2-24-15
Summary:
Laccases contain one type-1 copper site (T1), where the substrate is oxidized, and a trinuclear copper cluster consisting of one type-2 (T2) and two type-3 (T3) copper, where the reduction of molecular oxygen to water takes place (Gianfreda, Xu, & Bollag, 1999; Giardina et al., 2010; Yaropolov, Skorobogat’ko, Vartanov, & Varfolomeev, 1994). The primary structure of the protein directly influences the REDOX potential (E0) of the T1 site, and determines the efficiency of catalysis on substrate oxidation. From this perspective, laccases can be divided into three groups: low-, medium-, and high- potential. The low- potential laccases (isolated mainly from trees) are characterized by T1 redox potential of 0.43 V versus NHE and a methionine axial ligand at the T1 site. The intermediate laccases with T1 redox potential in the range 0.47-0.7 V versus NHE are isolated from many microorganisms and are characterized by a leucine axial ligand. High-potential laccases have a E0 above 0.7 V versus NHE; these are found solely in wood degrading fungi and are characterized by a phenylalanine axial ligand.
Another important aspect of laccases is the ability for secretion. Fungi are excellent secretors of many types of enzymes due to their reliance on absorptive nutrition to obtain nutrients. Secreted fungal enzymes undergo pos-translational modification to target them to the exterior of the cell; laccase is heavily N-glycosylated. To determine the ability of a given laccase to be secreted, the total number of N-glycosylation sites (Asn/Xxx/Ser/Thr/Cys when Xxx ?!= Pro) need simply to be be counted. When fully functional, this program will be an invlauable tool in the field of bioelectrochemistry, and will help to bridge the knowledge gap between electrochemists, biomedicalengineers, and biologists.
Electrochemically relevant amino acids: ^AA influences on laccase REDOX potentials.pdf
Similar idea, but no focus on secretion: ^In silico study of structural determinants modulating laccase REDOX potential.pdf
T1 AA sequence: H-C-H-X3-H-X3-[AG]-[LM]
TNC AA seq: G-X-[FYW]X[LIVMFYW][CST]X8-G[LM]-X[LIVMFYW]
Copper binding protein domains: http://prosite.expasy.org
^Laccase seqs.csv from PDB
Inputs --> Outputs:
laccase_seqs.csv --> low-potential laccases (name and seq) list
laccase_seqs.csv --> mid-potential laccases list
laccase_seqs.csv --> high-potential laccases list
High-potential laccases list --> COUNT N-Glycosylation sites
Sort High-potential laccase dictionary by count of N-Glycosylation sites
create csv file of ranked High-potential laccases,
write script to find N-Glycosylation sites (Asn/Xxx/Ser/Thr/Cys when Xxx ?!= Pro)
I plan on writing all of my own programs for the project, but I am unsure how to write the RegEx for each pattern.
If seq = A[^p]STC
Pseudocode:
import csv file
if line contains high redox pattern
return to high potential list
if line contains mid redox pattern
return to mid potential list
if line contains low redox pattern
return to low potential list