformational changes on the nanosecond time scale. Time-dependent order parameters were determined in order to separate motions occurring on different time scales. As an alternative approach, slow conformational changes were identified from the backbone torsion angle variances and a "conformationally filtered" order parameters were calculated for well-defined conformation states. A comparison of the data obtained for the free and pheromone-bound protein showed that some residues are more rigid in the bound form, but larger portion of the protein becomes more flexible upon the pheromone binding. This finding is in a general agreement with the NMR results. The higher flexibility observed on the fast (fs--ps) time scale was typically observed for the residues exhibiting higher conformational freedom on the ns time scale. An inspection of the hydrogen bond network provided a structural explanation for the flexibility differences between the free and pheromone-bound proteins in the simulations.
Návaznosti
| LC06030, projekt VaV |
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| MSM0021622413, záměr |
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