Insights on the structure and stability of Licanantase: A trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans

Fernando Abarca, Sebastian E. Gutierrez-Maldonado, Pilar Parada, Patricio Martinez, Alejandro Maass, Tomas Perez-Acle

Resultado de la investigación: Article

1 Cita (Scopus)

Resumen

Licanantase (Lic) is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery frombioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can formstable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction, a suitable model for Lic was produced using the de novo algorithm "Rosetta Fold-and-Dock". To assess the structural stability of our model, Molecular Dynamics (MD) and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic's secondary and tertiary structure.

Idioma originalEnglish
Número de artículoe457
PublicaciónPeerJ
Volumen2014
N.º1
DOI
EstadoPublished - 1 ene 2014

Huella dactilar

Acidithiobacillus thiooxidans
molecular dynamics
Molecular Dynamics Simulation
lipoproteins
Lipoproteins
Acids
prediction
Molecular dynamics
acids
Protein Sequence Analysis
structure-activity relationships
Computational Biology
crosslinking
Sulfur
bioinformatics
Alanine
Computer Simulation
alanine
hydrogen
Copper

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Citar esto

Abarca, F., Gutierrez-Maldonado, S. E., Parada, P., Martinez, P., Maass, A., & Perez-Acle, T. (2014). Insights on the structure and stability of Licanantase: A trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans. PeerJ, 2014(1), [e457]. https://doi.org/10.7717/peerj.457
Abarca, Fernando ; Gutierrez-Maldonado, Sebastian E. ; Parada, Pilar ; Martinez, Patricio ; Maass, Alejandro ; Perez-Acle, Tomas. / Insights on the structure and stability of Licanantase : A trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans. En: PeerJ. 2014 ; Vol. 2014, N.º 1.
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abstract = "Licanantase (Lic) is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery frombioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can formstable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction, a suitable model for Lic was produced using the de novo algorithm {"}Rosetta Fold-and-Dock{"}. To assess the structural stability of our model, Molecular Dynamics (MD) and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic's secondary and tertiary structure.",
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Abarca, F, Gutierrez-Maldonado, SE, Parada, P, Martinez, P, Maass, A & Perez-Acle, T 2014, 'Insights on the structure and stability of Licanantase: A trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans', PeerJ, vol. 2014, n.º 1, e457. https://doi.org/10.7717/peerj.457

Insights on the structure and stability of Licanantase : A trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans. / Abarca, Fernando; Gutierrez-Maldonado, Sebastian E.; Parada, Pilar; Martinez, Patricio; Maass, Alejandro; Perez-Acle, Tomas.

En: PeerJ, Vol. 2014, N.º 1, e457, 01.01.2014.

Resultado de la investigación: Article

TY - JOUR

T1 - Insights on the structure and stability of Licanantase

T2 - A trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans

AU - Abarca, Fernando

AU - Gutierrez-Maldonado, Sebastian E.

AU - Parada, Pilar

AU - Martinez, Patricio

AU - Maass, Alejandro

AU - Perez-Acle, Tomas

PY - 2014/1/1

Y1 - 2014/1/1

N2 - Licanantase (Lic) is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery frombioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can formstable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction, a suitable model for Lic was produced using the de novo algorithm "Rosetta Fold-and-Dock". To assess the structural stability of our model, Molecular Dynamics (MD) and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic's secondary and tertiary structure.

AB - Licanantase (Lic) is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery frombioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can formstable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction, a suitable model for Lic was produced using the de novo algorithm "Rosetta Fold-and-Dock". To assess the structural stability of our model, Molecular Dynamics (MD) and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic's secondary and tertiary structure.

KW - Acidithiobacillus thiooxidans

KW - Alanine-zipper

KW - Bioleaching

KW - Lipoprotein

KW - Molecular dynamics simulation

KW - Protein structure prediction

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