@article {49,
	title = {Activities of Topoisomerase I in Its Complex with SRSF1.},
	journal = {Biochemistry},
	year = {2012},
	month = {02/2012},
	abstract = {Human DNA topoisomerase I (topo I) catalyzes DNA relaxation and phosphorylates SRSF1. Whereas the structure of topo I complexed with DNA has been resolved, the structure of topo I in the complex with SRSF1 and structural determinants of topo I activities in this complex are not known. The main obstacle to resolving the structure is a contribution of unfolded domains of topo I and SRSF1 in formation of the complex. To overcome this difficulty, we employed a three-step strategy: identifying the interaction regions, modeling the complex, and validating the model with biochemical methods. The binding sites in both topo I and SRSF1 are localized in the structured regions as well as in the unfolded domains. One observes cooperation between the binding sites in topo I but not in SRSF1. Our results indicate two features of the unfolded RS domain of SRSF1 containing phosphorylated residues that are critical for the kinase activity of topo I: its spatial arrangement relative to topo I and the organization of its sequence. The efficiency of phosphorylation of SRSF1 depends on the length and flexibility of the spacer between the two RRM domains that uniquely determine an arrangement of the RS domain relative to topo I. The spacer also influences inhibition of DNA nicking, a prerequisite for DNA relaxation. To be phosphorylated, the RS domain has to include a short sequence recognized by topo I. A lack of this sequence in the mutants of SRSF1 or its spatial inaccessibility in SRSF9 makes them inadequate as topo I/kinase substrates.},
	issn = {1520-4995},
	doi = {10.1021/bi300043t},
	author = {Ishikawa, Takao and Krzy{\'s}ko, Krystiana A and Kowalska-Loth, Barbara and Skrajna, Aleksandra M and Czubaty, Alicja and Girstun, Agnieszka and Cieplak, Maja K and Lesyng, Bogdan and Staron, Krzysztof}
}
@article {48,
	title = {A genistein derivative, ITB-301, induces microtubule depolymerization and mitotic arrest in multidrug-resistant ovarian cancer.},
	journal = {Cancer chemotherapy and pharmacology},
	volume = {68},
	year = {2011},
	month = {10/2011},
	pages = {1033-44},
	abstract = {PURPOSE: To investigate the mechanistic basis of the anti-tumor effect of the compound ITB-301.

METHODS: Chemical modifications of genistein have been introduced to improve its solubility and efficacy. The anti-tumor effects were tested in ovarian cancer cells using proliferation assays, cell cycle analysis, immunofluorescence, and microscopy.

RESULTS: In this work, we show that a unique glycoside of genistein, ITB-301, inhibits the proliferation of SKOv3 ovarian cancer cells. We found that the 50\% growth inhibitory concentration of ITB-301 in SKOv3 cells was 0.5~μM. Similar results were obtained in breast cancer, ovarian cancer, and acute myelogenous leukemia cell lines. ITB-301 induced significant time- and dose-dependent microtubule depolymerization. This depolymerization resulted in mitotic arrest and inhibited proliferation in all ovarian cancer cell lines examined including SKOv3, ES2, HeyA8, and HeyA8-MDR cells. The cytotoxic effect of ITB-301 was dependent on its induction of mitotic arrest as siRNA-mediated depletion of BUBR1 significantly reduced the cytotoxic effects of ITB-301, even at a concentration of 10~μM. Importantly, efflux-mediated drug resistance did not alter the cytotoxic effect of ITB-301 in two independent cancer cell models of drug resistance.

CONCLUSION: These results identify ITB-301 as a novel anti-tubulin agent that could be used in cancers that are multidrug resistant. We propose a structural model for the binding of ITB-301 to α- and β-tubulin dimers on the basis of molecular docking simulations. This model provides a rationale for future work aimed at designing of more potent analogs.},
	keywords = {Antineoplastic Agents, Cell Line, Tumor, Cell Proliferation, Dose-Response Relationship, Drug, Drug Resistance, Multiple, Drug Resistance, Neoplasm, Female, Genistein, Glycosides, Humans, Inhibitory Concentration 50, Microtubules, Mitosis, Models, Molecular, Molecular Dynamics Simulation, Ovarian Neoplasms, Protein Binding, Tubulin},
	issn = {1432-0843},
	doi = {10.1007/s00280-011-1575-2},
	author = {Ahmed, Ahmed Ashour and Goldsmith, Juliet and Fokt, Izabela and Le, Xiao-Feng and Krzy{\'s}ko, Krystiana A and Lesyng, Bogdan and Bast, Robert C and Priebe, Waldemar}
}
@article {3,
	title = {A novel method to compare protein structures using local descriptors.},
	journal = {BMC bioinformatics},
	volume = {12},
	year = {2011},
	month = {08/2011},
	pages = {344},
	abstract = {BACKGROUND: Protein structure comparison is one of the most widely performed tasks in bioinformatics. However, currently used methods have problems with the so-called "difficult similarities", including considerable shifts and distortions of structure, sequential swaps and circular permutations. There is a demand for efficient and automated systems capable of overcoming these difficulties, which may lead to the discovery of previously unknown structural relationships.

RESULTS: We present a novel method for protein structure comparison based on the formalism of local descriptors of protein structure - DEscriptor Defined Alignment (DEDAL). Local similarities identified by pairs of similar descriptors are extended into global structural alignments. We demonstrate the method{\textquoteright}s capability by aligning structures in difficult benchmark sets: curated alignments in the SISYPHUS database, as well as SISY and RIPC sets, including non-sequential and non-rigid-body alignments. On the most difficult RIPC set of sequence alignment pairs the method achieves an accuracy of 77\% (the second best method tested achieves 60\% accuracy).

CONCLUSIONS: DEDAL is fast enough to be used in whole proteome applications, and by lowering the threshold of detectable structure similarity it may shed additional light on molecular evolution processes. It is well suited to improving automatic classification of structure domains, helping analyze protein fold space, or to improving protein classification schemes. DEDAL is available online at http://bioexploratorium.pl/EP/DEDAL.},
	keywords = {Algorithms, Animals, Bacterial Proteins, Carrier Proteins, Computational Biology, GTP Phosphohydrolases, Humans, Models, Molecular, Proteins, Saposins, Structural Homology, Protein},
	issn = {1471-2105},
	doi = {10.1186/1471-2105-12-344},
	author = {Daniluk, Pawe{\l} and Lesyng, Bogdan}
}
