Gunma University
Faculty of Engineering
Department of Chemistry and Chemical Biology
Biomolecular Science Laboratory (Sonoyama Group)

Original Papers

2006-Present

  1. Yokoyama, Y., Yamada, K., Higashi, Y., Ozaki, S., Wang, H., Koito, N., Watanabe, N., Sonoyama, M. and Mitaku, S. (2014)
    Dependence of purple membrane bump curvature on pH and ionic strength analyzed using atomic force microscopy combined with solvent exchange
    J. Phys. Chem. B 118, 9322-9328.
  2. Hasegawa, T., Shimoaka, T., Shioya, N., Morita, K., Sonoyama, M., Takagi, T., and Kanamori, T. (2014)
    Stratified dipole-arrays model accounting for perfluoroalkyl compounds-specific bulk properties
    ChemPlusChem, in press.
  3. Yoshino, M., Kikukawa, T., Takahashi, H., Takagi, T., Yokoyama, Y., Amii, H., Baba, T., Kanamori, T., and Sonoyama, M.
    hysicochemical studies of bacteriorhodopsin reconstituted in partially fluorinated phosphatidylcholine bilayers
    J. Phys. Chem. B 117, 5422-5429.
  4. Takahashi, H., Yoshino, M., Takagi, T., Amii, H., Baba, T., Kanamori, T., and Sonoyama, M. (2013)
    Non-ideal mixing of dimyristoylphosphatidylcholine with its partially fluorinated analogue in hydrated bilayers
    Chem. Phys. Lett. 559, 107-111.
  5. Yoshino, M., Takahashi, H., Takagi, T., Baba, T., Morita, K., Amii, H., Kanamori, T., and Sonoyama, M. (2012)
    Effect of partial fluorination in the myristoyl groups on thermal and interfacial properties of dimyristoylphosphatidylcholine
    Chem. Lett. 41, 1495-1497.
  6. Asada, A., and Sonoyama, M. (2011)
    Solubilizaiotn and structural stability of bacteriorhodopsin with a mild nonionic detergent n-octyl-β-thioglucoside
    Biosci. Biotech. Biochem. 75, 376-378.
  7. Yokoyama, Y., Negishi, L., Kitoh, T., Sonoyama, M., Asami, Y., and Mitaku, S. (2010)
    Effect of lipid phase transition on molecular assembly and structural stability of bacteriorhodopsin reconstituted into phosphatidylcholine liposomes with different acyl-chain lengths
    J. Phys. Chem. B. 114, 15706-15711.
  8. Sonoyama, M., Fukumoto, M., and Kuwabara, Y. (2010)
    Highly stable solubilization of membrane protein bacteriorhodopsin with a short chain phospholipid diheptanoylphosphatidylcholine
    Chem. Lett. 39, 876-877. [Editor's choice]
  9. Yokoyama, Y., Sonoyama, M., and Mitaku, S. (2010)
    Structural changes of bacteriorhodopsin in purple membranes induced by irreversible photobleaching with heterogeneous and homogeneous stability
    Photochem. Photobiol. 86, 297-301.
  10. Sonoyama, M., Kikukawa, T., Yokoyama, Y., Demura, M., Kamo, N., and Mitaku, S. (2009)
    Effect of molecular assembly on photocycle of reconstituted bacteriorhodopsin: Significant blue shift of the late M photointermediate in the liquid crystalline phase
    Chem. Lett. 38, 1134-135.
  11. Murayama, K., Sonoyama, M., Terada, T., Yokoyama, Y., Nara, M., Tomida, M., and Matsuda, S. (2009)
    Bisphenol A weakens calcium binding affinity of sites III and IV in C-terminal domain of bovine brain calmodulin
    Chem. Lett. 38, 1062-1063.
  12. Uchiyama, T., Sonoyama, M.,Hamada, Y., Dukor, R. K., Nafie, L. A., Hayashi, F., and Oosawa, K. (2008)
    Raman optical activity of flagellar filaments of Salmonella: Unusually intense ROA from L-type self-assembled protein filaments and their possible higher level chiral organization
    Vib. Spectrosc. 48,65-68.
  13. Shibakami, M., Tsuihiji, H., Miyoshi, S., Nakamura, M., Mitaku, S., and Sonoyama, M. (2008)
    Reconstitution of bacteriorhodopsin into cyclic lipid vesicles
    Biosci. Biotech. Biochem. 72, 1623-1625.
  14. Ke, R., Sakiyama, N., Sawada, R., Sonoyama, M., and Mitaku, S. (2008)
    Vertebrate genomes code excess proteins with charge periodicity of 28 residues
    J. Biochem. 143, 661-665.[Abstract]
  15. Imai, K., Asakawa, N., Tsuji, T., Akazawa, F., Ino, A., Sonoyama, M., and Mitaku, S. (2008)
    SOSUI-GramN: high performance prediction for sub-cellular localization of proteins in Gram-negative bacteria
    Bioinformation 2, 417-421.
  16. Ghimire, G. D., Tanizawa, H., Sonoyama, M., and Mitaku, S. (2008)
    Physicochemical properties of GPCR amino acid sequences for understanding GPCR-G-protein coupling
    Chem-Bio. Informatics J. 8, 49-57.
  17. Yokoyama, Y., Sonoyama, M., Nakano, T., and Mitaku, S. (2007)
    Structural change of bacteriorhodopsin in the purple membrane above pH 10 decreases heterogeneity of the irreversible photobleaching components
    J. Biochem. 142, 325-333.
  18. Sakiyama, N., Ke, R., Sawada, R., Sonoyama, M., and Mitaku, S. (2007)
    Nuclear proteins with charge periodicity of 28 residues from vertebrate genomes
    Chem-Bio. Informatics J. 7, 69-78.
  19. Sawada, R., Ke, R., Tsuji, T., Sonoyama, M., and Mitaku, S. (2007)
    Ratio of membrane proteins in total proteomes of prokaryota
    BIOPHYSICS 3, 37-45.
  20. Sakiyama, N., Ke, R., Sawada, R., Sonoyama, M., and Mitaku, S. (2007)
    Nuclear localization of proteins with a charge periodicity of 28 residues Chem-Bio. Informatics J. 7, 35-48.
  21. Ke, R., Sakiyama, N., Sawada, R., Sonoyama, M., and Mitaku, S. (2007) Human genome encodes many proteins with charge periodicity of 28 residues
    Jpn. J. Appl. Phys. 46, 6083-6086.
  22. Kameda, T., Nuzeki, T., and Sonoyama, M. (2007)
    In-situ observation of tryptophan in larval cocoon silk of the hornet Vespa simillima xanthoptera Cameron by ultraviolet resonance Raman spectroscopy
    Biosci. Biotech. Biochem. 71, 1353-1355.
  23. Uchiyama, T., Sonoyama, M., Hamada, Y., Komatsu, M., Dukor, R. K., Nafie, L. A., and Oosawa, K. (2006)
    Raman spectroscopic study on the L-type straight flagellar filament of Salmonella
    Vib. Spectrosc. 42, 192-194.
  24. Sugiyama, H., Sonoyama, M., Ghimire, G. D., and Mitaku, S. (2006)
    Heterogeneity in regeneration of bacteriorhodopsin from bacterio-opsin and all-trans retinal at high temperatures: Implications for dynamic structural fluctuations
    Biosci. Biotech. Biochem. 70, 1350-1355.
  25. Ghimire, G. D., Imai, K., Akazawa, F., Tsuji, T., Sonoyama, M., and Mitaku, S. (2006)
    Physicochemical properties of amino acid sequences of G-proteins for understanding GPCR-G-protein interaction
    Chem-Bio. Informatics J. 6, 1-16.
  26. Endo, O., Furuta, T., Ozaki, H., Sonoyama, M., and Mazaki, Y. (2006)
    Structures of 17,19-hexatriacontadiyne monolayers on Au(111) studied by infrared reflection absorption spectroscopy and scanning tunneling microscopy
    J. Phys. Chem. B 110, 13100-13106.

2001-2005

  1. Uchikoga, N., Takahashi, S. Y., Ke, R. C., Sonoyama, M., and Mitaku, S. (2005)
    Electric charge balance mechanism of extended soluble proteins
    Protein Sci. 14, 74-80.
  2. Sasaki, T., Sonoyama, M., Demura, M., and Mitaku, S. (2005)
    Photobleaching of bacteriorhodopsin solubilized with Triton X-100 Photochem. Photobiol. 81, 1131-1137.
  3. Imai, K., Asakawa, N., Tsuji, T., Sonoyama, M., and Mitaku, S. (2005)
    Secondary structure breakers and hair-pin structures in myoglobin and hemoglobin
    Chem-Bio. Informatics J. 5, 65-77.
  4. Gomi, M., Sawada, R., Sonoyama, M., and Mitaku, S. (2005) Comparative proteomics of the prokaryota using secretary proteins
    Chem-Bio. Informatics J. 5, 56-64.
  5. Ghimire, G. D., Sugiyama, H., Sonoyama, M., and Mitaku, S. (2005)
    Regeneration of bacteriorhodopsin from thermally unfolded bacterio-opsin and all-trans retinal at high temperatures
    Biosci. Biotech. Biochem. 69, 252-254.
  6. Yokoyama, Y., Sonoyama, M., and Mitaku, S. (2004)
    Inhomogeneous stability of bacteriorhodopsin in purple membrane against photobleaching at high temperature
    Proteins 54, 442-454.
  7. Yang, M. Y., Yao, J. M., Sonoyama, M., and Asakura, T. (2004)
    Spectroscopic characterization of heterogeneous structure of Samia cynthia ricini silk fibroin induced by stretching and molecular dynamics simulation
    Macromolecules 37, 3497-3504.
  8. Sonoyama, M., and Mitaku, S. (2004)
    High-temperature intermediate state of bacteriorhodopsin prior to the premelting transition of purple membrane revealed by reactivity with hydrolysis reagent hydroxylamine
    J. Phys. Chem. B 108, 19496-19500.
  9. Sonoyama, M., Hasegawa, T., Nakano, T., and Mitaku, S. (2004)
    Isomerization of retinal chromophore and conformational changes in membrane protein bacteriorhodopsin by solubilization with a mild non-ionic detergent, n-octyl-b-glucoside: an FT-Raman and FT-IR spectroscopic study, Vib. Spectrosc. 35, 115-119.
  10. Shibakami, M., Sonoyama, M., Goto, R., Mori, M., Suzuki, H., and Mitaku, S. (2004)
    Thermotropic behavior of membranes containing DMPC and chemically and stereochemically pure sphingomyelin upon cholesterol addition
    J. Phys. Soc. Jpn. 73, 3484-3488.
  11. Gomi, M., Sonoyama, M., and Mitaku, S. (2004) High performance system for signal peptide prediction: SOSUIsignal
    Chem-Bio. Informatics J. 4, 142-147.
  12. Endo, O., Fukushima, Y., Ozaki, H., Sonoyama, M., and Tukada, H. (2004)
    "Edge-on" orientation of alkyl chains on an iodine-covered Au(111) surface studied by infrared reflection absorption spectroscopy
    Surf. Sci. 569, 99-104.
  13. Yokoyama, Y., Sonoyama, M., and Mitaku, S. (2002)
    Irreversible photobleaching of bacteriorhodopsin in a high-temperature intermediate state,
    J. Biochem. 131, 785-790.
  14. Yamane, T., Sonoyama, M., Asakura, T., and Furukawa, Y. (2002)
    Raman spectrum of model peptide (Ala-Gly)(15) for Bombyxmori silk fibroin with Silk I form and theoretical calculation according to repeated b-turn type II structural model
    Sen-I Gakkaishi 58, 327-331.
  15. Hasegawa, T., Nishijo, J., Sonoyama, M., and Nakano, T. (2002)
    Analysis of thermal phase transition via time-resolved infrared spectra using partial least-squares regression modeling parameters
    Appl. Spectrosc. 56, 288-294.
  16. Tsunoda, K., Sugiura, M., Sonoyama, M., Yajima, H., Ishii, T., Taniyama, J., and Itoh, H. (2001)
    Characterization of water contribution to excimer laser ablation of collagen J. Photochem. Photobiol. A: Chem. 145, 195-200.
  17. Sakai, H., Tanaka, M., Imai, K., Sonoyama, M., and Mitaku, S. (2001)
    Effect of carbonic anhydrase II in molten globule state on physical properties of dimyristoylphosphatidylcholine liposome
    Jpn. J. Appl. Phys. 40, 3521-3525.

1992-2000

  1. Sonoyama, M., Yajima, H., Nakano, T., Matsumoto, M., Tsukushi, I., and Ishii, T. (2000) First observation of precursory structural changes of aliphatic parts in the a-g polymorphic transition of DL-norleucine by temperature-scanning time-resolved FT-IR spectroscopy
    Chem. Lett. 29, 558-559.
  2. Sonoyama, M., and Nakano, T. (2000)
    Infrared rheo-optics of Bombyx mori fibroin film by dynamic step-scan FT-IR spectroscopy combined with digital signal processing
    Appl. Spectrosc. 54, 968-973.
  3. Sakai, H., Imai, K., Tanaka, M., Sonoyama, M., and Mitaku, S. (2000)
    Ultrasonic properties of a binary system of a soluble protein, a-lactalbumin and dimyristoyl phosphatidylcholine membrane
    Jpn. J. Appl. Phys. 39, 2948-2949.
  4. Miyazawa, M., Sonoyama, M., and Saito, H. (2000)
    FT-IR studies on secondary structures of wild silkworm fibroin films, Int. J. Wild Silkmoth & Silk 5, 47-50.
  5. Mitaku, S., Ono, M., Hirokawa, T., Boon-Chieng, S., and Sonoyama, M. (1999)
    Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI predictio system
    Biophys. Chem. 82, 165-171.
  6. Miyazawa, M., and Sonoyama, M. (1998)
    Second derivative near infrared studies on the structural characterization of proteins
    J. Near Infrared Sepctrosc. 6, 253-257.
  7. Yajima, H., Ishii, T., Ikekita, M., Taketera, K., Watanabe, T., Sonoyama, M., and Tarutani, O. (1997)
    Secondary structure of hog thyroglobulins with different iodine content
    Res. Comm. Biochem. Cell. Mol. Biol. 1, 171-184.
  8. Sonoyama, M., Shoda, K., Katagiri, G., Ishida, H., Nakano, T., Shimada, S., Yokoyama, T., and Toriumi, H. (1997)
    Amplitude spectrum analysis of dynamic FT-IR spectra of uniaxially drawn poly(ethylene terephthalate) film with a variable-temperature polymer stretcher
    Appl. Spectrosc. 51, 598-600.
  9. Sonoyama, M., Shoda, K., Katagiri, G., and Ishida, H. (1997)
    Amplitude spectrum approach in dynamic FT-IR spectroscopy of uniaxially oriented poly(ethylene terephthalate) films .1. Draw ratio dependence
    Appl. Spectrosc. 51, 346-349.
  10. Sonoyama, M., Miyazawa, M., Katagiri, G., and Ishida, H. (1997)
    Dynamic FT-IR spectroscopic studies of silk fibroin films
    Appl. Spectrosc. 51, 545-547.
  11. Ikekita, M., Yajima, H., Murata, T., Takatera, K., Watanabe, T., Sonoyama, M., Tezuka, Y., Ishii, T., and Tarutani, O. (1997)
    Carbohydrate analysis of porcine thyroglobulin isoforms with different iodine contents
    Biochim. Biophys. Acta 1336, 557-565.
  12. Sonoyama, M., Shoda, K., Katagiri, G., and Ishida, H. (1996)
    Dynamic step-scan two-dimensional Fourier transform infrared studies of uniaxially drawn poly(ethylene terephthalate) film
    Appl. Spectrosc. 50, 377-381.
  13. Sonoyama, M., Motoki, A., Okamoto, G., Hirano, M., Ishida, H., and Katoh, S. (1996)
    Secondary structure and thermostability of the photosystem II manganese-stabilizing protein of the thermophilic cyanobacterium Synechococcus elongatus
    Biochim. Biophys. Acta 1297, 167-170.
  14. Miyazawa, M., and Sonoyama, M. (1995)
    NIR studies of fibroin secondary structures
    J. Spectrosc. Soc. Jpn. 44, 13-15.
  15. Vonderviszt, F., Sonoyama, M., Tasumi, M., and Namba, K. (1992)
    Conformational adaptability of the terminal regions fo flagellin
    Biophys. J. 63, 1672-1677.