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. 2022 Dec 23;14(6):1239–1245. doi: 10.1007/s12551-022-01033-6

A fortunate period of overlap with Prof. Haruki Nakamura

Damien Hall 1,2,✉
PMCID: PMC9786412  PMID: 36589736

Abstract

The author recounts a period of overlap with Prof. Haruki Nakamura that stretched from 2007 till the present day. Starting as a short-term research fellow in his laboratory, the author has also been a coauthor, academic colleague, and joint journal editorial board member of Prof. Nakamura.

I first met Prof. Haruki Nakamura in June of 2007 after coming to Osaka to talk with him about the possibility of taking on a short-term research position in his laboratory. At that stage, he was the Professor in charge of the Laboratory for Bioinformatics and Computational Structural Biology located within the Institute for Protein Research (IPR) at Osaka University as well as the Director of the Protein Data Bank in Japan (PDBj)—the Asian hub of the worldwide PDB. Since that time, he has been an interesting constant in my life and is someone that I have come to admire as much for his character and work ethic as for his scientific prowess, the latter of which is truly remarkable. In this Commentary, I thought I might recount some of the interesting ways my scientific career has intertwined with Prof. Nakamura’s, hopefully shining a light on some of the positive ways that scientists can interact with each other as well as highlighting some of the points that I genuinely admire about Prof. Nakamura.

Moving to Japan

I moved to Japan in October 2006. Prior to this, I worked at the Department of Chemistry at the University of Cambridge with the late Sir Prof. Christopher Dobson. During my time in Cambridge (2003–2006), my research was concerned with protein folding and transport in complex media, which produced papers detailing kinetic models of amyloid formation (Hall and Edskes 2004; Carulla et al. 2005; Hall et al. 2005) and novel considerations of chaperone action (Hall 2006, 2002; Hall and Dobson 2006). During my time at Cambridge, I was supported by a Human Frontiers Science Program (HFSP) Fellowship, and through this scheme, I met and eventually married a Japanese scientist funded by the same program. At the conclusion of a HFSP fellowship, the scheme provided funds to return to your own (or to your partner’s) country. We thought we might try Japan for a few years and so I went there in 2005 to scout out some likely places to continue my work. At that time, I visited three research centers, one at the National Institute for Material Science (NIMS) in Ibaraki-ken, one at Saitama-ken (near Tokyo), and one in Kyoto City. After traveling to these three centers, I was officially offered an ICYS (International Center for Young Scientists) Fellowship at NIMS (which provided independent laboratory space, salary, and research funds), or a non-independent Assistant Professor position located at an institute in Kyoto City. I leaned towards the NIMS position but upon discussion with my partner I was overruled (she indicated a strong preference for jointly living and working somewhere closer to her family), so I took the job in Kyoto. Although the city of Kyoto was beautiful, the institutional facilities fantastic, and the research laboratory filled with very kind workmates, I quickly realized that I had made a mistake. The professor, whose laboratory I had joined, was an authoritarian with a philosophical perspective that was not entirely in sympatico with my own outlook - so I quietly resigned after 6 months (while industriously filling my evenings looking for a new place to do research).

Joining the Nakamura laboratory

Perhaps, there were fewer scientists competing for positions in 2007, or the gloss of my previous positions at the NIH and University of Cambridge still shone bright, but I luckily managed to secure a few research offers from my evening search activities. Among the opportunities on offer, I was particularly fortunate to be able to split my research time between two different laboratories, one at the Tokyo Institute of Technology from Monday to Tuesday (led by the experimental biophysicist Prof. Fumio Arisaka1) and one at the Institute for Protein Research at Osaka University from Wednesday to Friday (led by the theoretical and computational biophysicist Prof. Haruki Nakamura). This balance of experiment and theory was perfect for me even if it required a lot of time snoozing during my commute on the train!

After meeting and interviewing with Prof. Nakamura, we decided upon a number of potential likely computational topics, two of which resulted later that year in publications concerned with protein adsorption and protein diffusion on curved surfaces (Hall 2008a, b) (particularly telling is the acknowledgement offered in these two papers). The Nakamura group covered two floors with one devoted to the team of data curators and scientists associated with the PDBj and another associated with the laboratory of bioinformatics and computational structural biology. I was part of the latter section although there was a significant overlap between the two. Within a few weeks of entering the group, I was genuinely impressed by how smart my colleagues were2 . At the time, there were around seven senior scientists with a single student in the laboratory. Such a balance, having only one, or just a few high-quality students immersed within a larger number of mature scientists, was not an accident of timing but rather (as I came to later learn) a characteristic feature of the Nakamura laboratory. Covering everything in the computational realm from quantum level to macroscopic and relational/informatics simulation and theory (with all types of atomistic and coarse-graining levels in between) the group placed a heavy emphasis on techniques for facilitating structural prediction using atomic-level experimental data (X-ray, nuclear magnetic resonance (NMR), and electron microscopy data) as well as estimating protein structure from informatics analysis of sequence data. Starting with Prof. Nakamura’s original contributions in analyzing the effects of electrostatic interactions on protein structure and protein–ligand interactions (Nakamura and Wada 1985; Nakamura et al. 1985a, b, 1988, 1991; Nakamura and Nishida 1987; Nakamura 1988, 1993, 1996), the group concentrated on developing original code, some of which included writing their own molecular dynamics routines and analysis tools (Morikami et al. 1992; for a modern description, see Kasahara et al. 2016; MyPresto5 2022), original methods for estimating likely protein–protein interfaces (Kinoshita and Nakamura 2005; Suzuki et al. 2016), protein–protein interactions (Patil and Nakamura 2005, 2006), protein–ligand association (Kawabata et al. 2013), homology alignment (Standley et al. 2005), and software for visualization and grouping of the ever-growing number of structures deposited within the PDBj (Kinjo et al. 2016).

Every Thursday at 10 am, the group had a laboratory meeting. I recall vividly the quality of those laboratory meetings and still to this day think they are among the best that I have ever attended (I have always used these as the model when later running meetings myself). After an hour of general business discussion (which focused everyone’s attention on the fact that they were part of a laboratory which depended on collective funding and future planning), two speakers gave scientific talks, with the first reviewing a series of papers and the second presenting their own work. Questioning was vigorous and proceeded freely until it became unproductive (usually at that stage Professor Nakamura would interject with a summarizing point outlining the two sides of the problem with a suggestion of the way to resolve the difference). Due to the preponderance of senior scientists within the laboratory, the discussion was substantial, i.e., the questions and answers were pointed without any bloviation—at the time I felt like it was academic heaven! Up till that point in my life, I had a very individual viewpoint of science just concentrating on problems that I found interesting3. After 6 months, the lesson I took from my first encounter with the Nakamura laboratory was that high-level science was a serious business requiring long-term planning and deliberate engagement with scientific institutions.

Starting my own laboratory in Japan

I could have happily stayed in the Nakamura laboratory but young scientific careers must undergo a maturation process for healthy development and so I applied for a few independent group leader positions within Japan. With the support of Prof. Nakamura and Prof. Arisaka, I received a Japan Science and Technology (JST) Wakate Fellowship allowing me to run my own laboratory within the Institute for Basic Medical Science at the University of Tsukuba. As one of fifteen newly appointed Independent Assistant Professors, I received generous start-up funds, salary for a postdoctoral fellow, and block funding for 5 years. My laboratory theme was “The Physical Biochemistry of Disease,” and under this thematic umbrella, I engaged in research on amyloidosis (Hall and Edskes 2009, 2012; Hall and Hirota 2009; Sasahara et al. 2010; Hall 2012; Hall and Huang 2012) and physical aspects of signal transduction (Hall and Hoshino 2010; Hall 2010). Mine was among the first intake of the JST Independent Assistant Professors scheme, and within this group, I was the only foreigner included in the program. To justify the inclusion of a foreigner, I was asked, in addition to my scientific research, to each year engage in one “international” activity. I didn’t really understand this requirement (nor did anyone else in the program) so I decided to interpret this in a way that would be both interesting and fun. As a result, each year I ran a 10-week series of five evening lectures4 grouped within a single theme, with the lecture followed by a wine and cheese night in which the audience got to engage directly with the guest speaker. Over my time at Tsukuba, the various series themes ranged from international policy makers from the Japanese government, foreign embassy–associated science advisors, and Japanese scientists successfully engaging in international associations. The last-mentioned theme was the first that I ran in 2009, and first on the list of invitees was Prof. Nakamura who kindly agreed to give a talk on the PDBj and how it interfaced with all nearby nations by acting as the Asian nexus for submission of protein structures. In this first Wakate Symposium series run in 2009, I had a number of high-powered speakers lined up to give talks, and the Tsukuba University administration was quite nervous about the potential for embarrassment to the program associated with lack of an audience and the apparent strangeness of a wine and cheese after the event. As the initial speaker, Prof. Nakamura set the tenor for the entire program, giving an extremely detailed and professional talk and making a real effort to engage with all one hundred participants (administration officials, academic staff, and student attendees) throughout the wine and cheese follow-up that ran on for about 2 h. After this first successful event, the university administration became significantly less nervous and I even received a few “good job” comments. This was another interesting lesson that I learned from Prof. Nakamura: if you commit to supporting a colleague, do so wholeheartedly and make that commitment excellent.

During my time at Tsukuba, a number of world-shaking events occurred, one of which was the largest earthquake to ever hit Japan, which happened on March 11th of 2011, and which was also coupled with a devastating tsunami and a series of nuclear disasters in the neighboring prefecture of Fukushima. This was a period of genuine tragedy for Japan with nearly 20,000 recorded deaths from the tsunami and significant displacement of the population from the nuclear disaster. Immediately following the nuclear accident, many foreigners either left or refused to visit Japan. Over the following year as society slowly began to recover (and as someone who remained) I found myself asked to participate in a number of scientific events that were often technically above the pay grade of an Assistant Professor5. Usually upon inquiry, I found that I had received a recommendation from either Prof. Nakamura or Prof. Arisaka—I was always touched by their support. This was another lesson that I learned about interacting with junior colleagues—sometimes a small effort on your part can yield large consequences for the person you are helping.

Moving to Australia

At the conclusion of my Wakate Fellowship at the University of Tsukuba, I was set to return to my home country to work at the Australian National University (ANU) with the support of an ANU Senior Research Fellowship. However, prior to starting in Australia, there was a lag period of 6 months (associated with a go-slow from the Australian government in approving Australian visas for foreign nationals), so I needed a job for 6 months. During this time I was fortunate to be able to get a fixed 6-month position as an Assistant Professor with a former laboratory mate from the Nakamura laboratory, Daron Standley, who by this stage was an Associate Professor running his own laboratory of computational biophysics within the Immunology Frontier Research Center (IFREC) in Osaka. This period was a happy, though intensely busy, one, that resulted in an edited special Issue (Hall and dos Remedios 2013) and a number of publications describing novel methods for solving the flexible docking problem (Hall et al. 2014, 2015a) and other problems related to protein association (Furukawa et al. 2014; Hall et al. 2015b). During this time, I took the liberty of once again joining (and presenting at) the Nakamura laboratory meetings located in the next-door building, a situation which allowed me to become re-acquainted with some old friends, notably Assoc. Prof. Akira Kinjo, and also meet a new group of smart Nakamura laboratory members, notable among these were then Visiting Professor Junichi Higo, Visiting Assoc. Prof. Ikuo Fukuda, and two very talented students Gert Bekker and Shinichi Iida.

After receiving final approval for my wife’s visa, I left for Australia in November 2013. However, soon after starting within Australia, I received a visiting fellowship for collaborative work at the Institute for Protein Research (IPR) in 2014. Following this, I then received an appointment as a Tokunin Associate Professor (2014–2018) which required that I spend from three to 6 months each year in Japan conducting collaborative research and teaching coursework within the Osaka University postgraduate program. These appointments corresponded with Prof. Nakamura’s appointment as Director of the IPR and I strongly suspect that my connection and good relations with him played a prominent role in my nomination for these honors. The collaborative research aspect from that time resulted in a number of joint publications concerned with protein folding and aggregation (Hall et al. 2016a, b; Hall et al. 2016a, b; Zhao et al. 2016; Hall 2017; Hall et al. 2018a; Hirota et al. 2019; Wakayama et al. 2019) along with the collation of two special Issues for Biophysical Reviews (Hall and Harding 2016; Hall et al. 2018a). Practically speaking, these fellowships/joint appointments allowed my half-Japanese family to regularly spend some time back in Japan each year and it also allowed me to easily meet the yearly knowledge performance index (KPI) requirement associated with the Australian academia (as my salary was converted to an external research award). As part of the IPR joint appointment program, I also received a lot of practical experience in preparing formal lecture courses and organizing large national (both in Japan and Australia) and international conferences, of which I ran five in total from 2014 to 2018. During Prof. Nakamura’s tenure as Director of the IPR (2014–2018), there was significant government pressure for the IPR to showcase its international engagement role, and throughout this time, the IPR was hosting an international conference nearly every month. Although it was an exciting period for those able to attend, such organizational demands placed significant pressure on all the IPR academic staff (myself included). At this time, in a moment of candid conversation, I asked Prof. Nakamura when he and the other IPR staff could relax a little from such a hectic workload. His reply, “when we retire or die,” made me laugh but I realized that he was only half joking. Throughout my association with the IPR, I had excellent support from Prof. Nakamura and would like to think that I inherited some of his stoicism when dealing with extra duties. It was also during this period that I began to grow up as a scientist—my working time involved engaging in activities that were not just immediately concerned with my own research but which rather represented a service to the scientific community. As part of these extra duties, I became the Deputy Editor of Biophysical Reviews in 2015.

To the USA and back to Japan

After finishing my 5-year fellowship in Australia, I next moved to the USA in 2019, funded by the US Department of Energy via the Oak Ridge Institute for Science and Education—ORISE. Prior to my move, one of Prof. Nakamura’s final acts as Director of the IPR was to nominate me as an IPR Guest Associate Professor—an appointment that I took with me when working as an ORISE Established Scientist at the National Institutes of Health in Bethesda, Maryland. My research work there involved investigating amyloid formation in yeast with the goal of both modelling this process computationally and solving the three-dimensional structure of the amyloid prion via cryo-electron microscopy. My work situation at the NIH was scientifically ideal (resulting in a few high-quality publications (Hall 2020a, b) and another edited special Issue (Hall et al. 2020). My position also allowed me sufficient time and space to engage with my newfound appointment as Chief Editor of the Biophysical Reviews journal which occurred in 2019. Part of my new duties as Chief Editor, was to develop initiatives for the journal and one of these was the Biophysical Reviews national biophysical society partnership program—which aimed to highlight the workings and research strengths of a single country’s biophysical society. Due to my previous associations, I approached some representatives of the Biophysical Society of Japan (BSJ) about the possibility of having them participate as the first example. In arranging this special issue (Komatsuzaki et al. 2020; Hall 2020c), Prof. Nakamura, as a then Associate Editor of Biophysical Reviews and former President of the BSJ, was instrumental in helping to organize meetings and introduce potential participants. With two successful national society issues completed (Komatsuzaki et al. 2020; dos Remedios et al. 2022) and a third one scheduled later for 2023 (Anashkina et al. 2022), I thank Prof. Nakamura once again for his help in launching this program.

At the start of the COVID-19 pandemic in 2020, I cut short my stay in the USA in order to avoid being locked out from my family who had remained in Japan (unfortunately working from home in another country was not an option available with my US funding and visa). In order to facilitate a rapid move back to Japan, I initially inquired about a makeshift position at the IPR but for a number of reasons this turned out to be not possible. So I wrote to Professor Hideki Kandori, to whom I had been previously introduced by Prof. Nakamura. With a suitable degree of urgency, Prof. Kandori kindly organized a position at his institution in Nagoya which allowed for a quick return to Japan that just beat the curfew on foreign entry. Midway through that first year back, I obtained a more permanent position resulting in a move to my present research center at the WPI-Nano Life Science Institute within Kanazawa University. Since being back in Japan, in addition to my service to the Biophysical Reviews journal, I have published two scientific papers, one on the simulation of the spread of the COVID-19 viral infection (Ando et al. 2021) and another on the simulation of measurement of dynamic membrane surfaces using high-speed atomic force microscopy (Hall and Foster 2022) within the BSJ English language journal Biophysics and Physicobiology (BPPB). As Japan starts to open up again, I am very grateful to both Prof. Kandori and Prof. Nakamura for their assistance in facilitating a quick return to Japan prior to the lockdown—an action which has practically meant me being able to see and interact with my children in person during the first 2 years (and worst uncertainties) of the pandemic.

Conclusions

The last few years have been testing for all scientists in different ways. Both during this time and prior to it, I have greatly benefitted from a continuing association with a number of close colleagues—prominent among these being Prof. Haruki Nakamura. It has been a real pleasure both working with him directly and watching him in action from afar. I would not describe him as an overly sentimental person, but rather someone who projects an inherent toughness. He has consistently made excellent scientific decisions and has greatly influenced, for the better, the institutions he has been associated with and the way Japanese (and world) biophysics is organized and practiced. Presenting a cool demeanor he is definitely someone that you would choose to be on your side in a crisis yet he is also capable of great kindness and I have actually never heard someone speak ill of him—quite an amazing achievement in itself! Without tending towards a hagiography, I hope that this Commentary has presented a suitable picture of someone that has both been excellent scientifically, acted honorably, and been steadfast in support of colleagues—a suitably rare combination in both science and life to be remarkable. Happy 70th birthday Haruki.

Funding

DH acknowledges funding associated with the receipt of a “Tokunin” Assistant Professorship carried out at the WPI-Center for Nano Life Science, Kanazawa University. DH also acknowledges the University of Aalto, for an appointment to their Affiliated Researcher Program carried out within the Department of Applied Physics. This work was supported, in part, by KAKENHI Start-Up grant 21K20633 awarded to. D.H.

Declarations

Conflict of interest

The author declares no competing interests.

Footnotes

1

I have previously written about Prof. Arisaka (Hall et al. 2018b).

2

Within the laboratory, at that time, I got to meet and chat with some truly great scientists including (then) Assist. Prof. Yu Takano, (then) Dr. Narutoshi Kamiya, (then) Dr. Daron Standley, (then) Assoc. Prof. Akira Kinjo, (then) Assist. Prof. Takeshi Kawabata, (then) Assist. Prof. Kengo Kinoshita, and (then) Dr. Yasushige Yonezawa. All of these scientists have since gone on to prominent positions with many contributing to this Issue. I remember even the student at that time, Rossen Apostolov, was exceptional (he had previously won a gold medal at the Chemistry Olympiad and spoke nearly perfect Japanese after 6 months of learning). Rossen is now a senior development scientist within the GROMACS consortium.

3

My PhD was conducted in a laboratory of one person; my first and second research positions were funded by fellowships in laboratories immune from granting pressures.

4

Known as the “Wakate Symposia.”

5

During this period, I frequently found myself being invited to speak at conferences and sharing the stage with Nobel prize winners and other similar high-level scientists.

Publisher's note

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References

  1. Anashkina AA, Rubin AB, Gudimchuk NB, Vanin AF, Tsygankov AA, Orlov YL (2022) An open call for contributions to a special issue of Biophysical Reviews highlighting the research themes of VII Congress of Russian Biophysicists 2023. Biophys Rev, pp.1–2. 10.1007/s12551-022-00998-8 [DOI] [PMC free article] [PubMed]
  2. Ando S, Matsuzawa Y, Tsurui H, Mizutani T, Hall D, Kuroda Y. Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19. Sci Rep. 2021;11(1):1–10. doi: 10.1038/s41598-021-86027-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Carulla N, Caddy GL, Hall DR, Zurdo J, Gairí M, Feliz M, Giralt E, Robinson CV, Dobson CM. Molecular recycling within amyloid fibrils. Nature. 2005;436(7050):554–558. doi: 10.1038/nature03986. [DOI] [PubMed] [Google Scholar]
  4. Dos Remedios C, Cranfield C, Whelan D, Cox C, Shearwin K, Ho J, Allen T, Shibuya R, Hibino E, Hayashi K, Li A (2022) A special issue of the Australian Society for Biophysics. Biophysical Reviews, pp.1–2. 10.1007/s12551-022-00936-8 [DOI] [PMC free article] [PubMed]
  5. Furukawa Y, Teraguchi S, Ikegami T, Dagliyan O, Jin L, Hall D, Dokholyan NV, Namba K, Akira S, Kurosaki T, Baba Y. Intrinsic disorder mediates cooperative signal transduction in STIM1. J Mol Biol. 2014;426(10):2082–2097. doi: 10.1016/j.jmb.2014.03.006. [DOI] [PubMed] [Google Scholar]
  6. Hall D, Li A, Cooke R (2020) Biophysics of human anatomy and physiology—a Special Issue in honor of Prof. Cristobal dos Remedios on the occasion of his 80th birthday. Biophys Rev 12(4):731–739. 10.1007/s12551-020-00745-x [DOI] [PMC free article] [PubMed]
  7. Hall D, Dobson CM. Expanding to fill the gap: a possible role for inert biopolymers in regulating the extent of the ‘macromolecular crowding’effect. FEBS Lett. 2006;580(11):2584–2590. doi: 10.1016/j.febslet.2006.04.005. [DOI] [PubMed] [Google Scholar]
  8. Hall D, Dos Remedios CG. Foreword to the biophysics of protein-protein and protein-ligand interactions in dilute and crowded media—a special issue in honor of Allen Minton’s 70th birthday. Biophys Rev. 2013;5(2):57–60. doi: 10.1007/s12551-013-0118-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hall D, Edskes H. Silent prions lying in wait: a two-hit model of prion/amyloid formation and infection. J Mol Biol. 2004;336(3):775–786. doi: 10.1016/j.jmb.2003.12.004. [DOI] [PubMed] [Google Scholar]
  10. Hall D, Edskes H. A model of amyloid’s role in disease based on fibril fracture. Biophys Chem. 2009;145(1):17–28. doi: 10.1016/j.bpc.2009.08.004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hall D, Edskes H. Computational modeling of the relationship between amyloid and disease. Biophys Rev. 2012;4(3):205–222. doi: 10.1007/s12551-012-0091-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hall D, Foster AS (2022) Practical considerations for feature assignment in high-speed AFM of live cell membranes. Biophys Physicobiol e190016. 10.2142/biophysico.bppb-v19.0016 [DOI] [PMC free article] [PubMed]
  13. Hall D, Harding SE. Foreword to ‘Quantitative and analytical relations in biochemistry’—a special issue in honour of Donald J Winzor’s 80th birthday. Biophys Rev. 2016;8(4):269–277. doi: 10.1007/s12551-016-0227-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hall D, Hirota N. Multi-scale modelling of amyloid formation from unfolded proteins using a set of theory derived rate constants. Biophys Chem. 2009;140(1–3):122–128. doi: 10.1016/j.bpc.2008.11.013. [DOI] [PubMed] [Google Scholar]
  15. Hall D, Hoshino M. Effects of macromolecular crowding on intracellular diffusion from a single particle perspective. Biophys Rev. 2010;2(1):39–53. doi: 10.1007/s12551-010-0029-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hall D, Huang L. On the use of size exclusion chromatography for the resolution of mixed amyloid aggregate distributions: I. Equilibrium partition models. Anal Biochem. 2012;426(1):69–85. doi: 10.1016/j.ab.2012.04.001. [DOI] [PubMed] [Google Scholar]
  17. Hall D. On the role of the macromolecular phase transitions in biology in response to change in solution volume or macromolecular composition: action as an entropy buffer. Biophys Chem. 2002;98(3):233–248. doi: 10.1016/S0301-4622(02)00072-8. [DOI] [PubMed] [Google Scholar]
  18. Hall D. Protein self-association in the cell: a mechanism for fine tuning the level of macromolecular crowding? Eur Biophys J. 2006;35(3):276–280. doi: 10.1007/s00249-005-0016-8. [DOI] [PubMed] [Google Scholar]
  19. Hall D. Analysis and interpretation of two-dimensional single-particle tracking microscopy measurements: effect of local surface roughness. Anal Biochem. 2008;377(1):24–32. doi: 10.1016/j.ab.2008.02.019. [DOI] [PubMed] [Google Scholar]
  20. Hall D (2008b) Kinetic models describing biomolecular interactions at surfaces. In: Handbook of Surface Plasmon Resonance. Royal Society of Chemistry Publishing, pp 81–122
  21. Hall D. Effect of heterogeneity on the characterization of cell membrane compartments: I. Uniform Size and Permeability. Anal Biochem. 2010;398(2):230–244. doi: 10.1016/j.ab.2009.11.033. [DOI] [PubMed] [Google Scholar]
  22. Hall D. Semi-automated methods for simulation and measurement of amyloid fiber distributions obtained from transmission electron microscopy experiments. Anal Biochem. 2012;421(1):262–277. doi: 10.1016/j.ab.2011.10.012. [DOI] [PubMed] [Google Scholar]
  23. Hall D. A composite polynomial approach for analyzing the indefinite self-association of macromolecules studied by sedimentation equilibrium. Biophys Chem. 2017;228:10–16. doi: 10.1016/j.bpc.2017.06.002. [DOI] [PubMed] [Google Scholar]
  24. Hall D. A simple method for modeling amyloid kinetics featuring position biased fiber breakage. Biophys Physicobiol. 2020;17:30–35. doi: 10.2142/biophysico.BSJ-2020003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Hall D. On the nature of the optimal form of the holdase-type chaperone stress response. FEBS Lett. 2020;594(1):43–66. doi: 10.1002/1873-3468.13580. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Hall D. Biophysical Reviews’ national biophysical society partnership program. Biophys Rev. 2020;12(2):187–192. doi: 10.1007/s12551-020-00693-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Hall D, Hirota N, Dobson CM. A toy model for predicting the rate of amyloid formation from unfolded protein. J Mol Biol. 2005;351(1):195–205. doi: 10.1016/j.jmb.2005.05.013. [DOI] [PubMed] [Google Scholar]
  28. Hall D, Kardos J, Edskes H, Carver JA, Goto Y. A multi-pathway perspective on protein aggregation: implications for control of the rate and extent of amyloid formation. FEBS Lett. 2015;589(6):672–679. doi: 10.1016/j.febslet.2015.01.032. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Hall D, Li S, Yamashita K, Azuma R, Carver JA, Standley DM. A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein. Biophys Chem. 2014;190:50–55. doi: 10.1016/j.bpc.2014.01.005. [DOI] [PubMed] [Google Scholar]
  30. Hall D, Li S, Yamashita K, Azuma R, Carver JA, Standley DM. RNA–LIM: a novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure. Anal Biochem. 2015;472:52–61. doi: 10.1016/j.ab.2014.11.004. [DOI] [PubMed] [Google Scholar]
  31. Hall D, Zhao R, Dehlsen I, Bloomfield N, Williams SR, Arisaka F, Goto Y, Carver JA. Protein aggregate turbidity:simulation of turbidity profiles for mixed-aggregation reactions. Anal Biochem. 2016;498:78–94. doi: 10.1016/j.ab.2015.11.021. [DOI] [PubMed] [Google Scholar]
  32. Hall D, Zhao R, So M, Adachi M, Rivas G, Carver JA, Goto Y. Recognizing and analyzing variability in amyloid formation kinetics: simulation and statistical methods. Anal Biochem. 2016;510:56–71. doi: 10.1016/j.ab.2016.07.013. [DOI] [PubMed] [Google Scholar]
  33. Hall D, Kinjo AR, Goto Y. A new look at an old view of denaturant induced protein unfolding. Anal Biochem. 2018;542:40–57. doi: 10.1016/j.ab.2017.11.011. [DOI] [PubMed] [Google Scholar]
  34. Hall D, Takagi J, Nakamura H. Foreword to ‘Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines’, a special issue in Honour of Fumio Arisaka’s 70thbirthday. Biophys Rev. 2018;10(2):105–129. doi: 10.1007/s12551-018-0401-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Hirota N, Edskes H, Hall D. Unified theoretical description of the kinetics of protein aggregation. Biophys Rev. 2019;11(2):191–208. doi: 10.1007/s12551-019-00506-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Kasahara K, Ma B, Goto K, Dasgupta B, Higo J, Fukuda I, Mashimo T, Akiyama Y, Nakamura H. myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme. Biophys Physicobiol. 2016;13:209–216. doi: 10.2142/biophysico.13.0_209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Kawabata T, Sugihara Y, Fukunishi Y, Nakamura H. LigandBox: a database for 3D structures of chemical compounds. Biophysics. 2013;9:113–121. doi: 10.2142/biophysics.9.113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Kinjo AR, Bekker GJ, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, Nakamura H (2016) Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic acids research, p.gkw962. 10.1093/nar/gkw962 [DOI] [PMC free article] [PubMed]
  39. Kinoshita K, Nakamura H. Identification of the ligand binding sites on the molecular surface of proteins. Protein Sci. 2005;14(3):711–718. doi: 10.1110/ps.041080105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Komatsuzaki T, Nakamura H, Tame J, Yanaka S, Nagai T, Nagayama K. Editorial for the Special Issue of Biophysical Reviews focused on the Biophysical Society of Japan with select scientific content from the 57th BSJ annual meeting, Miyazaki, Japan, Japan. Biophys Rev. 2020;12(2):183–185. doi: 10.1007/s12551-020-00691-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Morikami K, Nakai T, Kidera A, Saito M, Nakamura H (1992) PRESTO (PRotein Engineering SimulaTOr): A vectorized molecular mechanics program for biopolymers. Comput Chemi 16(3):243–248. 10.1016/0097-8485(92)80010-W
  42. MyPresto5 (2022) https://www.mypresto5.jp/en/ (last accessed December 5th 2022)
  43. Nakamura H, Nishida S. Numerical calculations of electrostatic potentials of protein-solvent systems by the self-consistent boundary method. J Phys Soc Jpn. 1987;56:1609–1622. doi: 10.1143/JPSJ.56.1609. [DOI] [Google Scholar]
  44. Nakamura H, Wada A. Nature of the charge distribution in proteins. III. Electric multipole structures. J Phys Soc Jpn. 1985;54(10):4047–4052. doi: 10.1143/JPSJ.54.4047. [DOI] [Google Scholar]
  45. Nakamura H. Numerical calculations of reaction fields of protein-solvent systems. J Phys Soc Jpn. 1988;57(11):3702–3706. doi: 10.1143/JPSJ.57.3702. [DOI] [Google Scholar]
  46. Nakamura H. Reproduction of correct electrostatic field by charges and dipoles on a closed surface. J Mol Graph. 1993;11(1):30–36. doi: 10.1016/0263-7855(93)85004-A. [DOI] [PubMed] [Google Scholar]
  47. Nakamura H. Roles of electrostatic interaction in proteins. Q Rev Biophys. 1996;29(1):1–90. doi: 10.1017/S0033583500005746. [DOI] [PubMed] [Google Scholar]
  48. Nakamura H, Komatsu K, Umeyama H. Electrostatic complementarities between guest ligands and host enzymes. J Phys Soc Jpn. 1985;54(9):3257–3260. doi: 10.1143/JPSJ.54.3257. [DOI] [Google Scholar]
  49. Nakamura H, Komatsu K, Nakagawa S, Umeyama H. Visualization of electrostatic recognition by enzymes for their ligands and cofactors. J Mol Graph. 1985;3(1):2–11. doi: 10.1016/0263-7855(85)80007-2. [DOI] [Google Scholar]
  50. Nakamura H, Oda Y, Iwai S, Inoue H, Ohtsuka E, Kanaya S, Kimura S, Katsuda C, Katayanagi K, Morikawa K. How does RNase H recognize a DNA. RNA hybrid? Proc Natl Acad Sci. 1991;88(24):11535–11539. doi: 10.1073/pnas.88.24.115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Nakamura H, Sakamoto T, Wada A. A theoretical study of the dielectric constant of protein. Protein Eng Des Sel. 1988;2(3):177–183. doi: 10.1093/protein/2.3.177. [DOI] [PubMed] [Google Scholar]
  52. Patil A, Nakamura H. HINT: a database of annotated protein-protein interactions and their homologs. Biophysics. 2005;1:21–24. doi: 10.2142/biophysics.1.21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Patil A, Nakamura H. Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. FEBS Lett. 2006;580(8):2041–2045. doi: 10.1016/j.febslet.2006.03.003. [DOI] [PubMed] [Google Scholar]
  54. Sasahara K, Hall D, Hamada D. Effect of lipid type on the binding of lipid vesicles to islet amyloid polypeptide amyloid fibrils. Biochemistry. 2010;49(14):3040–3048. doi: 10.1021/bi9019252. [DOI] [PubMed] [Google Scholar]
  55. Shirai H, Ikeda K, Yamashita K, Tsuchiya Y, Sarmiento J, Liang S, Morokata T, Mizuguchi K, Higo J, Standley DM, Nakamura H. High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations. Proteins Struct Funct Bioinforma. 2014;82(8):1624–1635. doi: 10.1002/prot.24591. [DOI] [PubMed] [Google Scholar]
  56. Standley DM, Toh H, Nakamura H. GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures. BMC Bioinforma. 2005;6(1):1–19. doi: 10.1186/1471-2105-6-221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Suzuki H, Kawabata T, Nakamura H. Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Bioinformatics. 2016;32(4):619–620. doi: 10.1093/bioinformatics/btv614. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Wakayama R, Uchiyama S, Hall D. Ionic liquids and protein folding—old tricks for new solvents. Biophys Rev. 2019;11(2):209–225. doi: 10.1007/s12551-019-00509-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Zhao R, So M, Maat H, Ray NJ, Arisaka F, Goto Y, Carver JA, Hall D. Measurement of amyloid formation by turbidity assay—seeing through the cloud. Biophys Rev. 2016;8(4):445–471. doi: 10.1007/s12551-016-0227-5. [DOI] [PMC free article] [PubMed] [Google Scholar]

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