| |  Research | | | Resources | | |  Teaching | | | Group |
|
|
Type: Seminar (2 SWS)
Ects: 4.0
Lecturer: Burkhard Rost
Time: Monday, 12:00 - 13:30
Room: MI 01.09.034
Language: English
Content
Topics related to the research interests of the group: protein sequence analysis, sequence based predictions,
protein structure prediction and analysis; interaction networks.
Pre-meeting
Thursday, Feb 23rd, 14:30
The rules and hints for preparation of the seminar discussed given in the pre-meeting are also summarised in our Checklist.
April 23 Lars von den Driesch: Structural Evolution of Enzymes
Advisor: Andrea Schafferhans
April 30 Johannes Höffler: Integral membrane proteins and their classification
Advisor: Edda Klopmann
May 7 Christiane Gasperi:Potassium channels
Advisor: Edda Klopmann
May 14 Stefan Huber: Mutations in protein kinases and their role in human disease
Advisor: Christian Schäfer
May 21 Kinga Balazs: The 1000 genomes project
Advisor: Lothar Richter
June 4 Nikos Papadopoulos: HIV mutational pathways
Advisor: Lothar Richter
June 11 Andre Seitz: Physical and Genetic Interaction networks
Advisor: Arthur Dong
June 18 Alexander Grün: The power of interaction networkds for associating genes with diseases
Advisor: Tobias Hamp
June 25 Verena Friedl: Disease Networks
Advisor: Arthur Dong
July 2 Paul Kerbs: Intrinsically Disordered Proteins in Human Diseases
Advisor: Esmeralda Vicedo
July 9 Milot Mirdita: Use of GPUs for bioinformatics
Advisor: Laszlo Kajan
July 16 Harold Tientcheu: Structural alignment and structure classification
Advisor: Andrea Schafferhans
Structural alignment and structure classification
Structure comparisons are the basis for many protein structure and function analyses. This seminar shall give an overview of structure comparison methods and explain the classification scheme behind SCOP/qCOPS.
Literature:
- Frank,K. et al. (2010) COPS benchmark: interactive analysis of database search methods. Bioinformatics (Oxford, England), 26, 574-5. www.ncbi.nlm.nih.gov/pubmed/20080504
- Suhrer,S.J. et al. (2009) COPS--a novel workbench for explorations in fold space. Nucleic acids research, 37, W539-44. www.pubmedcentral.nih.gov/articlerender.fcgi
- Sippl,M.J. (2008) On distance and similarity in fold space. Bioinformatics (Oxford, England), 24, 872-3. www.ncbi.nlm.nih.gov/pubmed/17127679
- Sippl,M.J. and Wiederstein,M. (2008) Structural bioinformatics A note on difficult structure alignment problems. Bioinformatics, 24, 426-427.
- Sippl,M.J. et al. (2008) A discrete view on fold space. Bioinformatics (Oxford, England), 24, 870-1. bioinformatics.oxfordjournals.org/cgi/content/abstract/24/6/870
- Suhrer,S.J. et al. (2007) QSCOP--SCOP quantified by structural relationships. Bioinformatics (Oxford, England), 23, 513-4. www.ncbi.nlm.nih.gov/pubmed/17127679
- Please search additional related literature and follow references!
Structural evolution of enzymes
The paradigm that "sequence determines structure and structure determines function" is central to the annotation of protein function. This seminar shall give an overview of studies that have analysed the relation between structural similarity and relatedness of enzyme function and the conclusions that have been reached with respect to evolution of new enzymes. It shall also review databases that can be used for such analyses.
Literature:
- Rison,S.C.G. and Thornton,J.M. (2002) Pathway evolution, structurally speaking. Current Opinion in Structural Biology, 12, 374-382. www.ncbi.nlm.nih.gov/pubmed/12127458
- Lee,D.A. et al. (2010) GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Research, 38, 720-737. discovery.ucl.ac.uk/1299034/
- Furnham,N. et al. (2011) FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic acids research, 44, 1-7. www.ncbi.nlm.nih.gov/pubmed/22006843
- Please search additional related literature and follow references!
Integral membrane protein structures and their classification
Dr. Edda Kloppmann
The important class of integral membrane proteins (IMPs) provides the link between cell and environment or between different cell compartments and is for example involved in ion transport, signaling and cell adhesion. Structures of these proteins are particularly difficult to solve. Nevertheless, a significant number of structures is known today. This talk shall give an overview of IMP structure and how their orientation in the membrane can be determined from structure. A short introduction to the prediction of transmembrane segments from protein sequence shall be included.
Literature: - Lomize et al. (2006) Positioning of proteins in membranes: A computational approach. Protein Science 15: 1318-1333.
- Tusnády et al. (2005) TMDET: web server for detecting transmembrane domains by using 3D structure of proteins. Bioinformatics 21: 1276-1277.
Potassium channels
Dr. Edda Kloppmann
Potassium channels form pores accross membranes selective for K+-ions. They constitute a major class of ion channels and occur in most organisms.
Literature: - Y Jiang, A Lee, J Chen, V Ruta, M Cadene, BT Chait & R MacKinnon. X-ray structure of a voltage-dependent K+ channel. Nature (2003) 423: 33–41.
- ...
Mutations in protein kinases and their role in human disease
Dipl. Bioinf. Christian Schaefer
Protein kinases represent one of the largest protein families. Due to their role in a variety of biological processes, mutations play an important part in some human diseases. In this seminar, an overview of the protein family shall be presented. Furthermore, a selection of known genotype-phenotype relationships shall be discussed with the main focus on distinct features of disease-causing mutations.
Literature: - Lahiry P, Torkamani A, Schork NJ, Hegele RA. Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat Rev Genet. 2010 Jan;11(1):60-74.
- Torkamani A, Schork NJ. Distribution analysis of nonsynonymous polymorphisms within the human kinase gene family. Genomics. 2007 Jul;90(1):49-58
- ...
The power of protein interaction networks for associating genes with diseases
Tobias Hamp
Recent years have seen a large increase of known protein-protein interactions (PPIs) on the one hand and of known disease causing genes on the other hand. Computational biologists have combined these two types of data and now predict so far unknown disease genes with help of PPI networks. This seminar is supposed to give an introduction to current state-of-the-art methods.
Literature: - S. Navlakha and C. Kingsford. The power of protein interaction networks for associating genes with diseases. Bioinformatics (2010) 26(8): 1057–1063.
- Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R, 2010 Associating Genes and Protein Complexes with Disease via Network Propagation. PLoS Comput Biol 6(1): e1000641.
- Marc Vidal, Michael E. Cusick, Albert-László Barabási, Interactome Networks and Human Disease, Cell, 144(6): 986-998,
Alternative splicing and evolution
Tobias Hamp
Alternative splicing is universal and, as we recently learned, much more frequent than expected. This talk will give an introduction to what we know, remains to be discovered and how computational biology can come into play.
Literature: - I. I. Artamonova and M. S. Gelfand. Comparative Genomics and Evolution of Alternative Splicing: The Pessimists' Science. Chemical Reviews (2007) 107(8): 3407-3430.
- H. Keren, L.-M. Galit and G. Ast. Alternative splicing and evolution: diversification, exon definition and function. Nature Reviews Genetics (2010) 11: 345-355.
Disease Networks
Dr. Arthur Dong
Molecular studies of diseases have traditionally focused on single genes (so called monogenic diseases). However, most common diseases are surprisingly complex, involving the interplay of multiple genes and proteins. The increasing availability of genome-scale data and the rise of systems biology ushered in a new era of network-based disease studies.
Literature:
Physical and Genetic Interaction Networks
Dr. Arthur Dong
Proteins are the main molecular actors in a cell, but they rarely carry out their functions alone. Instead, they physically interact with each other in most biological processes. The physical interactions can be either permanent, as in protein complexes, or transient, as in signal transduction. Proteins can also be highly correlated without interacting with each other physically; for example, one protein may induce or suppress another protein, or two proteins may participate in the same pathway. Such indirect interactions are termed genetic interactions. Both physical and genetic interactions in a cell form complex networks, with intriguing properties. In this study we combine the two types of networks to obtain further insights.
Literature: - Kelley, R. and Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5):561-566
Intrinsically Disordered Proteins in Human Diseases
Diplom. Biol. Esmeralda Vicedo
Intrinsically disordered proteins (IDPs) lack stable tertiary and/or secondary structures under physiological conditions in vitro.IDPs are involved in regulation, signaling, and control and their functions are tuned via alternative splicing and posttranslational modifications.Numerous IDPs are associated with human diseases, including cancer, cardiovascular disease, amyloidoses, neurodegenerative diseases, and diabetes. Overall, intriguing interconnections among intrinsic disorder, cell signaling, and human diseases suggest that protein conformational diseases may result not only from protein misfolding, but also from misidentification, missignaling, and unnatural or nonnative folding.
Literature:
Protein design and engineering
Dr. Marc Offman
Proteins are central to most biological processes and their spectrum of functions is seemingly endless. Given that proteins are found in almost any living forms and each organism had to adapt to evolutionary pressure over million of years, a large number of different proteins have evolved. Some of these proteins could potentially be used as drugs, others need to be adapted (engineered), and for some purposes new proteins need to be designed. In protein engineering/design either known proteins are adapted in order to meet certain criteria such as increased stability, function, activity and recognition, or novel protein folds are created. Given the fact that proteins are large, complicated molecules with a huge number of degrees of freedom, protein engineering seems to be an unsolvable task. Nevertheless, methods are under constant development and show some success, as engineered proteins can already be used as therapeutics and as tools for cell biology.
Reference
Molecular Dynamics
Dr. Marc Offman
|
|
|
|
Imprint |
Sitemap |
Contact