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..Cold ion trap laser spectroscopy …… reveals the molecular recognition of a binding motif, SIVSF, which mimics theadrenergic receptor. As described by S. Ishiuchi, M. Fujii, and co-workers in theirCommunication on page 5626 ff. , SIVSF distinguishes the difference in the molecularstructures of various ligands and recognizes whether the ligand is the proper one or not.

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- 20 -

o N N N s

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i A01 1. L▲D.P. Tran, K. Takemura, K. Kuwata and *A. Kitao "Protein-Ligand Dissociation Simulated by Parallel Cascade Selection

Molecular Dynamics" J. Chem. Theory Comput., , 14, 404−417 (2018). 2. ▲ *N. Yoshida, *M. Higashi, H.Motoki, S. Hirota "Theoretical Analysis of the domain-swapped dimerization of cytochrome

c: An MD and 3D-RISM approach " J. Chem. Phys., , 148, 025102 (2018). 3. ▲ F. Lu, N. Kitamura, T. Takaya, K. Iwata, *T. Nakanishi, *Y. Kurashige "Experimental and theoretical investigation of

fluorescence solvatochromism of dialkoxyphenyl-pyrene molecules" Phys. Chem. Chem. Phys., , 20, 3258-3264 (2018)

4. ▲*P. Pongprayoon and *T. Mori "The critical role of dimer formation in monosaccharides binding to human serum albumin"Phys. Chem. Chem. Phys., , 20(5), 3249-3257 (2018).

5. L▲*A. Kitao and K. Takemura, "High anisotropy and frustration: the keys to regulating protein function efficiency in crowded environments" Curr. Opin. Struct. Biol., , 42, 50-58 (2017).

6. L▲*K. Yagi and B. Thomsen, “Infrared spectra of protonated water clusters, H+(H2O)4, in Eigen and Zundel forms studied by vibrational quasi-degenerate perturbation theory” J. Phys. Chem. A, , 121 (12), 2386-2398 (2017).

7. ▲*T. Kawasaki and *K. Kim "Identifying time scales for violation/preservation of Stokes-Einstein relation in supercooled water" Sci. Adv., 3(8), , e1700399 (7pages) (2017).

8. L▲ H.M. Dokainish, D. Yamada, T. Iwata, H. Kandori and *A. Kitao "Electron Fate and Mutational Robustness in the Mechanism of (6-4) Photolyase-Mediated DNA Repair" ACS Catalysis, , 7(7), 4835-4845 (2017).

9. L▲M. Kamiya, and *S. Hayashi "Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation” J. Phys. Chem. B, , 121, 3842-3852 (2017).

10. ▲*T. Furuta, and M. Sakurai "Structural Dynamics of the Heterodimeric ABC Transporter TM287/288 Induced by ATP and Substrate Binding" Biochemistry, , 55(48), 6730-6738 (2016).

11. ▲W.-L. Hsu, T.Furuta, and *M. Sakurai "ATP Hydrolysis Mechanism in a Maltose Transporter Explored by QM/MM Metadynamics Simulation" J. Phys. Chem. B, , 120(43), 11102-11112 (2016).

12. L▲Y. Nishihara and *A. Kitao "Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor" Proc. Natl. Acad. Sci. U.S.A., , 112(25), 7737-7742 (2015).

13. L▲R. Harada and *A. Kitao "Non-targeted parallel cascade selection molecular dynamics (nt-PaCS-MD) for enhancement of the conformational sampling of proteins" J. Chem. Theory Comput., , 11(11), 5493-5502 (2015).

14. ▲N. Kikkawa, L. Wang, and *A. Morita "Microscopic Barrier Mechanism of Ion Transport through Liquid-Liquid Interface" J. Am. Chem. Soc., 137(25), 8022-8025 (2015).

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19. *H. Torii "Amide I vibrational properties affected by hydrogen bonding out-of-plane of the peptide group" J. Phys. Chem. Lett., , 6 (4), 727-733 (2015).

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A02 1. L▲ M. Mizuno, A. Nakajima, H. Kandori, and *Y. Mizutani “Structural Evolution of a Retinal Chromophore in the

Photocycle of Halorhodopsin from Natronobacterium pharaonis” J. Phys. Chem. A, , 122, 2411-2423 (2018). 2. ▲H. Oikawa, T. Takahashi, S. Kamonprasertsuk and *S. Takahashi “Microsecond resolved single-molecule FRET time

series measurements based on the line confocal optical system combined with hybrid photodetectors” Phys. Chem. Chem. Phys., , 20(5), 3277-3285 (2018).

3. L▲T. Sekiguchi, M. Tamura, H.Oba, P. Çarçarbal, R. R. Lozada-Garcia, A. Zehnacker-Rentien, G. Grégoire, *S. Ishiuchi, and *M. Fujii “Molecular recognition by a short partial peptide of adrenergic receptor – Bottom-up approach” Angew. Chem. Int. Ed., , in press (2018).

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, 20, 3395 - 3402 (2018). 5. L▲T. Oshima, T. Ichiba, K. S. Qin, K. Muraoka, J. J. M. Vequizo, K. Hibino, R. Kuriki, S. Yamashita, K. Hongo, T. Uchiyama,

K. Fujii, D. Lu, R. Maezono, A. Yamakata, H. Kato, K. Kimoto, M. Yashima, Y. Uchimoto, M. Kakihana, O. Ishitani, H. Kageyama and K. Maeda* "Undoped Layered Perovskite Oxynitride Li2LaTa2O6N for Photocatalytic CO2 Reduction with Visible Light" Angew. Chem. Int. Ed., , in press (2018).

6. ▲*T. Takaya, M. Anan, and *K. Iwata "Vibrational relaxation dynamics of β-carotene and its derivatives with substituents on terminal rings in electronically excited states as studied by femtosecond time-resolved stimulated Raman spectroscopy in the near-IR region" Phys. Chem. Chem. Phys., , 20(5), 3320-3327 (2018).

7. L▲*Y. Mizutani "Time-resolved Resonance Raman Spectroscopy and Application to Studies on Ultrafast Protein Dynamics,", Bull. Chem. Soc. Jpn., 90, 1344 - 1371 (2017).

8. ▲*M. Shibata, *H. Nishimasu, N. Kodera, S. Hirano, T. Ando, T. Uchihashi and *O. Nureki "Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy" Nat. Commun., , 8, 1430 (2017).

9. ▲T. Kozai, T. Sekiguchi, T. Satoh, H. Yagi, *K. Kato and *T. Uchihashi" Two-step process for disassembly mechanism of proteasome α7 homo-tetradecamer by α6 revealed by high-speed atomic force microscopy" Sci. Rep., , 7, 15373 (2017).

10. ▲S. Yoshidomi, M. Mishima, S. Seyama, *M. Abe, Y. Fujiwara, and *T. Ishibashi "Direct Detection of a Chemical Equilibrium between a Localized Singlet Diradical and Its σ-Bonded Species by Time Resolved UV-vis and IR Spectroscopy: Notable Nitrogen-Atom Effects" Angew. Chem. Int. Ed., , 56, 2984-2988 (2017).

11. ▲M. Kondoh, M. Mizuno, and *Y. Mizutani “Importance of Atomic Contacts in Vibrational Energy Flow in Proteins” J. Phys. Chem. Lett., , 7, 1950–1954 (2016).

12. L▲H. Kuramochi, S.Takeuchi, K. Yonezawa, H. Kamikubo, M. Kataoka, T. Tahara “Probing ultrafast photoreceptive responses inside photoactive yellow protein with time-domain Raman” Nat. Chem., , 9, 660-666 (2016).

13. ▲K. Matsuzaki, R. Kusaka, S. Nihonyanagi, S. Yamaguchi, T. Nagata, T. Tahara “Partially hydrated electrons at the air/water interface observed by UV-excited time-resolved heterodyne-detected vibrational sum frequency generation spectroscopy” J. Am. Chem. Soc., , 138, 7551-7557 (2016).

14. L▲*T. Ikeya, T. Hanashima, S. Hosoya, M. Shimazaki, S. Ikeda, M. Mishima, P. Güntert and *Y. Ito "In-cell structure determination of proteins at near-physiological concentration" Sci. Rep., , 6, 38312 (2016).

15. L▲#H. Isojima, #R. Iino, Y. Niitani, H. Noji, *M. Tomishige (#Equal contribution) “Direct observation of intermediate states during the stepping motion of kinesin-1” Nat. Chem. Biol., , 12, 290-297 (2016).

16. L▲#M. Baba, #K. Iwamoto, R. Iino, H. Ueno, M. Hara, A.Nakanishi, J. Kishikawa, *H. Noji, and *K. Yokoyama (#Equal contribution) “Rotation of artificial rotor axles in rotary molecular motors” Proc. Natl. Acad. Sci. U.S.A., , 113, 11214-11219 (2016) .

17. ▲M. Saito, S. Kamonprasertsuk, S. Suzuki, K. Nanatani, H. Oikawa, K. Kushiro, M. Takai, P.-T. Chen, E. H.-L. Chen, R. P.-Y. Chen, and *S.Takahashi “Significant Heterogeneity and Slow Dynamics of the Unfolded Ubiquitin Detected by Confocal Method of Single-Molecule Fluorescence Spectroscopy” J. Phys. Chem. B, , 120(34), 8818-8829 (2016).

18. L▲T. Otosu, K. Ishii, T. Tahara “Microsecond protein dynamics observed at the single molecule level” Nat. Commun., , 6, 7685 (2015).

19. ▲M. Miyazaki, R.Ohara, K. Daigoku, K. Hashimoto, J. R. Woodward, C. Dedonder, *C. Jouvet, and *M, Fujii “Electron-Proton Decoupling in Excited State Hydrogen Atom Transfer in the Gas Phase” Angew. Chem. Int. Ed., , 54(50), 15089-15093 (2015).

20. ▲K. Mizuse, K. Kitano, H. Hasegawa and *Y. Ohshima "Quantum unidirectional rotation directly imaged with molecules" Sci. Adv., , 1, e1400185 (2015).

21. LH. Yomoda, Y. Makino, Y. Tomonaga, T. Hidaka, *I. Kawamura, T. Okitsu, A. Wada, *Y. Sudo, *A. Naito "Color Discriminating Retinal Configurations of Sensory Rhodopsin I by Photo-Irradiation Solid State NMR Spectroscopy." Angew. Chem. Int. Ed., , 53 (27), 6960-6964 (2014).

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A03 1. L▲A. Pushkarev, K. Inoue, 12 , *H. Kandori, and *O. Beja, “A distinct abundant group of microbial rhodopsins

discovered via functional metagenomics” Nature, in press (2018). 2. L▲*H. Kandori, K. Inoue and S. P. Tsunoda, “Light-driven sodium-pumping rhodopsin: A new concept of active transport”,

Chem. Rev., , in press (2018). 3. ▲ K. Mase, Y. Sasaki, *Y. Sagara, 2 , *N. Yanai, and *N. Kimizuka, "Stimuli-responsive dual-color photon upconversion: an S-T

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with tailorable properties using pyrene-fluorescence as a probe”, Sci. Rep., , 7, 3416 (2017). 5. ▲ M. Yamashina, M. Akita, T. Hasegawa, S. Hayashi, and *M. Yoshizawa, "Polyaromatic nanocapsule as a sucrose receptor

in water", Science Adv., , 3, e1701126 (2017). 6. ▲K. Yazaki, M. Akita, S. Prusty, D. K. Chand, T. Kikuchi, H. Sato, and *M. Yoshizawa, "Polyaromatic molecular peanuts",

Nat. Commun., , 8, 15914 (2017). 7. LR. Taniguchi, 9 , Y. Otani, 4 , *J. Aoki, and *O. Nureki, "Structural insights into ligand recognition by the

lysophosphatidic acid receptor LPA6", Nature, , 548, 356-360 (2017). 8. L▲*K. Oohora, 4 , and *T. Hayashi, "Manganese(V) porphycene complex responsible for inert C–H bond

hydroxylation in a myoglobin matrix", J. Am. Chem. Soc., , 139, 18460–18463 (2017). 9. L▲ W. Piao, *K. Hanaoka, T. Fujisawa, S. Takeuchi, 3 , T. Tahara, T. Nagano, and *Y. Urano, “Development of an

azo-based photosensitizer activated under mild hypoxia for photodynamic therapy”, J. Am. Chem. Soc., , 139, 13713-13719 (2017).

10. ▲B. Maity, S. Abe, and *T. Ueno, “Observation of gold sub-nanocluster nucleation within a crystalline protein cage”, Nat. Commun., ,8, 1480 (2017).

11. L*Y. Shomura, 10 , S. Hirota, and *Y. Higuchi, "Structural basis of the redox switches in the NAD+-reducing soluble [NiFe]-hydrogenase", Science, , 357, 928-932 (2017).

12. L▲K. Yuyama, M. Ueda, S. Nagao, *S. Hirota, *T. Sugiyama, and *H. Masuhara, "A single spherical assembly of protein amyloid fibrils formed by laser trapping", Angew. Chem. Int. Ed., , 56, 6739-6743 (2017).

13. L▲ K. Inoue, S. Ito, Y. Kato, Y. Nomura, M. Shibata, T. Uchihashi, S. P. Tsunoda, and *H. Kandori, "Natural light-driven inward proton pump", Nat. Commun., 7, , 13415 (2016).

14. L▲ D. Yamada, H. M. Dokainish, T. Iwata, 5 , A. Kitao and *H. Kandori, "Functional conversion of CPD and (6-4) photolyases by mutation", Biochemistry, , 55, 4173-4183 (2016).

15. L▲K. Inoue, Y. Nomura and *H. Kandori, "Asymmetric functional conversion of eubacterial light-driven ion pumps", J. Biol. Chem., , 291, 9883-9893 (2016).

16. ▲Y.-G. Huang, 12 , and *O Sato, "Superior thermoelasticity and shape-memory nanopores in a porous supramolecular organic framework", , Nat. Commun., 7, 11564 (2016).

17. ▲ S. Kanegawa, 3 , H. Okajima, A. Sakamoto, T. Iwata, H. Kandori, K. Yoshizawa, and *O. Sato, “Directional electron transfer in crystals of [CrCo] dinuclear complexes achieved by chirality-assisted preparative Mmethod”, J. Am. Chem. Soc., , 138, 14170-14173 (2016).

18. L▲H. E. Kato, K. Inoue, 19 , *H. Kandori, and *O. Nureki, “Structural basis for Na+ transport mechanism by a light-driven Na+ pump”, Nature, , 521, 48-53 (2015).

19. ▲ M. Yamashina, 3 , S. Takeuchi, T. Tahara, and *M. Yoshizawa, "Preparation of highly fluorescent host-guest complexes with tunable color upon encapsulation", J. Am. Chem. Soc., , 137, 9266-9269 (2015).

20. ▲ P. Duan, *N. Yanai, Y. Kurashige, and *N. Kimizuka, “Aggregation-induced photon upconversion through control of the triplet energy landscapes of the solution and solid states”, Angew. Chem. Int. Ed., 5 , 4, 7554-7549 (2015).

21. L▲ K. Inoue, 4 , S. Hayashi, H. Kandori, and *Y. Sudo, “Converting a light-driven proton pump into a light-gated proton channel”, J. Am. Chem. Soc., , 137, 3291-3299 (2015).

22. ▲ S. Horiuchi, 2 , K. Yamamoto, 4 , Y. Kurashige, T. Yanai, and *T. Murahashi, “Multinuclear metal binding ability of a carotene”, Nat. Commun., , 6, 7742 (2015).

23. ▲Y. Ishikawa, 3 , Y. Kurashige, T. Yanai, and *T. Murahashi, “Modulation of benzene or naphthalene binding to palladium cluster sites by the backside-ligand effect”, Angew. Chem. Int. Ed., , 54, 2482-2486 (2015).

24. ▲S. Kang, H. Zheng, *T. Liu, 12 , and *O. Sato, “A ferromagnetically coupled Fe42 cyanide-bridged nanocage”, Nat. Commun., , 6, 5955 (2015).

25. L▲*O. P. Ernst, D. T. Lodowski, M. Elstner, P. Hegemann, L. S. Brown, and H. Kandori, “Microbial and animal rhodopsins: Structures, functions, and molecular mechansims” Chem. Rev., , 114, 126-163 (2014).

26. ▲M. Yamashina, Y. Sei, M. Akita, and *M. Yoshizawa, “Safe storage of radical initiators within a polyaromatic nanocapsule”, Nat. Commun., , 5, 4662 (2014).

27. ▲Z.-S. Yao, 11 , and *O. Sato, “Molecular motor-driven abrupt anisotropic shape change in a single crystal of a Ni complex”, Nat. Chem., , 6, 1079-1083 (2014).

28. ▲*M. J. Hollamby, 11 , and *T. Nakanishi, “Directed assembly of optoelectronically active alkyl‒π-conjugated

- 23 -

molecules by adding n-alkanes or π-conjugated species”, Nat. Chem , , 6, 690-696 (2014). 29. ▲N. Kishi, M. Akita, M. Kamiya, S. Hayashi, H.-F. Hsu, and *M. Yoshizawa, “Facile catch and release of fullerenes using a

photoresponsive molecular tube”, J. Am. Chem. Soc., , 135, 12976-12979 (2013).

i guN Physical Chemistry Chemical Physics i goO

Themed collection “Complex molecular systems: supramolecules, biomolecules and interfaces” p. 2917 -3852) Guest Edited by T. Tahara, A. Kitao, Y. Mizutani, H. Kandori and M. Fujii Royal Society of Chemistry, 2018

URL : http://www.yawaraka.org/

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Interntional Advisory Board, IABM. Sheves (Professor, Weizmann Institute of Science, Israel), J. E. Straub (Professor, Boston University,

USA), S. R. Meech (Professor, University of East Anglia, UK), P. M. Champion (Professor, Northeastern University, USA)

All IAB members participated in the associated international symposium held on June 26-28 and were greatly impressed by the

productivity and scope of the research presented, as well as by the full range of scientific work, collaboration, and outreach

conducted during the project. The number of papers published by the SMS group in high-impact journals was truly impressive, with approximately 115

papers appearing in journals having an impact factor of ~10 or higher. Nearly 700 papers have been published in total, and over

- 34 -

350 invited talks at international meetings were delivered by members of the collaboration. The group also organized five major

9ternational symposia and is in the process of editing a special issue for the prestigious international journal Physical Chemistry

Chemical Physics (PCCP), published by the Royal Society of Chemistry (RSC), entitled “Complex Molecular Systems:

Supramolecules, Biomolecules and Interfaces.”

Importantly, this KAKENHI grant has “seeded” 145 new collaborations, resulting in numerous joint publications. The IAB also

noted a particularly strong record of prizes awarded to both the leaders and the participants within this research collaboration. In the following, we outline specific new scientific directions that have been pioneered and highlight some of the new scientific

concepts that have evolved as a direct result of this project.

u 6 26 28 (2017) o gN e o e

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Phys. Chem. Chem. Phys. g guW 2018 1 30 O

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Nc go o o O

New Concepts and Outstanding Achievements 1) Structural and Dynamic Encapsulation:

2) Dual Ensemble Protein Folding: 2 2

3) Functional Compactness in Biomolecules and Soft Molecular Crystals:

4) Discovery and Engineering of Cationic Protein Pumps

5) Functional Conversion of Ion Pumps N c N i Q

iO 6) Decoding Molecular Softness a e

7) Innovative Probes of Molecular Interfaces

Conclusions

The research accomplishments resulting from this KAKENHI grant were truly outstanding. The breadth of topics explored

through the large number of new collaborations greatly exceeded the high expectations of the IAB. The depth of scientific research

and the significant new concepts developed as a result of this project establish Japan as a world leader in the pioneering area of Soft Molecular

Systems. The IAB commends MEXT for its support of the fundamental

research that has been explored within this project. We enthusiastically

recommend that future extensions of the research developed in this

innovative project be supported.

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