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Molecular basis for the differential interaction of plant mitochondrial VDAC proteins with tRNAs.

Salinas T, El Farouk-Ameqrane S, Ubrig E, Sauter C, Duchêne AM, Maréchal-Drouard L - Nucleic Acids Res. (2014)

Bottom Line: To further identify specific features and critical amino acids required for tRNA binding, 21 VDAC34 mutants were constructed and analyzed by northwestern.This allowed us to show that the β-barrel structure of VDAC34 and the first 50 amino acids that contain the α-helix are essential for RNA binding.Altogether the work shows that during evolution, plant mitochondrial VDAC proteins have diverged so as to interact differentially with nucleic acids, and this may reflect their involvement in various specialized biological functions.

View Article: PubMed Central - PubMed

Affiliation: Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France laurence.drouard@ibmp-cnrs.unistra.fr.

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Plant VDAC architecture and tRNA binding regions. When performing modeling, VDAC 34 and 36 architecture models show no significant differences due to their high sequence identity (75%). Thus, this figure focuses on VDAC 34 features. (A) Topological arrangement of VDAC34. The N-terminal α-helix is indicated by an orange dashed box and the 19 β-strands of the β-barrel are depicted by open boxes (green frames). Amino acid residues different in VDAC36 are under gray background. G2, K47 and K48 residues are under pink background. (B) 3D model of VDAC34 generated using Modeler (25) and the mouse mitochondrial VDAC1 crystal structure as a template (PDB ID: 3EMN). It displays a characteristic VDAC architecture with the N-terminal helix in orange docked along the inner channel wall at the midpoint with the β-strands in green. Key residues for tRNA binding, G2 at one entry and K47K48 at the opposite entry, are highlighted by dotted volumes and are indicated by pink arrows. The N-terminus including the helix partially closes the pore and leaves a channel of about 25 × 15 Å (top right). The pore diameter is 25 Å large at the extremities and could be open more widely by moving the N-terminal region out of the channel (bottom right).
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Figure 6: Plant VDAC architecture and tRNA binding regions. When performing modeling, VDAC 34 and 36 architecture models show no significant differences due to their high sequence identity (75%). Thus, this figure focuses on VDAC 34 features. (A) Topological arrangement of VDAC34. The N-terminal α-helix is indicated by an orange dashed box and the 19 β-strands of the β-barrel are depicted by open boxes (green frames). Amino acid residues different in VDAC36 are under gray background. G2, K47 and K48 residues are under pink background. (B) 3D model of VDAC34 generated using Modeler (25) and the mouse mitochondrial VDAC1 crystal structure as a template (PDB ID: 3EMN). It displays a characteristic VDAC architecture with the N-terminal helix in orange docked along the inner channel wall at the midpoint with the β-strands in green. Key residues for tRNA binding, G2 at one entry and K47K48 at the opposite entry, are highlighted by dotted volumes and are indicated by pink arrows. The N-terminus including the helix partially closes the pore and leaves a channel of about 25 × 15 Å (top right). The pore diameter is 25 Å large at the extremities and could be open more widely by moving the N-terminal region out of the channel (bottom right).

Mentions: In order to gain an insight into the organization of tRNA binding sites in VDACs we built 3D models of S. tuberosum VDACs and of their mutants (Supplemental Figure S6) based on the crystal structure of the mouse VDAC1 (3). Sequence alignment with mammal proteins unambiguously showed that VDAC34 and VDAC36 adopt a β-barrel structure composed of 19 antiparallel β-strands (Figure 6A), in agreement with ProtScale prediction of 19 hydrophobic segments separated by hydrophilic loops (not shown). The N-terminal extremity contains a short α-helix that is positioned inside the β-barrel close to strands 10–15 (Figure 6B). The amphiphilic nature of the α-helix (Supplemental Figure S6) allows its anchoring to the β-barrel wall via hydrophobic contacts and exposes polar and charged side chains inside the pore. As observed in mammal VDAC1, this N-terminal helix is positioned at the midpoint of the pore and restricts its inner diameter to about 15 Å, whereas both entries of the barrel have a diameter of at least 25 Å (Figure 6B). Hydrophilic residues are mainly found in the loops connecting the β-strands or inside the pore alternating with hydrophobic residues that point towards the membrane. This organization provides pores with an inner channel that is mainly positively charged to guide anions through the OMM (Supplemental Figure S6).


Molecular basis for the differential interaction of plant mitochondrial VDAC proteins with tRNAs.

Salinas T, El Farouk-Ameqrane S, Ubrig E, Sauter C, Duchêne AM, Maréchal-Drouard L - Nucleic Acids Res. (2014)

Plant VDAC architecture and tRNA binding regions. When performing modeling, VDAC 34 and 36 architecture models show no significant differences due to their high sequence identity (75%). Thus, this figure focuses on VDAC 34 features. (A) Topological arrangement of VDAC34. The N-terminal α-helix is indicated by an orange dashed box and the 19 β-strands of the β-barrel are depicted by open boxes (green frames). Amino acid residues different in VDAC36 are under gray background. G2, K47 and K48 residues are under pink background. (B) 3D model of VDAC34 generated using Modeler (25) and the mouse mitochondrial VDAC1 crystal structure as a template (PDB ID: 3EMN). It displays a characteristic VDAC architecture with the N-terminal helix in orange docked along the inner channel wall at the midpoint with the β-strands in green. Key residues for tRNA binding, G2 at one entry and K47K48 at the opposite entry, are highlighted by dotted volumes and are indicated by pink arrows. The N-terminus including the helix partially closes the pore and leaves a channel of about 25 × 15 Å (top right). The pore diameter is 25 Å large at the extremities and could be open more widely by moving the N-terminal region out of the channel (bottom right).
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Related In: Results  -  Collection

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Figure 6: Plant VDAC architecture and tRNA binding regions. When performing modeling, VDAC 34 and 36 architecture models show no significant differences due to their high sequence identity (75%). Thus, this figure focuses on VDAC 34 features. (A) Topological arrangement of VDAC34. The N-terminal α-helix is indicated by an orange dashed box and the 19 β-strands of the β-barrel are depicted by open boxes (green frames). Amino acid residues different in VDAC36 are under gray background. G2, K47 and K48 residues are under pink background. (B) 3D model of VDAC34 generated using Modeler (25) and the mouse mitochondrial VDAC1 crystal structure as a template (PDB ID: 3EMN). It displays a characteristic VDAC architecture with the N-terminal helix in orange docked along the inner channel wall at the midpoint with the β-strands in green. Key residues for tRNA binding, G2 at one entry and K47K48 at the opposite entry, are highlighted by dotted volumes and are indicated by pink arrows. The N-terminus including the helix partially closes the pore and leaves a channel of about 25 × 15 Å (top right). The pore diameter is 25 Å large at the extremities and could be open more widely by moving the N-terminal region out of the channel (bottom right).
Mentions: In order to gain an insight into the organization of tRNA binding sites in VDACs we built 3D models of S. tuberosum VDACs and of their mutants (Supplemental Figure S6) based on the crystal structure of the mouse VDAC1 (3). Sequence alignment with mammal proteins unambiguously showed that VDAC34 and VDAC36 adopt a β-barrel structure composed of 19 antiparallel β-strands (Figure 6A), in agreement with ProtScale prediction of 19 hydrophobic segments separated by hydrophilic loops (not shown). The N-terminal extremity contains a short α-helix that is positioned inside the β-barrel close to strands 10–15 (Figure 6B). The amphiphilic nature of the α-helix (Supplemental Figure S6) allows its anchoring to the β-barrel wall via hydrophobic contacts and exposes polar and charged side chains inside the pore. As observed in mammal VDAC1, this N-terminal helix is positioned at the midpoint of the pore and restricts its inner diameter to about 15 Å, whereas both entries of the barrel have a diameter of at least 25 Å (Figure 6B). Hydrophilic residues are mainly found in the loops connecting the β-strands or inside the pore alternating with hydrophobic residues that point towards the membrane. This organization provides pores with an inner channel that is mainly positively charged to guide anions through the OMM (Supplemental Figure S6).

Bottom Line: To further identify specific features and critical amino acids required for tRNA binding, 21 VDAC34 mutants were constructed and analyzed by northwestern.This allowed us to show that the β-barrel structure of VDAC34 and the first 50 amino acids that contain the α-helix are essential for RNA binding.Altogether the work shows that during evolution, plant mitochondrial VDAC proteins have diverged so as to interact differentially with nucleic acids, and this may reflect their involvement in various specialized biological functions.

View Article: PubMed Central - PubMed

Affiliation: Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France laurence.drouard@ibmp-cnrs.unistra.fr.

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