python for biofuel cell development parker evans
TRANSCRIPT
OverviewElectricity reviewWhat are fuel cells?Why do we need Python?Methods
◦Anaconda Python distribution ◦Spyder IDE◦Biopython◦Regular Expressions
The programThe resultsFuture Directions
Why Fuel Cells?Fuel cells simply
steal electrons from biological processes
Implantable sensors◦ Glucose monitors ◦ Heart rate etc.
Terawatts (10¹²W) of power + CLEAN water from wastewater
How do you make a fuel cell?
Grow fungus Filter proteins
Adsorb proteins to electrode
Collect electricity!
Collect additional
products (ie. drinking water)
Laccase Sequence SourceThere are 2,674 fungal laccase protein
sequences in the UniProt databaseApproximately half (50.2%) of these
are protein fragments under 100kb◦Laccase average seq. length: 453AA
Min = 100; Max = 906
Fragments were removed using UniProt’s built in feature
The remaining 1,331 sequences were run through the regex_fasta program
T1 Cu Site – REDOX Potential REDOX potential of laccase
determines the voltage of the system
Pardo et al. found the REDOX potential is directly determined by the axial amino acid (AA)◦L = low, M= med., F = high
ThÖny-Meyer et al. found that the T1 copper motif is highly conserved:◦HCHXXXHXXXXL/M/F
REDOX Potential
162 of 1331 sequences, 12%, contained phenylalanine axial amino acids at the T1 copper center
N-Glycosylation - SecretionThe program secretome.P uses
the occurrence of N-Gycosylation sites to determine the probabilitity that a given protein will be secreted
I used the regular expression behind their open-source program to find N-Glycosylation sites in my program◦N[^P](S|T)[^P]
N-Glycosylation
Of the 162 high REDOX potential laccases, 9 contained N-Glycosylation sites
Interestingly none of these sites contained serine
ResultsMy motif finder pipeline narrowed
the thousands of candidate organisms to less than 0.5% of the initial input while retaining the optimal features of the candidate proteins
The prospective species are:
ResourcesReiss, R., Ihssen, J., Richter, M.,
Eichhorn, E., Schilling, B., & Thöny-Meyer, L. (2013). Laccase versus laccase-like multi-copper oxidase: a comparative study of similar enzymes with diverse substrate spectra. PloS one, 8(6), e65633.
Pardo, I., & Camarero, S. (2015). Laccase engineering by rational and evolutionary design.Cellular and Molecular Life Sciences, 1-14.