Research - Institute of Biophysics - Bionanoscience Research Unit - Biomolecular Electronics Research Group

András DÉR
scientific adviser

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László FÁBIÁN research associate
Balázs LEITGEB research associate
Sándor VALKAI research associate
András KINCSES junior research associate
Zoltán NÁSZTOR junior research associate
Szilvia KREKIC Ph.D. student

BIOELECTRONICS OF ION-TRANSPORTING MEMBRANE PROTEINS

Bioelectronics has a double meaning in scientific literature. On the one hand, as a branch of basic biophysical sciences, it deals with electric phenomena appearing on any organization level of living systems (A). On the other hand, as a recently developed discipline of information technological science, it explores the potential of biological materials for application in molecular electronics (B). In both disciplines, interfaces between structural units play a crucial role. Our main goal is to develop novel experimental methods based on integrated micro- and nanotechnological platforms, as well as theoretical models, to study biological interfaces, and utilize them in both branches of bioelectronics. Besides its impact on basic biophysical science, this research is expected to have various applications in molecular electronics.


A) Electric signals associated to membrane transport processes

Electric phenomena, ubiquitous in living systems, carry a lot of information about basic physiological processes that are inaccessible to other techniques (e.g., ECG or EEG). All they can be traced back to the cellular level, namely to membrane-coupled signal- and energy transduction processes. The importance of methodological developments aiming at the detection of the associated electric signals is underpinned, e.g., by the Nobel Prize given for the patch clamp technique (Neher and Sackmann, 1991).

However, application of the most commonly used microelectrode methods to the investigation of transmembrane ionic currents often fails due to technical limitations, while alternative optical techniques still suffer from fundamental sensitivity and time resolution problems. Active pump currents, therefore, are still measured on suspensions of cell organelles or cells by macroelectrode methods, in whose elaboration our institute in Szeged played a determining role. The generalization of one of our techniques allowed the detection of intramolecular electric signals in all the three spatial dimensions.




Recent developments in nanotechnology offer the opportunity of a natural extension of our techniques to the investigation of interfaces of single cells or cellular monolayers forming biological barriers. In line with this, we have measured electric signals associated to the signal transduction processes of the phototaxis of Chlamydomonas cells by a modified light gradient method. Comparing the signals detected with and without a pre-orienting light, it was possible to separate signal components generated in different regions of the plasma membrane (eye spot, flagellae). The method represents an ideal tool for in vivo testing point mutants of the visual pigment of Chlamydomonas, „Channelrhodopsin”, that plays a key role in a whole new branch of neuro-electrophysiological applications (optogenetics).

Besides proceeding with the topics above, we are going to utilize our expertise to establish various lab-on-a-chip measuring platforms for the investigation of the active and passive electric properties of living cells and endothelial tissues, combined with a microscopic control. Endothelial membranes play a role analogous to cell membranes on a higher level of hierarchy, hence they may serve as an ideal model system to investigate the primary processes associated with inflammation and related diseases. The research is going to be carried out in cooperation with the group of Prof. Mária Deli (Lab of Neurobiology).


B) Protein-based integrated optical switching

Since the start of integrated electronics, the expansion of development has been described by “Moore’s law”: the density (performance) of integrated electronic circuits doubles about every 1.8 years. While this “law” has remained proven valid for a remarkable period of 30 years, there is a general perception that the evolutionary development has reached a limit. It is agreed that future development needs revolutionary new principles. Presently, all possible candidates are explored in the search for new routes. Molecular electronics combined with optical data processing is regarded as being among the most promising emerging alternative technologies.

Coupling of optical data-processing devices with microelectronics, as well as sensory functions, is one of the biggest challenges in molecular electronics. Suitable nonlinear optical (NLO) materials with high stability and sensitivity are being intensively researched. In addition to organic and inorganic crystals, biological molecules have also been considered for use in optoelectronics, among which bR has generated the most interest.




We suggested the application of this protein as an active, programmable nonlinear optical material in all-optical integrated circuits, and demonstrated the first integrated optical switching by bR, with a switching speed of ca. 1 μs. Based on these findings, a USA patent was registered in 2005. Based on these findings, a USA patent [Light-driven integrated optical device (US 6,956,984 B2)] was registered in 2005. Later on, we improved the switching time to ca. 10 ns, still behind the state of the art (some 100ps). Eventually, using the picosecond BR-K and the subpicosecond BR-I transitions, we have recently demonstrated switching speeds increased by several orders of magnitude, to subpicosecond switching times, well beyond the present state of the art. This superior performance brings biomaterials to the frontline of modern photonic technology.

A novel, all-optical biosensor was also created using a thin bacteriorhodopsin film of unique nonlinear optical properties as an active element of the device. The passive part of the sensor consisted of an integrated optical Mach-Zehnder interferometer produced by the direct laser writing technique. After a thorough optical test, the sensor was successfully applied to detect protein-protein interactions (antigen-antibody reactions).

On behalf of the Bionics Innovation Center, we are further developing the method, in order to make it suitable for sensitive, label-free detection of bacteria from body fluids.

In addition to its impact on basic biophysical science, we expect our Bioelectronics research to have various applications in molecular electronics and medical diagnostics.

Selected publications

Dér, A., Oroszi, L., Kulcsár, Á., Zimányi, L., Tóth-Boconádi, R., Keszthelyi, L., Stoeckenius, W., Ormos, P. (1999) Interpretation of spatial charge displacements in bacteriorhodopsin in terms of structural changes during the photocycle PROC. NATL. ACAD. SCI. USA 96: 2776-2781

Dér, A. and Keszthelyi, L. (2001) Charge motion during the photocycle of bacteriorhodopsin. (Review) BIOCHEMISTRY (M) 66:1234-1248.

Dér, A., Keszthelyi, L. (eds.) BIOELECTRONIC APPLICATIONS OF PHOTCHROMIC PIGMENTS, IOS Press, 2001. NATO Science Series, 335.

Tóth-Boconádi, R., Dér, A., Taneva, S.G., Keszthelyi, L. (2006) Excitation of the L intermediate of bacteriorhodopsin: Electric responses to test X-ray structures. BIOPHYS. J. 90: 2651-2655

Ormos, P., Fábián L., Oroszi L., Ramsden, J.J., Wolff, E.K., Dér, A. (2002) Protein-based integrated optical switching and modulation. APPL. PHYS. LETT. 80: 4060-4062

Dér, A., Valkai, S., Fábián, L., Ormos, P., Ramsden, J.J., Wolff, E.K. (2007) Integrated Optical Switching Based on The Protein Bacteriorhodopsin. PHOTOCHEM. PHOTOBIOL. 83: 393-396

Fábián, L., Wolff, E.K., Oroszi, L., Ormos, P., Dér, A. (2010) Fast integrated optical switching by the protein bacteriorhodopsin. APPLIED PHYSICS LETTERS 97: 10.1063/1.3462940.

Dér, A., Valkai, S., Mathesz, A., Ando, I., Wolff, E.K., Ormos, P. (2010) Protein-based all-optical sensor device. SENSORS AND ACTUATORS B 151: 26-29

Fábián, L., Heiner, Z., Mero, M., Kiss, M., Wolff, E.K., Ormos, P., Osvay, K., Dér, A. (2011) Protein-based ultrafast photonic switching. OPTICS EXPRESS 19:18861-18870

Kincses, A., Tóth-Boconádi, R., Dér, A. (2012) 2D measurement of ion currents associated to the signal transduction of the phototactic alga Chlamydomonas reinhardtii. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 114: 147-152

Mathesz, A., Fábián, L., Valkai, S., Alexandre, D., Marques, P.V.S., Ormos, P., Wolff, E.K., Dér, A. (2013) High-speed integrated optical logic based on the protein bacteriorhodopsin. BIOSENSORS & BIOELECTRONICS 46: 48-52

Fábián L, Mathesz A, Dér A. (2015) New trends in biophotonics. (review article) ACTA BIOLOGICA SZEGEDIENSIS 59:(Suppl 2) pp. 189-202.

Mathesz A, Valkai S, Ujvárosy A, Aekbote B, Sipos O, Stercz B, Kocsis B, Szabó D, Dér A. (2015)Integrated optical biosensor for rapid detection of bacteria. OPTOFLUIDICS MICROFLUIDICS AND NANOFLUIDICS 2: pp. 14-20.

Walter FR, Valkai S, Kincses A, Petneházi A, Czeller T, Veszelka S, Ormos P, Deli MA, Dér A. (2016) A versatile lab-on-a-chip tool for modeling biological barriers. SENSORS AND ACTUATORS B-CHEMICAL 222: pp. 1209-1219.

Hofmeister effects

Water is the third most abundant molecule in the Universe (after H and CO), and the most abundant in Earth. The major part of living organisms is made up by water (on each level of organization). If water is extracted, proteins do not function. “Water is a matrix providing stability and flexibility of proteins at the same time.” (Philip Ball)

Some unique physical-chemical properties: high electric dipole moment, network of H-bonds, fast proton exchange. According to molecular dynamics modelling, such cluster-formations are more frequent at lower than at higher temperatures:

The reason is the change of H-bond strength versus temperature. What could be the consequence of this on proteins? Temperature change is the most straightforward tool to change the strength of H-bonds, however, this has an impact on the Brownian motion of protein molecules, as well. Addition of salts which do not affect pH, and do not specifically interact with proteins might help this problem. Unspecific effects of neutral salts on protein aggregation and conformation have been known for a long time, and, after their first investigator, are called Hofmeister effects. According to the investigations, the effects are dominated by anions, rather than cations. In 1888, Hofmeister ordered the anions according to their ability of precipitating globular proteins from water:

SO4-- > F- > CH4COO- > Cl- > Br- > I- > ClO4-, SCN- (1)

Cl- has the least effect (in the middle of the row), while those on the left-hand side of (1) are called kosmotrops (increase of aggregation: “salting out”), and the right-hand-side ones are called chaotrops (increase of solubility: “salting in”). Interestingly, the same row was found for protein conformation and activity, too: Normally, kosmotrops stabilize conformation and increase activity, while chaotrops destabilize conformation and decrease activity. Disturbingly, however, the tendency is just the opposite in some cases. Such exceptions make the elaboration of a coherent theory of Hofmeister effects rather difficult.

Recently, we have given a theoretical groun¬ding of the effects based on the salt dependence of solute-water interfacial tension. We also showed that the relation between interfacial tension and protein structural stability is straightforwardly linked to protein conformational fluctuations, providing a keystone for the microscopic interpretation of HE. Using bR and photoactive yellow protein as model objects, we pointed out that Hofmeister salts affect the magnitude of protein conformational fluctuations, and, inasmuch as modifing water structure at the protein-water interface, they can be used to identify major conformational changes associated to protein function. We called the attention to the importance of the interplay between the interfacial properties of the protein and conformational dynamics.

In the future, we are going to utilize HE as research tool to reveal the role of interfacial water structure in crucial steps of biological processes, such as protein folding or function. The spectrum of the target proteins spans from highly ordered β-amyloid structures via model polypeptides and fully functional proteins of well-defined, but flexible, conformation to intrinsically disordered proteins. We are going to apply a complex methodological approach involving both powerful experimental techniques and molecular dynamics simulations. The results are expected to have important general implications concerning the effect of water structure on protein stabilty and dynamics.

Selected publications

Dér, A.; Ramsden, J.J. (1998) Evidence for loosening of a protein mechanism. NATURWISSENSCHAFTEN, 85: 353-355.

Neagu, A., Neagu., M., Dér, A. (2001) Fluctuations and the Hofmeister effect. BIOPHYS. J. 81: 1285

Dér, A., Neagu, A., Neagu, M. (2001) Active transport modulated by barrier fluctuations. In: Dér, A Keszthelyi (ed.) BIOELECTRONIC APPLICATIONS OF PHOTOCHROMIC PIGMENTS, IOS Press, pp. 225-243

Dér, A., Kelemen, L., Fábián, L., Taneva, S.G., Fodor, E., Páli, T., Cupane, A., Cacace, M.G., Ramsden, J.J. (2007). Interfacial Water Structure Controls Protein Conformation. JOUNAL OF PHYSICAL CHEMISTRY B 111: 5344-5350

Dér, A. (2008). Salts, interfacial water and protein conformation. BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT 22: 629-633

Khoroshyy, P. , Dér, A., Zimányi, L. (2013). Effect of Hofmeister cosolutes on the photocycle of photoactive yellow protein at moderately alkaline pH. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B 120: 111-119

Szalontai, B., Nagy, G., Krumova, S., Fodor, E., Páli, T., Taneva, S.G., Garab, G., Peters, J., Dér, A. (2013). Hofmeister ions control protein dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS 1830: 4564-4572

Bogár F, Bartha F, Násztor Z, Fábián L, Leitgeb B, Dér A. (2014) On the Hofmeister Effect: Fluctuations at the Protein-Water Interface and the Surface Tension. JOURNAL OF PHYSICAL CHEMISTRY B 118:(29) pp. 8496-8504.

Násztor Z, Bogár F, Dér A. (2016) The Interfacial Tension Concept, as Revealed by Fluctuations. (review article) CURRENT OPINION IN COLLOID AND INTERFACE SCIENCE 23: pp. 29-40.

Molecular dynamics simulation of bioactive peptides

Since the different peptides possess relevant biological effects, it is therefore important to identify the structural and conformational properties of these bioactive molecules in detail. For the peptides, studying the three-dimensional structure, folding processes, and mode of action proves to be often difficult using experimental methods. However, applying the appropriate theoretical methods, not only the structural and folding features of peptides, but also their mode of action could be investigated in sufficient detail. Consequently, the molecular modeling proves to be a very useful and suitable tool, and an opportunity arises to determine the structural and conformational properties of peptides by means of various theoretical methods. These computational studies, as well as the results obtained by the different calculations have important contributions to the better understanding of various biological processes, and furthermore, they provide a good basis for the rational design of potent and novel peptides, peptidomimetics, as well as drugs.

We perform molecular modeling calculations on a variety of biologically active peptides, which are as follows: opioid peptides; polyalanine and polyglutamine peptides; alanine-based peptides; antimicrobial peptides; peptaibols. In the course of these theoretical studies, the structural properties, folding processes, structure-activity relationships, as well as mode of action of bioactive peptides are investigated applying different molecular modeling methods.




The effects of Hofmeister salts on various peptides and proteins are examined by means of theoretical methods including ab initio and molecular dynamics calculations. The spectrum of biologically relevant target molecules spans from the highly ordered beta-amyloid structures via proteins and model peptides of flexible, but well-defined structure (e.g. Trp-cage miniprotein and photoactive yellow protein) to the intrinsically disordered proteins.

We carried out different molecular modeling calculations on bioactive peptaibol molecules, in order to determine their characteristic structural and conformational properties. Furthermore, the interactions of peptaibols with various micelles and membranes are studied, as well as the micelle- and membrane-bound conformations of these peptides are identified and characterized. Additionally, applying the data regarding the biological activities of peptaibol molecules, the possible relationships between their structural features and bioactivity are investigated, and structure-activity relationship studies are performed.

Selected publications

Leitgeb, B., Szekeres, A., Manczinger, L., Vágvölgyi, C. and Kredics, L. (2007). The history of alamethicin: A review of the most extensively studied peptaibol. CHEM. BIODIVERS. 4(6): 1027-1051.

Leitgeb, B. (2007). Structural investigation of endomorphins by experimental and theoretical methods: Hunting for the bioactive conformation. CHEM. BIODIVERS. 4(12): 2703-2724.

Janzsó, G., Bogár, F., Hudoba, L., Penke, B., Rákhely, G. and Leitgeb, B. (2011). Exploring and characterizing the folding processes of Lys- and Arg-containing Ala-based peptides: a molecular dynamics study. COMPUT. BIOL. CHEM. 35(4): 240-250.

Leitgeb, B., Janzsó, G., Hudoba, L., Penke, B., Rákhely, G. and Bogár, F. (2011). Helix and H-bond formations of alanine-based peptides containing basic amino acids. STRUCT. CHEM. 22(6): 1287-1295.

Leitgeb, B. (2012). Conformational similarities and dissimilarities between the stereoisomeric forms of endomorphin-2. CHEM. BIOL. DRUG DES. 79(3): 313-325.

Leitgeb, B. (2012). Spatial relationships between the pharmacophores of endomorphin-2: a comparative study of stereoisomers. CENT. EUR. J. CHEM. 10(6): 1791-1798.

Kredics, L., Szekeres, A., Czifra, D., Vágvölgyi, C. and Leitgeb, B. (2013). Recent results in alamethicin research. CHEM. BIODIVERS. 10(5): 744-771.

Násztor, Z., Horváth, J. and Leitgeb, B. (2013). Structural characterization of the short peptaibols trichobrachins by molecular-dynamics methods. CHEM. BIODIVERS. 10(5): 876-886.

Leitgeb, B. (2014). Characteristic structural features of indolicidin: effects of the cis-trans isomerism on its conformation. CHEM. BIOL. DRUG DES. 83(1): 132-140.

Násztor, Z., Horváth, J. and Leitgeb, B. (2015). Studying the structural and folding features of long-sequence trichobrachin peptides. CHEM. BIODIVERS. 12(9): 1365-1377.

Horváth, J., Násztor, Z., Bartha, F., Bogár, F. and Leitgeb, B. (2016). Characterizing the structural and folding properties of long-sequence hypomurocin B peptides and their analogs. BIOPOLYMERS (PEPT. SCI.) in press.