PD Dr. Basem Soboh

Hi, my name is Basem soboh. I come from Palestine. The major focus of my work is to understanding how complex iron-sulphur cofactors are assembled. After I completed my Diploma and PhD-degrees in Thauer Lab (MPI-Marburg), i investigated the in vitro biosynthesis of the iron-molybdenum cofactor of Nitrogenase at University of California-Berkeley. During my Habilitation, an in vitro Synthesis of active [NiFe]-hydrogenase has been elucidated. Since 2016 i started to work in the groups of Heberle and Schlesinger. Using a combinations of molecular biology, anaerobic protein biochemistry and biophysical methods, we are currently “watching” the in vitro stepwise synthesis and assembly of hydrogenase cofactor over time.

basem

Fachbereich Physik

Institut für experimentelle Physik

Experimentelle Molekulare Biophysik

Wissenschaftlicher Angestellter

Adresse Arnimallee 14
Raum 0.1.43
14195 Berlin
Telefon (030) 838-56098
Fax (030) 838-453337
E-Mail basem.soboh@fu-berlin.de

Basem Soboh born 1974 in Palestine-Gaza

Habilitation 2016, University of Halle (Institute of Biology-Microbiology)

Ph.D. (Dr. rer. nat.) 2004, University of Marburg (PhD Thesis in MPI, Thauer Lab)

Diploma in Biology 2001, Marburg (Microbiology, Biochemistry, Genetics & Virology)

Bachelor of science 1996, Alazhr University-Gaza (Microbiology & Chemistry)


Research Assistant:

University of California-Berkeley/Ludden Lab (2005-2008)

University of Halle/Sawers Lab (2008-2015)

Freie University Berlin/Heberle Lab (2016)

My research focuses on the in vitro biosynthesis of complex Fe-S cofactors. We currently employ hydrogenases that make or oxidize hydrogen gas. [NiFe]-hydrogenase has a complicated catalytic active site that contains nickel and iron bound to the protein in addition to unique non-protein ligands. The biosynthesis of hydrogenases is a multi-step process that requires the coordinated activity of several accessory proteins. My interest lies in determining how this complex cofactor is assembled and incorporated into these enzymes.

Our strategy concept of an in vitro system is based on the isolation of active maturation machinery, followed by “watching” the stepwise synthesis and assembly of cofactor over time. This concept involves a broad range of methodologies ranging from microbiology, molecular biology and protein biochemistry to biophysical methods. This includes cloning, manipulation of genes, overexpression,anaerobic isolation of protein complexes and intermediates, that bound cofactor precursors in preparative amounts and X-ray crystallography. The analytical methods include anoxic enzyme kinetics, UV-vis spectroscopy, FPLC, functional protein-protein interaction (thermophoresis), metal detection (ICP-MS), and native gel electrophoresis. Spectroscopic methods like infrared spectroscopy, surface-enhanced IR absorption spectroscopy (SEIRAS), and Raman spectroscopy are well established in our Lab (Dr. Stripp). All methods are performed in a glove box including isotope editing of the carbonyl ligands of cofactor.

Recently we could demonstrate the in vitro synthesis of active [NiFe]-hydrogenase using only purified components. This finding allows us to exert much greater control over the hydrogenase maturation machinery. It provides the possibility to study each of maturation steps individually at molecular level. This study includes determination of the temporal sequence of events and analysis of the compositions of functional complexes at each maturation step along the path of cofactor biosynthesis. A more thorough spectroscopic and structural investigation of an all-pure-component-based in vitro system is required to conclusively trace the intermediates of the assembly process of [NiFe]-hydrogenase.


Working model for maturation of the large subunit pro-protein of [NiFe]-hydrogenases to active hydrogenase (i) Incorporation of the Fe(CN)2CO moiety into the precursor of the hydrogenase large subunit (pro-protein); (ii) Nickel insertion; (iii) Endoproteolytic cleavage associated with a conformational change; and (iv) formation of the heterodimeric enzyme complex exhibiting hydrogenase activity.

Selected publications related to my current research


Stripp ST., Lindenstrauss U., Sawers RG. and Soboh B. (2015) Identification of an Isothiocyanate on the HypEF Complex Suggests a Route for Efficient Cyanyl-Group Channeling during [NiFe]-Hydrogenase Cofactor Generation. PLoS One e0133118. doi: 10.1371/journal.pone.0133118.

Stripp ST., Lindenstrauss U., Granich C., Sawers RG. and Soboh B. (2014) The influence of oxygen on [NiFe]-hydrogenase cofactor biosynthesis and how ligation of carbon monoxide precedes cyanation. Plos ONE 9 e107488. doi: 10.1371/journal.pone.0107488.

Soboh B., Lindenstrauss U., Granich C., Javaid M., Herzberg M., Claudia T. and Stripp ST. (2014) [NiFe]-hydrogenase maturation in vitro: analysis of the roles of the HybG and HypD accessory proteins. Biochemical journal. 1;464(2):169-77.

Soboh B., Stripp ST., Muhr E., Granich C., Braussemann M., Herzberg M., Heberle J. and Sawers RG. (2012) [NiFe]-hydrogenase maturation: isolation of a HypC-HypD complex carrying diatomic CO and CN- ligands.FEBS Lett., 586(21) 3882-3887

Soboh B., Kuhns M., Braussemann M., Waclawek M., Muhr E., Pierik AJ. and Sawers RG. (2012) Evidence for an oxygen-sensitive iron-sulfur cluster in an immature large subunit species of Escherichia coli [NiFe]-hydrogenase 2. Biochem Biophys Res Commun. 424(1),158-163

Petkun S., Shi R., Li Y., Asinas A., Munger C., Zhang L., Waclawek M., Soboh B., Sawers RG. and Cygler M. (2011) Structure of Hydrogenase Maturation Protein HypF with Reaction Intermediates Shows Two Active Sites. Structure 19 (12), 1773–1783

Soboh B., Boyd ES., Zhao D, Peters JW. and Rubio LM. (2010) Substrate specificity and evolutionary implications of a NifDK enzyme carrying NifB-co at its active site. FEBSLett. 584(8),1487-92

Curatti L., Hernandez JA., Igarashi RY., Soboh B., Zhao D. and Rubio LM. (2007). In vitro synthesis of the iron-molybdenum cofactor of nitrogenase from iron, sulfur, molybdenum and homocitrate using purified proteins. Proc. Natl. Acad. Sci. 104 (45), 17626-31

George SJ., Igarashi RY., Piamonteze C., Soboh B., Cramer SP. and Rubio LM. (2007) Identification of a Mo-Fe-S cluster on NifEN by Mo K-edge EXAFS. J. Am. Chem. Soc.,129(11),3060-3061

Soboh B., Linder D. and Hedderich R. (2004) A multisubunit membrane-bound [NiFe] hydrogenase and a NADH-dependent Fe-only hydrogenase in the fermenting bacterium Thermoanaerobacter tengcongensis. Microbiology 150, 2451-2463