Publications   (Last update 2026.3)   *Corresponding author,  #Contributed equally

56.  Hydrophobic hydration of analgesics and diltiazem complexes explored by electrochemical impedance spectroscopy and diffusion-ordered spectroscopy.
Koga, R., Kinoshita, T., Ishiguro, M., Fujita, M., Chatani, H., Kataoka, H., Yokoyama, H., Hanawa, T., Shitanda, I. & *Goto, S.
Phys. Chem. Chem. Phys. 28, 1159-1172 (2026).   PubMed

55.  Comparative study on the effects of the inclusion complexes of non-steroidal anti-inflammatory drugs with 2-hydroxypropyl-β-cyclodextrins on dissociation rates and supersaturation.
Oshite, Y., Wada-Hirai, A., Ichii, R., Kuroda, C., Hasegawa, K., Hiroshige, R., Yokoyama, H., Tsuchida, T. & *Goto, S.
RSC Pharm. 1, 80-97 (2024).   DOI

54.  Quantification of crystallinity during indomethacin crystalline transformation from α- to γ-polymorphic forms and of the thermodynamic contribution to dissolution in aqueous buffer and solutions of solubilizer.
Hasegawa, K., *Goto, S., Kataoka, H., Chatani, H., Kinoshita, T., Yokoyama, H.. & Tsuchida, T.
RSC Adv. 14, 4129-4141 (2024).   PubMed

53.  Wnt activation disturbs cell competition and causes diffuse invasion of transformed cells through NF-ƒČB-MMP21 pathway.
Nakai, K., Lin, H., Yamano, S., Tanaka, S., Kitamoto, S., Saitoh, H., Sakuma, K., Kurauchi, J., Akter, E., Konno, M., Ishibashi, K., Kamata, R., Ohashi, A., Koseki, J., Takahashi, H., Yokoyama, H.., Shiraki, Y., Enomoto, A., Abe, S., Hayakawa, Y., Ushiku, T., Mutoh, M., Fujita, Y. & Kon, S.
Nat. Commun. 14, 7048 (2023).   PubMed

52.  Using singular value decomposition to analyze drug/β-cyclodextrin mixtures: insights from X-ray powder diffraction patterns.
Hasegawa, K., *Goto, S., Tsunoda, C., Kuroda, C., Okumura, Y., Hiroshige, R., Wada-Hirai, A., Shimizu, S., Yokoyama, H.. & Tsuchida, T.
Phys. Chem. Chem. Phys. 25, 29266-29282 (2023).   PubMed

51.  Effect of cyclodextrin complex formation on solubility changes of each drug due to intermolecular interactions between acidic NSAIDs and basic H2 blockers.
Tsunoda, C., Hasegawa, K., Hiroshige, R., Kasai, T., Yokoyama, H.. & *Goto, S.
Mol. Pharm. 20, 5032-5042 (2023).   PubMed

50.  Effects of local anesthetics on liposomal membranes determined by their inhibitory activity of lipid peroxidation.
Horizumi, Y., *Goto, S., Takatsuka, M. & Yokoyama, H.
Mol. Pharm. 20, 2911-2918 (2023).   PubMed

49.  Higher-order structure formation using refined monomer structures of lipid raft markers, Stomatin, Prohibitin, Flotillin, and HflK/C-related proteins.
Yokoyama, H. & *Matsui, I.
FEBS Open Bio 13, 926-937 (2023).   PubMed

48.  Crystal structure of the motor domain of centromere]associated protein E in complex with a non]hydrolysable ATP analogue.
Shibuya, A., Suzuki, A., Ogo, N., Sawada, J., Asai, A. & *Yokoyama, H.
FEBS Lett. 597, 1138-1148 (2023).   PubMed   PDB ID: 8HFH

47.  Optimization of the stability constants of the ternary system of diclofenac/famotidine/β-cyclodextrin by nonlinear least-squares method using theoretical equations.
Tsunoda, C., *Goto, S, Hiroshige, R., Kasai, T., Okumura, Y. & Yokoyama, H.
Int. J. Pharm. 638, 122913 (2023).   PubMed

46.  Interaction mode of hydroxypropyl-β-cyclodextrin with vaccine adjuvant components Tween 80 and Triton X-100 revealed by fluorescence increasing-quenching analysis.
Kurosawa, Y., *Goto, S., Mitsuya, K., Otsuka, Y. & Yokoyama, H.
Phys. Chem. Chem. Phys. 25, 6203-6213 (2023).   PubMed

45.  Structural and mutational studies suggest key residues to determine whether stomatin SPFH domains form dimers or trimers.
Komatsu, T., Matsui, I. & *Yokoyama, H.
Biochem. Biophys. Rep. 32, 101384 (2022).   PubMed   PDB ID: 8GN9

44.  Trajectory of the spectral/structural rearrangements for photo-oxidative reaction of neat ketoprofen and its cyclodextrin complex.
Hiroshige, R., *Goto, S., Tsunoda, C., Ichii, R., Shimizu, S., Otsuka, Y., Makino, K., Takahashi, H. & Yokoyama, H.
J. Incl. Phenom. Macrocycl. Chem. 102, 791-800 (2022).   DOI

43.  Fluorescence changes of dyes/NSAIDs adsorbed on fluorocarbon polymers.
Mitsuya, K., *Goto, S., Kurosawa, Y., Yokoyama, H. & Hanawa, T.
Mater. Chem. Phys. 290, 126552 (2022).   DOI

42.  Structural basis for peptide recognition by archaeal oligopeptide permease A.
*Yokoyama, H., Kamei, N., Konishi, K., Hara, K., Ishikawa, Y., Matsui, I., Forterre, P. & Hashimoto, H.
Proteins: Struct. Funct. Bioinf. 90, 1434-1442 (2022).   PubMed   PDB ID: 7FI3

41.  Crystal structures of human glyoxalase I and its complex with TLSC702 reveal inhibitor binding mode and substrate preference.
Usami, M., Ando, K., Shibuya, A., Takasawa, R. & *Yokoyama, H.
FEBS Lett. 596, 1458-1467 (2022).   PubMed   PDB ID: 7WT2 7WT0 7WT1 7WSZ

40.  Preparation, crystallization, and X-ray data collection of archaeal oligopeptide permease A.
*Yokoyama, H., Kamei, N., Konishi, K., Hara, K., Ishikawa, Y., Matsui, I., Forterre, P. & Hashimoto, H.
Crystallogr. Rep. 66, 1300-1305 (2021).   DOI

39.  Structure and comparison of the motor domain of centromere-associated protein E.
Shibuya, A., Ogo, N., Sawada, J., Asai, A. & *Yokoyama, H.
Acta Crystallog. D77, 280-287 (2021).   PubMed   PDB ID: 6M4I

38.  Inactive dimeric structure of the protease domain of stomatin operon partner protein.
*Yokoyama, H., Suzuki, K., Hara, K., Matsui, I. & Hashimoto, H.
Acta Crystallog. D76, 515-520 (2020).   PubMed   PDB ID: 6M4B

37.  The lipid raft markers stomatin, prohibitin, flotillin, and HflK/C (SPFH)-domain proteins form an operon with NfeD proteins and function with apolar polyisoprenoid lipids.
Yokoyama, H. & *Matsui, I.
Crit. Rev. Microbiol. 46, 38-48 (2020).   PubMed

36.  Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab.
Yokoyama, H., Mizutani, R., Noguchi, S. & *Hayashida, N.
Sci. Rep. 9, 18494 (2019).   PubMed   PDB ID: 6KDH 6KDI

35.  Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms.
Yokoyama, H., Mizutani, R., Noguchi, S. & *Hayashida, N.
Acta Crystallog. F75, 80-88 (2019).   PubMed   PDB ID: 6IDG 6IDH

34.  Molecular modeling and simulation of human stomatin and predictions for its membrane association.
Kondo, Y., *Yokoyama, H., Matsui, I. & Miyazaki, S.
J. Data Mining Genomics Proteomics, 9, 216 (2018).   DOI

33.  Structural and thermodynamic basis of the enhanced interaction between kinesin spindle protein Eg5 and STLC-type inhibitors.
*,#Yokoyama, H., #Sawada, J., Sato, K., Ogo, N., Kamei, N., Ishikawa, Y., Hara, K., *Asai, A. & Hashimoto, H.
ACS Omega, 3, 12284-12294 (2018).   PubMed   PDB ID: 5ZO7 5ZO8 5ZO9

32.  Structure of proliferating cell nuclear antigen (PCNA) bound to an APIM peptide reveals the universality of PCNA interaction.
Hara, K., Uchida, M., Tagata, R., Yokoyama, H., Ishikawa, Y., Hishiki, A. & *Hashimoto, H.
Acta Crystallog. F74, 214-221 (2018).   PubMed

31.  Dynamic feature of mitotic arrest deficient 2-like protein 2 (MAD2L2) and structural basis for its interaction with chromosome alignment-maintaining phosphoprotein (CAMP).
Hara, K., Taharazako, S., Ikeda, M., Fujita, H., Mikami, Y., Kikuchi, S., Hishiki, A., Yokoyama, H., Ishikawa, Y., Kanno, SI., Tanaka, K. & *Hashimoto, H.
J. Biol. Chem. 292, 17658-17667 (2017).   PubMed

30.  Role of the mobility of antigen binding site in high affinity antibody elucidated by surface plasmon resonance.
Fukuda, N., Suwa, Y., Uchida, M., Kobashigawa, Y., Yokoyama, H. & *Morioka, H.
J. Biochem. 161, 37-43 (2017).   PubMed

29.  Structure of a novel DNA-binding domain of helicase-like transcription factor (HLTF) and its functional implication in DNA damage tolerance.
Hishiki, A., Hara, K., Ikegaya, Y., Yokoyama, H., Shimizu, T., Sato, M. & *Hashimoto, H.
J. Biol. Chem. 290, 13215-13223 (2015).   PubMed

28.  Crystallographic study of a novel DNA-binding domain of human HLTF involved in the template-switching pathway to avoid the replication arrest caused by DNA damage.
Ikegaya, Y., Hara, K., Hishiki, A., Yokoyama, H. & *Hashimoto, H.
Acta Crystallog. F71, 668-670 (2015).   PubMed

27.  Structural basis of new allosteric inhibition in kinesin spindle protein Eg5.
*,#Yokoyama, H., #Sawada, J., Katoh, S., Matsuno, K., Ogo, N., Ishikawa, Y., Hashimoto, H., Fujii, S. & *Asai, A.
ACS Chem. Biol. 10, 1128-1136 (2015).   PubMed   PDB ID: 3WPN

26.  Structural biology of DNA (6-4) photoproducts formed by ultraviolet radiation and interactions with their binding proteins.
*Yokoyama, H. & Mizutani, R.
Int. J. Mol. Sci. 15 (11), 20321-20338 (2014).   PubMed

25.  Crystal structure of the stomatin operon partner protein from Pyrococcus horikoshii indicates the formation of a multimeric assembly.
*Yokoyama, H. & Matsui, I.
FEBS Open Bio 4, 804-812 (2014).   PubMed   PDB ID: 3WWV

24.  Structures and metal-binding properties of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center.
*Yokoyama, H. & Fujii, S.
Biomolecules 4 (3), 600-615 (2014).   PubMed

23.  Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease.
*Yokoyama, H., Kobayashi, D., Takizawa, N., Fujii, S. & Matsui, I.
J. Synchrotron Rad. 20, 933-937 (2013).   PubMed   PDB ID: 3WG5

22.  Domain structures and inter-domain interactions defining the holoenzyme architecture of archaeal D-Family DNA polymerase.
*Matsui, I., Matsui, E., Yamasaki, K. & Yokoyama, H.
Life 3 (3), 375-385 (2013).   PubMed

21.  Clustering of OB-fold domains of the partner protease complexed with trimeric stomatin from Thermococcales.
Yokoyama, H., Matsui, E., Hiramoto, K., Forterre, P. & *Matsui, I.
Biochimie 95, 1494-1501 (2013).   PubMed

20.  Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab.
*Yokoyama, H., Mizutani, R. & Satow, Y.
Acta Crystallog. D69, 504-512 (2013).   PubMed   PDB ID: 3VW3

19.  Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form.
*Yokoyama, H., Tsuruta, O., Akao, N. & Fujii, S.
Biochem. Biophys. Res. Commun. 422, 745-750 (2012).   PubMed   PDB ID: 4EVB 4EVC 4EVD 4EVE

18.  Crystal structure of a membrane stomatin-specific protease in complex with a substrate peptide.
*Yokoyama, H., Takizawa, N., Kobayashi, D., Matsui, I. & Fujii, S.
Biochemistry 51, 3872-3880 (2012).   PubMed   PDB ID: 3VIV

17.  Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides.
*Yokoyama, H., Mizutani, R., Satow, Y., Sato, K., Komatsu, Y., Ohtsuka, E. & Nikaido, O.
Acta Crystallog. D68, 232-238 (2012).   PubMed   PDB ID: 1KEG

16.  A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP).
Tsuruta, O., *Yokoyama, H. & Fujii, S.
Acta Crystallog. F68, 134-140 (2012).   PubMed   PDB ID: 3T9J 3TA8

15.  Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii.
*Matsui, I., Urushibata, Y., Shen, Y., Matsui, E. & Yokoyama, H.
FEBS Lett. 585, 452-458 (2011).   PubMed   PDB ID: 3O59

14.  Three-dimensional structure of membrane protein stomatin and function of stomatin-specific protease.
*Yokoyama, H.
Yakugaku Zasshi 130 (10), 1289-1293 (2010).   PubMed

13.  Binding of sulphatide to recombinant haemagglutinin of influenza A virus produced by a baculovirus protein expression system.
Takahashi, T., Satoh, H., Takaguchi, M., Takafuji, S., Yokoyama, H., Fujii, S. & *Suzuki, T.
J. Biochem. 147, 459-462 (2010).   PubMed

12.  Unusual thermal disassembly of the SPFH domain oligomer from Pyrococcus horikoshii.
Kuwahara, Y., Unzai, S., Nagata, T., Hiroaki, Y., Yokoyama, H., Matsui, I., Ikegami, T., Fujiyoshi, Y. & *Hiroaki, H.
Biophys. J. 97, 2034-2043 (2009).   PubMed

11.  The solution structure of the C-terminal domain of NfeD reveals a novel membrane-anchored OB-fold.
Kuwahara, Y., Ohno, A., Morii, T., Yokoyama, H., Matsui, I., Tochio, H., Shirakawa, M. & *Hiroaki, H.
Protein Sci. 17, 1915-1924 (2008).   PubMed

10.  Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin.
Yokoyama, H., Hamamatsu, S., Fujii, S. & *Matsui, I.
J. Synchrotron Rad. 15, 254-257 (2008).   PubMed   PDB ID: 3BPP

9.  Crystal structure of a core domain of stomatin from Pyrococcus horikoshii illustrates a novel trimeric and coiled-coil fold.
Yokoyama, H., Fujii, S. & *Matsui, I.
J. Mol. Biol. 376, 868-878 (2008).   PubMed   PDB ID: 3BK6

8.  Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii.
Yokoyama, H., Matsui, E., Akiba, T., Harata, K. & *Matsui, I.
J. Mol. Biol. 358, 1152-1164 (2006).   PubMed   PDB ID: 2DEO

7.  A novel thermostable membrane protease forming an operon with a stomatin homolog from the hyperthermophilic archaebacterium Pyrococcus horikoshii.
Yokoyama, H. & *Matsui, I.
J. Biol. Chem. 280, 6588-6594 (2005).   PubMed

6.  Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii.
Matsui, E., Abe, J., Yokoyama, H. & *Matsui, I.
J. Biol. Chem. 279, 16687-16696 (2004).   PubMed

5.  A 21-amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11-like and prefers manganese ion as the cofactor.
Shen, Y., Tang, X.-F., Yokoyama, H., Matsui, E. & *Matsui, I.
Nucleic Acids Res. 32, 158-168 (2004).   PubMed

4.  Distinct domain functions regulating de novo DNA synthesis of thermostable DNA primase from hyperthermophile Pyrococcus horikoshii.
Matsui, E., Nishio, M., Yokoyama, H., Harata, K., Darnis, S. & *Matsui, I.
Biochemistry 42, 14968-14976 (2003).   PubMed

3.  Complex formation of double-stranded DNA (6-4) photoproducts and anti-(6-4) photoproduct antibody Fabs.
Yokoyama, H., Mizutani, R. & *Satow, Y.
Nucleic Acids Symp. Ser. 44, 151-152 (2000).   PubMed

2.  Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation.
Yokoyama, H., Mizutani, R., *Satow, Y., Komatsu, Y., Ohtsuka, E. & Nikaido, O.
J. Mol. Biol. 299, 711-723 (2000).   PubMed   PDB ID: 1EHL

1.  Crystal structures of the 64M-2 and 64M-3 antibody Fabs complexed with DNA (6-4) photoproducts.
Yokoyama, H., Mizutani, R., *Satow, Y., Komatsu, Y., Ohtsuka, E. & Nikaido, O.
Nucleic Acids Symp. Ser. 42, 267-268 (1999).   PubMed