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Teraherz vibrational spectroscopy of E. coli and molecular constituents: Computational modeling and experiment

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DOI: 10.4236/abb.2013.43A065    4,562 Downloads   7,603 Views   Citations

ABSTRACT

In this paper we present the results of our research of E. coli cells and cellular components, DNA and protein thioredoxin, using highly resolved sub-Terahertz (THz) vibrational spectroscopy. In this combined research, the results from experimental spectroscopy are analyzed via molecular dynamics (MD) simulation of vibrational modes and absorption spectra from E. coli cells and constituents in the sub-THz range. Simplified models of DNA macromolecules with a short sequencing have been constructed for several E. coli strains with the goal to predict their absorption spectra. The similarity between spectral characteristics of E. coli cells and cellular components observed in experiments helps us to better understand the mechanism of material interaction with THz radiation and to add genetic information to the characteristic signatures from biological objects. Modeling results supported by experimental characterization using a spectroscopic sensor prototype developed and built by Vibratess confirm that an optical, label and reagent free technique can be used to examine, detect, and identify bacterial cells with high accuracy and selectivity to the level of strains.

Conflicts of Interest

The authors declare no conflicts of interest.

Cite this paper

Globus, T. , Sizov, I. and Gelmont, B. (2013) Teraherz vibrational spectroscopy of E. coli and molecular constituents: Computational modeling and experiment. Advances in Bioscience and Biotechnology, 4, 493-503. doi: 10.4236/abb.2013.43A065.

References

[1] Finlay, B.B. (2010) The art of bacterial warfare. Scientific American, 302, 56-63. doi:10.1038/scientificamerican0210-56
[2] Globus, T., Moyer, A., Gelmont, B., Khromova, T., Lvovska, M., Sizov, I. and Ferrance, J. (2012) Highly resolved sub-Terahertz vibrational spectroscopy of biological macromolecules and cells. IEEE Sensors Journal, 13, 72-79. doi:10.1109/JSEN.2012.2224333
[3] Globus, T., Woolard, D., Crowe, T.W., Khromova, T., Gelmont, B. and Hessler J. (2006) Terahertz fourier transform characterization of biological materials in a liquid phase. Journal of Physics D: Applied Physics, 39, 3405-3413. doi:10.1088/0022-3727/39/15/028
[4] Globus, T., Dorofeeva, T., Sizov, I., Gelmont, B., Lvovska, M., Khromova, T., Chertihin, O. and Koryakina Y. (2012) Sub-THz vibrational spectroscopy of bacterial cells and molecular components. American Journal of Biomedical Engineering, 2, 143-154.
[5] Bykhovski, A., Globus, T., Khromova, T., Gelmont, B., Woolard, D.L. and Bykhovskaia, M. (2006) An analysis of the THz frequency signatures in the cellular components of biological agents. SPIE Defense and Security Symposium, 6212, 132-141.
[6] Alijabbari, N., Chen, Y., Sizovm I., Globus, T. and Gelmont, B. (2012) Molecular dynamics modeling of the subTHz vibrational absorption of thioredoxin from E. coli. Journal of Molecular Modeling, 18, 2209-2218. doi:10.1007/s00894-011-1238-6
[7] Sizov, I., Gelmont, B. and Globus, T. (2011) Statistical model for E. coli DNA sequence using Monte-Carlo technique for Markov chain. Study of sub-THz molecular vibrations. DTRA CBD S&T Conference, Las-Vegas, 5 October 2011.
[8] Bykhovski, A., Li, X., Globus, T., Khromova, T., Gelmont, B., Woolard, D., Samuels, A. and Jensen, J. (2005) THz absorption signature detection of genetic material of E. coli and B. subtilis. SPIE Proceedings of Chemical and Biological Standoff Detection III, 5995, 2005.
[9] Bykhovski, A., Globus, T., Khromova, T., Gelmont, B. and Woolard, D. (2007) Resonant Terahertz spectroscopy of bacterial thioredoxin in water: Simulation and experiment. ISSSR-Proceedings, 888-896.
[10] Globus, T. (2010) Low-Terahertz resonance spectroscopy for fingerprinting of biological and organic materials. DTRA CBD S&T Conference, Orlando, 15-19 November 2010.
[11] Globus, T., Bykhovskaia, M., Woolard, D. and Gelmont, B. (2003) Sub-millimeter wave absorption spectra of artificial RNA molecules. Journal of Physics D: Applied Physics, 36, 1314-1322. doi:10.1088/0022-3727/36/11/312
[12] Globus, T., Woolard, D., Bykhovskaia, M., Gelmont, B., Werbos, L. and Samuels, A. (2003) THz spectroscopic sensing of DNA and related biological materials. International Journal of High Speed Electronics, 13, 903. doi:10.1142/S0129156403002083
[13] Bykhovskaia, M., Gelmont, B., Globus, T., Woolard, D., Samuels, A., Ha-Duong, T. and Zakrzewska, K. (2001) Prediction of DNA far IR absorption spectra basing on normal mode analysis. Theoretical Chemistry Accounts, 106, 22-27. doi:10.1007/s002140100259
[14] Globus, T., Bykhovskaia, M., Gelmont, B. and Woolard, D. (2001) Far-infrared phonon modes of selected RNA molecules. Proceedings of SPIE, Instrumentation for Air Pollution and Global Atmospheric Monitoring, 4574, 119. doi:10.1117/12.455149
[15] Li, X., Globus, T., Gelmont, B., Salay, L. and Bykhovski, A. (2008) Terahertz absorption of DNA decamer duplex. The Journal of Physical Chemistry A, 112, 12090-12096. doi:10.1021/jp806630w
[16] Heilweil, E.J. and Plusquelic, D.F. (2008) Terahertz spectroscopy of biomolecules, In: Terahertz Spectroscopy, CRC Press, Taylor & Francis Group, LLC, London and New York, 269-297.
[17] Plusquellic, D.F., Siegrist, K., Heilweil, E.J. and Esenturk, O. (2007) Applications of Terahertz spectroscopy in biosystems. ChemPhysChem, 8, 2412-2431. doi:10.1002/cphc.200700332
[18] Zhang, H., Siegrist, K., Douglas, K.O., Gregurick, S.K. and Plusquellic, D.F. (2008) THz investigations of condensed phase biomolecular systems. Methods in Cell Biology, 90, 417-434. doi:10.1016/S0091-679X(08)00818-2
[19] Korter, T.M. and Plusquellic, D.F. (2004) Continuouswave Terahertz spectroscopy of biotin: Vibrational anharmonicity in the far-infrared. Chemical Physics Letters, 385, 45-51. doi:10.1016/j.cplett.2003.12.060
[20] Li, T., Hassanali, A.A., Kao, Y.T., Zhong, D. and Singer S.J. (2007) Hydration dynamics and time scales of coupled water-protein fluctuations. Journal of the American Chemical Society, 129, 3376-3382. doi:10.1021/ja0685957
[21] Furse, K.E. and Corcelli, S.A. (2010) Molecular dynamics simulations of DNA solvation dynamics. The Journal of Physical Chemistry Letters, 1, 1813-1820. doi:10.1021/jz100485e
[22] Qiu, W., Wang, L., Lu, W., Boechler, A., Sanders, D.A.R. and Zhong, D. (2007) Dissection of complex protein dynamics in human thioredoxin. Proceedings of the National Academy of Sciences of the United States of America, 104, 5366-5371. doi:10.1073/pnas.0608498104
[23] Globus, T., Moyer, A., Gelmont, B., Sizov, I. and Khromova, T. (2011) Dissipation time in molecular dynamics and discriminative capability for sub-Terahertz spectroscopic characterization of bio-simulants. DTRA CBD S&T Conference, Las-Vegas, 14-18 November 2011.
[24] Globus, T., Moyer, A., Gelmont, B., Lichtenberger, A., Ferrance, J., Weikle, R. and Lvovska, M. (2011) Sub-Terahertz spectroscopy of bio-materials with high spectral and spatial resolution. Nano DDS, Salt Lake City, 2011.
[25] Parthasarathy, R., Bykhovski, A., Gelmont, B., Globus, T., Swami, N. and Woolard, D.L. (2007) Enhanced coupling of sub-Terahertz radiation with semiconductor periodic slot arrays, Physical Review Letters, 98, Article ID: 153906. doi:10.1103/PhysRevLett.98.153906
[26] Gelmont, B., Parthasarathy, R., Globus, T., Bykhovski, A. and Swami, N. (2008) Terahertz (THz) electromagnetic field enhancement in periodic subwavelength structures. IEEE Sensors Journal, 8, 791-796. doi:10.1109/JSEN.2008.923222
[27] Gelmont, B. and Globus, T. (2011) Edge effect in perfectly conducting periodic subwavelength structures. IEEE Transactions on Nanotechnology, 10, 83-87. doi:10.1109/TNANO.2010.2064785
[28] Gelmont, B., Globus, T., Bykhovski, A., Lichtenberger, A., Swami, N., Parthasarathy, R. and Weikle, R. (2012) Method of local electro-magnetic field enhancement of Terahertz (THz) radiation in sub wavelength regions and improved coupling of radiation to materials through the use of the discontinuity edge effect. US Patent No. 8309930.
[29] Woolard, D., Brown, E., Pepper, M. and Kemp, M. (2005) Terahertz frequency sensing and imaging: A time of reckoning future applications? Proceedings of the IEEE, 93, 1722. doi:10.1109/JPROC.2005.853539
[30] Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham III, T.E., Wang, J., Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Tsui, V., Gohlke, H., Radmer, R.J., Duan, Y., Pitera, J., Massova, I., Seibel, G.L., Singh, U.C., Weiner, P.K. and Kollman, P.A. (2004) AMBER 8. University of California, San Francisco.
[31] Case, D.A., Darden, T.A., Cheatham III, T.E., Simmerling, C.L., Wang, J., Duke, R.E., Luo, R., Crowley, M., Ross, W.S., Zhang, W., Merz, K.M., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossváry, I., Wong, K.F., Paesani, F., Vanicek, J., Wu, X., Brozell, S.R., Steinbrecher, T., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Mathews, D.H., Seetin, M.G., Sagui, C., Babin, V. and Kollman, P.A. (2008) AMBER 10. University of California, San Francisco.
[32] Likic, V.A., Gooley, P.R., Speed, T.P. and Strehler, E.E. (2005) A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics. Protein Science, 14, 2955-2963. doi:10.1110/ps.051681605
[33] Lewars, B.G. (2003) Computational chemistry: Introduction to the theory and applications of molecular and quantum mechanics. Springer, Berlin.
[34] Bykhovski, A., Globus, T., Khromova, T., Gelmont, B. and Woolard, D. (2008) Resonant Terahertz Spectroscopy of Bacterial Thioredoxin in Water: Simulation and Experiment. In: Selected Topics in Electronics and Systems. Spectral Sensing Research for Water Monitoring Applications and Frontier Science and Technology for Chemical, Biological and Radiological Defense. World Scientific Publishing Co., Singapore City, 48, 367-375.
[35] Globus, T., Alijabbary, N., Chen, Y., Sizov, I. and Gelmont, B. (2010) Molecular dynamics modeling of subTHz vibrational absorption of thioredoxin from E. coli. DTRA CBD S&T Conference, Orlando, 15-19 November 2010.
[36] Karplus, M. and Kushick, J.N. (1981) Method for estimating the configurational entropy of macromolecules. Macromolecules, 14, 325-332. doi:10.1021/ma50003a019
[37] Levy, R.M., Karplus, M., Kushick, J. and Perahia, D. (1984) Evaluation of the configurational entropy for proteins: Application to molecular dynamics simulations of an alfa-helix. Macromolecules, 17, 1370-1374. doi:10.1021/ma00137a013
[38] Durbin, R., Eddy, S., Krogh, A. and Mitchison, G. (1998) Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, 368.
[39] Ching, W.-K., Ng, M.K. and Ching, W. (2005) Markov chains: Models, algorithms and applications. Springer, 208.
[40] Studier, F.W. and Moffatt, B.A. (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. Journal of Molecular Biology, 189, 113-130. doi:10.1016/0022-2836(86)90385-2
[41] Grodberg, J. and Dunn, J.J. (1988) ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification. Journal of Bacteriology, 170, 245-253.
[42] Phillips, T.A., VanBogelen, R.A. and Neidhardt, F.C. (1984) Lon gene product of Escherichia coli is a heat-shock protein. Journal of Bacteriology, 159, 283-287.
[43] Welch, R.A., Burland, V., Plunkett III, G., Redford, P., Roesch, P., Rasko, D., Buckles, E.L., Liou, S.-R., Boutin, A., Hackett, J., Stroud, D., Mayhew, G.F., Rose, D.J., Zhou, S., Schwartz, D.C., Perna, N.T., Mobley, H.L.T., Donnenberg, M.S. and Blattner, F.R. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 99, 17020-17024. doi:10.1073/pnas.252529799
[44] Kendall, M.M., Gruber, C.C., Rasko, D.A., Hughes, D.T. and Sperandio, V. (2011) Hfq virulence regulation in enterohemorrhagic Escherichia coli O157:H7 strain 86-24. Journal of Bacteriology, 193, 6843-6851. doi:10.1128/JB.06141-11

  
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