Electrical properties of the protein molecule in two - terminal device
Keywords:
proteins, impedance, aminoacids, complex networks, electrical properties, conformational changes
Abstract
Here we present a mathematical model of the single protein molecule in two-terminal device as complex irregular impedance network. It is applied for the prediction of the response of the electronic nanobiosensor based on the single molecule of G-protein coupled receptor (GPCR) family protein. The protein molecule is modeled as a complex network of elementary impedances where nodes correspond to alpha-carbon atoms of the protein aminoacids residues, and links correspond to some electrical interaction between them. Links connect each pair of aminoacids close enough in space and each link corresponds to an elementary impedance. The impedance value depends on the kin of the corresponding pair of aminoacids and distance between them. Correspondingly, conformational changes of the GPCR molecule transmit to the variation of its electrical properties. The change of rhodopsin molecule impedance with photon capture is calculated. The results for the different values of model parameters are presented and discusse.
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References
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Tzong-Zeng Wu. A piezoelectric biosensor as an olfactory receptor for odour detection: electronic nosc. Biosensors and Bioelectronics. 1999;14:9-18.
Joachim C, Gimzewski JK, Aviram A. Electronics using hybrid-molecular and mono-molecular devices. Nature. 2000;408:541-8.
Bayley H, Cremer PS. Stochastic sensors inspired by biology. Nature. 2001;413:226-30.
Firestein S. How the olfactory system makes sense of scents. Nature. 2001;413:211-8.
Xie Q, Archontis G, Skourtis SS. Protein electron transfer: a numerical study of tunneling through uctuationg bridges. Chem. Phys. Lett. 1999;12:237-46.
Bezrukov SM, Winterhalter W. Examining noise sources at the single-molecule level: l/f noise of an open maltoporin channel. Phys. Rev. Lett. 2000;85:202-5.
Lameh J, Cone RI, Maeda S, Philip M, Corbani M, N’adasdi L, et al. Structure and function of G protein coupled receptors. Pharmaceutical Research. 1990;7:1213-21.
Shacham S, Topf M, Avisar N, Glaser F, Marantz Y, Bar-Haim S, et al. Modeling the 3D structure of GPCRs from sequence. Medical RFesearch Reviews. 2001;21:472-83.
Vaidehi N, Floriano WB, Trabanino R, Hall SE, Freddolino P, Choi EJ, et al. Prediction of structure and function of G protein coupled receptors. PNAS. 2002;99:12622-7.
Chou KC, Elrod DW. Bioinformatical analysis of G-protein-coupled receptors. Journal of Proteome Research. 2002;1:429-33.
Gether U, Kobilka BK. G protein-coupled receptors. Journ. Bio. Chem. 1998;273:17979-82.
Palezewski K, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, et al. Crystal structure of Rhodopsin: A G protein- coupled receptor. Science. 2000;289:739-45.
Yaegle PL, Choi G, Albert AD. Studies on the structure of g-protein-coupled receptor rhodopsin including the putative g-protein binding site in unactivated and activated forms. Biochemistry. 2001;40:11932-7.
Choi G, Landin J, Galan JF, Birge RR, Albert AD, Yeagle PL. Structural studies on metharhodopsin II, the activated form of the g-protein coupled receptor rhodopsin. Biochemistry. 2002;41:7318-24.
Sakmar TP, Menon ST, Marin EP, Awad ES. RHODOPSIN: Insights from recent structural studies. Annu. Biomol. Struct. 2002;31:443-82.
Pilpel Y, Lancet D. The variable and conserved interfaces of modeled olfactoty receptor protein. Protein Science. 1999;8:969-77.
Crasto C, Singer MS, Shepherd GM. The olfactory receptor family album. Genome Biology. 2001;2:1027.1-4.
Liu AH, Zhang X, Stolovitzky GA, Califano A, Firestein SJ. Electronics using hybrid-molecular and monomolecular devices. Nature. 2000;408:541-8.
Research Collaboratory for Structural Bioinformatics, Protein data bank, publisher State University of New Jersey. Address http://www.rcsb.org/pdb
Yand H, Luo G, Karnchanaphanurach P, Louie TM, Rech I, Cova S, et al. Protein conformational dynamics probed by single-molecule electron transfer. Sciences. 2003;302:262-6.
Kobilka B, Gether U, Seifert M, Lin S, Ghanouni P. Examination of ligand-induced conformational changes in the beta 2 andrenergic receptor. Life Sciences. 1998;62:1509-12.
Kobilka B, Gether U, Seifert M, Lin S, Ghanouni P. Characterization of ligand-induced conformational states in the beta 2 andrenergic receptor. J. Receptor and Signal Transduction Research. 199;19:293-300.
Xueyu Song. An inhomogeneous model of protein dielectric properties: intrinsic polarizabilities of amino acids. J. Chem. Phys. 2002;116:9359-83.
Rammal R, Tannous C, Tremblay AMS. l/f noise in random resistor networks: fractals and percolating systems. Phys. Rev. A. 1985;31:2662-71.
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. The large-scale organization of metabolic networks. Nature. 2000;407:651-4.
Albert R, Barabasi AL. Statistical mechanics of complex networks. Rev. Mod. Phys. 2002;74:47-97.
Published
2007-06-05
Cited
How to Cite
Akimov, V. I., Shestopalova, A. V., Tulupenko, V. N., Alfinito, E., Penneta, C., & Reggiani, L. (2007). Electrical properties of the protein molecule in two - terminal device. Biophysical Bulletin, 1(18), 23-27. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/12616
Section
Molecular biophysics
Copyright (c) 2007 Biophysical visnik
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