Forschungsbericht 2011



General methods and tools for systems and synthetic biology

Institut: V-1
Projektleitung: An-Ping Zeng
Mitarbeiter/innen: Julian da Luz
Uwe Jandt
Chenwei Ma
Wael Sabra
Wei Wang
Zhen Chen
Donna Dietz
Yu Bo
Libang Zhou
Feng Geng
Jibin Sun
Laufzeit: 01.01.2007 — 31.12.2018
Finanzierung:Technische Universität Hamburg-Harburg (TUHH)

 

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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Chen, Z and Zeng, A P: Protein design in systems metabolic engineering for industrial strain development Biotechnol J, 8(5): S. 523--533, 2013.
  • 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.
  • 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.
  • 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.
  • 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.