Faculty Information - Shimono Kazumi

Shimono Kazumi

Department / Course FACULTY OF PHARMACEUTICAL SCIENCES Department of Pharmaceutical Sciences

Job

Book and thesis
1.	2023/01	Papers	Recent advances in signaling and activation mechanism in microbial rhodopsins: Report for the session 6 at the 19th International Conference on Retinal Proteins Biophysics and Physicobiology,pp.e201009 (Co-authored)
2.	2022/04	Papers	Estimation of the Diffusion Coefficients of Small Molecules by Diffusion Measurements with Agar-gel and Theoretical Molecular Modeling Chem-Bio Informatics Journal 22,pp.13-20 (Co-authored)
3.	2021/05	Papers	Protonation state of a histidine residue in human oligopeptide transporter 1 (hPEPT1) regulates hPEPT1-mediated efflux activity Biological and Pharmaceutical Bulletin 44 (59),pp.678-685 (Co-authored)
4.	2020/11	Papers	Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules Molecules 25 (22),pp.5340 (Co-authored)
5.	2019/02	Papers	Transport of 2,4-dichloro phenoxyacetic acid by human Na⁺-coupled monocarboxylate transporter 1 (hSMCT1, SLC5A8) Drug Metabolism and Pharmacokinetics 34 (1),pp.95-103 (Co-authored)
6.	2018/06	Papers	Production of a Light-Gated Proton Channel by Replacing the Retinal Chromophore with Its Synthetic Vinylene Derivative J Phys Chem Lett 9 (11),pp.2857-2862 (Co-authored)
7.	2018/06	Papers	Interhelical interactions between D92 and C218 in the cytoplasmic domain regulate proton uptake upon N-decay in the proton transport of Acetabularia rhodopsin II J Photochem Photobiol B 183,pp.35-45 (Co-authored)
8.	2018/03	Papers	The phenomenon of albumin-mediated hepatic uptake of organic anion transport polypeptide substrates: Prediction of the in vivo uptake clearance from the in vitro uptake by isolated hepatocytes using a facilitated-dissociation model Drug Metabolism and Disposition 46 (3),pp.259-267 (Co-authored)
9.	2017/09	Papers	Carbidopa is an activator of aryl hydrocarbon receptor with potential for cancer therapy Biochemical Journal 474 (20),pp.3391-3402 (Co-authored)
10.	2017/03	Papers	Existence of two O-like intermediates in the photocycle of Acetabularia rhodopsin II, a light-driven proton pump from a marine alga Biophysics and Physicobiology 14,pp.49-55 (Co-authored)
11.	2016/10	Papers	Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor Nature Communications 7,pp.13235 (Co-authored)
12.	2016/08	Books	Cell-free synthesis of membrane proteins Advanced Methods in Structural Biology,pp.123-135 (Co-authored)
13.	2016/06	Papers	X-ray Crystallographic Structure of Thermophilic Rhodopsin: Implications for High Thermal Stability and Optogenetic Function Journal of Biological Chemistry 291 (23),pp.12223-12232 (Co-authored)
14.	2015/11	Papers	Structural Basis for Slow Photocycle and Late Proton Release in Acetabularia Rhodopsin I from a Marine Plant, Acetabularia acetabulum Acta Crystallographica Section D: Biological Crystallography 71 (11),pp.2203-2216 (Co-authored)
15.	2015/03	Papers	Converting a light-driven proton pump into a light-gated ion channel Journal of American Chemical Society 137 (9),pp.3291-3299 (Co-authored)
16.	2014/11	Papers	Electrophysiological characterization of human Na+/taurocholate cotransporting polypeptide (hNTCP) heterologously expressed in Xenopus laevis oocytes Archives of Biochemistry and Biophysics 562,pp.115-121 (Co-authored)
17.	2014/01	Papers	A common variant of leucine-rich repeat containing 16A (LRRC16A) gene is associated with gout susceptibility Human Cell 27 (1),pp.1-4 (Co-authored)
18.	2013/02	Papers	A study of the interaction of drugs with liposomes with isothermal titration calorimetry Jouranl of Biophysical Chemistry 4 (1),pp.11-21 (Co-authored)
19.	2013/02	Papers	Thermodynamic Parameters of Anion Binding to Halorhodopsin from Natronomonas pharaonis by Isothermal Titration Calorimetry Biophysical Chemistry 172,pp.61-67 (Co-authored)
20.	2012/11	Papers	The Photo-induced Proton Release in Proteorhodopsin at Low pH: The Possibility of the pKa Decrease of Asp227 Biochemistry 51 (46),pp.9290-9301 (Co-authored)
21.	2012/03	Books	Photoinduced Proton Transfers of Microbial Rhodopsins Molecular Photochemistry - Various Aspects,pp.89-108 (Co-authored)
22.	2011/10	Papers	Photochemistry of Acetabularia Rhodopsin II from a Marine Plant, Acetabularia acetabulum Biochemistry 50 (41),pp.8888-8898 (Co-authored)
23.	2011/09	Papers	Crystal structure of the eukaryotic light-driven proton pumping rhodopsin, Acetabularia rhodopsin II from marine alga Journal of Molecular Biology 411 (5),pp.986-998 (Co-authored)
24.	2011/01	Papers	Photochemistry of a Putative New Class of Sensory Rhodopsin (SRIII) coded by xop2 of Haloarcular marismortui Journal of Photochemistry and Photobiology B-Biology 102,pp.45-54 (Co-authored)
25.	2009/10	Papers	Production of functional bacteriorhodopsin by an Escherichia coli cell-free protein synthesis system supplemented with steroid detergent and lipid Protein Science 18 (10),pp.2160-2171 (Co-authored)
26.	2008/07	Papers	A long-lived M-like state of phoborhodopsin that mimics the active state Biophysical Journal 95 (2),pp.753-760 (Co-authored)
27.	2007/03	Papers	Participation of the surface structure of Pharaonis phoborhodopsin, ppR and its A149S and A149V mutants, consisting of the C-terminal alpha-helix and E-F loop, in the complex-formation with the cognate transducer pHtrII, as revealed by site-directed C-13 solid-state NMR Photochemistry and Photobiology 83 (2),pp.339-345 (Co-authored)
28.	2006/10	Papers	Assignment of the hydrogen-out-of-plane and -in-plane vibrations of the retinal chromophore in the K intermediate of pharaonis phoborhodopsin Biochemistry 45 (39),pp.11836-11843 (Co-authored)
29.	2006/04	Papers	Importance of specific hydrogen bonds of archaeal rhodopsins for the binding to the transducer protein Journal of Molecular Biology 357 (4),pp.1274-1282 (Co-authored)
30.	2005/09	Papers	Hydrogen-bonding alterations of the protonated Schiff base and water molecule in the chloride pump of Natronobacterium pharaonis Biochemistry 44 (37),pp.12279-12286 (Co-authored)
31.	2005/08	Papers	Formation of a long-lived photoproduct with a deprotonated Schiff base in proteorhodopsin, and its enhancement by mutation of Asp227 Biochemistry 44 (32),pp.10828-10838 (Co-authored)
32.	2005/03	Papers	Structural changes of the complex between pharaonis phoborhodopsin and its cognate transducer upon formation of the m photointermediate Biochemistry 44 (8),pp.2909-2915 (Co-authored)
33.	2005/02	Papers	Correlation of the O-intermediate rate with the pK(a) of Asp-75 in the dark, the counterion of the Schiff base of Pharaonis phoborhodopsin (sensory rhodopsin II) Biophysical Journal 88 (2),pp.1215-1223 (Co-authored)
34.	2004/11	Papers	Role of charged residues of pharaonis phoborhodopsin (sensory rhodopsin II) in its interaction with the transducer protein Biochemistry 43 (43),pp.13748-13754 (Co-authored)
35.	2004/08	Papers	Amino acid residues regulating the color among archaeal rhodopsins Recent Research Developments in Photochemistry and Photobiology 7,pp.19-38 (Co-authored)
36.	2004/06	Papers	Transient movement of helix F revealed by photo-induced inactivation by reaction of a bulky SH-reagent to cysteine-introduced pharaonis phoborhodopsin (sensory rhodopsin II) Photochemical & Photobiological Sciences 3 (6),pp.537-542 (Co-authored)
37.	2004/05	Papers	FTIR spectroscopy of the O photointermediate in pharaonis phoborhodopsin Biochemistry 43 (18),pp.5204-5212 (Co-authored)
38.	2004/05	Papers	Role of Arg-72 of pharaonis phoborhodopsin (sensory rhodopsin II) on its photochemistry Biophysical Journal 86 (5),pp.3112-3120 (Co-authored)
39.	2004/05	Papers	Conformation and dynamics of the [3-C-13]Ala,[1-C-13]val-labeled truncated pharaonis transducer, pHtrII(1-159), as revealed by site-directed C-13 solid-state NMR: Changes due to association with phoborhodopsin (sensory rhodopsin II) Biophysical Journal 86 (5),pp.3131-3140 (Co-authored)
40.	2004/03	Papers	Proton release and uptake of pharaonis phoborhodopsin (Sensory rhodopsin II) reconstituted into phospholipids Biochemistry 43 (11),pp.3195-3203 (Co-authored)
41.	2003/12	Papers	Hydrogen bonding alteration of Thr-204 in the complex between pharaonis phoborhodopsin and its transducer protein Biochemistry 42 (48),pp.14166-14172 (Co-authored)
42.	2003/11	Papers	Interaction of Natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II) with its cognate transducer probed by increase in the thermal stability Photochemistry and Photobiology 78 (5),pp.511-516 (Co-authored)
43.	2003/07	Papers	Roles of Ser130 and Thr126 in chloride binding and photocycle of pharaonis halorhodopsin Journal of Biochemistry 134 (1),pp.151-158 (Co-authored)
44.	2003/07	Papers	Ser-130 of Natronobacterium pharaonis halorhodopsin is important for the chloride binding Biophysical Chemistry 104 (1),pp.209-216 (Co-authored)
45.	2003/06	Papers	Importance of the broad regional interaction for spectral tuning in Natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II) Journal of Biological Chemistry 278 (26),pp.23882-23889 (Co-authored)
46.	2003/05	Papers	Vibrational modes of the protonated Schiff base in pharaonis phoborhodopsin Biochemistry 42 (25),pp.7801-7806 (Co-authored)
47.	2003/02	Papers	Dynamic structure of pharaonis phoborhodopsin (sensory rhodopsin II) and complex with a cognate truncated transducer as revealed by site-directed C-13 solid-state NMR FEBS Letters 536,pp.237-240 (Co-authored)
48.	2003/01	Papers	Arg-72 of pharaonis phoborhodopsin (Sensory rhodopsin II) is important for the maintenance of the protein structure in the solubilized state Photochemistry and Photobiology 77 (1),pp.96-100 (Co-authored)
49.	2002/12	Papers	FTIR spectroscopy of the M photointermediate in pharaonis phoborhodopsin Biophysical Journal 83 (6),pp.3482-3489 (Co-authored)
50.	2002/10	Papers	Illumination accelerates the decay of the o-intermediate of pharaonis phoborhodopsin (sensory rhodopsin II) Photochemistry and Photobiology 76 (4),pp.462-466 (Co-authored)
51.	2002/08	Papers	Role of Asp193 in chromophore-protein interaction of pharaonis phoborhodopsin (sensory rhodopsin II) Biophysical Journal 83 (2),pp.1130-1135 (Co-authored)
52.	2002/07	Papers	Association between a photo-intermediate of a M-lacking mutant D75N of pharaonis phoborhodopsin and its cognate transducer Journal of Photochemistry and Photobiology B-Biology 67 (3),pp.171-176 (Co-authored)
53.	2002/07	Papers	Tyr-199 and charged residues of pharaonis phoborhodopsin are important for the interaction with its transducer Biophysical Journal 83 (1),pp.427-432 (Co-authored)
54.	2002/05	Papers	A pharaonis phoborhodopsin mutant with the same retinal binding site residues as in bacteriorhodopsin Biochemistry 41 (20),pp.6504-6509 (Co-authored)
55.	2002/04	Papers	Probing the proton channel and the retinal binding site of Natronobacterium pharaonis sensory rhodopsin II Biophysical Journal 82 (4),pp.2156-2164 (Co-authored)
56.	2002/04	Papers	Interaction of Asn105 with the retinal chromophore during photoisomerization of pharaonis phoborhodopsin Biochemistry 41 (14),pp.4554-4559 (Co-authored)
57.	2002/01	Papers	Association of pharaonis phoborhodopsin with its cognate transducer decreases the photo-dependent reactivity by water-soluble reagents of azide and hydroxylamine Biochimica et Biophysica Acta-Biomembranes 1558 (1),pp.63-69 (Co-authored)
58.	2001/11	Papers	Photochemistry and photoinduced proton-transfer by pharaonis phoborhodopsin Biochemistry-Moscow 66 (11),pp.1277-1282 (Co-authored)
59.	2001/12	Papers	Internal water molecules of pharaonis phoborhodopsin studied by low-temperature infrared Spectroscopy Biochemistry 40 (51),pp.15693-15698 (Co-authored)
60.	2001/12	Papers	Environment around the chromophore in pharaonis phoborhodopsin: mutation analysis of the retinal binding site Biochimica et Biophysica Acta-Biomembranes 1515 (2),pp.92-100 (Co-authored)
61.	2001/09	Papers	Pharaonis phoborhodopsin binds to its cognate truncated transducer even in the presence of a detergent with a 1 : 1 stoichiometry Photochemistry and Photobiology 74 (3),pp.489-494 (Co-authored)
62.	2001/09	Papers	Selective reaction of hydroxylamine with chromophore during the photocycle of pharaonis phoborhodopsin Biochimica et Biophysica Acta-Biomembranes 1514 (1),pp.152-158 (Co-authored)
63.	2001/08	Papers	Structural changes of pharaonis phoborhodopsin upon photoisomerization of the retinal chromophore: Infrared spectral comparison with bacteriorhodopsin Biochemistry 40 (31),pp.9238-9246 (Co-authored)
64.	2001/02	Papers	Photo-induced proton transport of Pharaonis phoborhodopsin (sensory rhodopsin II) is ceased by association with the transducer Biophysical Journal 80 (2),pp.916-922 (Co-authored)
65.	2000/10	Papers	Involvement of two groups in reversal of the bathochromic shift of pharaonis phoborhodopsin by chloride at low pH Biophysical Chemistry 87,pp.225-230 (Co-authored)
66.	2000/07	Papers	Effects of three characteristic amino acid residues of Pharaonis phoborhodopsin on the absorption maximum Photochemistry and Photobiology 72 (1),pp.141-145 (Co-authored)
67.	1999/11	Papers	Light-induced proton uptake and release of pharaonis phoborhodopsin detected by a photoelectrochemical cell Journal of Physical Chemistry B 103 (46),pp.10311-10315 (Co-authored)
68.	1999/06	Papers	Positioning proton-donating residues to the Schiff-base accelerates the M-decay of pharaonis phoborhodopsin expressed in Escherichia coli Biophysical Chemistry 79 (3),pp.187-192 (Co-authored)
69.	1998/08	Papers	V108M mutant of pharaonis phoborhodopsin: Substitution caused no absorption change but affected its M-state Journal of Biochemistry 124 (2),pp.404-409 (Co-authored)
70.	1997/12	Papers	Functional expression of pharaonis phoborhodopsin in Escherichia coli FEBS Letters 420 (1),pp.54-56 (Co-authored)