2010

Zhang, G., Lukoszek, R., Mueller-Roeber, B., Ignatova, Z. (2010) Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.  Nucleic Acids Res. In press.

Zhang, G., Ignatova, Z. (2010) Folding at the birth of the nascent chain: coordinating translation with co-translational folding. Curr Opin Struct Biol. In press.

Czech, A., Fedyunin, I., Zhang, G., Ignatova Z. (2010) Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations. Mol Biosyst. 6(10):1767-72.

Valleriani, A., Ignatova, Z., Nagar, A., and Lipowsky, R. (2010) Turn-over of messenger RNA: Polysome statistics beyond the steady state. Eur. Phys. Lett., 89, 2010, 58003.

Zhang, G., Fedyunin, I., Miekley, O., Valleriani, A., Moura, A. and Ignatova, Z. (2010) Global and local depletion of ternary complex transiently stalls the ribosomes and limits translational elongation. Nucl. Acid. Res., 38(14):4778-87.

Yuryev, R., Ignatova, Z., Kasche, V. and Galunsky, B. (2010) Comparative investigation of thermodynamic and pH stability of wild type and mutant penicillin amidase from A. feacalis, Prot. J., 29(3):181-7.

2009

Zhang, G., Hubalewska, M., and Ignatova, Z. (2009) Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nature Struct. Mol. Biol. 16, 274-280.

Zhang, G. and Ignatova, Z. (2009) Isolation of homogeneous ribosome-nascent complexes from coupled cell-free transcription-translation system. Nature Protocols, on-line

Zhang, G. and Ignatova, Z. (2009) A generic algorithm to predict translation rates: Implications for protein biogenesis, PLoS One 4, e5036.

Martinez-Perez, I.M., Ignatova, Z., and Zimmermann, K.-H. (2009) Exploiting the features of the finite state automata for biomolecular computing. Recent Patents DNA Gene Seq.. in press.

Martinez-Perez, I.M., Zimmermann, K.-H.* and Ignatova, Z. (2009) An autonomous DNA model for finite state automata. Int. J. Bioinform. Res. Appl. 5, 81-96.

Ignatova, Z. and Gierasch, L.M. (2009) A method for direct measurement of protein stability in vivo. Meth. Mol. Biol. 490, 165-178.

2008

Hinz, J., Gierasch, L.M., and Ignatova, Z. (2008) Cross-seeding in vivo: an approach for direct determination of mechanism of aggregation in living cells. Biochem. 47, 4196-4200.

Ignatova, Z. and Gierasch, L.M. (2008) A fluorescent window into protein folding and aggregation in cells. Meth. Cell. Biol. 89, 59-70.

Ignatova, Z., Martinez-Perez, I.M., and Zimmermann, K.-H. (2008) DNA computing models. Springer

2007

Ignatova, Z., Thakur, A.K., Wetzel, R.B., and Gierasch, L.M. (2007) In vivo aggregation of polyglutamine tracts is a multistep process with early involvement of flanking sequences. J. Biol. Chem.282, 36736-36743.

Ignatova, Z., Krishnan, B., Bombardier, J.P., Marcelino, A.M., Hong, J. and Gierasch, L.M. (2007) From the test tube to the cell: Exploring the folding and aggregation of a ß-clam protein. Biopolymers 88, 157-163.

Ignatova, Z. and Gierasch, L.M. (2007) Effect of osmolytes on protein folding and aggregation in cells. Meth. Enzymol. 428, 355-372.

Martinez-Perez, I.M., Zhang, G., Ignatova, Z., and Zimmermann, K.-H. (2007) Computational genes: a tool for early molecular diagnosis and therapy of cancer. BMC. Bioinformatics 8, 365.

2006

Ignatova, Z. and Gierasch, L.M. (2006) Extended polyglutamine tracts cause aggregation and structural perturbation of an adjacent b-barrel protein. J. Biol. Chem. 281, 12959-12967.

Ignatova, Z. and Gierasch, L.M. (2006) Inhibition of protein aggregation in vivo and in vitro by a natural osmoprotectants. Proc. Nac. Acad. Sci. USA 103, 13357-13361. Comment: Fisher, M.T. (2006) Proline to the rescue, Proc. Natl. Acad. Sci. USA 103, 13365-13366.

2005

Ignatova, Z. (2005) Monitoring protein stability in vivo. (Review) Microb. Cell. Fact. 4, 1-6.

Ignatova, Z. and Gierasch, L.M. (2005) Aggregation of a slow-folding mutant of a b-clam protein proceeds through a monomeric nucleus. Biochemistry 44, 7266-7274.

Ignatova, Z., Wischnewski, F., Notbohm, H., and Kasche, V. (2005) Pro-sequence and Ca²⁺-binding: implications for the folding and activity of penicillin amidase. J. Mol. Biol. 348, 999-1014.

Viegas, S., Schmidt, D., Arraiano, C.M., Kasche, V. and Ignatova, Z. (2005) Effect of the increased stability of the penicillin amidase mRNA on the protein expression levels. FEBS Lett. 579, 5069-5073.

Kasche, V., Ignatova, Z., Märkl, H., Plate, W., Punckt, N., Schmidt, D., Ernst, B (2005) Ca²⁺ is required for transport and maturation and is yield determining factor in high cell density fermentations of penicillin amidase. Biotechnol. Prog. 21, 432-438.

Martinez-Perez, I.M., Ignatova, Z., Zhang, G. and Zimmermann, K.-H. (2005) Biomolecular autonomous solution of the Hamiltonian path problem via hairpin formation. Int. J. Bioinform. Res. Appl. 1, 389-398.

Publications of AG Baumann