Microscopic modeling of charge transport in sensing proteins
© Reggiani et al.; licensee Springer. 2012
Received: 6 January 2012
Accepted: 22 June 2012
Published: 22 June 2012
Sensing proteins (receptors) are nanostructures that exhibit very complex behaviors (ions pumping, conformational change, reaction catalysis, etc). They are constituted by a specific sequence of amino acids within a codified spatial organization. The functioning of these macromolecules is intrinsically connected with their spatial structure, which modifications are normally associated with their biological function. With the advance of nanotechnology, the investigation of the electrical properties of receptors has emerged as a demanding issue. Beside the fundamental interest, the possibility to exploit the electrical properties for the development of bioelectronic devices of new generations has attracted major interest. From the experimental side, we investigate three complementary kinds of measurements: (1) current-voltage (I-V) measurements in nanometric layers sandwiched between macroscopic contacts, (2) I-V measurements within an AFM environment in nanometric monolayers deposited on a conducting substrate, and (3) electrochemical impedance spectroscopy measurements on appropriate monolayers of self-assembled samples. From the theoretical side, a microscopic interpretation of these experiments is still a challenging issue. This paper reviews recent theoretical results carried out within the European project, Bioelectronic Olfactory Neuron Device, which provides a first quantitative interpretation of charge transport experiments exploiting static and dynamic electrical properties of several receptors. To this purpose, we have developed an impedance network protein analogue (INPA) which considers the interaction between neighboring amino acids within a given radius as responsible of charge transfer throughout the protein. The conformational change, due to the sensing action produced by the capture of the ligand (photon, odour), induces a modification of the spatial structure and, thus, of the electrical properties of the receptor. By a scaling procedure, the electrical change of the receptor when passing from the native to the active state is used to interpret the macroscopic measurement obtained within different methods. The developed INPA model is found to be very promising for a better understanding of the role of receptor topology in the mechanism responsible of charge transfer. Present results point favorably to the development of a new generation of nano-biosensors within the lab-on-chip strategy.
Receptors are proteins of relevant interest because of the fundamental role they play in living environments at a cellular level[1, 2]. At present, the best known (and studied) are bacteriorhodopsin (bR), a light sensitive protein whose action is related to a proton pump, and some of the G protein-coupled receptors, a large class of proteins that are sensitive to the light or more generally to the capture of single or a few specific molecules (ligands). The activation of a receptor is driven by the capture of an external ligand and starts with a conformational change followed by a biological chain of events finally detected by the brain. The intriguing question is whether this biological chain of detection could be replaced by an electrical chain monitored by the change of an electrical property of the single protein induced by the change of conformation. To answer this question, the investigation of the electrical properties of a protein is the essential step.
To this purpose, we mention recent experiments on the current-voltage (I-V) characterization of bR monolayers sandwiched between metallic contacts[4, 5]. Measurements were carried out in dark and when the sample was irradiated with a green light to which bR is sensitive. At increasing voltages, the current was found to exhibit a superlinear behavior which is common to both the illumination conditions. Furthermore, for each voltage value, the current is found to be significantly enhanced up to about a factor of three by the presence of light. These results, besides confirming the very low electrical conductivity of bR, suggest an underlying tunneling mechanism of charge transport[6, 7]. On the other hand (most interesting for technological applications), following the I-V response, it is possible to monitor the protein activation, i.e., the conformational change. By implementing an atomic force microscope (AFM) technique, I-V measurements on bR were extended to higher applied voltages (near to about 10 V) where a cross over from direct to injection (or Fowler Nordheim) tunneling regime was evident[8, 9]. On the same subject, recent electrical experiments have been performed on the rat olfactory receptor (OR) OR I7 and on the human OR 17-40 properly deposited on a functionalized gold substrate with the technique of molecular self-assembly. These measurements[10, 11] showed the possibility to monitor the sensing action of the protein and, in turn, their conformational change by means of the modification of the electrochemical impedance spectrum in the presence of a controlled flux of specific odorants (heptanal, octanal). From a theoretical side, a microscopic interpretation of all these experiments is still a challenging issue.
The aim of the present work is to report on a microscopic model, recently developed by the authors[3, 12–16], which is able to interpret the electrical properties of a single protein and their modifications due to the sensing action in terms of the change of the protein tertiary structure. By implementing an impedance network protein analogue (INPA), the theoretical model is henceforth called INPA model. To this scope, we further included in the model a sequential tunneling mechanism[14–16] able to account for the superlinear I-V characteristics experimentally evidenced in bR and similar proteins at increasing applied voltages. Then, the model is validated on available experiments and its predictability discussed in the perspective of further experimental confirmations.
Model and materials
The INPA model is briefly summarized below. Each protein is associated with a topological network (graph) consisting of nodes and links. Once the tertiary structure of the protein is given by the protein database (PDB) or similarly, the graph reproduces its main features. To this purpose, the nodes are in correspondence with the amino acids, taken as single interacting centers, and their position coincides with the related C α atom. Each couple of nodes is connected with a link when their distance is less than an assigned interacting radius, R C . In this way, the protein network analogue becomes a set of intercrossing spheres of radius R C . In principle, all the values of R C from zero to tens of nanometers (the protein size) are possible. Actually, this value depends on the kind of interaction under consideration[12, 18–20]. In the present case, as interaction, we consider the transfer of charge. Accordingly, R C is taken in the range 5 to 15 Å, as will be detailed in the following. Finally, the network gives a skeleton of the protein topology in a fixed conformation.
where, is the cross-sectional area between the spheres centered on the i j nodes, respectively; li,j is the distance between these centers; ρ is the resistivity taken to be the same for every amino acid with the indicative value, ρ = 1010Ω m (here, the microscopic mechanism responsible of charge transfer is not specified); is the imaginary unit; ε0 is the vacuum permittivity; and ω is the circular frequency of the applied harmonic voltage. The relative dielectric constant pertaining to the couple of i j amino acids, εi,j, is expressed in terms of the intrinsic polarizability of the i j amino acids.
where Vi,j is the potential drop between the i-th and j-th node; m is an electron effective mass (taken as the bare one); e is the electron charge; ℏ is the reduced Planck constant; and Φ is the barrier height. The model has been further implemented to include also injection tunneling.
Comparison between theory and experiments
As anticipated above, the INPA is able to interpret the behavior of the I-V characteristics carried out in bR with an electrode-bilayer-electrode structure and when the protein is illuminated or less by green light. To this purpose, the model is applied to the PDB entries 2NTU (for the native state) and 2NTW (for the activated state of bR). The comparison between theory and experiments proceeds as follows. The theoretical model describes the I-V modifications of a single protein when it undergoes a conformational change. On the other hand, the experimental results are carried out on a macroscopic sample that contains a macroscopic number of proteins. To compare the results, we normalize the current value obtained for the single protein in its native state at 1 V to that of the experiment in dark. For the case of bR, the normalization corresponds to multiply the current of the single protein by a factor 108 to 109. The same normalization factor is used for the single protein in its activated state, which is then compared with the experimental value under green light.
The microscopic modeling of the electrical properties of a sensing protein is briefly reviewed with the objective of providing a unifying theoretical interpretation of available experiments. In this framework, protein tertiary structure plays a primary role. Indeed, by determining the network structure, its conformational change induces the network change and, consequently, the change of the electrical properties of the protein. The possibility to monitor the conformational change by means of electrical measurements is identified as the key point for a better knowledge of charge transport in biological materials and for exploiting new frontiers of application of sensing proteins. The qualitative and quantitative agreements between the numerical results and experiments pose the INPA, implemented to account for a sequential tunneling mechanism of charge transfer, as a physical plausible model to investigate the electrical properties in other proteins pertaining to or less to the receptor family.
LR is full professor in Physics of Matter at the Engineering Faculty of Salento University. JM received a PhD in micro-electronics from Montpellier University and has a post doc position at the Dipartimento di Ingegneria dell’ Innovazione of the Salento University. CP is an associate professor in Physics of Matter at the Science Faculty of Salento University.
The collaboration of Dr. Eleonora Alfinito is deeply acknowledged. This research is carried out within the Bioelectronic Olfactory Neuron Device (BOND) Project sponsored by the Commission of the European Community (CEC) within the 7th Program (grant agreement: 228685-2).
- American Institute of Physics: Olfaction and electronic nose. In Proceeding 13 International Symposium: April 15–17 2009; Brescia, Italy. Edited by: Pardo M, Sberveglieri G. AIP Press; 2009:115–118.Google Scholar
- Bioelectronic Olfactory Neuron Device (BOND): Collaborative project FP7-NMP-2008-SMALL-2, GA number 228685. [http://bondproject.org/] 
- Alfinito E, Millithaler JF, Reggiani L, Zine N, Jaffrezic-Renault N: Topological and electrical properties of 17–40 human olfactory receptor for the realization of a nanobiosensor. RCS Adv 2011, 1: 123–127.Google Scholar
- Jin YD, Friedman N, Sheves M, He T, Cahen D: Bacteriorhodopsin (bR) as an electronic conduction medium: current transport through bR-containing monolayers. PNAS 2006, 103: 8601–8606. 10.1073/pnas.0511234103View ArticleGoogle Scholar
- Jin YD, Friedman N, Sheves M, Cahen D: Bacteriorhodopsin-mnolayer-based planar metal-insulator-metal junctions via mimetic vesicle fusion: preparation, characterization and bio-optoelectronic characteristics. Adv Funct Mater 2007, 17: 1417–1428. 10.1002/adfm.200600545View ArticleGoogle Scholar
- Simmons JG: Generalized formula for the elctron tunnel effect between similar electrodes separated by a thin insulating film. J Appl Phys 1963, 34: 1793–1803. 10.1063/1.1702682View ArticleGoogle Scholar
- Wang W, Lee T, Reed WA: Electron tunnelling in self-assembled monolayers. Rep Prog Phys 2005, 68: 523–544. 10.1088/0034-4885/68/3/R01View ArticleGoogle Scholar
- Casuso I, Fumagalli L, Samitier J, Padrós E, Reggiani L, Akimov V, Gomila G: Electron transport through supported biomembranes at the nanoscale by conductive atomic force microscopy. Nanotechnology 2007, 18: 465503–465511. 10.1088/0957-4484/18/46/465503View ArticleGoogle Scholar
- Casuso I, Fumagalli L, Samitier J, Padrós E, Reggiani L, Akimov V, Gomila G: Nanoscale electrical conductivity of the purple membrane monolayer. Phys Rev E 2007, 76: 041919–041924.View ArticleGoogle Scholar
- Hou Y, Helali S, Zhang A, Jaffrezic-Renault N, Martelet C, Minic J, Gorojankina T, Persuy M-A, Pajot-Augy E, Salesse R, Bessueille F, Samitier J, Errachid A, Akimov V, Reggiani L, Pennetta C, Alfinito E: Immobilization of rhodopsin on a self-assembled multilayer and its specific detection by electrochemical impedance spectroscopy. Biosens Bioelectron 2006, 21: 1393–1402. 10.1016/j.bios.2005.06.002View ArticleGoogle Scholar
- Hou Y, Jaffrezic-Renault N, Martelet C, Zhang A, Minic J, Gorojankina T, Persuy M-A, Pajot-Augy E, Salesse R, Akimov V, Reggiani L, Pennetta C, Alfinito E, Ruiz O, Gomila G, Samitier J, Errachid A: A novel detection strategy for odorant molecules based on controlled bioengineering of rat olfactory receptor I7. Biosens Bioelectron 2007, 22: 1550–1555. 10.1016/j.bios.2006.06.018View ArticleGoogle Scholar
- Alfinito E, Pennetta C, Reggiani L: A network model to correlate conformational change and the impedance spectrum of single proteins. Nanotechnology 2008, 19: 065202–065214. 10.1088/0957-4484/19/6/065202View ArticleGoogle Scholar
- Alfinito E, Pennetta C, Reggiani L: Topological change and impedance spectrum of rat olfactory I7: a comparative analysis with bovine rhodopsin and bacteriorhodopsin. J Appl Phys 2009, 105: 084703–084708. 10.1063/1.3100210View ArticleGoogle Scholar
- Alfinito E, Reggiani L: Detecting conformational change by current transport in bacteriorhodopsin. Europhys Lett 2009, 85: 68002–68008. 10.1209/0295-5075/85/68002View ArticleGoogle Scholar
- Alfinito E, Reggiani L: The role of topology in electrical properties of bR and rat-olfactory receptor. Phys Rev E 2010, 81: 032902–032905.View ArticleGoogle Scholar
- Alfinito E, Millithaler J-F, Reggiani L: Charge transport in purple membrane monolayers: a sequential tunneling approach. Phys Rev E 2011, 83: 042902–042905.View ArticleGoogle Scholar
- Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The protein deata bank. Nucleic Acids Res 2000, 28: 235–242. 10.1093/nar/28.1.235View ArticleGoogle Scholar
- Tirion MM: Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996, 77: 1905–1908. 10.1103/PhysRevLett.77.1905View ArticleGoogle Scholar
- Micheletti C, Carloni P, Maritan A: Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models. Proteins 2004, 55: 635–647. 10.1002/prot.20049View ArticleGoogle Scholar
- Juanico B, Sanejouand YH, Piazza F, De Los Rios P: Discrete breathers in nonlinear network models of proteins. Phys Rev Lett 2007, 99: 238104–238107.View ArticleGoogle Scholar
- Pennetta C, Akimov V, Alfinito E, Reggiani L, Gorojankina T, Minic J, Pajot E, Persuy MA, Salesse R, Casuso I, Errachid A, Gomila G, Ruiz O, Samitier J, Hou Y, Jaffrezic N, Ferrari G, Fumagalli L, Sampietro M: Towards the realization of nanobiosensors based on G-protein-coupled receptors. In Nanodevices for the Life Sciences (Nanotechnology of the Life Science). Volume 4. Edited by: Kumar CSSR. Weinheim: Wiley-VCH; 2006:217–240.Google Scholar
- Hianik T: Biological membranes and membrane mimics. In Bioelectrochemistry: Fundamentals, Experimental Techniques and Applications. Edited by: Bartlett PN. England: Wiley J & Sons; 2008:87–148.View ArticleGoogle Scholar
- Benilova IV, Vidic M, Pajot-Augy E, Soldatkin AP, Martelet C, Jaffrezic-Renault N: Electrochemical study of human olfactory receptor OR 17–40 stimulation by odorants in solution. Mater Sci Eng C 2008, 28: 633–639. 10.1016/j.msec.2007.10.040View ArticleGoogle Scholar
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