Zum Hauptinhalt springen

Research

Research

Research

Research

Understanding our research

Basic understanding

DNA is the molecule that carries the information of life in all living organisms. But on its own, this information is useless without proteins — the second key class of biomolecules. Proteins perform nearly all essential tasks in the cell: they build structures, transport molecules, regulate processes, and, most importantly, act as enzymes — catalysts that speed up chemical reactions necessary for life. Converting DNA-encoded information into proteins is one of nature’s most fundamental processes. You can think of DNA as the blueprint, and proteins as the builders and catalysts that bring the plan to life.

The Grininger lab focuses on proteins. We take a two-step approach: first, we study selected proteins to understand what they do and how they work in detail. Then, since proteins are natural catalysts, we explore how they can be reprogrammed to catalyze new reactions. For example, we rebuild enzymes to synthesize products of interest for biotechnology and health care.

Advanced understanding

Proteins are essential building blocks of life and are found in every living organism. They serve both structural and functional roles. Structurally, proteins can form stable frameworks. For example, the protein keratin provides strength to hair, nails, and skin, while the protein collagen is the main component of connective tissue. Functionally, proteins perform a wide range of tasks. They are responsible for binding and transporting molecules such as oxygen, vitamins, hormones, or other proteins. And, they are catalyzing chemical reactions. For example, enzymes such as hexokinase, citrate synthase, and malate dehydrogenase convert sugars and other nutrients into energy and essential metabolic intermediates. The enzyme ATP synthase drives the production of ATP, the universal energy carrier of the cell, by using the energy stored in a proton gradient. Other enzymes, including fatty acid synthase, are responsible for building up lipids, ensuring the proper balance of cellular energy and membrane components.

Proteins exist in many different architectures, and their structural complexity often mirrors the complexity of their functions. Some of the most remarkable examples are multidomain enzymes — large proteins in which several distinct catalytic units are connected within a single polypeptide chain. These domains work together to perform cascade or multistep reactions efficiently, passing intermediate products directly from one active site to the next. A prominent example of such systems are multienzyme complexes involved in fatty acid and polyketide synthesis. The Grininger Lab focuses on these multidomain proteins to understand how their internal organization enables complex reaction sequences, and to harness this principle for designing new catalytic pathways in biotechnology.

Expert understanding

The Grininger Lab investigates the fascinating world of multidomain enzymes — complex molecular machines that can perform entire reaction sequences within a single protein scaffold. We aim to uncover how these enzymes are organized, how their catalytic domains communicate, and how they achieve the precise coordination required for efficient cascade reactions. A particular focus lies on large multienzyme systems such as fatty acid synthases, which serve as model systems to understand the structural and mechanistic basis of multistep catalysis. By combining biochemical, structural, and biophysical methods, we explore how architecture, flexibility, and dynamics define enzymatic function.

Building on this understanding, we apply protein engineering and design to reprogram multidomain enzymes for new purposes. By modifying their domain composition or catalytic properties, we investigate how these molecular assembly lines can be adapted to catalyze novel chemical transformations and produce compounds of technological or pharmaceutical relevance. In doing so, the Grininger Lab bridges fundamental research and applied biotechnology, aiming to develop efficient, sustainable, and enzyme-based alternatives to traditional chemical synthesis.

Lab expertise: Handling large multidomain proteins

Research in the Grininger lab relies on the high-quality recombinant production of these enzymes, which allows for targeted modifications through molecular biology techniques. Using this approach, the lab has made significant contributions in recent years to the quantitative understanding of the function and mechanism of these complex biosynthetic systems. It has addressed key catalytic functions of the individual enzymatic domains of FASs and PKSs (e.g. 1–3), as well as their interplay within the compartmentalized architecture for product synthesis (4,5). Work towards the functional characterization is accompanied by investigations into the structure and conformational dynamics of these multi-domain proteins (e.g. 5–7). Building on the deep mechanistic understanding, the lab has developed engineering strategies; for example, modifying FASs to produce fatty acids of varying chain lengths (8,9), and engineering PKSs to incorporate fluorinated substrates during synthesis (10).

1.    Rittner, A., Paithankar, K. S., Huu, K. V. & Grininger, M. Characterization of the Polyspecific Transferase of Murine Type I Fatty Acid Synthase (FAS) and Implications for Polyketide Synthase (PKS) Engineering. ACS Chem. Biol. 13, 723–732 (2018).
2.    Stegemann, F. & Grininger, M. Transacylation Kinetics in Fatty Acid and Polyketide Synthases and its Sensitivity to Point Mutations**. ChemCatChem 13, 2771–2782 (2021).
3.    Gusenda, C., Calixto, A. R., Da Silva, J. R., Fernandes, P. A. & Grininger, M. The Kinetics of Carbon‐Carbon Bond Formation in Metazoan Fatty Acid Synthase and Its Impact on Product Fidelity. Angew. Chem. Int. Ed. e202412195 (2024) doi:10.1002/anie.202412195.
4.    Klaus, M., Buyachuihan, L. & Grininger, M. Ketosynthase Domain Constrains the Design of Polyketide Synthases. ACS Chem. Biol. 15, 2422–2432 (2020).
5.    Klaus, M. et al. Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS Au jacsau.1c00043 (2021) doi:10.1021/jacsau.1c00043.
6.    Gipson, P. et al. Direct structural insight into the substrate-shuttling mechanism of yeast fatty acid synthase by electron cryomicroscopy. Proc Natl Acad Sci U A 107, 9164–9169 (2010).
7.    Ciccarelli, L. et al. Structure and conformational variability of the Mycobacterium tuberculosis fatty acid synthase multienzyme complex. Structure 21, 1251–1257 (2013).
8.    Gajewski, J. et al. Engineering fatty acid synthases for directed polyketide production. Nat Chem Biol 13, 363–365 (2017).
9.    Gajewski, J., Pavlovic, R., Fischer, M., Boles, E. & Grininger, M. Engineering fungal de novo fatty acid synthesis for short chain fatty acid production. Nat Commun 8, 14650 (2017).
10.  Rittner, A. et al. Chemoenzymatic synthesis of fluorinated polyketides. Nat. Chem. 14, 1000–1006 (2022).

CHAIN LENGTH CONTROL in fatty acid biosynthesis

The biosynthesis of fatty acids (FAs) with defined chain lengths is of great interest to the chemical industry. Short-chain fatty acids (SCFAs, ≤C8) are widely used in the food, pharmaceutical, and cosmetic sectors, whereas medium-chain fatty acids (MCFAs, C10–C14) serve as valuable components in lubricants, fragrances, paint additives, and pharmaceuticals. The biotechnological production of short- and medium-chain fatty acids (SMCFAs) represents a sustainable alternative to land-intensive coconut and palm oil extraction.

We engineer eukaryotic multienzyme fatty acid synthases (FASs) from yeast and mouse to produce FAs of defined chain length (1-3). Our strategy follows the principle of minimizing invasive modifications to the enzymes in order to maintain high catalytic efficiency. We achieve this by modulating the relative activity of the carbon–carbon bond-forming ketoacyl synthase (KS) domain and the fatty acid–releasing thioesterase (TE) and MPT domains (4).

Recently, we have engineered the mammalian FAS from mouse to produce SMCFAs by reducing the efficiency of the KS in elongating longer-chain acyl intermediates (5) and by incorporating a TE with broad chain-length specificity. In these FAS variants, the promiscuous TE preferentially hydrolyzes short- and medium-chain acyl intermediates into free fatty acids, as these are poor substrates for the engineered KS. Consequently, the engineered systems yield FAs with narrow and tunable chain-length distributions (Ludig and Zhai et al. accepted).

1.   Gajewski, J. et al. Engineering fatty acid synthases for directed polyketide production. Nat Chem Biol 13, 363–365 (2017).
2.   Gajewski, J., Pavlovic, R., Fischer, M., Boles, E. & Grininger, M. Engineering fungal de novo fatty acid synthesis for short chain fatty acid production. Nat Commun 8, 14650 (2017).
3.   Zhu, Z. et al. Expanding the product portfolio of fungal type I fatty acid synthases. Nature chemical biology 13, 360–362 (2017).
4.   Gusenda, C., Calixto, A. R., Da Silva, J. R., Fernandes, P. A. & Grininger, M. The Kinetics of Carbon‐Carbon Bond Formation in Metazoan Fatty Acid Synthase and Its Impact on Product Fidelity. Angew. Chem. Int. Ed. e202412195 (2024) doi:10.1002/anie.202412195.
5.   Heil, C. S., Wehrheim, S. S., Paithankar, K. S. & Grininger, M. Fatty Acid Biosynthesis: Chain-Length Regulation and Control. Chembiochem : a European journal of chemical biology 20, 2298–2321 (2019).

Structure of fatty acid synthases

In eukaryotes, de novo fatty acid synthesis is catalyzed by the large, multifunctional enzyme complex fatty acid synthase (FAS). The catalytic domains are organized on large polypeptide chains that assemble into higher-order oligomeric complexes. FASs perform iterative rounds of chain elongation, with each cycle extending the growing acyl chain by two carbon atoms. The structural studies on fatty acid synthases (FAS), both fungal and mammalian, have led to numerous high-impact publications over the past two decades. The Grininger Lab’s contributions — including the yeast FAS structure, its inhibited state (1), assembly intermediates (2), and the process of post-translational modification (3), as well as domain structures of mammalian FAS (4,5).

1.    Johansson, P. et al. Inhibition of the fungal fatty acid synthase type I multienzyme complex. Proc Natl Acad Sci U A 105, 12803–12808 (2008).
2.    Fischer, M. et al. Analysis of the co-translational assembly of the fungal fatty acid synthase (FAS). Sci. Rep. 10, 895 (2020).
3.    Johansson, P. et al. Multimeric options for the auto-activation of the Saccharomyces cerevisiae FAS type I megasynthase. Structure 17, 1063–1074 (2009).
4.    Rittner, A., Paithankar, K. S., Huu, K. V. & Grininger, M. Characterization of the Polyspecific Transferase of Murine Type I Fatty Acid Synthase (FAS) and Implications for Polyketide Synthase (PKS) Engineering. ACS Chem. Biol. 13, 723–732 (2018).
5.    Rittner, A., Paithankar, K. S., Himmler, A. & Grininger, M. Type I fatty acid synthase trapped in the octanoyl-bound state. Protein Sci 29, 589–605 (2020).

Engineering of the flavin-binding protein dodecin

Dodecin is found in both archaea and bacteria. The best-characterized examples are from the archaeon Halobacterium salinarum1 and Streptomycetes2,3 and Mycobacteria4. Dodecin is a small flavin-binding protein of approximately 70 amino acids that assembles into dodecameric complexes with cubic symmetry and a diameter of about 7 nm. Each subunit features a spherical β-sheet core and surface-exposed helices, conferring remarkable conformational stability, robustness, and high solubility.
 
The native function of dodecin is to store and protect flavin cofactors1,4. By tightly binding these molecules, it helps to regulate the intracellular flavin pool, preventing harmful oxidative reactions caused by free flavins and ensuring cofactors are available when required. Although not an enzyme, dodecin plays an essential role in flavin homeostasis and redox balance in both archaea and bacteria.

1.  Grininger, M., Staudt, H., Johansson, P., Wachtveitl, J. & Oesterhelt, D. Dodecin is the key player in flavin homeostasis of Archaea. J Biol Chem 284, 13068–13076 (2009).
2.  Ludwig, P. et al. Characterization of the small flavin-binding dodecin in the roseoflavin producer Streptomyces davawensis. Microbiology 164, 908–919 (2018).
3.  Bourdeaux, F. et al. Comparative biochemical and structural analysis of the flavin-binding dodecins from Streptomyces davaonensis and Streptomyces coelicolor reveals striking differences with regard to multimerization. Microbiology 165, 1095–1106 (2019).
4.  Bourdeaux, F. et al. Flavin Storage and Sequestration by Mycobacterium tuberculosis Dodecin. ACS Infect. Dis. 4, 1082–1092 (2018).

Designing next-generation polyketide compounds

Polyketides are bioactive natural products produced polyketide synthases (PKSs). The architecture of PKSs makes them prime engineering targets to produce new therapeutics (1). We develop polyketide modifcation strategies, and have recently focused the MAT domain to reprogram PKS (2). Using this platform, we also synthesized fluorinated polyketides from small fluorinated building blocks, demonstrating strong potential for creating next-generation antibiotics and other drugs (3).

(1) Grininger, M. Enzymology of assembly line synthesis by modular polyketide synthases. Nat Chem Biol 19, 401–415 (2023).
(2) Klaus, M. & Grininger, M. Engineering strategies for rational polyketide synthase design. Natural product reports 35, 1070–1081 (2018).
(3) Rittner, A. et al. Chemoenzymatic synthesis of fluorinated polyketides. Nat. Chem. 14, 1000–1006 (2022).