Detail publikace

Tertiary Structure Prediction of Potential Efflux-Pump Protein in Clostridium beijerinckii NRRL B-598

Originální název

Tertiary Structure Prediction of Potential Efflux-Pump Protein in Clostridium beijerinckii NRRL B-598

Anglický název

Tertiary Structure Prediction of Potential Efflux-Pump Protein in Clostridium beijerinckii NRRL B-598

Jazyk

en

Originální abstrakt

The fields of computational biochemistry and structural biology are growing rapidly. With various computational tools the whole workflow for in silico modeling of three-dimensional protein structures can be compiled. Here, we present a method for tertiary structure prediction for arcB1, a putative efflux pump gene, recently identified in the genomic sequence of Clostridium beijerinckii NRRL B-598. The strain C. beijerinckii NRRL B-598, formerly misidentified as C. pasteurianum, is an oxygen tolerant heterofermentative anaerobe with the ability of acetone-butanol fermentation, with butanol as the main product. Unfortunately, the mechanism of butanol efflux remains unknown. The translated AcrB1 protein sequence had a high similarity to the already described efflux-pump of Escherichia coli. To study these sequences in a structural context, we constructed a homology model for C. beijerinckii NRRL B-598 and compared it with the corresponding experimentally determined structure from E. coli. The predicted protein model helps us to understand its function and confirm that acrB1 is a gene for nonspecific efflux pump — a potential pump capable of butanol efflux.

Anglický abstrakt

The fields of computational biochemistry and structural biology are growing rapidly. With various computational tools the whole workflow for in silico modeling of three-dimensional protein structures can be compiled. Here, we present a method for tertiary structure prediction for arcB1, a putative efflux pump gene, recently identified in the genomic sequence of Clostridium beijerinckii NRRL B-598. The strain C. beijerinckii NRRL B-598, formerly misidentified as C. pasteurianum, is an oxygen tolerant heterofermentative anaerobe with the ability of acetone-butanol fermentation, with butanol as the main product. Unfortunately, the mechanism of butanol efflux remains unknown. The translated AcrB1 protein sequence had a high similarity to the already described efflux-pump of Escherichia coli. To study these sequences in a structural context, we constructed a homology model for C. beijerinckii NRRL B-598 and compared it with the corresponding experimentally determined structure from E. coli. The predicted protein model helps us to understand its function and confirm that acrB1 is a gene for nonspecific efflux pump — a potential pump capable of butanol efflux.

BibTex


@inproceedings{BUT141676,
  author="Pavlína {Cicková} and Karel {Sedlář} and Kristýna {Kupková} and Jan {Kolek} and Petra {Patáková} and Ivo {Provazník}",
  title="Tertiary Structure Prediction of Potential Efflux-Pump Protein in Clostridium beijerinckii NRRL B-598",
  annote="The fields of computational biochemistry and structural biology are growing rapidly. With various 
computational tools the whole workflow for in silico modeling of three-dimensional protein structures can be 
compiled. Here, we present a method for tertiary structure prediction for arcB1, a putative efflux pump gene, 
recently identified in the genomic sequence of Clostridium beijerinckii NRRL B-598. The strain C. beijerinckii
NRRL B-598, formerly misidentified as C. pasteurianum, is an oxygen tolerant heterofermentative anaerobe 
with the ability of acetone-butanol fermentation,  with butanol as the main product. Unfortunately, the 
mechanism of butanol efflux remains unknown. The translated AcrB1 protein sequence had a high similarity to 
the already described efflux-pump of Escherichia coli. To study these sequences in a structural context, we 
constructed a homology model for  C. beijerinckii  NRRL B-598 and compared  it with  the corresponding 
experimentally determined structure from E. coli. The predicted protein model helps us to understand its 
function and confirm that acrB1 is a gene for nonspecific efflux pump — a potential pump capable of butanol 
efflux.",
  address="Ocean Design",
  booktitle="Proceedings of the 5th International Conference on Chemical Technology",
  chapter="141676",
  edition="1",
  howpublished="online",
  institution="Ocean Design",
  year="2017",
  month="october",
  pages="26--30",
  publisher="Ocean Design",
  type="conference paper"
}