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Toward understanding the conformational dynamics of RNA ligation.

Swift RV, Durrant J, Amaro RE, McCammon JA - Biochemistry (2009)

Bottom Line: This study describes a recent 70 ns molecular dynamics simulation of TbREL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of T. brucei insect and bloodstream forms.In this work, a model of TbREL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between TbREL1 and T4 Rnl2.Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093-0365, USA.

ABSTRACT
Members of the genus Trypanosoma, which include the pathogenic species Trypanosoma brucei and Trypanosoma cruzi, edit their post-transcriptional mitochondrial RNA via a multiprotein complex called the editosome. In T. brucei, the RNA is nicked prior to uridylate insertion and deletion. Following editing, nicked RNA is religated by one of two RNA-editing ligases (TbREL). This study describes a recent 70 ns molecular dynamics simulation of TbREL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of T. brucei insect and bloodstream forms. In this work, a model of TbREL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between TbREL1 and T4 Rnl2. The simulation captures TbREL1 dynamics in the state immediately preceding RNA ligation, providing insights into the functional dynamics and catalytic mechanism of the kinetoplastid ligation reaction. Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily.

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Equilibrated ribofuranose pseudorotation angle for the 3′-OH nucleotide as depicted within the active site (left panel) and in polar coordinates (right panel; equilibration data colored gray and dynamics data black).
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fig3: Equilibrated ribofuranose pseudorotation angle for the 3′-OH nucleotide as depicted within the active site (left panel) and in polar coordinates (right panel; equilibration data colored gray and dynamics data black).

Mentions: A 70 ns MD simulation followed in which unrestrained dynamics were performed with a 1 fs time step. The duration of the simulation was sufficient to equilibrate the system on the basis of rmsd values [overall α-carbon (Figure S1 of the Supporting Information) and the 3′-terminal sugar pucker phase angle (Figure 3)], while allowing us to sample functionally relevant conformations local to the step 2 intermediate. The temperature bath was maintained by Langevin dynamics at 310 K, and pressure was maintained with the hybrid Nose Hoover-Langevin piston method at 1 atm (25) using period and decay times of 100 and 50 fs, respectively. The particle mesh Ewald algorithm was used to treat long-range electrostatics (26). A multiple-time step algorithm was employed in which bonded interactions were computed at every time step, short-range nonbonded interactions were computed every two time steps, and full electrostatics were computed every two time steps. The water hydrogen−oxygen and hydrogen−hydrogen distances were constrained using the SHAKEH algorithm (27) to be within 0.0005 Å of the nominal lengths. All minimization and MD simulations were carried out with NAMD 2.6 (28) using the Amber ff99SB force field (21). Simulations were performed on the TeraGrid ABE cluster. A typical benchmark for the 57575-atom system on 128 processors was 0.21 days per nanosecond of simulation. System configurations were sampled every 50 ps, generating 1400 coordinate snapshots for subsequent analysis.


Toward understanding the conformational dynamics of RNA ligation.

Swift RV, Durrant J, Amaro RE, McCammon JA - Biochemistry (2009)

Equilibrated ribofuranose pseudorotation angle for the 3′-OH nucleotide as depicted within the active site (left panel) and in polar coordinates (right panel; equilibration data colored gray and dynamics data black).
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651658&req=5

fig3: Equilibrated ribofuranose pseudorotation angle for the 3′-OH nucleotide as depicted within the active site (left panel) and in polar coordinates (right panel; equilibration data colored gray and dynamics data black).
Mentions: A 70 ns MD simulation followed in which unrestrained dynamics were performed with a 1 fs time step. The duration of the simulation was sufficient to equilibrate the system on the basis of rmsd values [overall α-carbon (Figure S1 of the Supporting Information) and the 3′-terminal sugar pucker phase angle (Figure 3)], while allowing us to sample functionally relevant conformations local to the step 2 intermediate. The temperature bath was maintained by Langevin dynamics at 310 K, and pressure was maintained with the hybrid Nose Hoover-Langevin piston method at 1 atm (25) using period and decay times of 100 and 50 fs, respectively. The particle mesh Ewald algorithm was used to treat long-range electrostatics (26). A multiple-time step algorithm was employed in which bonded interactions were computed at every time step, short-range nonbonded interactions were computed every two time steps, and full electrostatics were computed every two time steps. The water hydrogen−oxygen and hydrogen−hydrogen distances were constrained using the SHAKEH algorithm (27) to be within 0.0005 Å of the nominal lengths. All minimization and MD simulations were carried out with NAMD 2.6 (28) using the Amber ff99SB force field (21). Simulations were performed on the TeraGrid ABE cluster. A typical benchmark for the 57575-atom system on 128 processors was 0.21 days per nanosecond of simulation. System configurations were sampled every 50 ps, generating 1400 coordinate snapshots for subsequent analysis.

Bottom Line: This study describes a recent 70 ns molecular dynamics simulation of TbREL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of T. brucei insect and bloodstream forms.In this work, a model of TbREL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between TbREL1 and T4 Rnl2.Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093-0365, USA.

ABSTRACT
Members of the genus Trypanosoma, which include the pathogenic species Trypanosoma brucei and Trypanosoma cruzi, edit their post-transcriptional mitochondrial RNA via a multiprotein complex called the editosome. In T. brucei, the RNA is nicked prior to uridylate insertion and deletion. Following editing, nicked RNA is religated by one of two RNA-editing ligases (TbREL). This study describes a recent 70 ns molecular dynamics simulation of TbREL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of T. brucei insect and bloodstream forms. In this work, a model of TbREL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between TbREL1 and T4 Rnl2. The simulation captures TbREL1 dynamics in the state immediately preceding RNA ligation, providing insights into the functional dynamics and catalytic mechanism of the kinetoplastid ligation reaction. Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily.

Show MeSH