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Active site specific pharmacophore-based screening for methyltransferase inhibitors

Journal of Pharmacy Research 2013年第1期7卷 121-126页

作者： Thangaraju Tamilvanan Waheeta Hopper Department of Bioinformatics School of Bioengineering Faculty of Engineering & Technology SRM University Kattankulathur 603203 Tamil Nadu India

Background Dengue hemorrhagic fever is a mosquito-borne, re-emerging infectious disease in many areas of the world, which affects 50–100 million human and causes 24,000 deaths every year. Currently, no specific drug is available for dengue fever. Dengue fever is caused by Flavivirus . Methyltransferase (MTase) is particularly important for viral replication, which also plays a key role in normal physiology and human infection through methylating DNA. The flaviviral MTase (NS5) which catalyzes both guanine N-7 and ribose 2′-OH methylation during viral cap formation, serve as a promising flavivirus drug target. The present work is to identify lead molecules for Flavivirus NS5 MTase using computational approaches like structure-based pharmacophore and induced fit docking. Methods Energy-optimized pharmacophore models were generated for the RTP, SAH and SAM ligands based on their binding mode at the different parts of the active site of MTase. Pharmacophore-based screening of the Asinex database was performed. The short-listed compounds were subjected for induced fit docking. Results The pharmacophore sites were predicted for RTP, SAH and SAM with seven features of which, minimum of three pharmacophore features were taken as the basis for screening the ligands. At the end of docking analysis, three compounds having high binding capability for RTP, SAH and SAM binding sites of MTase were observed. Conclusions These results suggest that the selected compounds could be novel leads to inhibit MTase and may stop viral replication further. Also, these three lead compounds could be serving as building blocks for designing drug-like molecules for the treatment of dengue hemorrhagic fever.

关键词： Dengue NS5 methyltransferase Structure-based pharmacophore Induced fit docking

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Pharmacological activation of ischemic tolerance signaling pathways ameliorates gentamycin nephrotoxicity

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Biochimica et Biophysica Acta (BBA) - Bioenergetics 2014年 1837卷 e61-e61页

作者： Stanislovas S. Jankauskas Irina B. Pevzner Ljubava D. Zorova Valentina A. Babenko Egor Y. Plotnikov Dmitry B. Zorov Faсulty of Bioengineering and Bioinformatics MSU Research Institute of Mitoengineering MSU Russia Research Institute of Mitoengineering Lomonosov Moscow State University Russia International Laser Center Lomonosov Moscow State University Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Russia AN Belozersky Institute Lomonosov Moscow State University Russia

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Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015

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BMC genomics 2016年第6期17 Suppl 6卷 487页

作者： Jerry W. Shay Noriko Homma Ruyun Zhou Muhammad Imran Naseer Adeel G. Chaudhary Mohammed Al-Qahtani Nobutaka Hirokawa Maryam Goudarzi Albert J. Fornace Saleh Baeesa Deema Hussain Mohammed Bangash Fahad Alghamdi Hans-Juergen Schulten Angel Carracedo Ishaq Khan Hanadi Qashqari Nawal Madkhali Mohamad Saka Kulvinder S. Saini Awatif Jamal Jaudah Al-Maghrabi Adel Abuzenadah Adeel Chaudhary Mohammed Al Qahtani Ghazi Damanhouri Heba Alkhatabi Anne Goodeve Laura Crookes Nikolas Niksic Nicholas Beauchamp Adel M. Abuzenadah Jim Vaught Bruce Budowle Mourad Assidi Abdelbaset Buhmeida Leena Merdad Sudhir Kumar Sayaka Miura Karen Gomez Mahmood Rasool Ahmed Rebai Sajjad Karim Hend F. Nour Eldin Heba Abusamra Elham M. Alhathli Nada Salem Mohammed H. Al-Qahtani Hossam Faheem Ashok Agarwa Eberhard Nieschlag Joachim Wistuba Oliver S. Damm Mohd A. Beg Taha A. Abdel-Meguid Hisham A. Mosli Osama S. Bajouh Serdar Coskun Muhammad Abu-Elmagd Ashraf Dallol Sahar Hakamy Wejdan Al-Qahtani Asia Al-Harbi Shireen Hussain Burak Ozkosem Rick DuBois Safia S. Messaoudi Maryam T. Dandana Touhami Mahjoub Wassim Y. Almawi S. Abdalla M. Nabil Al-Aama Asmaa Elzawahry Tsuyoshi Takahashi Sachiyo Mimaki Eisaku Furukawa Rie Nakatsuka Isao Kurosaka Takahiko Nishigaki Hiromi Nakamura Satoshi Serada Tetsuji Naka Seiichi Hirota Tatsuhiro Shibata Katsuya Tsuchihara Toshirou Nishida Mamoru Kato Sajid Mehmood Naeem Mahmood Ashraf Awais Asif Muhammad Bilal Malik Siddique Mehmood Aadil Hussain Qazi Mohammad Sajid Jamal Mughees Uddin Siddiqui Mohammad A. Alzohairy Mohammad A. Al Karaawi Taoufik Nedjadi Heba Al-Khattabi Adel Al-Ammari Ahmed Al-Sayyad Hédia Zitouni Nozha Raguema Marwa Ben Ali Wided Malah Raja Lfalah Wassim Almawi Mohammed Elanbari Andrey Ptitsyn Sana Mahjoub Rabeb El Ghali Bechir Achour Nidhal Ben Amor Brahim N’siri Hamid Morjani Esam Azhar Vera Chayeb Maryam Dendena Hedia Zitouni Khedija Zouari-Limayem Bassem Refaat Ahmed M. Ashshi Sarah A. Batwa Hazem Ramadan Amal Awad Ahmed Ateya Adel Galal Ahmed El-Shemi Ahmad Ashshi Mohammed Basalamah Youjin Na Cha University of Texas Southwestern Medical Center Dallas USA Department of Cell Biology and Anatomy Graduate School of Medicine the University of Tokyo Tokyo Japan Center of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Department of Biochemistry and Molecular & Cellular Biology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Oncology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Radiation Medicine Lombardi Comprehensive Cancer Center Georgetown University Washington USA Center of Excellence in Genomic Medicine Research (CEGMR) King Abdulaziz University Jeddah Kingdom of Saudi Arabia King Fahd Medical Research Centre King Abdulaziz University Jeddah Saudi Arabia Centre of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Sheffield Diagnostic Genetic Service Sheffield Children’s NHS Foundation Trust Western Bank Sheffield UK Center of Innovations in Personalized Medicine King Abdulaziz University Jeddah Saudi Arabia President ISBER Editor-in-Chief Biopreservation & Biobanking ᅟ USA Institute of Applied Genetics Department of Molecular and Medical Genetics University of North Texas Health Science Center Fort Worth USA Department of Dental Public Health Faculty of Dentistry King Abdulaziz University Jeddah Saudi Arabia Institute for Genomics and Evolutionary Medicine Temple University Philadelphia USA Center of Excellence in Genomic Medicine King Abdulaziz University Jeddah Kingdom of Saudi Arabia Laboratory of Molecular and Cellular Screening Processes (Bioinformatics Group) Centre of Biotechnology of Sfax Sfax Tunisia Fujitsu Technology Solutions International ᅟ ᅟ Case Western Reserve University School of Medicine and Lerner College of Medicine Cleveland Clinic Foundation Cleveland USA American Center for Reproductive Medicine Andrology Center Cleveland USA Center for Reproductive Medicine and

O1 Regulation of genes by telomere length over long distances Jerry W. Shay O2 The microtubule destabilizer KIF2A regulates the postnatal establishment of neuronal circuits in addition to prenatal cell survival, cell migration, and axon elongation, and its loss leading to malformation of cortical development and severe epilepsy Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa O3 Integration of metagenomics and metabolomics in gut microbiome research Maryam Goudarzi, Albert J. Fornace Jr. O4 A unique integrated system to discern pathogenesis of central nervous system tumors Saleh Baeesa, Deema Hussain, Mohammed Bangash, Fahad Alghamdi, Hans-Juergen Schulten, Angel Carracedo, Ishaq Khan, Hanadi Qashqari, Nawal Madkhali, Mohamad Saka, Kulvinder S. Saini, Awatif Jamal, Jaudah Al-Maghrabi, Adel Abuzenadah, Adeel Chaudhary, Mohammed Al Qahtani, Ghazi Damanhouri O5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesis Heba Alkhatabi O6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic service Anne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas Beauchamp O7 Targeted sequencing panels and their utilization in personalized medicine Adel M. Abuzenadah O8 International biobanking in the era of precision medicine Jim Vaught O9 Biobank and biodata for clinical and forensic applications Bruce Budowle, Mourad Assidi, Abdelbaset Buhmeida O10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumors Jaudah Al-Maghrabi O11 The CEGMR biobanking unit: achievements, challenges and future plans Abdelbaset Buhmeida, Mourad Assidi, Leena Merdad O12 Phylomedicine of tumors Sudhir Kumar, Sayaka Miura, Karen Gomez O13 Clinical implementation of pharmacogenomics for colorectal cancer treatment Angel Carracedo, Mahmood Rasool O14 From association to causality: translation of GWAS findings for genomic me

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Dynamic mechanical finite element model of biological cells for studying cellular pattern formation

Dynamic mechanical finite element model of biological cells ...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society

作者： Jieling Zhao Hammad Naveed Sema Kachalo Youfang Cao Wei Tian Jie Liang Bioinformatics Program Department of Broengineering University of Illinois at Chicago CAS-MPG partner Institute for Computational Biology Intel Graphics Unit Intel Corporation Department of Bioengineering University of Illinois at Chicago Faculty of Department of Bioengineering University of Illinois at Chicago

ISBN: (纸本)9781457702150

Understanding the geometric, topologic, and mechanical properties of cells and their interactions is critical for studying tissue pattern formation and organ development. Computational model and tools for simulating cell pattern formation have broad implications in studying embryogenesis, blood-vessel development, tissue regeneration, and tumor growth. Although a number of cell modeling methods exist, they do not simultaneously account for detailed cellular shapes as well as dynamic changes in cell geometry and topology. Here we describe a dynamic finite element cell model (dFEMC) for studying populations of cells and tissue development. By incorporating details of cell shape, cell growth and shrinkage, cell birth and death, cell division and fusion, our method can model realistically a variety problems of cell pattern formation. We give two examples of applying our method to the study of cell fusion and cell apoptosis. The dFEMC model developed here provides a general computational framework for studying dynamics pattern formation of tissue.

关键词： Pattern formation embryo pattern formation cytology Mechanical properties Histogenic Process Cell Fusion Organogenesis

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Proceedings of the Frontiers of Retrovirology Conference 2016

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Retrovirology 2016年第1期13卷 1-40页

作者： Irena Zurnic Sylvia Hütter Nicole Stanke Tobias Kern Fabian Lindel Gesche Gerresheim Martin Hamann Erik Müllers Dirk Lindemann Ute Lehmann Juliane Reh Paul Lesbats Peter Cherepanov Melanie Mann Erik Serrao Alan Engelman Claire Da Silva Santos Kevin Tartour Andrea Cimarelli Rya Burdick Jianbo Chen Jaya Sastri Wei-Shau Hu Vinay Pathak Oliver T. Keppler Patrícia de Sousa-Pereira Hanna-Mari Baldauf Marcel Stern Karine Pradeau Sylvia Eiler Nicolas Levy Marc Ruff Sarah Lennon Sarah Cianferani Stéphane Emiliani Vincent Parissi Sylvie Rato Miguel Munoz Angela Ciuffi Antonio Rausell Amalio Telenti Alexander Zhyvoloup Ian Anderson Chen- Hsuin Lee Ariberto Fassati Anat Melamed Delphine Planas Petronela Ancuta Yuwei Zhang Huicheng Chen Annie Bernier Annie Gosselin Janos Kriston-Vizi Robin Ketteler Andy Merritt Charles Bangham Jocelyn Turpin Anthony Rodari Benoit Van Driessche Mathilde Galais Nadége Delacourt Sylvain Fauquenoy Caroline Vanhulle Anna Kula Carine Van Lint Ernst J. Wolvetang Arsène Burny Olivier Rohr Thijs van Montfort Renee van der Sluis Ben Berkhout Dave Speijer Gang Wang Na Zhao Atze T. Das Mirte Scherpenisse Bo Meng Andrzej Rutkowski Lars Dölken Andrew Lever Neil Berry Claire Ham Neil Almond Hoi Ping Mok Nicholas Norton Axel Fun Jack Hirst Mark Wills Chris Hellmund Harriet Groom Thomas Schuster Benedikt Asbach Ralf Wagner Christine Gross Martina Kalmer Andrea K. Thoma-Kress Norbert Donhauser Sebastian Millen Sandra M. Müller-Schmucker Veit Wiesmann Thomas Wittenberg Jan Gettemans Minghua Li Shan-Lu Liu Eric O. Freed Janis Müller Jan Münch Simone Joas Clement Wesley Gnanadurai Edina Lump Christina M. Stürzel Daniel Sauter Frank Kirchhoff Katharina Mack Kathrin Starz Christina Stürzel Xaver Sewald Nasim Motamedi Pradeep Uchil Ruoxi Pi Christin Herrmann Walther Mothes Mark Ladinsky Pamela Bjorkman Jagadish Beloor Priti Kumar Thomas Murooka Thorsten Mempel Michael Brehm Dale Greiner Erica Parrish Nicholas F. Parrish Beatrice H. Hahn Frederic Bibollet-Ruche Ulrike Sauermann Katharina Töpfer Tina Schultheiss Chris Molecular Virology and Gene Therapy Molecular Medicine Leuven Belgium Molecular Virology Technical University Dresden Dresden Germany Center for Regenerative Therapies Dresden Dresden Germany Potsdam University Potsdam Germany The Francis Crick Institute London Great Britain Institute of Clinical and Molecular Virology Friedrich-Alexander-Universität Erlangen-Nuremberg Erlangen Germany Dana Farber Cancer Institute Boston MA United States CIRI Lyon France National Cancer Institute Frederick MD United States Virology Max von Pettenkofer-Institut LMU Munich Munich Germany Institute of Medical Virology University of Frankfurt Frankfurt a. M. Germany German Center for Infection Research Munich Germany Institute of Medical Virology University Hospital Frankfurt Frankfurt a. M. Germany CIBIO/InBIO University of Porto Vairão Portugal Faculty of Sciences University of Porto Porto Portugal Virology Max von Pettenkofer Institute LMU Munich Germany Institute for Medical Virology Frankfurt a. M. Germany Integrative structural Biology IGBMC Illkirch France Institut Pluridisciplinaire Hubert Curien Strasbourg France Institut Cochin Paris France CNRS UMR5234 MFP Lab Bordeaux France Associated International Laboratory (LIA) Microbiology and Immunology CNRS/Université de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology Bordeaux/Hamburg France Institute of Microbiology University Hospital Center and University of Lausanne Lausanne Switzerland Imagine Institute Paris Descartes University Paris France J. Craig Venter Institute La Jolla CA United States Infection University College London London Great Britain Medicine Imperial College London Great Britain Microbiology & Infection University of Montreal Montreal Great Britain CRCHUM Montreal Canada University College London LMCB London Great Britain MRC Technology Centre for Therapeutic Discovery London Great Britain Section of Virology Department of Medicine Imperial Co

Oral presentationsSession 1: Entry & uncoatingO1 Host cell polo-like kinases (PLKs) promote early prototype foamy virus (PFV) replicationIrena Zurnic, Sylvia Hütter, Ute Lehmann, Nicole Stanke, Juliane Re... 详细信息

Oral presentations

Session 1: Entry & uncoating

O1 Host cell polo-like kinases (PLKs) promote early prototype foamy virus (PFV) replication

Irena Zurnic, Sylvia Hütter, Ute Lehmann, Nicole Stanke, Juliane Reh, Tobias Kern, Fabian Lindel, Gesche Gerresheim, Martin Hamann, Erik Müllers, Paul Lesbats, Peter Cherepanov, Erik Serrao, Alan Engelman, Dirk Lindemann

O2 A novel entry/uncoating assay reveals the presence of at least two species of viral capsids during synchronized HIV-1 infection

Claire Da Silva Santos, Kevin Tartour, Andrea Cimarelli

O3 Dynamics of nuclear envelope association and nuclear import of HIV-1 complexes

Rya Burdick, Jianbo Chen, Jaya Sastri, Wei-Shau Hu, Vinay Pathak

O4 Human papillomavirus protein E4 potently enhances the susceptibility to HIV infection

Oliver T. Keppler

Session 2: Reverse transcription & integration

O5 Structure and function of HIV-1 integrase post translational modifications

Karine Pradeau, Sylvia Eiler, Nicolas Levy, Sarah Lennon, Sarah Cianferani, Stéphane Emiliani, Marc Ruff

O6 Regulation of retroviral integration by RNA polymerase II associated factors and chromatin structure

Vincent Parissi

Session 3: Transcription and latency

O7 A novel single-cell analysis pipeline to identify specific biomarkers of HIV permissiveness

Sylvie Rato, Antonio Rausell, Miguel Munoz, Amalio Telenti, Angela Ciuffi

O8 A capsid-dependent integration program linking T cell activation to HIV-1 gene expression

Alexander Zhyvoloup, Anat Melamed, Ian Anderson, Delphine Planas, Janos Kriston-Vizi, Robin Ketteler, Chen-Hsuin Lee, Andy Merritt, Petronela Ancuta, Charles Bangham, Ariberto Fassati

O9 Characterisation of new RNA polymerase III and RNA polymerase II transcriptional promoters in the Bovine Leukemia Virus genome

Anthony Rodari, Benoit Van Driessche, Mathilde Galais, Nadége Delacourt, Sylv

关键词： Human Immunodeficiency Virus Infection Simian Immunodeficiency Virus Feline Immunodeficiency Virus Bovine Leukemia Virus Prototype Foamy Virus

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FANTOM5 CAGE profiles of human and mouse samples

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Scientific Data 2017年第1期4卷 1-10页

作者： Noguchi, Shuhei Arakawa, Takahiro Fukuda, Shiro Furuno, Masaaki Hasegawa, Akira Hori, Fumi Ishikawa-Kato, Sachi Kaida, Kaoru Kaiho, Ai Kanamori-Katayama, Mutsumi Kawashima, Tsugumi Kojima, Miki Kubosaki, Atsutaka Manabe, Ri-Ichiroh Murata, Mitsuyoshi Nagao-Sato, Sayaka Nakazato, Kenichi Ninomiya, Noriko Nishiyori-Sueki, Hiromi Noma, Shohei Saijyo, Eri Saka, Akiko Sakai, Mizuho Simon, Christophe Suzuki, Naoko Tagami, Michihira Watanabe, Shoko Yoshida, Shigehiro Arner, Peter Axton, Richard A. Babina, Magda Kenneth Baillie, J. Barnett, Timothy C. Beckhouse, Anthony G. Blumenthal, Antje Bodega, Beatrice Bonetti, Alessandro Briggs, James Brombacher, Frank Carlisle, Ailsa J. Clevers, Hans C. Davis, Carrie A. Detmar, Michael Dohi, Taeko Edge, B. Albert S. Edinger, Matthias Ehrlund, Anna Ekwall, Karl Endoh, Mitsuhiro Enomoto, Hideki Eslami, Afsaneh Fagiolini, Michela Fairbairn, Lynsey Farach-Carson, Mary C. Faulkner, Geoffrey J. Ferrai, Carmelo Fisher, Malcolm E. Forrester, Lesley M. Fujita, Rie Furusawa, Jun-Ichi Geijtenbeek, Teunis B. Gingeras, Thomas Goldowitz, Daniel Guhl, Sven Guler, Reto Gustincich, Stefano Ha, Thomas J. Hamaguchi, Masahide Hara, Mitsuko Hasegawa, Yuki Herlyn, Meenhard Heutink, Peter Hitchens, Kelly J. Hume, David A. Ikawa, Tomokatsu Ishizu, Yuri Kai, Chieko Kawamoto, Hiroshi Kawamura, Yuki I. Kempfle, Judith S. Kenna, Tony J. Kere, Juha Khachigian, Levon M. Kitamura, Toshio Klein, Sarah Peter Klinken, S. Knox, Alan J. Kojima, Soichi Koseki, Haruhiko Koyasu, Shigeo Lee, Weonju Lennartsson, Andreas MacKay-Sim, Alan Mejhert, Niklas Mizuno, Yosuke Morikawa, Hiromasa Morimoto, Mitsuru Moro, Kazuyo Morris, Kelly J. Motohashi, Hozumi Mummery, Christine L. Nakachi, Yutaka Nakahara, Fumio Nakamura, Toshiyuki Nakamura, Yukio Nozaki, Tadasuke Ogishima, Soichi Ohkura, Naganari Ohno, Hiroshi Ohshima, Mitsuhiro Okada-Hatakeyama, Mariko Okazaki, Yasushi Orlando, Valerio Ovchinnikov, Dmitry A. Passier, Robert Patrikakis, Margaret Pombo, Ana Pradhan-Bhatt, Swati Qin, Xian-Yang Rehli, Michael Rizzu, Patrizia Roy, S Division of Genomic Technologies RIKEN Center for Life Science Technologies Yokohama Kanagawa 230-0045 Japan RIKEN Omics Science Center Yokohama Kanagawa 230-0045 Japan Department of Medicine Karolinska Institutet Stockholm 14186 Sweden Karolinska University Hospital Center for Metabolism and Endocrinology Stockholm 14186 Sweden Scottish Centre for Regenerative Medicine University of Edinburgh 5 Little France Drive Edinburgh EH164UU United Kingdom Department of Dermatology and Allergy Charite University Medicine Berlin Charitéplatz 1 Berlin 10117 Germany Roslin Institute and Royal School of Veterinary Studies University of Edinburgh Edinburgh EH259RG United Kingdom Australian Infectious Diseases Research Centre University of Queensland St Lucia 4072 QLD Australia School of Chemistry and Molecular Biosciences University of Queensland St Lucia 4072 QLD Australia Bio-Rad Laboratories Pty Ltd Hercules 94547 CA United States University of Queensland Diamantina Institute University of Queensland Woolloongabba 4102 QLD Australia IRCCS Fondazione Santa Lucia Via del Fosso di Fiorano 64 Rome 00143 Italy Australian Institute for Bioengineering and Nanotechnology University of Queensland Brisbane St Lucia 4072 QLD Australia Division of Immunology Institute of Infectious Diseases and Molecular Medicine University of Cape Town Anzio Road Observatory 7925 South Africa Immunology of Infectious Diseases Faculty of Health Sciences South African Medical Research Council University of Cape Town Anzio Road 7925 South Africa International Centre for Genetic Engineering and Biotechnology Cape Town Component Anzio Road 7925 South Africa Hubrecht Institute Royal Netherlands Academy of Arts and Sciences Uppsalalaan 8 3584 Netherlands University Medical Centre Utrecht Postbus 85500 Utrecht 3508 Netherlands Genomics Cold Spring Harbor Laboratory Cold Spring Harbor New York 11797 NY United States Institute of Pharmaceutical Sciences ETH Zurich Vladi

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

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Parameters that affect estimation of nucleolar proteins' mobility in living cells by the FRAP method with the example of protein fibrillarin

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Cell and Tissue Biology 2012年第2期6卷 128-136页

作者： Barygina, V.V. Mironova, A.A. Zatsepina, O.V. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Moscow Russian Federation Faculty of Biology Moscow State University Moscow Russian Federation Faculty of Bioengineering and Bioinformatics Moscow State University Moscow Russian Federation

The fluorescence recovery after photobleaching (FRAP) method, in combination with confocal laser scanning microscopy, represents one of the basic approaches to studying the properties of proteins in living mammalian cells. However, the data of different authors on the dynamic properties of the same protein and even in cells of the same type can differ greatly. Until now, the reasons for such discrepancies have not been specifically analyzed. In the present work, using the example of nucleolar protein fibrillarin fused with EGFP, we studied the effect of the area of the irradiated region (the region of interest (ROI)) and temperature conditions of experiments on the main dynamic characteristics of the protein-the portion of the mobile fraction of protein and the half-recovery time of fluorescence after photobleaching (t _1/2). The obtained results have shown that both parameters affect markedly the estimation of the fibrillarin-EGFP mobility in HeLa cells. It was concluded that, in FRAP experiments the ROI area can be standardized and, where possible, minimized. In addition, when analyzing the dynamic characteristics of the nucleolar proteins, which participate in the temperature-dependent enzymatic reactions, it is necessary to maintain standard temperature conditions. © 2012 Pleiades Publishing, Ltd.

关键词： area of ROI photobleaching fibrillarin fluorescence half-recovery time (t 1/2) FRAP mobile protein fraction temperature conditions

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Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities

Bioinformatic analysis of alpha/beta-hydrolase fold enzymes ...

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作者： Suplatov, D.A. Besenmatter, W. Švedas, V.K. Svendsen, A. Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics Belozersky Institute of Physicochemical Biology Lenin Hills 1/7 Moscow 119991 Russia Novozymes A/S Krogshoejvej 36 2880 Bagsvaerd Denmark

Superfamily of alpha-beta hydrolases is one of the largest groups of structurally related enzymes with diverse catalytic functions. Bioinformatic analysis was used to study how lipase and amidase catalytic activities are implemented into the same structural framework. Subfamily-specific positions-conserved within lipases and peptidases but different between them-that were supposed to be responsible for functional discrimination have been identified. Mutations at subfamily-specific positions were used to introduce amidase activity into Candida antarctica lipase B (CALB). Molecular modeling was implemented to evaluate influence of selected residues on binding and catalytic conversion of amide substrate by corresponding library of mutants. In silico screening was applied to select reactive enzyme-substrate complexes that satisfy knowledge-based criteria of amidase catalytic activity. Selected CALB variants with substitutions at subfamily-specific positions Gly39, Thr103, Trp104, and Leu278 were produced and showed significant improvement of experimentally measured amidase activity. Based on these results, we suggest that value of subfamily-specific positions should be further explored in order to develop a systematic tool to study structure-function relationship in enzymes and to use this information for rational enzyme engineering. © 2012 The Author.

关键词： Catalyst activity

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[Verification of the PREFAB alignment database].

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Biofizika 2012年第2期57卷 205-211页

作者： Astakhova, T.V. Lobanov, M.N. Poverennaia, I.V. Roǐtberg, M.A. Iakovlev, V.V. Institute of Mathematical Problems of Biology Russian Academy of Sciences Pushchino Moscow Region Russia Institute of Protein Research Russian Academy of Sciences Pushchino Moscow Region Russia Faculty of Bioengineering and Bioinformatics Moscow State University Moscow Russia

The verification of the PREFAB database containing golden standard protein alignments was performed. It has revealed a significant number of differences between the sequences from PREFAB and PDB databases. It was shown that compared to the sequences given in the PDB database 575 alignments refered to a sequence with a gap;such alignments were excluded. Furthermore, compared to the PDB-sequences a single substitute or the insertions were found for 440 aminoacid sequences from PREFAB database;these sequences were edited. SCOP domain analysis has shown that only 502 alignments in the resulting set contain the sequences from the same family. Finally, eliminating duplicates, we have created a new golden standard alignment database PREFAB-P based on PREFAB;the PREFAB-P database contains 581 alignments.

关键词： amino acid sequence golden standard PDB structure SCOP classification

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31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part one: National Harbor, MD, USA. 9-13 November 2016

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J Immunother Cancer 2016年第SUPPL 1期4卷 1-1页

作者： Andreas Lundqvist Vincent van Hoef Xiaonan Zhang Erik Wennerberg Julie Lorent Kristina Witt Laia Masvidal Sanz Shuo Liang Shannon Murray Ola Larsson Rolf Kiessling Yumeng Mao John-William Sidhom Catherine A. Bessell Jonathan Havel Jonathan Schneck Timothy A. Chan Eliot Sachsenmeier David Woods Anders Berglund Rupal Ramakrishnan Andressa Sodre Jeffrey Weber Roberta Zappasodi Yanyun Li Jingjing Qi Philip Wong Cynthia Sirard Michael Postow Walter Newman Henry Koon Vamsidhar Velcheti Margaret K. Callahan Jedd D. Wolchok Taha Merghoub Lawrence G. Lum Minsig Choi Archana Thakur Abhinav Deol Gregory Dyson Anthony Shields Cara Haymaker Marc Uemura Ravi Murthy Marihella James Daqing Wang Julie Brevard Catherine Monaghan Suzanne Swann James Geib Mark Cornfeld Srinivas Chunduru Sudhir Agrawal Cassian Yee Jennifer Wargo Sapna P. Patel Rodabe Amaria Hussein Tawbi Isabella Glitza Scott Woodman Wen-Jen Hwu Michael A. Davies Patrick Hwu Willem W. Overwijk Chantale Bernatchez Adi Diab Erminia Massarelli Neil H. Segal Vincent Ribrag Ignacio Melero Tara C. Gangadhar Walter Urba Dirk Schadendorf Robert L. Ferris Roch Houot Franck Morschhauser Theodore Logan Jason J. Luke William Sharfman Fabrice Barlesi Patrick A. Ott Laura Mansi Shivaani Kummar Gilles Salles Cecilia Carpio Roland Meier Suba Krishnan Dan McDonald Matthew Maurer Xuemin Gu Jaclyn Neely Satyendra Suryawanshi Ronald Levy Nikhil Khushalani Jennifer Wu Jinyu Zhang Fahmin Basher Mark Rubinstein Mark Bucsek Guanxi Qiao Cameron MacDonald Bonnie Hylander Elizabeth Repasky Shilpak Chatterjee Anusara Daenthanasanmak Paramita Chakraborty Kyle Toth Megan Meek Elizabeth Garrett-Mayer Michael Nishimura Chrystal Paulos Craig Beeson Xuezhong Yu Shikhar Mehrotra Fei Zhao Kathy Evans Christine Xiao Alisha Holtzhausen Brent A. Hanks Nicole Scharping Ashley V. Menk Rebecca Moreci Ryan Whetstone Rebekah Dadey Simon Watkins Robert Ferris Greg M. Delgoffe Jonathan Peled Sean Devlin Anna Staffas Melissa Lumish Kori Porosnicu Rodriguez Katya Ahr Miguel Perales Sergio Giralt Ying Taur Eric Pam Karolinska Institutet Stockholm Stockholms Lan Sweden Weill Cornell Medical College New York NY USA Nova Southeastern University Cell Therapy Institute Fort Lauderdale FL USA Johns Hopkins University School of Medicine Baltimore MD USA Immunology Program Johns Hopkins University School of Medicine Columbia MD USA Memorial Sloan Kettering Cancer Center New York NY USA Johns Hopkins Medical Institute Baltimore MD USA University of Rochester Monrovia MD USA NYU Langone Medical Center New York NY USA H. Lee Moffitt Cancer Center Tampa FL USA Ludwig Collaborative Laboratory Memorial Sloan Kettering Cancer Center New York NY USA Immune Monitoring Core Facility Memorial Sloan Kettering Cancer Center New York NY USA Leap Therapeutics Cambridge MA USA Department of Medicine Memorial Sloan Kettering Cancer Center New York NY USA Case Western Reserve University Cleveland OH USA Cleveland Clinic Main Campus Cleveland OH USA University of Virginia Cancer Center Charlottesville VA USA Stony Brook University Medical Center Stony Brook NY USA Karmanos Cancer Institute Detroit MI USA University of Texas MD Anderson Cancer Center Houston TX USA Idera Pharmaceuticals Inc. Cambridge MA USA Institut Gustave Roussy Villejuif Ile-de-France France Center for Applied Medical Research (CIMA) University of Navarra Pamplona Navarra Spain University of Pennsylvania Philadelphia PA USA Earle A. Chiles Research Institute Providence Cancer Center Portland OR USA Universitätsklinikum Essen Essen Nordrhein-Westfalen Germany University of Pittsburgh Pittsburgh PA USA CHU Rennes Service Hématologie Clinique and INSERM 0203 Unité d’Investigation Clinique Rennes Bretagne France Centre Hospitalier Régional Universitaire de Lille Lille Nord-Pas-de-Calais France Simon Cancer Center Indiana University Indianapolis IN USA University of Chicago School of Medicine Chicago IL USA Johns Hopkins University School of Medicine Lutherville MD USA Multidisciplinary Oncology and Therapeuti

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