Structure and Biochemistry of Polyunsaturated Fatty Acid Double Bond Isomerase from Propionibacterium Acnes

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Structure and Biochemistry of Polyunsaturated Fatty Acid Double Bond Isomerase from Propionibacterium Acnes Structure and biochemistry of polyunsaturated fatty acid double bond isomerase from Propionibacterium acnes PhD Thesis In partial fulfillment of the requirements for the degree “Doctor of Philosophy (PhD)” in the Molecular Biology Program at the Georg August University Göttingen, Faculty of Biology Submitted by Alena Liavonchanka Born in Vysoki Borak, Belarus 2007 Affidavit Hereby I declare that my thesis entitled “Structure and biochemistry of polyunsaturated fatty acid double bond isomerase from Propionibacterium acnes” has been written independently and with no other sources and aids than quoted. Alena Liavonchanka Göttingen, 28.09.2007 2 To all my teachers 3 List of publications Liavonchanka, A., and Feussner, I. (2006) Lipoxygenases: occurrence, functions and catalysis. J Plant Physiol 163, 348-357. Liavonchanka, A., Hornung, E., Feussner, I., and Rudolph, M. (2006) In-house SIRAS phasing of the polyunsaturated fatty-acid isomerase from Propionibacterium acnes. Acta Crystallograph Sect F Struct Biol Cryst Commun 62, 153-156. Liavonchanka, A., Hornung, E., Feussner, I., and Rudolph, M. G. (2006) Structure and mechanism of the Propionibacterium acnes polyunsaturated fatty acid isomerase. Proc Natl Acad Sci U S A 103, 2576-2581. 4 Table of contents Acknowledgements............................................................................................................. 7 Abstract............................................................................................................................... 9 1. Introduction................................................................................................................... 10 1.1 Physiological action of CLA and possible mechanisms............................................. 11 1.2 Biosynthesis of CLA................................................................................................... 15 1.3 Comparative analysis of enzymatic mechanisms involved in carbon-carbon double bond isomerization and conjugated PUFA synthesis........................................................ 22 1.4 Aim of the work.......................................................................................................... 32 2. Materials and methods .................................................................................................. 33 2.1 Chemicals.................................................................................................................... 33 2.2 Recombinant DNA...................................................................................................... 33 2.3 PCR based mutagenesis .............................................................................................. 34 2.4 Bacterial growth.......................................................................................................... 34 2.5 Protein solubility analysis and activity test................................................................. 35 2.6 Protein purification ..................................................................................................... 35 2.6.1 Affinity chromatography on Glutathione Sepharose ............................................... 35 2.6.2 Ni2+ affinity chromatography................................................................................... 36 2.6.3 Ion exchange chromatography on Source 30Q Sepharose ...................................... 36 2.6.4 SDS-PAGE analysis of protein fractions................................................................. 36 2.7 Immunoblotting........................................................................................................... 37 2.8 Spectroscopic assays................................................................................................... 37 2.9 Crystallization............................................................................................................. 37 2.9.1 Preliminary screening .............................................................................................. 37 2.9.2 Optimized conditions for PAI crystallization .......................................................... 38 2.10 Data collection, structure determination and refinement.......................................... 38 2.11 GC and GC-MS analysis of lipids ............................................................................ 39 2.11.1 Extraction and derivatization of lipids................................................................... 39 2.11.2 GC and GC-MS analysis of lipids ......................................................................... 40 2.12 HPLC analysis of FA................................................................................................ 40 2.13 Kinetic measurements............................................................................................... 41 2.14 Cofactor exchange .................................................................................................... 41 2.15 Anaerobic photoreduction and redox potential measurement .................................. 42 5 2.17 MALDI TOF analysis............................................................................................... 42 3. Results........................................................................................................................... 45 3.1 PAI structure ............................................................................................................... 45 3.1.1 PAI purification and biochemical properties ........................................................... 45 3.1.2 Crystallization, data collection, structure determination, and refinement ............... 45 3.1.3 Structure of PAI and PAI-CLA complex................................................................. 50 3.1.3.1 Overall structure description of free PAI.............................................................. 50 3.1.3.2 FAD cofactor ........................................................................................................ 52 3.1.3.3 Structure of PAI-CLA and PAI-CLnA complexes ............................................... 53 3.1.3.4 Gating mechanism for substrate entry .................................................................. 56 3.2 PAI reaction mechanism............................................................................................. 58 3.2.1 Structure-based mechanism of FA isomerization.................................................... 58 3.2.2 Hydrogen transfer during LA isomerization............................................................ 61 3.2.3 Active site engineering by site-directed mutagenesis.............................................. 64 3.2.4 Enzyme-substrate complex formation, anaerobic reduction, cofactor exchange .... 66 3.3 FA hydratase from Streptococcus pyogenes (SPH).................................................... 70 3.3.1 Cloning, purification and spectral properties........................................................... 70 3.3.2 SPH produces hydroxy FA species.......................................................................... 73 3.4 (9Z,11E)-CLA producing FA isomerases................................................................... 78 3.4.1 Bifidobacterium breve isomerase (BBI) .................................................................. 78 4. Discussion..................................................................................................................... 81 4.1. PAI structure and reaction mechanism ...................................................................... 81 4.2. Putative bifunctional FA hydratases-isomerases ....................................................... 90 5. Summary and conclusions ............................................................................................ 94 6. Supplementary material. ............................................................................................... 96 7. References................................................................................................................... 107 8. Abbreviations.............................................................................................................. 118 9. Curriculum vitae ......................................................................................................... 120 6 List of figures Fig. 1 Structures of LA, (9Z,11E)-CLA and (10E,12Z)-CLA. ......................................... 11 Fig. 2 Possible mechanisms of CLA action...................................................................... 14 Fig. 3 Structures of EPA and conjugated triene product produced by PFI....................... 18 Fig. 4 Scheme of LA conversion to hydroxy FAs by Lactobacillus sp............................ 19 Fig.5 The routes of LA metabolism in anaerobic bacteria of human gut. ........................ 21 Fig. 6 Schematic overview of enzymatic mechanisms for carbon-carbon double bond isomerization............................................................................................................. 23 Fig. 7 Reaction mechanism of IDI type 1......................................................................... 24 Fig. 8 Scheme of proposed CTI reaction mechanism....................................................... 25 Fig. 9 Reaction mechanism of ECI................................................................................... 26 Fig. 10 The reaction mechanism of KSI. .......................................................................... 27 Fig. 11 Analysis of active
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