General methods and tools for systems and synthetic biology

Stichworte

• Stoffflussanalyse
• synthetische Biologie
• Systembiologie
• Systems Biology

Publikationen

• Ma, C W and Xiu, Z L and Zeng, A P: A new concept to reveal protein dynamics based on energy dissipation. PLoS One, 6(10): S. e26453, 2011. , DOI: 10.1371/journal.pone.0026453
• Stelzer, M and Sun, J and Kamphans, T and Fekete, S P and Zeng, A P: An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks. Integr Biol (Camb), 3(11): S. 1071--1086, 2011. , DOI: 10.1039/c1ib00008j
• Flipphi, M and Sun, J and Robellet, X and Karaffa, L and Fekete, E and Zeng, A P and Kubiecek, C P: Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus spp. Fungal Genet Biol, 46 Suppl 1: S. S19--S44, 2009.
• Chen, Z and Meyer, W and Rappert, S and Sun, J and Zeng, A P: Coevolutionary analysis enabled rational deregulation of allosteric enzyme inhibition in Corynebacterium glutamicum for lysine production. Appl Environ Microbiol, 77(13): S. 4352--4360, 2011. , DOI: 10.1128/AEM.02912-10
• Schomburg, K T and Ardao, I and Gotz, K and Rieckenberg, F and Liese, A and Zeng, A P and Rarey, M: Computational biotechnology: prediction of competitive substrate inhibition of enzymes by buffer compounds with protein-ligand docking. J Biotechnol, 161(4): S. 391--401, 2012. , DOI: 10.1016/j.jbiotec.2012.08.002
• Chen, Z and Bommareddy, R R and Frank, D and Rappert, S and Zeng, A P: Deregulation of feedback inhibition of phosphoenolpyruvate carboxylase for improved lysine production in Corynebacterium glutamicum. Appl Environ Microbiol, 80(4): S. 1388--1393, 2014. , DOI: 10.1128/AEM.03535-13
• Ma, C W and Xiu, Z L and Zeng, A P: Discovery of intramolecular signal transduction network based on a new protein dynamics model of energy dissipation. PLoS One, 7(2): S. e31529, 2012. , DOI: 10.1371/journal.pone.0031529
• Ma, C W and Xiu, Z L and Zeng, A P: Exploring signal transduction in heteromultimeric protein based on energy dissipation model. J Biomol Struct Dyn, 2013. , DOI: 10.1080/07391102.2013.855145
• Geng, F and Chen, Z and Zheng, P and Sun, J and Zeng, A P: Exploring the allosteric mechanism of dihydrodipicolinate synthase by reverse engineering of the allosteric inhibitor binding sites and its application for lysine production. Appl Microbiol Biotechnol, 97(5): S. 1963--1971, 2013. , DOI: 10.1007/s00253-012-4062-8
• He, Feng Q and Sauermann, Ulrike and Beer, Christiane and Winkelmann, Silke and Yu, Zheng and Sopper, Sieghart and Zeng, An-Ping and Wirth, Manfred: Identification of molecular sub-networks associated with cell survival in a chronically SIVmac-infected human CD4+ T cell line.. Virology journal, 11(1): S. 152, jan 2014. , DOI: 10.1186/1743-422X-11-152, http://www.virologyj.com/content/11/1/152
• Chen, Z and Rappert, S and Sun, J and Zeng, A P: Integrating molecular dynamics and co-evolutionary analysis for reliable target prediction and deregulation of the allosteric inhibition of aspartokinase for amino acid production. J Biotechnol, 154(4): S. 248--254, 2011. , DOI: 10.1016/j.jbiotec.2011.05.005
• Zhou, Libang; Zeng, An-Ping : Metabolic engineering of Corynebacterium glutamicum for increasing lysine production by using a lysine riboswitch. ACS Synthetic Biology, 2014 (accepted).
• He, F and Chen, H and Probst-Kepper, M and Geffers, R and Eifes, S and Del Sol, A and Schughart, K and Zeng, A P and Balling, R: PLAU inferred from a correlation network is critical for suppressor function of regulatory T cells. Mol Syst Biol, 8: S. 624, 2012. , DOI: 10.1038/msb.2012.56
• Ma, C W and Luddecke, J and Forchhammer, K and Zeng, A P: Population shift of binding pocket size and dynamic correlation analysis shed new light on the anticooperative mechanism of PII protein. Proteins, 82(6): S. 1048--1059, 2014. , DOI: 10.1002/prot.24477
• Chen, Z and Zeng, A P: Protein design in systems metabolic engineering for industrial strain development. Biotechnol J, 8(5): S. 523--533, 2013. , DOI: 10.1002/biot.201200238
• Chen, Z and Rappert, S and Zeng, A P: Rational Design of Allosteric Regulation of Homoserine Dehydrogenase by a Non-Natural Inhibitor L-Lysine. ACS Synth Biol, 2013. , DOI: 10.1021/sb400133g
• He, F and Balling, R and Zeng, A P: Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives. J Biotechnol, 144(3): S. 190--203, 2009. , DOI: 10.1016/j.jbiotec.2009.07.013
• Chen, Z and Wilmanns, M and Zeng, A P: Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development. Trends Biotechnol, 28(10): S. 534--542, 2010. , DOI: 10.1016/j.tibtech.2010.07.004
• Chen, L and Chen, Z and Zheng, P and Sun, J and Zeng, A P: Study and reengineering of the binding sites and allosteric regulation of biosynthetic threonine deaminase by isoleucine and valine in Escherichia coli. Appl Microbiol Biotechnol, 97(7): S. 2939--2949, 2013. , DOI: 10.1007/s00253-012-4176-z
• Chen, Zhen and Rappert, Sugima and Zeng, An-Ping: Rational Design of Allosteric Regulation of Homoserine Dehydrogenase by a Nonnatural Inhibitor L-Lysine. ACS Synthetic Biology, 4(2): S. 126--131, feb 2015. , DOI: 10.1021/sb400133g, http://pubs.acs.org/doi/abs/10.1021/sb400133g
• Ma, Cheng-Wei and Xiu, Zhi-Long and Zeng, An-Ping: Exploring signal transduction in heteromultimeric protein based on energy dissipation model. Journal of Biomolecular Structure and Dynamics, 33(1): S. 134--146, jan 2015. , DOI: 10.1080/07391102.2013.855145, http://www.tandfonline.com/doi/full/10.1080/07391102.2013.855145
• Zeng, An-Ping: Fundamentals and Application of New Bioproduction Systems. Springer, , 2013
• Schopke, B and Zeng, A P: Inference of responsive metabolic pathways from time-series transcriptomic data with consideration of the metabolic network structure. Integr Biol (Camb), 4(8): S. 889--896, 2012. , DOI: 10.1039/c2ib20031g