Bio-knowledge-based filters improve residue-residue contact prediction accuracy.

Motivation: Residue-residue contact prediction through direct coupling analysis has reached impressive accuracy, but yet higher accuracy will be needed to allow for routine modelling of protein structures. One way to improve the prediction accuracy is to filter predicted contacts using knowledge about the particular protein of interest or knowledge about protein structures in general. Results: We focus on the latter and discuss a set of filters that can be used to remove false positive contact predictions. Each filter depends on one or a few cut-off parameters for which the filter performance was investigated. Combining all filters while using default parameters resulted for a test set of 851 protein domains in the removal of 29% of the predictions of which 92% were indeed false positives. Availability and implementation: All data and scripts are available at http://comprec-lin.iiar.pwr.edu.pl/FPfilter/. Supplementary information: Supplementary data are available at Bioinformatics online.

Forecasting residue-residue contact prediction accuracy.

MOTIVATION: Apart from meta-predictors, most of today's methods for residue-residue contact prediction are based entirely on Direct Coupling Analysis (DCA) of correlated mutations in multiple sequence alignments (MSAs). These methods are on average ∼40% correct for the 100 strongest predicted contacts in each protein. The end-user who works on a single protein of interest will not know if predictions are either much more or much less correct than 40%, which is especially a problem if contacts are predicted to steer experimental research on that protein. RESULTS: We designed a regression model that forecasts the accuracy of residue-residue contact prediction for individual proteins with an average error of 7 percentage points. Contacts were predicted with two DCA methods (gplmDCA and PSICOV). The models were built on parameters that describe the MSA, the predicted secondary structure, the predicted solvent accessibility and the contact prediction scores for the target protein. Results show that our models can be also applied to the meta-methods, which was tested on RaptorX. AVAILABILITY AND IMPLEMENTATION: All data and scripts are available from http://comprec-lin.iiar.pwr.edu.pl/dcaQ/. CONTACT: malgorzata.kotulska@pwr.edu.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Correlated mutations select misfolded from properly folded proteins.

MOTIVATION: The recently developed direct coupling analysis (DCA) method has greatly improved the accuracy with which residue-residue contacts can be predicted from multiple sequence alignments. Contact prediction accuracy, though, is still often not sufficient for complete ab initio protein structure prediction. DCA can, however, support protein structure studies in several ways. RESULTS: We show that DCA can select the better structure from among properly folded and misfolded variants. This idea was tested by comparing obsolete PDB files with their more correctly folded successors and by the comparison of structures with deliberately misfolded decoy models from the Decoys 'R' Us database. The DCA method systematically predicts more contacts for properly folded structures than for misfolded ones. The method works much better for X-ray structures than for NMR structures. AVAILABILITY AND IMPLEMENTATION: All data are available from http://comprec-lin.iiar.pwr.edu.pl/dcaVSmisfolds/ and http://swift.cmbi.ru.nl/dcaVSmisfolds/ . CONTACT: malgorzata.kotulska@pwr.edu.pl . SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cellular stress induced by photodynamic reaction with CoTPPS and MnTMPyPCl5 in combination with electroporation in human colon adenocarcinoma cell lines (LoVo and LoVoDX).

Two porphyrins, CoTPPS and MnTMPyPCl5, were tested for their photodynamic activity and potential novel use in a therapy of human cancers. We investigated an effect of photodynamic reaction (PDR), electroporation (EP) and their combination (electro-photodynamic reaction [EP-PDR]) on human colon adenocarcinoma cell lines (LoVo and resistant to doxorubicin LoVoDX), human breast adenocarcinoma (wild type MCF-7/WT and resistant to doxorubicin MCF-7/DOX), and human melanoma (Me45). The efficiency of macromolecules transport was examined with cytofluorymetry by assessing the degree of propidium iodide (PI) penetration. Additionally, cellular ultrastructure after EP was evaluated. We determined cyto- and photo-cytotoxic effect on the cells viability (MTT assay) after standard PDR and PDR combined with EP. Intracellular distribution and mitochondrial colocalization of both porphyrins was also performed. The experiments proved that both complexes exhibit desirable photodynamic properties on LoVo LoVoDX cells, and EP effectively supports photodynamic method in this type of cancer. The application of EP provided shorter time of incubation (only 10 min) and enhanced effect of applied therapy. The porphyrins did not affect the MCF-7 and Me45 cell lines.

The influence of electroporation on in vitro photodynamic therapy of human breast carcinoma cells.

Phototoxicity of drugs used in cancer photodynamic therapy could be augmented by increased accumulation of a photosensitizer in target cells. The intracellular delivery mode that enhances drug transportation could facilitate therapy by reducing the exposure time. Doses of the administered drug and related side effects could be lowered, whilst maintaining the same therapeutic efficiency. Electroporation supports transport of many drugs by creating electric field-induced transient nanopores in the plasma membrane. In this study, the electroporation- assisted transport of a photosensitizer was tested in vitro in human breast carcinoma cell lines: wild-type (MCF-7/WT) and doxorubicin-resistant (MCF-7/DOX). The efficacy of photodynamic therapy alone and in combination with electroporation was evaluated by cell viability with MTT test, using a haematoporphyrin derivative as a model. The data presented show up to 10-fold greater efficacy of the combined method, with very significantly reduced drug exposure times.

Cyanines as efficient photosensitizers in photodynamic reaction: photophysical properties and in vitro photodynamic activity.

The purpose of the present study was to explore the potential application of cyanines in photodynamic treatment. The photophysical features of four cyanines (KF570, HM118, FBF-749, and ER-139) were investigated by elemental and spectral analyses. Two malignant cell lines (MCF-7/WT and MCF-7/DOX) were used to test the potential for use in the photodynamic therapy. The cytotoxic effects of these dyes were determined by the MTT assay after 4 and 24 h of incubation with the cyanine. KF570 and HM118 were irradiated with red light (630-nm filter) and FBF-749 and ER-139 with green light (435-nm filter). The results showed that the cyanine HM118 demonstrated a major phototoxic effect. It was also noted that the efficiency of photodynamic therapy was higher in the doxorubicin-resistant cell line (MCF-7/DOX).