Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation

MACEK, Pavel, Petr NOVÁK, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation. Journal of Physical Chemistry B. USA: The American Chemical Society, vol. 111, No 20, p. 5731-5739. ISSN 1089-5639. 2007.

Basic information

• Original name: Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation
• Name in Czech: Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation
• Authors: MACEK, Pavel (203 Czech Republic), Petr NOVÁK (203 Czech Republic), Lukáš ŽÍDEK (203 Czech Republic) and Vladimír SKLENÁŘ (203 Czech Republic, guarantor).
• Edition: Journal of Physical Chemistry B, USA, The American Chemical Society, 2007, 1089-5639.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10610 Biophysics
• Country of publisher: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• Impact factor: Impact factor: 2.918
• RIV identification code: RIV/00216224:14310/07:00022171
• Organization unit: Faculty of Science
• UT WoS: 000246569400028
• Keywords in English: Molecular dynamics; order parameter; NMR relaxation; motional analysis
• Tags: molecular dynamics, motional analysis, NMR relaxation, order parameter

Abstract

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.

Abstract (in Czech)

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.

Links

• LC06030, research and development project: Name: Biomolekulární centrum

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre

• MSM0021622413, plan (intention): Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment