Effect of aqueous medium on low-frequency dynamics, chemical activity and physical properties of a spherical virus

References

• Aggarwal, A., May, E. R., Brooks, C. L., & Klug, W. S. (2016). Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature. Physical Review E, 93(1), 012417. doi: 10.1103/physreve.93.012417
   PubMed Web of Science ®Google Scholar
• Allen, G. L., Bayles, R. A., Gile, W. W., & Jesser, W. A. (1986). Small particle melting of pure metals. Thin Solid Films, 144(2), 297–308. doi: 10.1016/0040-6090(86)90422-0
   Web of Science ®Google Scholar
• Alonso, J. M., Górzny, M. L., & Bittner, A. M. (2013). The physics of tobacco mosaic virus and virus-based devices in biotechnology. Trends in Biotechnology, 31(9), 530–538. doi: 10.1016/j.tibtech.2013.05.013
   PubMed Web of Science ®Google Scholar
• Arrhenius, S. (1889). Über die dissociationswärme und den einfluss der temperatur auf den dissociationsgrad der elektrolyte. Zeitschrift Für Physikalische Chemie, 4(1), 96–116. doi: 10.1515/zpch-1889-0408
   Google Scholar
• Blanco, E., Ruso, J. M., Sabín, J., Prieto, G., & Sarmiento, F. (2007). Thermal stability of lysozyme and myoglobin in the presence of anionic surfactants. Journal of Thermal Analysis and Calorimetry, 87(1), 211–215. doi: 10.1007/s10973-006-7842-5
   Web of Science ®Google Scholar
• Chen, S., & Kucernak, A. (2004). Electrocatalysis under conditions of high mass transport rate: oxygen reduction on single submicrometer-sized Pt particles supported on carbon. The Journal of Physical Chemistry B, 108(10), 3262–3276. doi: 10.1021/jp036831j
   Web of Science ®Google Scholar
• Chung, W.-J., Oh, J.-W., Kwak, K., Lee, B. Y., Meyer, J., Wang, E., … Lee, S.-W. (2011). Biomimetic self-templating supramolecular structures. Nature, 478(7369), 364–368. doi: 10.1038/nature10513
   PubMed Web of Science ®Google Scholar
• Dash, J. G. (1999). History of the search for continuous melting. Reviews of Modern Physics, 71(5), 1737–1743. doi: 10.1103/RevModPhys.71.1737
   Web of Science ®Google Scholar
• Dudowicz, J., Freed, K. F., & Douglas, J. F. (2005). The glass transition temperature of polymer melts. The Journal of Physical Chemistry B, 109(45), 21285–21292. doi: 10.1021/jp0523266
   PubMed Web of Science ®Google Scholar
• Duval, E. (1992). Far-infrared and Raman vibrational transitions of a solid sphere: Selection rules. Physical Review B, 46(9), 5795–5797. doi: 10.1103/PhysRevB.46.5795
   Web of Science ®Google Scholar
• Dykeman, E. C., Sankey, O. F., & Tsen, K. T. (2007). Raman intensity and spectra predictions for cylindrical viruses. Physical Review E, 76(1), 011906–011917. doi: 10.1103/PhysRevE.76.011906
   Web of Science ®Google Scholar
• Dyre, J. C. (2006). Colloquium: The glass transition and elastic models of glass-forming liquids. Reviews of Modern Physics, 78(3), 953–972. doi: 10.1103/RevModPhys.78.953
   Web of Science ®Google Scholar
• Farrant, J. (1970). Mechanisms of injury and protection in living cells and tissues at low temperatures. In A. U. Smith (Ed.), Current trends in cryobiology (p. 139). New York: Plenum; Tappel, A. L. (1966). In H. T. Meryman (Ed.), Cryobiology (p. 163). London: Academic.
   Google Scholar
• Flynn, C. E., Lee, S. W., Peelle, B. R., & Belcher, A. M. (2003). Viruses as vehicles for growth, organization and assembly of materials. Acta Materialia, 51(19), 5867–5880. doi: 10.1016/j.actamat.2003.08.031
   Web of Science ®Google Scholar
• Ford, L. H. (2003). Estimate of the vibrational frequencies of spherical virus particles. Physical Review E, 67, 051924. doi: 10.1103/PhysRevE.67.051924
   Web of Science ®Google Scholar
• Forrest, J. A., Dalnoki-Veress, K., & Dutcher, J. R. (1997). Interface and chain confinement effects on the glass transition temperature of thin polymer films. Physical Review E, 56(5), 5705–5716. doi: 10.1103/PhysRevE.56.5705
   Web of Science ®Google Scholar
• Ghavanloo, E., & Fazelzadeh, S. A. (2015). Nonlocal shell model for predicting axisymmetric vibration of spherical shell-like nanostructures. Mechanics of Advanced Materials and Structures, 22(7), 597–603. doi: 10.1080/15376494.2013.828816
   Web of Science ®Google Scholar
• Górzny, M., Walton, A. S., & Evans, S. D. (2010). Synthesis of high-surface-area platinum nanotubes using a viral template. Advanced Functional Materials, 20(8), 1295–1300. doi: 10.1002/adfm.200902196
   Web of Science ®Google Scholar
• Green, J. L., Fan, J., & Angell, C. A. (1994). The protein-glass analogy: New insight from homopeptide comparisons. The Journal of Physical Chemistry, 98(51), 13780–13790. doi: 10.1021/j100102a052
   Web of Science ®Google Scholar
• Gupta, S. K., Sahoo, S., Jha, P. K., Arora, A. K., & Azhniuk, Y. M. (2009). Observation of torsional mode in CdS1-xSex nanoparticles in a borosilicate glass. Journal of Applied Physics, 106(2), 024307–024314. doi: 10.1063/1.3171925
   Web of Science ®Google Scholar
• Gupta, S. K., Talati, M., & Jha, P. K. (2008). Shape and size dependent melting point temperature of nanoparticles. Materials Science Forum, 570, 132–137. doi: 10.4028/www.scientific.net/MSF.570.132
   Google Scholar
• Jackson, C. L., & McKenna, G. B. (1991). The glass transition of organic liquids confined to small pores. Journal of Non-Crystalline Solids, 131–133(1), 221–224. doi: 10.1016/0022-3093(91)90305-P
   Google Scholar
• Jansson, H., & Swenson, J. (2010). The protein glass transition as measured by dielectric spectroscopy and differential scanning calorimetry. Biochimica et Biophysica Acta - Proteins and Proteomics, 1804(1), 20–26. doi: 10.1016/j.bbapap.2009.06.026
   Web of Science ®Google Scholar
• Jerome, B. (1999). Dynamics of glass-forming materials confined in thin films. Journal of Physics: Condensed Matter, 11(10A), A189–A197. doi: 10.1088/0953-8984/11/10A/014
   Web of Science ®Google Scholar
• Jiang, Q., & Yang, C. C. (2008). Size effect on the phase stability of nanostructures. Current Nanoscience, 4(2), 179–200. doi: 10.2174/157341308784340949
   Web of Science ®Google Scholar
• Jiang, Q., Shi, H. X., & Li, J. C. (1999). Finite size effect on glass transition temperatures. Thin Solid Films, 354(1–2), 283–286. doi: 10.1016/S0040-6090(99)00537-4
   Web of Science ®Google Scholar
• Kahn, D., Kim, K. W., & Stroscio, M. A. (2001). Quantized vibrational modes of nanospheres and nanotubes in the elastic continuum model. Journal of Applied Physics, 89(9), 5107. doi: 10.1063/1.1356429
   Web of Science ®Google Scholar
• Katava, M., Stirnemann, G., Zanatta, M., Capaccioli, S., Pachetti, M., Ngai, K. L., … Paciaroni, A. (2017). Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion. Proceedings of the National Academy of Sciences of the United States of America, 114(35), 9361–9366. doi: 10.1073/pnas.1707357114
   PubMed Web of Science ®Google Scholar
• Khodadadi, S., Malkovskiy, A., Kisliuk, A., & Sokolov, A. P. (2010). A broad glass transition in hydrated proteins. Biochimica et Biophysica Acta - Proteins and Proteomics, 1804(1), 15–19. doi: 10.1016/j.bbapap.2009.05.006
   Web of Science ®Google Scholar
• Koga, K., Ikeshoji, T., & Sugawara, K. I. (2004). Size- and temperature-dependent structural transitions in gold nanoparticles. Physical Review Letters, 92(11), 115507–115511. doi: 10.1103/PhysRevLett.92.115507
   PubMed Web of Science ®Google Scholar
• Koh, Y. P., McKenna, G. B., & Simon, S. L. (2006). Calorimetric glass transition temperature and absolute heat capacity of polystyrene ultrathin films. Journal of Polymer Science Part B: Polymer Physics, 44(24), 3518–3527. doi: 10.1002/polb.21021
   Web of Science ®Google Scholar
• Kresten, L. L., Piana, S., Dror, R. O., & Shaw, D. E. (2011). How fast-folding proteins fold. Science, 334(6055), 517–520. doi: 10.1126/science.1208351
   PubMed Web of Science ®Google Scholar
• Ku, T., Lu, P., Chan, C., Wang, T., Lai, S., Lyu, P., & Hsiao, N. (2009). Predicting melting temperature directly from protein sequences. Computational Biology and Chemistry, 33(6), 445–450. doi: 10.1016/j.compbiolchem.2009.10.002
   PubMed Web of Science ®Google Scholar
• Lamb, H. (1882). On the Vibrations of an Elastic Sphere. Proceedings of the London Mathematical Society, 1, 189–212. doi: 10.1112/plms/s1-14.1.50
   Google Scholar
• Lee, W. A., & Knight, G. J. (1970). Ratio of the glass transition temperature to the melting point in polymers. British Polymer Journal, 2(1), 73–80. doi: 10.1002/pi.4980020112
   Google Scholar
• Leslie, S. B., Israeli, E., Lighthart, B., Crowe, J. H., & Crowe, L. M. (1995). Trehalose and sucrose protect both membranes and proteins in intact bacteria during drying. Applied and Environmental Microbiology, 61(10), 3592–3597. URL: https://aem.asm.org/content/61/10/3592.
   PubMed Web of Science ®Google Scholar
• Lošdorfer Božič, A., & Šiber, A. (2018). Electrostatics-driven inflation of elastic icosahedral shells as a model for swelling of viruses. Biophysical Journal, 115(5), 822–829. doi: 10.1016/j.bpj.2018.07.032
   PubMed Web of Science ®Google Scholar
• Lu, H. M., & Meng, X. K. (2010). Morin temperature and Néel temperature of hematite nanocrystals. The Journal of Physical Chemistry C, 114(49), 21291–21295. doi: 10.1021/jp108703b
   Web of Science ®Google Scholar
• Mallamace, F., Corsaro, C., Mallamace, D., Vasi, S., Vasi, C., Baglioni, P., … Stanley, H. E. (2016). Energy landscape in protein folding and unfolding. Proceedings of the National Academy of Sciences of the United States of America, 113(12), 3159–3163. doi: 10.1073/pnas.1524864113
   PubMed Web of Science ®Google Scholar
• Mamedov, K. K., Abdullaev, A. B., Shalumov, B. Z., Mekhtiev, M. I., Alyanov, M. A., & Gumbatov, D. O. (1987). Low‐temperature heat capacity and thermodynamic properties of silicon‐dioxide‐based binary vitreous systems. Physica Status Solidi (A), 99(2), 413–421. doi: 10.1002/pssa.2210990211
   Web of Science ®Google Scholar
• May, E. R. (2014). Recent developments in molecular simulation approaches to study spherical virus capsids. Molecular Simulation, 40(10-11), 878–888. doi: 10.1080/08927022.2014.907899
   PubMed Web of Science ®Google Scholar
• Monkos, K. (2015). Determination of the glass-transition temperature of proteins from a viscometric approach. International Journal of Biological Macromolecules, 74, 1–4. doi: 10.1016/j.ijbiomac.2014.11.029
   PubMed Web of Science ®Google Scholar
• Morozov, V. N., & Gevorkian, S. G. (1985). Low‐temperature glass transition in proteins. Biopolymers, 24(9), 1785–1799. doi: 10.1002/bip.360240909
   Web of Science ®Google Scholar
• Murray, D. B., & Saviot, L. (2007). Damping by bulk and shear viscosity for confined acoustic phonons of a spherical virus in water. Journal of Physics: Conference Series, 92(1), 012036–012040. doi: 10.1088/1742-6596/92/1/012036
   Google Scholar
• Nanda, K. K. (2009). Size-dependent melting of nanoparticles: Hundred years of thermodynamic model. Pramana, 72(4), 617–628. doi: 10.1007/s12043-009-0055-2
   Web of Science ®Google Scholar
• Pankhurst, Q. A., Connolly, J., Jones, S. K., & Dobson, J. (2003). Applications of magnetic nanoparticles in biomedicine. Journal of Physics D: Applied Physics, 36(13), R167–R181. doi: 10.1088/0022-3727/36/13/201
   Web of Science ®Google Scholar
• Park, H., Heldman, N., Rebentrost, P., Abbondanza, L., Iagatti, A., Alessi, A., … Belcher, A. M. (2016). Enhanced energy transport in genetically engineered excitonic networks. Nature Materials, 15(2), 211–216. doi: 10.1038/nmat4448
   PubMed Web of Science ®Google Scholar
• Pauling, L. (1948). Nature of forces between large molecules of biological interest. Nature, 161(4097), 707–709. doi: 10.1038/161707a0
   PubMed Web of Science ®Google Scholar
• Qi, W. H., & Wang, M. P. (2005). Size- and shape-dependent superheating of nanoparticles embedded in a matrix. Materials Letters, 59(18), 2262–2266. doi: 10.1016/j.matlet.2004.06.079
   Web of Science ®Google Scholar
• Raichura, A., Dutta, M., & Stroscio, M. A. (2003). Quantized acoustic vibrations of single-wall carbon nanotube. Journal of Applied Physics, 94(6), 4060. doi: 10.1063/1.1600846
   Web of Science ®Google Scholar
• Sartor, G., Mayer, E., & Johari, G. P. (1994). Calorimetric studies of the kinetic unfreezing of molecular motions in hydrated lysozyme, hemoglobin, and myoglobin. Biophysical Journal, 66(1), 249–258. doi: 10.1016/S0006-3495(94)80774-X
   PubMed Web of Science ®Google Scholar
• Shenton, W., Douglas, T., Young, M., Stubbs, G., & Mann, S. (1999). Inorganic-organic nanotube composites from template mineralization of tobacco mosaic virus. Advanced Materials, 11(3), 253–256. doi: 10.1002/(SICI)1521-4095(199903)11:3 < 253::AID-ADMA253 > 3.0.CO;2-7
   Web of Science ®Google Scholar
• Shi, F. G. (1994). Size dependent thermal vibrations and melting in nanocrystals. Journal of Materials Research, 9(5), 1307–1314. doi: 10.1557/JMR.1994.1307
   Web of Science ®Google Scholar
• Siepi, M., Politi, J., Dardano, P., Amoresano, A., De Stefano, L., Monti, D. M., & Notomista, E. (2017). Modified denatured lysozyme effectively solubilizes fullerene c60 nanoparticles in water. Nanotechnology, 28(33), 335601–335616. doi: 10.1088/1361-6528/aa744e
   PubMed Web of Science ®Google Scholar
• Steinbach, P. J., & Brooks, B. R. (1993). Protein hydration elucidated by molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America, 90(19), 9135–9139. doi: 10.1073/pnas.90.19.9135
   PubMed Web of Science ®Google Scholar
• Stillinger, F. H., & Stillinger, D. K. (1990). Computational study of transition dynamics in 55-atom clusters. Journal of Chemical Physics, 93(8), 6013–6024. doi: 10.1063/1.459488
   Web of Science ®Google Scholar
• Sun, J., & Simon, S. L. (2007). The melting behavior of aluminum nanoparticles. Thermochimica Acta, 463(1–2), 32–40. doi: 10.1016/j.tca.2007.07.007
   Web of Science ®Google Scholar
• Talati, M., & Jha, P. K. (2006). Acoustic phonon quantization and low-frequency Raman spectra of spherical viruses. Physical Review E, 73(1), 011901–011907. doi: 10.1103/PhysRevE.73.011901
   Web of Science ®Google Scholar
• Terki, F., Levelut, C., Prat, J. L., Boissier, M., & Pelous, J. (1997). Low-frequency dynamics in an optical strong glass: Vibrational and relaxational contributions. Journal of Physics: Condensed Matter, 9(19), 3955–3971. doi: 10.1088/0953-8984/9/19/015
   Web of Science ®Google Scholar
• Teslyuk, I., Vasylkiv, Y., Nastishin, Y., & Vlokh, R. (2007). Structural phase transition in lysozyme crystals. Ferroelectrics, 346(1), 49–55. doi: 10.1080/00150190601180216
   Web of Science ®Google Scholar
• Tsen, K. T., Dykeman, E. C., Sankey, O. F., Lin, N. T., Tsen, S. W., & Kiang, J. G. (2006). Observation of the low frequency vibrational modes of bacteriophage M13 in water by Raman spectroscopy. Virology Journal, 3(1), 79–90. [Mismatch] doi: 10.1186/1743-422X-3-79
   PubMedGoogle Scholar
• Zhang, C. Y., & Zhang, N. H. (2018). Influence of Microscopic Interactions on the Flexible Mechanical Properties of Viral DNA. Biophysical Journal, 115(5), 763–772. doi: 10.1016/j.bpj.2018.07.023
   PubMed Web of Science ®Google Scholar
• Zheng, K., Lu, M., Liu, Y., Chen, Q., Taccardi, N., Hüser, N., & Boccaccini, A. R. (2016). Monodispersed lysozyme-functionalized bioactive glass nanoparticles with antibacterial and anticancer activities. Biomedical Materials, 11(3), 035012–035025. doi: 10.1088/1748-6041/11/3/035012
   PubMed Web of Science ®Google Scholar
• Zhong, C., Wang, Y., Ma, G., & Li, R. (2016). Measurement of the onset temperature of irreversible inactivation of proteins using FITC as a fluorescent reporter. Analytical Methods, 8(18), 3809–3815. doi: 10.1039/C5AY03234B
   Web of Science ®Google Scholar
• Zhou, Y., Vitkup, D., & Karplus, M. (1999). Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state. Journal of Molecular Biology, 285(4), 1371–1375. doi: 10.1006/jmbi.1998.2374
   PubMed Web of Science ®Google Scholar