Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1

David Alberto Díaz; George Emilio Barreto; Janneth González Santos

doi:10.1007/978-3-319-01568-2_7

Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1

David Alberto Díaz
, George Emilio Barreto
, Janneth González Santos

Universidad Javeriana

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Pseudomonas aeruginosa is a bacterium resistant to a large number of antibiotics and disinfectants. Since the antigens are responsible for producing this resistance, and most of these are proteins, the objective of this work was to predict by computational means the 3D structure and function of PA2481 protein, determining whether is involved in the antibiotic resistance of this bacterium. In order to do this, the primary structure was analyzed computationally by using servers PROSITE, PFAM, BLAST, PROTPARAM, GLOBPLOT, and PROTSCALE. The secondary structure was obtained by the consensus of algorithms SOPM, PREDATOR, DPM, DSC, and GOR4. The 3D structure was predicted with the I-TASSER server and its stereochemical conformation was evaluated with the STRUCTURE ASSESSMENT tool. The final model was visualized with PyMol program. As a result, the 3D structure of PA2481 is proposed according to its stereochemical conformation; two domains are identified as cytochrome c. The function of the protein may be related to electron transport and proton pumping to generate ATP in Pseudomonas aeruginosa. These results allow a better understanding of the role this protein plays in the physiology of this bacterium.

Original language	English
Title of host publication	Advances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013
Publisher	Springer Verlag
Pages	47-55
Number of pages	9
ISBN (Print)	9783319015675
DOIs	https://doi.org/10.1007/978-3-319-01568-2_7
Publication status	Published - 2014
Externally published	Yes
Event	2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013 - Manizales, Colombia Duration: 25 Sep 2013 → 27 Sep 2013

Publication series

Name	Advances in Intelligent Systems and Computing
Volume	232
ISSN (Print)	2194-5357

Conference

Conference	2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013
Country/Territory	Colombia
City	Manizales
Period	25/09/13 → 27/09/13

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Cystic fibrosis
External otitis
Hypothetical protein
PA2481
Pseudomonas aeruginosa
Structural modeling

Access to Document

10.1007/978-3-319-01568-2_7

Cite this

Díaz, D. A., Barreto, G. E., & Santos, J. G. (2014). Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1. In Advances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013 (pp. 47-55). (Advances in Intelligent Systems and Computing; Vol. 232). Springer Verlag. https://doi.org/10.1007/978-3-319-01568-2_7

Díaz, David Alberto ; Barreto, George Emilio ; Santos, Janneth González. / Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1. Advances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013. Springer Verlag, 2014. pp. 47-55 (Advances in Intelligent Systems and Computing).

@inproceedings{89af2b4fbe6f40bab797a66c07c55fa9,

title = "Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1",

abstract = "Pseudomonas aeruginosa is a bacterium resistant to a large number of antibiotics and disinfectants. Since the antigens are responsible for producing this resistance, and most of these are proteins, the objective of this work was to predict by computational means the 3D structure and function of PA2481 protein, determining whether is involved in the antibiotic resistance of this bacterium. In order to do this, the primary structure was analyzed computationally by using servers PROSITE, PFAM, BLAST, PROTPARAM, GLOBPLOT, and PROTSCALE. The secondary structure was obtained by the consensus of algorithms SOPM, PREDATOR, DPM, DSC, and GOR4. The 3D structure was predicted with the I-TASSER server and its stereochemical conformation was evaluated with the STRUCTURE ASSESSMENT tool. The final model was visualized with PyMol program. As a result, the 3D structure of PA2481 is proposed according to its stereochemical conformation; two domains are identified as cytochrome c. The function of the protein may be related to electron transport and proton pumping to generate ATP in Pseudomonas aeruginosa. These results allow a better understanding of the role this protein plays in the physiology of this bacterium.",

keywords = "Cystic fibrosis, External otitis, Hypothetical protein, PA2481, Pseudomonas aeruginosa, Structural modeling",

author = "D{\'i}az, \{David Alberto\} and Barreto, \{George Emilio\} and Santos, \{Janneth Gonz{\'a}lez\}",

year = "2014",

doi = "10.1007/978-3-319-01568-2\_7",

language = "English",

isbn = "9783319015675",

series = "Advances in Intelligent Systems and Computing",

publisher = "Springer Verlag",

pages = "47--55",

booktitle = "Advances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013",

note = "2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013 ; Conference date: 25-09-2013 Through 27-09-2013",

}

Díaz, DA, Barreto, GE & Santos, JG 2014, Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1. in Advances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013. Advances in Intelligent Systems and Computing, vol. 232, Springer Verlag, pp. 47-55, 2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013, Manizales, Colombia, 25/09/13. https://doi.org/10.1007/978-3-319-01568-2_7

Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1. / Díaz, David Alberto; Barreto, George Emilio; Santos, Janneth González.
Advances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013. Springer Verlag, 2014. p. 47-55 (Advances in Intelligent Systems and Computing; Vol. 232).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1

AU - Díaz, David Alberto

AU - Barreto, George Emilio

AU - Santos, Janneth González

PY - 2014

Y1 - 2014

N2 - Pseudomonas aeruginosa is a bacterium resistant to a large number of antibiotics and disinfectants. Since the antigens are responsible for producing this resistance, and most of these are proteins, the objective of this work was to predict by computational means the 3D structure and function of PA2481 protein, determining whether is involved in the antibiotic resistance of this bacterium. In order to do this, the primary structure was analyzed computationally by using servers PROSITE, PFAM, BLAST, PROTPARAM, GLOBPLOT, and PROTSCALE. The secondary structure was obtained by the consensus of algorithms SOPM, PREDATOR, DPM, DSC, and GOR4. The 3D structure was predicted with the I-TASSER server and its stereochemical conformation was evaluated with the STRUCTURE ASSESSMENT tool. The final model was visualized with PyMol program. As a result, the 3D structure of PA2481 is proposed according to its stereochemical conformation; two domains are identified as cytochrome c. The function of the protein may be related to electron transport and proton pumping to generate ATP in Pseudomonas aeruginosa. These results allow a better understanding of the role this protein plays in the physiology of this bacterium.

AB - Pseudomonas aeruginosa is a bacterium resistant to a large number of antibiotics and disinfectants. Since the antigens are responsible for producing this resistance, and most of these are proteins, the objective of this work was to predict by computational means the 3D structure and function of PA2481 protein, determining whether is involved in the antibiotic resistance of this bacterium. In order to do this, the primary structure was analyzed computationally by using servers PROSITE, PFAM, BLAST, PROTPARAM, GLOBPLOT, and PROTSCALE. The secondary structure was obtained by the consensus of algorithms SOPM, PREDATOR, DPM, DSC, and GOR4. The 3D structure was predicted with the I-TASSER server and its stereochemical conformation was evaluated with the STRUCTURE ASSESSMENT tool. The final model was visualized with PyMol program. As a result, the 3D structure of PA2481 is proposed according to its stereochemical conformation; two domains are identified as cytochrome c. The function of the protein may be related to electron transport and proton pumping to generate ATP in Pseudomonas aeruginosa. These results allow a better understanding of the role this protein plays in the physiology of this bacterium.

KW - Cystic fibrosis

KW - External otitis

KW - Hypothetical protein

KW - PA2481

KW - Pseudomonas aeruginosa

KW - Structural modeling

UR - https://www.scopus.com/pages/publications/84894832698

U2 - 10.1007/978-3-319-01568-2_7

DO - 10.1007/978-3-319-01568-2_7

M3 - Conference contribution

AN - SCOPUS:84894832698

SN - 9783319015675

T3 - Advances in Intelligent Systems and Computing

SP - 47

EP - 55

BT - Advances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013

PB - Springer Verlag

T2 - 2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013

Y2 - 25 September 2013 through 27 September 2013

ER -

Díaz DA, Barreto GE, Santos JG. Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1. In Advances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013. Springer Verlag. 2014. p. 47-55. (Advances in Intelligent Systems and Computing). doi: 10.1007/978-3-319-01568-2_7

Structural and functional prediction of the hypothetical protein PA2481 in Pseudomonas aeruginosa Pao1

Abstract

Publication series

Conference

UN SDGs

Keywords

Access to Document

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