Sühnel Laboratory

Biocomputing

Structural bioinformatics and computational genomics

We do research in the field of bioinformatics and computational biology with an emphasis on structural biology and computational genomics. In the structural biology field we have been interested in the identification and analysis of unusual motifs and interactions in three-dimensional structures of proteins and nucleic acids. Our research involves different techniques including quantum-chemical calculations, molecular dynamics simulations and structural bioinformatics approaches.

More specifically, we have worked and are working on

water-mediated interactions in nucleic acid base pairs,
the geometry and electronic structure of base tetrad motifs occurring in telomere structures, for example,
C-H...O-, C-H...N- and C-H...PI interactions,
the role of non-repetitive dipeptide motifs in proteins that correspond to transitions between different Ramachandran plot clusters.

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» Telomeric DNA sequences form DNA tetraplex structures, see for example the structure of the human telomeric repeat sequence (PDB ID: 143d). Quantum-chemical studies on building blocks such as the sandwiched G-tetrads shown can contribute to a better understanding of structure and function. (Meyer et al, 2005, 2007).

Our computational genomics work is currently aimed at the development of tools for an accelerated and improved annotation and analysis of prokaryotic genomes. In addition, a new genome browser type that encodes the nucleic acid sequence by physico-chemical dinucleotide properties is developed. We also apply mathematical methods to microscopical, FISH (fluorescence in situ hybridisation) and imaging techniques.

We have developed and are maintaining a variety of widely used databases and webtools shown in the right side bar.

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» Circular plot of features of the E. coli K12 genome generated with JPGV. CDS(PDB) stands for genes for which three-dimensional protein structures are available. Note, that the origin of replication correlates with the purine excess minimum (Romualdi et al, 2007).

The Sühnel Group was coordinating the Jena Centre for Bioinformatics - JCB between 2001 and 2007. Currently, J. Sühnel is acting as the coordinator of JenaAge - The Jena Centre for Systems Biology of Ageing. The group is also responsible for the maintenance of the institutional computer network including the internet link.

In-house collaborations with the Diekmann and Platzer labs.
External collaborations with M. Meyer, Revotar Biopharmaceuticals, Hennigsdorf, C. Skerka and P. Zipfel, Hans Knöll Institute, Jena, A. Gutermann, Medigene, Martinsried, P. Dittrich, Jena University, M. Hausmann, Heidelberg University and E.B. Pedersen, University of Southern Denmark, Odense.

Recent selected publications

Friedel M, Nikolajewa S, Sühnel J, Wilhelm T. (2009) DiProGB: The Dinucleotide Properties Genome Browser. Bioinformatics. Jul 15. Epub ahead of print. [PubMed]
Friedel M, Nikolajewa S, Sühnel J, Wilhelm T. (2009) DiProDB: a database for dinucleotide properties. Nucleic Acids Res. 37 (Database issue), D-37-40. [PubMed]
Meyer M, Sühnel J. (2008) Density functional study of adenine tetrads with N6-H6...N3 hydrogen bonds. J Phys Chem A. 112, 4336-4341. [PubMed]
Huehne R, Koch F-T, Sühnel J (2007) A comparative view of comprehensive information resources on three dimensional structures of biological macromolecules. Brief Funct Genomics Proteomics 6, 220-239. [PubMed]
Romualdi A, Felder M, Rose D, Gausmann U, Schilhabel M, Glöckner G, Platzer M, Sühnel J (2007) GenColors: annotation and comparative genomics of prokaryotes made easy. Methods Mol Biol. 395, 75-96. [PubMed]
Schwarz-Finsterle J, Stein S, Grossmann C, Schmitt E, Trakhtenbrot L, Rechavi G, Amariglio N, Cremer C, Hausmann M (2007) Comparison of triple helical COMBO-FISH and standard FISH by means of quantitative microscopic image analysis of abl/bcr positions in cell nuclei. J Biochem Biophys Methods. 70, 397-406. [PubMed]
Skerka C, Lauer N, Weinberger AA, Keilhauer CN, Sühnel J, Smith R, Schlötzer-Schrehardt U, Fritsche L, Heinen S, Hartmann A, Weber BH, Zipfel PF (2007) Defective complement control of factor H (Y402H) and FHL-1 in age-related macular degeneration. Mol Immunol. 44, 3398-3406. [PubMed]
Glöckner G, Schulte-Spechtel U, Schilhabel M, Felder M, Sühnel J, Wilske B, Platzer M (2006) Comparative genome analysis: selection pressure on the Borrelia vls cassettes is essential for infectivity. BMC Genomics 7, 211. [PubMed]
Nolte O, Müller M, Häfner B, Knemeyer JP, Stöhr K, Wolfrum J, Hakenbeck R, Denapaite D, Schwarz-Finsterle J, Stein S, Schmitt E, Cremer C, Herten DP, Hausmann M, Sauer M (2006) Novel singly labelled probes for life science applications (SMART PROBES). In: Biophotonics: Visions for Better Health Care (Popp J, Strehle M, Eds), Wiley-VCH, 167-230. [Amazon]
Meyer M, Hocquet A, Sühnel J (2005) Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. J Comput Chem. 26, 352-364. [PubMed]
Monajembashi S, Rapp A, Schmitt E, Dittmar H, Greulich KO, Hausmann M (2005) Spatial association of homologous pericentric regions in human lymphocyte nuclei during repair. Biophys J. 88, 2309-2322. [PubMed]
Romualdi A, Siddiqui R, Glöckner G, Lehmann R, Sühnel J (2005) GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness. Bioinformatics. 21, 3669-3671. [PubMed]
Wieland GD, Nehmann N, Müller D, Eibel H, Siebenlist U, Sühnel J, Zipfel PF, Skerka C (2005) Early growth response proteins EGR-4 and EGR-3 interact with immune inflammatory mediators NF-kappaB p50 and p65. J Cell Sci. 118, 3203-3212. [PubMed]

Last update: October 7, 2009

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