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Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution.

Carvalho HF, Roque AC, Iranzo O, Branco RJ - PLoS ONE (2015)

Bottom Line: However, previously unnoticed dynamical similarity was found between the relevant members Carboxypeptidase Pfu, Leishmanolysin, and Botulinum Neurotoxin Type A, despite sharing no structural similarity.These results suggest that distinct selective pressure mechanisms act on metalloproteases at structural and dynamical levels through the course of their evolution.The integration of these newly developed tools, if applied to other protein families, can lead to more accurate and descriptive protein classification systems.

View Article: PubMed Central - PubMed

Affiliation: UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.

ABSTRACT
Metalloproteases have evolved in a vast number of biological systems, being one of the most diverse types of proteases and presenting a wide range of folds and catalytic metal ions. Given the increasing understanding of protein internal dynamics and its role in enzyme function, we are interested in assessing how the structural heterogeneity of metalloproteases translates into their dynamics. Therefore, the dynamical profile of the clan MA type protein thermolysin, derived from an Elastic Network Model of protein structure, was evaluated against those obtained from a set of experimental structures and molecular dynamics simulation trajectories. A close correspondence was obtained between modes derived from the coarse-grained model and the subspace of functionally-relevant motions observed experimentally, the later being shown to be encoded in the internal dynamics of the protein. This prompted the use of dynamics-based comparison methods that employ such coarse-grained models in a representative set of clan members, allowing for its quantitative description in terms of structural and dynamical variability. Although members show structural similarity, they nonetheless present distinct dynamical profiles, with no apparent correlation between structural and dynamical relatedness. However, previously unnoticed dynamical similarity was found between the relevant members Carboxypeptidase Pfu, Leishmanolysin, and Botulinum Neurotoxin Type A, despite sharing no structural similarity. Inspection of the respective alignments shows that dynamical similarity has a functional basis, namely the need for maintaining proper intermolecular interactions with the respective substrates. These results suggest that distinct selective pressure mechanisms act on metalloproteases at structural and dynamical levels through the course of their evolution. This work shows how new insights on metalloprotease function and evolution can be assessed with comparison schemes that incorporate information on protein dynamics. The integration of these newly developed tools, if applied to other protein families, can lead to more accurate and descriptive protein classification systems.

No MeSH data available.


Structure- and dynamics-based alignments obtained for pair M3-M32.(A) Structure-based and (B) Dynamics-based alignment of M3 representative Neurolysin (blue, PDB ID: 1I1I) and M32 representative Carboxypeptidase Pfu (red, PDB ID: 1KA4). Produced alignments were obtained using the DaliLite and ALADYN web-servers (see Methods). Aligned residues colored in cartoon representation, non-aligned residues in colored ribbons and active site residues in surface representations (Neurolysin: H474, E475, H478 and E503; Carboxypeptidase Pfu H269, E270, H273 and E299). Colored arrows indicate modes of motion of aligned portions along the first mode.
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pone.0138118.g004: Structure- and dynamics-based alignments obtained for pair M3-M32.(A) Structure-based and (B) Dynamics-based alignment of M3 representative Neurolysin (blue, PDB ID: 1I1I) and M32 representative Carboxypeptidase Pfu (red, PDB ID: 1KA4). Produced alignments were obtained using the DaliLite and ALADYN web-servers (see Methods). Aligned residues colored in cartoon representation, non-aligned residues in colored ribbons and active site residues in surface representations (Neurolysin: H474, E475, H478 and E503; Carboxypeptidase Pfu H269, E270, H273 and E299). Colored arrows indicate modes of motion of aligned portions along the first mode.

Mentions: Both structures are mainly α-helical in content and characterized by a deep narrow channel that divide the structures into two domains, with a wider opening at one end and with the active site located at the bottom. This prevents activity towards large, folded substrates. Their structure-based alignment is shown in Fig 4A. The alignment produces a RMSD of 3.7 Å for 449 amino acids used with 15% sequence identity. Aligned regions consist on core regions surrounding the active sites and α-helices that constitute the channel base and walls. The respective dynamics-based alignment, shown in Fig 4B, produces a lower number of equivalent residues, with RMSD of 2.8 Å for 371 amino acids with 13.5% sequence identity (RMSIP of 0.870). It reveals that these regions undergo very similar deformations resembling hinge motions, most likely corresponding to channel opening for substrate access. The aligned portions in both structure- and dynamics-based alignments have high degree of identity.


Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution.

Carvalho HF, Roque AC, Iranzo O, Branco RJ - PLoS ONE (2015)

Structure- and dynamics-based alignments obtained for pair M3-M32.(A) Structure-based and (B) Dynamics-based alignment of M3 representative Neurolysin (blue, PDB ID: 1I1I) and M32 representative Carboxypeptidase Pfu (red, PDB ID: 1KA4). Produced alignments were obtained using the DaliLite and ALADYN web-servers (see Methods). Aligned residues colored in cartoon representation, non-aligned residues in colored ribbons and active site residues in surface representations (Neurolysin: H474, E475, H478 and E503; Carboxypeptidase Pfu H269, E270, H273 and E299). Colored arrows indicate modes of motion of aligned portions along the first mode.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4580569&req=5

pone.0138118.g004: Structure- and dynamics-based alignments obtained for pair M3-M32.(A) Structure-based and (B) Dynamics-based alignment of M3 representative Neurolysin (blue, PDB ID: 1I1I) and M32 representative Carboxypeptidase Pfu (red, PDB ID: 1KA4). Produced alignments were obtained using the DaliLite and ALADYN web-servers (see Methods). Aligned residues colored in cartoon representation, non-aligned residues in colored ribbons and active site residues in surface representations (Neurolysin: H474, E475, H478 and E503; Carboxypeptidase Pfu H269, E270, H273 and E299). Colored arrows indicate modes of motion of aligned portions along the first mode.
Mentions: Both structures are mainly α-helical in content and characterized by a deep narrow channel that divide the structures into two domains, with a wider opening at one end and with the active site located at the bottom. This prevents activity towards large, folded substrates. Their structure-based alignment is shown in Fig 4A. The alignment produces a RMSD of 3.7 Å for 449 amino acids used with 15% sequence identity. Aligned regions consist on core regions surrounding the active sites and α-helices that constitute the channel base and walls. The respective dynamics-based alignment, shown in Fig 4B, produces a lower number of equivalent residues, with RMSD of 2.8 Å for 371 amino acids with 13.5% sequence identity (RMSIP of 0.870). It reveals that these regions undergo very similar deformations resembling hinge motions, most likely corresponding to channel opening for substrate access. The aligned portions in both structure- and dynamics-based alignments have high degree of identity.

Bottom Line: However, previously unnoticed dynamical similarity was found between the relevant members Carboxypeptidase Pfu, Leishmanolysin, and Botulinum Neurotoxin Type A, despite sharing no structural similarity.These results suggest that distinct selective pressure mechanisms act on metalloproteases at structural and dynamical levels through the course of their evolution.The integration of these newly developed tools, if applied to other protein families, can lead to more accurate and descriptive protein classification systems.

View Article: PubMed Central - PubMed

Affiliation: UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.

ABSTRACT
Metalloproteases have evolved in a vast number of biological systems, being one of the most diverse types of proteases and presenting a wide range of folds and catalytic metal ions. Given the increasing understanding of protein internal dynamics and its role in enzyme function, we are interested in assessing how the structural heterogeneity of metalloproteases translates into their dynamics. Therefore, the dynamical profile of the clan MA type protein thermolysin, derived from an Elastic Network Model of protein structure, was evaluated against those obtained from a set of experimental structures and molecular dynamics simulation trajectories. A close correspondence was obtained between modes derived from the coarse-grained model and the subspace of functionally-relevant motions observed experimentally, the later being shown to be encoded in the internal dynamics of the protein. This prompted the use of dynamics-based comparison methods that employ such coarse-grained models in a representative set of clan members, allowing for its quantitative description in terms of structural and dynamical variability. Although members show structural similarity, they nonetheless present distinct dynamical profiles, with no apparent correlation between structural and dynamical relatedness. However, previously unnoticed dynamical similarity was found between the relevant members Carboxypeptidase Pfu, Leishmanolysin, and Botulinum Neurotoxin Type A, despite sharing no structural similarity. Inspection of the respective alignments shows that dynamical similarity has a functional basis, namely the need for maintaining proper intermolecular interactions with the respective substrates. These results suggest that distinct selective pressure mechanisms act on metalloproteases at structural and dynamical levels through the course of their evolution. This work shows how new insights on metalloprotease function and evolution can be assessed with comparison schemes that incorporate information on protein dynamics. The integration of these newly developed tools, if applied to other protein families, can lead to more accurate and descriptive protein classification systems.

No MeSH data available.