Biomolecular Interaction Laboratory / Ferenc Erdődi

Personal data: 

Ferenc Erdődi, D. Sc.
E-mail: erdodimed[at]unideb.hu
bioinkubator.unideb.hu

Services: 

The laboratory provides the following services:
• quantitative characterization of protein-protein and protein-ligand interactions using purified components: determination of the association and dissociation rate constants as well as the association/dissociation constants for the interaction
• characterization of antigen-antibody interaction including epitope mapping
• study of the binding of possible drug molecules to the target protein and /or to receptor
• characterization of protein-nucleic acid and protein-carbohydrate interactions
• separation of protein(s) from cell lysate or partially purified samples that bind to an immobilized partner (antibody, subunit, inhibitor etc.) via a sample recovering system: binding proteins are recovered in a form suitable for direct analyses by mass spectrometry or by immunological methods.

Infrastucture: 

Biacore-3000 equipment, accessories for sample preparations (centrifuges, vacuum filtering and ultrasonic degasing systems).

Methods: 

Technical description and limitations:
In both basic and applied science it is often required to uncover the mechanism of protein-protein and protein-ligand interactions. Surface plasmon resonance based binding study is the choice of technique nowadays for these assays since this measurement requires relatively low amount of samples and it can provide quantitative kinetic and thermodynamic data for the interaction of the binding partners.
In the Biomolecular Interaction Laboratory we study and characterize the interaction of biomolecules using Biacore-3000 equipment based on the principles of surface plasmon resonance. To carry out such studies relatively low amount of the binding partners are needed. One of the binding partners is immobilized on the surface of a sensor chip by covalent coupling, then the solution containing the other partner is injected over the surface and the interaction is detected and quantified. The equipment is suitable for multi-channel analyses at wide temperature (4-40°C) and flow rate (1-2 µl/min to 50-100 µl/min) range. It is also able to detect relatively weak (Ka~104) interactions. The equipment is supplied with user friendly software which makes possible the evaluation of the binding data for different kinetic mechanisms.

Previous projects:
We characterized previously the subunit interactions in myosin phosphatase and uncovered the regions in the myosin phosphatase target subunit (MYPT) that bound to the protein phosphatase-1 catalytic subunit (PP1c).
Since the installation of the Biacore-3000 instrument at the Medical and Health Science Center of the University of Debrecen different types of biomolecular interactions have been successfully characterized. It has been shown that the retinoblastoma protein (pRb) is a substrate of myosin phosphatase (PP1c-MYPT) and it binds to both the isolated PP1c and MYPT. However, effective dephosphorylation occurs only when MYPT targets the PP1c to pRb. This mechanism is supported by the stronger binding of MYPT to pRb than that of PP1c. We also probed binding of small molecules to enzymes immobilized on the sensorchip surface. We proved that flavopiridol, that influences the activity of glycogen phosphorylase can also bind to this enzyme in a wide concentration range. The reproducibility of binding of this small molecule to the enzyme has been proved by the overlay of the binding sensograms of five independent experiments at each flavopiridol concentration. In similar experiments the binding of tannins as well as pentagalloyl glucose (PGG), one of the major tannin constituent, to human salivary α-amylase (HAS) has been studied. These binding experiments confirmed the direct interaction of PGG with HAS and established a relative binding strength for different tannins and PGG. We assayed the interaction between transglutaminase-2 (TG2) and milk fat globulin EGF factor-8 (MFG-E8). The latter is a phagocytic integrin ß3 ligand and its interaction with TG2 may play an important role in integrin signaling. TG2 was immobilized and MFG-E8 was injected over the surfaces. The sensograms obtained clearly indicated the stable interaction of TG2 with MFG-E8 suggesting that these binding partners may form a complex under physiological conditions too.

Current projects:
Currently we investigate the binding characteristics of two tannin constituents, PGG and epigallocatcehin-3-gallate (EGCG), to protein phosphatase-1 catalytic subunit (PP1c). PGG and EGCG bind directly to PP1c and they inhibit the phosphatase activity. To uncover the mechanism in the inhibition competitive binding assays with phosphatase inhibitory toxins (okadaic acid, microcystin) are carried out. These initial results suggest that PGG and EGCG binds partly to the hydrophobic groove at the catalytic center of PP1c competing for binding with the inhibitory toxins.
Studies are initiated also to fish out interacting proteins from cell lysates for an immobilized partner and identify these binding proteins by mass spectrometry analyses.

Representative publications on the application of methods:

Toth A, Kiss E, Herberg FW, Gergely P, Hartshorne DJ, Erdodi F
Study of the subunit interactions in myosin phosphatase by surface plasmon resonance
EUR J BIOCHEM 267:(6) 1687-1697 (2000)

Kiss A, Lontay B, Bécsi B, Márkász L, Oláh É, Gergely P, Erdődi F
Myosin phosphatase interacts with and dephosphorylates the retinoblastoma protein in THP-1 leukemic cells: its inhibition is involved in the attenuation of daunorubicin-induced cell death by calyculin-A
CELL SIGNAL 20: 2059-2070 (2008)

Tóth B, Garabuczi É, Sarang Zs, Vereb Gy, Vámosi Gy, Aeschlimann D, Blaskó B, Bécsi B, Erdődi F, Lacy-Hulbert A, Zhang A, Falasca L, Birge RB, Balajthy Z, Melino G, Fésüs L, Szondy Zs
Transglutaminase 2 is needed for the formation of an efficient phagocyte portal in macrophages engulfing apoptotic cells
J IMMUNOL 182: 2084-2092 (2009)

Gyémánt Gy, Zajácz Á, Bécsi B, Ragunath C, Ramasubbu N, Erdődi F, Batta Gy, Kandra L
Evidence for pentagalloyl glucose binding to human salivary alpha-amylase through aromatic amino acid residues
BBA-PROTEINS PROTEOM 1794: 291-296 (2009)

Contact: 

Prof. Ferenc Erdődi, D. Sc erdodi[at]med.unideb.hu

Photos: 

 

Figure 1.

Biacore-3000 instrument and its major units for surface plasmon resonance (SPR) based detection of biomolecular interactions.

 

 

 

 

 

Figure 2.

The interaction of protein phosphatase-1 catalytic subunit (PP1c) with retinoblastoma protein immobilized on the sensorchip surface in the absence or in the presence of a PP1c-binding peptide

 

 

 

 

 

Figure 3.

Binding of flavopiridol to skeletal muscle glycogen phosphorylase. Sensograms were obtained in at least five independent binding experiments at each concentration.