Phanerochaete chrysosporium soluble proteome as a prelude for the analysis of heavy metal stress response

Ozcan, Servet
Yildirim, Volkan
Kaya, Levent
Albrecht, Dirk
Becher, Doerte
Hecker, Michael
Özcengiz, Gülay
A 2-D reference map in pI range 3-10 was constructed for the soluble protein fraction of Phancrochaete chrysosporium growing vegetatively under standard conditions. Functional annotation could be made for 517 spots out of 720 that were subjected to MALDI-TOF-MS analysis, according to the specific accession numbers from the P. chrysosporium genomic database. Further analysis of the data revealed 314 distinct ORFs, 118 of which yielded multiple spots on the master gel. Functional classification of the proteins was made according to the eukaryote orthologous groups defined in the organism's genome website. The functional class of PTMs, protein turnover and chaperones was represented with the highest number (63) of the identified ORFs. Six proteins were assigned to the hypothetical proteins and 29 were predicted to have a signal peptide sequence. Subcellular localization predictions were also made for the identified proteins. Of the protein spots detected on the master gel, 380 were found to be probably phosphorylated and 96 of these matched to the identified proteins. The reference map was efficiently used in the identification of the proteins differentially expressed under cadmium and copper stress. Three new ribosomal proteins as well as zinc-containing alcohol dehydrogenase, glucose-6-phosphate isomerase, flavonol/cinnamoyl-CoA reductase, H+-transporting two-sector ATPase, ribosomal protein S7, ribosomal protein S21e, elongation factor EF-1 alpha subunit were demonstrated as the most strongly induced.


Using artificially generated spectral data to improve protein secondary structure prediction from Fourier transform infrared spectra of proteins
Severcan, M; Haris, PI; Severcan, Feride (Elsevier BV, 2004-09-15)
Secondary structures of proteins have been predicted using neural networks from their Fourier transform infrared spectra. To improve the generalization ability of the neural networks, the training data set has been artificially increased by linear interpolation. The leave-one-out approach has been used to demonstrate the applicability of the method. Bayesian regularization has been used to train the neural networks and the predictions have been further improved by the maximum-likelihood estimation method. T...
Immobilization of tyrosinase in polysiloxane/polypyrrole copolymer matrices
Arslan, A; Kiralp, S; Toppare, Levent Kamil; Yagci, Y (Elsevier BV, 2005-04-01)
Immobilization of tyrosinase in conducting copolymer matrices of pyrrole functionalized polydimethylsiloxane/polypyrrole (PDMS/PPy) was achieved by electrochemical polymerization. The polysiloxane/polypyrrole/tyrosinase electrode was constructed by the entrapment of enzyme in conducting matrices during electrochemical copolymerization. Maximum reaction rate (V-max) and Michaelis-Menten constant were investigated for immobilized enzyme. Enzyme electrodes were prepared in two different electrolyte/sol vent sy...
Chemoselective Immobilization of Proteins by Microcontact Printing and Bio-orthogonal Click Reactions
Tolstyka, Zachary P.; Richardson, Wade; Bat, Erhan; Stevens, Caitlin J.; Parra, Dayanara P.; Dozier, Jonathan K.; Distefano, Mark D.; Dunn, Bruce; Maynard, Heather D. (Wiley, 2013-12-16)
Herein, a combination of microcontact printing of functionalized alkanethiols and site-specific modification of proteins is utilized to chemoselectively immobilize proteins onto gold surfaces, either by oxime- or copper-catalyzed alkyne-azide click chemistry. Two molecules capable of click reactions were synthesized, an aminooxy-functionalized alkanethiol and an azide-functionalized alkanethiol, and self-assembled monolayer (SAM) formation on gold was confirmed by IR spectroscopy. The alkanethiols were then...
Prediction of hexagonal lattice parameters of various apatites by artificial neural networks
Kockan, Umit; Evis, Zafer (International Union of Crystallography (IUCr), 2010-08-01)
In this study, the hexagonal lattice parameters of apatite compounds, M-10(TO4)(6)X-2, where M is Na+, Ca2+, Ba2+, Cd2+, Pb2+, Sr2+, Mn2+, Zn2+, Eu2+, Nd3+, La3+ or Y3+, T is As+5, Cr+5, P5+, V5+ or Si+4, and X is F-, Cl-, OH- or Br-, were predicted from their ionic radii by artificial neural networks. A multilayer perceptron network was used for training and the best results were obtained with a Bayesian regularization method. Four neurons were used in the hidden layer, utilizing a tangent sigmoid activati...
IR and turbidity studies of vitamin E-cholesterol-phospholipid membrane interactions
Severcan, Feride; Kazanci, Nadide; Baykal, Ülkü; Süzer, Şefik (Portland Press Ltd., 1995-8-1)
Binary and tertiary mixture of α-tocophenol, cholesterol and dimyristoylphosphatidylcholine in the form of multilamellar liposomes were investigated by Fourier Transform Infrared and visible spectroscopy. Results of the FTIR and turbidity experiments indicate that α T decreases or diminishes the effect of cholesterol on the frequency and the bandwidth of the C-H stretching, CH2 scissoring and C=O stretching bands in FTIR spectra and the turbidity measurements (recorded as absorbance values at 440 nm) in pho...
Citation Formats
S. Ozcan et al., “Phanerochaete chrysosporium soluble proteome as a prelude for the analysis of heavy metal stress response,” PROTEOMICS, pp. 1249–1260, 2007, Accessed: 00, 2020. [Online]. Available: