Bioinformatics for Biofuel Cell DevelopmentParker Evans

OverviewWhat are fuel cells?How do you make a fuel cell?Laccase Sequence Source

◦Laccase Sequence Histogram T1 Cu Site – REDOX Potential

◦REDOX Potential resultsN-Glycosylation – Secretion

◦N-Glycosylation resultsResultsResources

What are 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

Laccase Sequence Histogram

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:◦ Panus rudis, Moniliophthora roreri,

Cerrena unicolor, Heterobasidion irregulare, Cerrena sp., Fusarium oxysporum, Spongipellis sp., Fusarium solani

T. versicolor and P. ostreatus were identified as high REDOX potential laccases, but not secretors

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.

http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/fasta/matchregex.html

Feature based prediction of non-classical and leaderless protein secretion J. Dyrløv Bendtsen, L. Juhl Jensen, N. Blom, G. von Heijne and S. Brunak Protein Eng. Des. Sel., 17(4):349-356, 2004

Questions?https://github.com/evansparker/PLS-599

Water AnalogyVoltage =

electrical pressure

Current = electrical flow-rate

Resistance = electrical friction

R

C

V