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Œ¤‹†‹ĆŃPublications

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  1. Ito Y, Araki T, Shiga S, Konno H and Makabe K *

Surface Engineering of Top7 to Facilitate Structure Determination

International Journal of Molecular Science, 23(2), 701, 2022

DOI: 10.3390/ijms23020701

  1. Makabe K, Yokoyama T, Uehara S, Uchikubo-Kamo T, Shirouzu M, Kimura K, Tsumoto K, Asano R, Tanaka Y, Kumagai I*.

Anti-EGFR antibody 528 binds to domain III of EGFR at a site shifted from the cetuximab epitope

Scientific Reports, 11(1):5790., 2021

  1. Tajiri M, Yamada R, Hotsumi M, Makabe K, Konno H*.

The total synthesis of berberine and selected analogues, and their evaluation as amyloid beta aggregation inhibitors.

Eur J Med Chem., 215:113289., 2021

doi: 10.1016/j.ejmech.2021.113289.

  1. Shiga S, Makabe K*.

Structural analysis of the ƒŔ-sheet edge of peptide self-assembly using a model protein.

Proteins, 89(7):845-852, 2021

doi: 10.1002/prot.26063.

  1. Shigekazu Yano, Haruki Kanno, Haruna Tsuhako, Sonoka Ogasawara, Wasana Suyotha, Hiroyuki Konno, Koki Makabe, Keiko Uechi, Toki Taira*

Cloning, expression, and characterization of a GH 19-type chitinase with antifungal activity from Lysobacter sp. MK9-1 

Journal of Bioscience and Bioengineering, S1389-1723(20)30423-0., 2020 

doi: 10.1016/j.jbiosc.2020.11.005. 

  1. Koki Makabe, Ruka Hirota, Yoshihito Shiono, Yoshikazu Tanaka, and Takuya Koseki*

Biochemical and structural investigation of rutinosidase from Aspergillus oryzae

Applied and Environmental Microbiology, 87(3):e02438-20., 2020

doi: 10.1128/AEM.02438-20.

  1. Mayumi Hotsumi, Misato Tajiri, Koki Makabe, Hiroyuki Konno*

Design, synthesis and evaluation of diaryl ƒÁ-dihydropyrone derivatives as cyclocurcumin mimetics and inhibitors of the aggregation of amyloid ƒŔ

Bioorg Chem., 104:104302., 2020

doi: 10.1016/j.bioorg.2020.104302.

  1. Namioka S, Yoshida N, Konno H, Makabe K*.

Residue-specific binding mechanisms of Thioflavin T to a surface of flat ƒŔ-sheets within a peptide self-assembly mimic.

Biochemistry.  59(30) 2782-2787, (2020) Aug

doi: 10.1021/acs.biochem.0c00280

  1. Hideki Fujiwara, Shota Shiga, Koki Makabe*.

Cooperative unfolding of a single-layer ƒŔ-sheet protein, CPAP G-box.

Biochem Biophys Res Commun. 526(1), 105-109, (2020) Mar

doi: 10.1016/j.bbrc.2020.03.056.

  1. Saki Hemmi, Ryutaro Asano, Kouki Kimura, Mitsuo Umetsu, Takeshi Nakanishi, Izumi Kumagai and Koki Makabe*

Construction of a circularly connected VHH bispecific antibody (cyclobody) for the desirable positioning of antigen-binding sites

Biochem Biophys Res Commun., 1, 72-77 (2020) Feb

doi: 10.1016/j.bbrc.2019.12.018.

  1. Takafumi Itoh, Rattanaporn Intuy, Wasana Suyotha, Junji Hayashi, Shigekazu Yano,Koki Makabe, Mamoru Wakayama*, and Takao Hibi*

Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 ƒż-1,3-glucanase from Paenibacillus glycanilyticus FH11

The FEBS Journal, 287(12), 2524-2543, (2020) 

doi: 10.1111/febs.15161.

  1. Shigekazu Yano, Wasana Suyotha, Natsuki Oguro, Takashi Matsui, Shota Shiga, Takafumi Itoh, Takao Hibi, Yoshikazu Tanaka, Mamoru Wakayama and Koki Makabe*

Crystal structure of the catalytic unit of GH 87-type ƒż-1,3-glucanase Agl-KA from Bacillus circulans

Scientific Reports, 9(1), 15295 (2019) Oct

doi: 10.1038/s41598-019-51822-5.

  1. Yoshiya Miyasaka, Keigo Murakami, Koji Ito, Jiro Kumaki, Koki Makabe, Kuniyuki Hatori*

Condensed desmin and actin cytoskeletal communication in lipid droplets

Cytoskeleton, 76(9-10), 477-490 (2019) Sep

  1. Hotsumi M, Tajiri M, Nikaido Y, Sato T, Makabe K, Konno H*

Design, synthesis, and evaluation of a water soluble C5-monoketone type curcumin analogue as a potent amyloid ƒŔ aggregation inhibitor.

Bioorg Med Chem Lett., 29(16):2157-2161. (2019)

doi: 10.1016/j.bmcl.2019.06.052.

  1. Fujiwara H, Hongo K, Hori Y, Yoshida N, and Makabe K*

ƒŔ-sheet elasticity of peptide self-assembly mimic, PSAM, with a grafted sequence characterized by comprehensive analyses of isomorphous crystals

The Journal of Molecular Liquids, 290, 111161, (2019)  June 8

10.1016/j.molliq.2019.111161.

  1. Shiga S, Yamanaka M, Fujiwara W, Hirota S, Goda S, Makabe K*

Domain-swapping design by poly-proline rod insertion

ChemBioChem, 20(19), 2454-2457, (2019)  Oct 1

doi: 10.1002/cbic.201900179

  1. Hori Y, Fujiwara H, Fujiwara W, Makabe K*.

Grafting a short chameleon sequence from ƒżB crystallin into a ƒŔ-sheet scaffold protein. 

Proteins. 87(5), 416-424.(2019)

doi: 10.1002/prot.25663

  1. Intuy R, Itoh T, Suyotha W, Hayashi J, Yano S, Makabe K, Wakayama M, Hibi T.

X-ray crystallographic analysis of the catalytic domain of ƒż-1,3-glucanase FH1 from Paenibacillus glycanilyticus overexpressed in Brevibacillus choshinensis.

Acta Crystallogr F Struct Biol Commun. 74(Pt 12), 770-773 (2018) Dec

10.1107/S2053230X18013109

  1. Sato T, Hotsumi M, Makabe K, Konno H*

Design, synthesis and evaluation of curcumin-based fluorescent probes to

detect AƒŔ fibrils

Bioorganic & Medicinal Chemistry Letters,28(22), 3520-3525 (2018)

  1. Makabe K*, Nakamura T, Dhar D, Ikura T, Koide S, Kuwajima K

An overlapping region between the two terminal folding units of the outer surface protein A (OspA) controls its folding behavior

J Mol Biol. 430(12), 1799-1813 (2018) Jun

  1. Saito R, Saito Y, Nakazawa H, Hattori T, Kumagai I, Umetsu M, Makabe K*

Impact in stability during sequential CDR grafting to construct camelid VHH antibodies against zinc oxide and gold.

J Biochem. 164(1), 21-25, 2018 Jul

doi: 10.1093/jb/mvy016.

  1. Asano R, Nagai K, Makabe K, Takahashi K, Kumagai T, Kawaguchi H, Ogata H, Arai K, Umetsu M and Kumagai I

Structural considerations for functional anti-EGFR ~ anti-CD3 bispecific diabodies in light of domain order and binding affinity

Oncotarget, 2018 Feb 14;9(17):13884-13893.

doi.org/10.18632/oncotarget.24490

  1. Takenaka T, Nakamura T, Yanaka S, Yagi-Utsumi M, Chandak MS, Takahashi K, Paul S, Makabe K, Arai M, Kato K, Kuwajima K.

Formation of the chaperonin complex studied by 2D NMR spectroscopy.

PLoS One. 2017 Oct 23;12(10):e0187022. 

doi: 10.1371/journal.pone.0187022.

  1. Samori PY, Makabe K, Ohya N, Hatano B, Murakami S, Kijima T.

Role of Cys73 in the thermostability of farnesyl diphosphate synthase from Geobacillus stearothermophilus

3 Biotech 7:236, 2017

DOI 10.1007/s13205-017-0792-8

  1. Shibuya Y, Haga N, Asano R, Nakazawa H, Hattori T, Takeda D, Sugiyama A, Kurotani R, Kumagai I, Umetsu M, and Makabe K*

Generation of camelid VHH bispecific constructs via in-cell intein-mediated  protein trans-splicing

Protein Eng Des Sel., 30, 15-21, 2017

  1. Sasaki R, Kitazawa S, Kitahara R, Nakazawa H, Tanaka Y, Kumagai I, Umetsu M, and Makabe K*

Zinc ion-binding activity of an anti-ZnO VHH antibody, 4F2

Chem. Lett. 44, 1309-1311, 2015

doi:10.1246/cl.150537 

  1. Biancalana M, Makabe K, Yan S and Koide S

Aromatic cluster mutations produce focal modulations of ƒŔ-sheet structure

Protein Science, 24, 841-849, 2015

  1. Nakagawa A, Moriya K, Arita M, Yamamoto Y, Kitamura K, Ishiguro N, Kanzaki T, Oka T, Makabe K, Kuwajima K, Yohda M.

Dissection of the ATP-dependent conformational change cycle of a group II chaperonin.

J Mol Biol. 426, 447-459, 2014

10.1016/j.jmb.2013.09.034.

  1. Ochi A, Makabe K, Yamagami R, Hirata A, Sakaguchi R, Hou YM, Watanabe K, Nureki O, Kuwajima K, Hori H.

The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and non-substrate tRNA via an induced-fit process.

J Biol Chem. 2013 Aug 30;288(35):25562-74.

10.1074/jbc.M113.485128.

  1. Sekiguchi H, Nakagawa A, Moriya K, Makabe K, Ichiyanagi K, Nozawa S, Sato T, Adachi S, Kuwajima K, Yohda M, Sasaki YC.

ATP dependent rotational motion of group II chaperonin observed by X-ray single molecule tracking.

PLoS One 2013 May 29;8(5):e64176.

10.1371/journal.pone.0064176.

  1. Yagi-Utsumi M, Kunihara T, Nakamura T, Uekusa Y, Makabe K, Kuwajima K, Kato K.

NMR characterization of the interaction of GroEL with amyloid ƒŔ as a model ligand.

FEBS Lett. 587, 1605-9, 2013. 

10.1016/j.febslet.2013.04.007.

  1. Chandak MS, Nakamura T, Makabe K, Takenaka T, Mukaiyama A, Chaudhuri TK, Kato K, Kuwajima K.

The H/D-exchange Kinetics of the Escherichia coli Co-chaperonin GroES Studied by 2D-NMR and DMSO-Quenched Exchange Methods.

J Mol Biol. 425, 2541-60, 2013.

10.1016/j.jmb.2013.04.008.

  1. Nakamura T, Aizawa T, Kariya R, Okada S, Demura M, Kawano K, Makabe K, Kuwajima K.

Molecular mechanisms of the cytotoxicity of human ƒż-lactalbumin made lethal to tumor cells (HAMLET) and other protein-oleic acid complexes.

J Biol Chem. 288, 14408-14416, 2013.

10.1074/jbc.M112.437889.

  1. Makabe K*, Nakamura T, Kuwajima K.

Structural insights into the stability perturbations induced by N-terminal variation in human and goat ƒż-lactalbumin.

Protein Eng Des Sel. 26, 165-170, 2013

10.1093/protein/gzs093.

  1. Mukaiyama A, Nakamura T, Makabe K, Maki K, Goto Y, Kuwajima K.

The Molten Globule of ƒŔ2-Microglobulin Accumulated at pH 4 and Its Role in Protein Folding.

J Mol Biol. 425, 273-291, 2013

10.1016/j.jmb.2012.11.002. 

  1. Mukaiyama A, Nakamura T, Makabe K, Maki K, Goto Y, Kuwajima K.

Native-state Heterogeneity of ƒŔ2-Microglobulin as Revealed by Kinetic Folding and Real-time NMR Experiments.

J Mol Biol. 425, 257-272, 2013

10.1016/j.jmb.2012.11.004.

  1. Tomoyori K, Nakamura T, Makabe K (Equal contribution with the 1st author), Maki K, Saeki K, Kuwajima K.

Sequential Four-state Folding/unfolding of Goat ƒż-Lactalbumin and Its N-Terminal Variants

Proteins, 80, 2191-206, 2012.

10.1002/prot.24109

  1. Chen J, Yagi H, Sormanni P, Vendruscolo M, Makabe K, Nakamura T, Goto Y, Kuwajima K.

Fibrillogenic propensity of the GroEL apical domain: A Janus-faced minichaperone

FEBS Letters, 586, 1120-1127, 2012.

10.1016/j.febslet.2012.03.019

  1. Chen J, Makabe K, Nakamura T, Inobe T, Kuwajima K.

Dissecting a Bimolecular Process of MgATP2- Binding to the Chaperonin GroEL.

J Mol Biol. 410, 343-356, 2011.

  1. Biancalana M, Makabe K, Koide S.

Minimalist design of water-soluble cross-beta architecture.

Proc Natl Acad Sci U S A. 107, 3469-3474, 2010

  1. Nakamura T, Makabe K, Tomoyori K, Maki K, Mukaiyama A, Kuwajima K.

Different Folding Pathways Taken by Highly Homologous Proteins, Goat alpha-Lactalbumin and Canine Milk Lysozyme.

J Mol Biol. 396, 1361-1378, 2010.

  1. Ochi A, Makabe K, Kuwajima K, Hori H.

Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes.

J Biol Chem. 285, 9018-9029, 2010.

  1. Huang J, Makabe K, Biancalana M, Koide A, Koide S.

Structural Basis for Exquisite Specificity of Affinity Clamps, Synthetic Binding Proteins Generated through Directed Domain-interface Evolution.

J Mol Biol. 392, 1221-1231, 2009

  1. Biancalana M, Makabe K, Koide A, Koide S.

Molecular Mechanism of Thioflavin-T Binding to the Surface of beta-Rich Peptide Self-Assemblies.

J Mol Biol. 385, 1052-1063, 2009

  1. Makabe K, Koide S.

The promiscuity of beta-strand pairing allows for rational design of beta-sheet face inversion.

J Am Chem Soc. 130, 14370-14371, 2008

  1. Biancalana M, Makabe K (Equal contribution with the 1st author), Koide A, Koide S.

Aromatic cross-strand ladders control the structure and stability of beta-rich peptide self-assembly mimics.

J Mol Biol. 383, 205-213, 2008

  1. Huang J, Koide A, Makabe K, Koide S.

Design of protein function leaps by directed domain interface evolution.

Proc Natl Acad Sci U S A. 105, 6578-6583, 2008

  1. Makabe K, Biancalana M, Yan S, Tereshko V, Gawlak G, Miller-Auer H, Meredith SC, Koide S.

High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble beta-sheet scaffold.

J Mol Biol. 378, 459-467, 2008.

  1. Makabe K, Nakanishi T, Tsumoto K, Tanaka Y, Kondo H, Umetsu M, Sone Y, Asano R, Kumagai I. 

Thermodynamic consequences of mutations in Vernier zone residues of a humanized anti-human epidermal growth factor receptor (EGFR) murine antibody, 528.

J Biol Chem. 283, 1156-1166, 2008

  1. Makabe K, Yan S, Tereshko V, Gawlak G, Koide S.

ƒŔ-Strand flipping and slipping triggered by turn replacement reveal the opportunistic nature of ƒŔ-strand pairing

J Am Chem Soc. 129, 14661-14669 2007

  1. Onoda T, Rahman M, Nara H, Araki A, Makabe K, Tsumoto K, Kumagai I, Kudo T, Ishii N, Tanaka N, Sugamura K, Hayasaka K, Asao H.

Human CD4+ central and effector memory T cells produce IL-21: effect on cytokine-driven proliferation of CD4+ T cell subsets.

Int. Immunol. 10, 1191-1199, 2007

  1. Akamatsu N, Yamada Y, Hasegawa H, Makabe K, Asano R, Kumagai I, Murata K, Imaizumi Y, Tsukasaki K, Tsuruda K, Sugahara K, Atogami S, Yanagihara K, Kamihira S. 

High IL-21 receptor expression and apoptosis induction by IL-21 in follicular lymphoma. 

Cancer Lett. 256, 196-206, 2007

  1. Yan S, Gawlak G, Makabe K, Tereshko V, Koide A, and Koide S 

Hydrophobic Surface Burial Is the Major Stability Determinant of a Flat, Single-layer beta-Sheet. 

J Mol Biol. 368, 230-243, 2007

  1. Makabe K, McElheny D, Tereshko V, Hilyard A, Gawlak G, Yan S, Koide A and Koide S

Atomic structures of peptide self-assembly mimics. 

Proc Natl Acad Sci U S A. 103, 17753-17758, 2006

  1. Asano R, Sone Y, Makabe K, Tsumoto K, Hayashi H, Katayose Y, Unno M, Kudo T, Kumagai I.

Humanization of the bispecific epidermal growth factor receptor x CD3 diabody and its efficacy as a potential clinical reagent. 

Clin Cancer Res. 13, 4036-4042, 2006

  1. Makabe K, Tereshko V, Gawlak G, Yan S, Koide S. 

Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineering.

Protein Science 8, 1907-1914, 2006

  1. Makabe K, Asano R, Ito T, Tsumoto K, Kudo T, Kumagai I, Tumor-directed lymphocyte-activating cytokines: refolding-based preparation of recombinant human interleukin-12 and an antibody variable domain-fused protein by additive-introduced stepwise dialysis. 

Biochem Biophys Res Commun. 328, 98-105, 2005

  1. Hayashi H, Asano R, Tsumoto K, Katayose Y, Suzuki M, Unno M, Kodama H, Takemura S, Yoshida H, Makabe K, Imai K, Matsuno S, Kumagai I, Kudo T. A highly effective and stable bispecific diabody for cancer immunotherapy: cure of xenografted tumors by bispecific diabody and T-LAK cells. 

Cancer Immunol Immunother. 53, 497-509, 2004

  1. Asano R, Kudo T, Nishimura Y, Makabe K, Hayashi H, Suzuki M, Tsumoto K, Kumagai I. Efficient construction of a diabody using a refolding system: anti-carcinoembryonic antigen recombinant antibody fragment. 

J Biochem. 132 903-909, 2002

  1. Asano R, Kudo T, Makabe K (Equal contribution with the 1st author), Tsumoto K, Kumagai I. 

Antitumor activity of interleukin-21 prepared by novel refolding procedure from inclusion bodies expressed in Escherichia coli. 

FEBS Lett. 528, 70-76, 2002