May 29, 2008
RIKEN Harima InstituteResearch Promotion Division

Reports on Structural Biophysics Laboratory Periodical Review
Laboratory Leader: Chief Scientist, Masashi Miyano (Dr. Sci.)
Date: December 3, 2007
Venue: RIKEN Harima Institute (SPring-8)
Reviewers:
Prof. Bi-Cheng Wang
(Biochemistry & Molecular Biology, University of Georgia, USA)
Prof. Haruki Nakamura(Institute for Protein Research, Osaka University, Japan)
Prof. Shinya Yoshikawa(Graduate School of Life Science, University of Hyogo, Japan)
Prof. Yoshinori Satow(Graduate School of Pharmaceutical Sciences, The University of Tokyo, Japan)
Reports:
Reviewer1:
This research group has published articles in Science and Nature since 2000, suggesting extremely strong
research activity as a whole.

However, the reviewer does not understand why the chief scientist did not present any

concrete future research plan (or dream) in the review meeting. Unfortunately, this seems to be consistent to the factthat it is unclear what the research objective by driving the four research subjects in the last 7 years is. Therefore, thereviewer strongly encourages for the chief scientist to show his concrete future plan to the member of his researchgroup. All the members of Structural Biophysics Laboratory are quite talented and enthusiastic in their researchsubjects and thus, their future progress as the world-leading scientist is definitely promising. Setting the clear
objective to these young research group members from the Chief Scientist would surely stimulate their research
activities.
Reviewer2:
The most serious point of this research group is that the group leader does not make their research
objectives clear, although there are several research topics performed by the group. To the reviewer's
question at the periodical review meeting about the future goals, the group leader only answered thatthey are going to determine the crystal structures of membrane proteins as many as possible. Inaddition, it does not seem that this group has made much effort to develop or invent any novel
approaches for the structure analyses of membrane proteins, which are widely known to be very
difficult by the current conventional approaches. Probably, it is due to a lack of the scientificmotivation, by which the group wants to reveal any particular biological phenomenon with themembrane proteins.
This field is now very hot in the world, and so international collaborations are critical. However,this group has very rare international collaborations, and has no foreign staffs. The abilities of English
speaking of the members are not quite high except the group leader, as the Japanese researchers'
1standard.
It is not clear that how many original papers have been actually published from this group since
2000, because the corresponding authors are not identified from the publication list correctly. However,when I assume that the corresponding authors are the first or the last authors of the papers in the list,
the publication number becomes very few. In 2000, 1 (#10); in 2001, 1 (#17); in 2002, 0; in 2003, 1 (#31);
in 2004, 3 (#36-38); in 2005, 3 (#43, #56, #58); and in 2006, 3 (#64, #66, #74). Total only 12 papers are
considered to have been published from this group, although there are many collaborative papers withother researchers inside or out of RIKEN. My estimate of the corresponding authors may not be very
correct, but it is true that the name of the group leader does not appear frequently as the first or thelast author. Although the group published one Science and one Nature paper during the period, theresulted publications are not very satisfactory, considering the total research budget, 325 M yen, spentfrom years 2000 to 2006.
Thus, the reviewer does not consider that the current group leader is very suitable for continuing tohave the leadership of the "Structural Biophysics Laboratory", which should have a very important
position in RIKEN. This conclusion has also been confirmed by the fact that the group leader has not
succeeded in obtaining research grants from outside of RIKEN in 2004-2006.
Reviewer3:
Research objectives of this Laboratory are mainly in the three-dimensional structural andfunctional studies of lipid-related proteins. The proteins intensively studied are bovine rhodopsin,human leukotriene C4 synthase (LTC4S), and Bacillus celeus sphingomyelinase (Bc-SMase). These
are of biological and medical interest, hard to be structurally elucidated, and of high scientificsignificance.
The laboratory members are also focusing their efforts on development andimprovement of methods for protein crystallography using synchrotron radiation.
Rhodopsin is a G-protein coupled (photo)receptor (GPCR) embedded in the membrane. The
crystals of rhodopsin were obtained by their collaborators, and its structure was promptly determinedby this Laboratory in the early beginning of the laboratory startup. This structural study was in theforefront of the elucidation of GPCRs, breaking new ground in understanding its function, and ishighly evaluated.
Leukotriene synthase is a membrane-associated protein involved in metabolism of eicosanoid andglutathione. Human LTC4S is a membrane integral protein and a target in the structure-based drug
design. They expressed LTC4S in Schizosaccharomyces yeast and successfully determined its
three-dimensional structures.
Sphingomyelinases cleave sphingomyelin in cell membranes into ceramide and phosphocholine.
Its product ceramide is an important signaling molecule in cellular processes and also in diseases
including cancer and diabetes. They determined the structure of Bc-SMase that contains two
divalent metal ions of Co2+, Mg2+, or Ca2+. They also determined several other proteins including
long-chain fatty acyl CoA synthetase, which have high social impact because of biological and medical
interest.
They contributed to the startup and the success of the Protein 3000 structural genomics project inRIKEN. In this project, they developed fully-automated crystallization and crystal-observation
system TERA as well as protein expression procedures for structural and functional analyses. They
also have made efforts to determine accurate structures at ultra-high resolutions.
Theseachievements are highly remarked.
Management of the Laboratory appeared very good. Laboratory members are composed oftalented and skilled professionals in excellently-managed scientific atmosphere, and collaboratingwith a wide variety of researchers. The members cover most of the technical fields required inmodern protein crystallography: protein expression, purification, crystallization, functional analysis,
2and structure determination. Laboratory facilities are well equipped and maintained. They are
fully taking great advantage in using synchrotron X-rays of SPring-8 located in the same site.
Although future research plans were less spoken by the Chief Scientist of the laboratory in thePeriodical Review meeting, their directions seem highly promising since their past scientificachievements are measured in excellence. Their cooperative involvement in synchrotron X-ray
crystallography as well as in structural biology itself is fully anticipated. They are expected to play
important roles in protein research activities which will be carried out by using powerful XFEL
radiation in the near future.
Overall, the activities of the scientists of this Laboratory are assessed in a high and valuable rank.
Reviewer4:
The Structural Biophysics Laboratory, headed by Dr. Masashi Miyano, has continued to gain astrong reputation among national and international structural biology communities during the last
seven years. The lab clearly possesses a number of strong and unique attributes, including but notlimited to:Focus on lipid-related proteins and biologically important proteins.

Providing enabling technology within and outside RIKEN institutes.

A highly motivated and integrated team of experts.

During the past 7 years, the lab members have implemented the needed infrastructure related totheir mission and level of support. Notably, their accomplishments include:Successfully implemented a hetero host expression system, Schizosaccharomyces prombe formembrane protein expression.

Successfully determined several important lipid-related protein structures and a number ofother biomedical relevant protein structures.

Developed an automated high throughput robotic crystallization and observation system
named TERA.

Established successful collaborations with colleagues within RIKEN, and at other research
institutions in Japan and the USA.



74 original published papers, 36 reviews and 5 book chapters; some of which were published inhigh impact journals.

The Miyano group has focused on several areas of biomedical research, and has produced excellent
results in each of these areas. In close collaboration with colleagues at the University of Washington,
for example, Miyano’s group solved the first detailed structure of bovin rhodopsin in 2000.

This work,

which was published in Science, has now been cited over 2000 times. All other determined structuresfrom Miyano’s group are also from proteins that are of high biomedical relevance, and are targeted forpotential drug discovery. This group of structures includes a recent paper on human leukotriene C4synthase, published in Nature. Dr Miyano’s group has also engaged in the development of highthroughput structural genomics pipelines.

In these areas, the TERA crystallization and observation

system was developed in an impressively short period of time, and has partly served the critical needfor high-throughput crystallography in Japan’s structural genomics efforts.
As to the future plans, Dr. Miyano intends to keep the options open in searching for biologicallysignificant molecules that may not be currently identifiable, and for methodology development toadvance to the “Integral Life Science Research at SPring-8.” While he will continue to work on
obtaining the highest resolution possible for the lipid-related membrane structures that he is studying,
he will also work to develop integrated methods, including EM and XFEL, for structural studies. The
linking of XFEL with crystallography should be an important extension of the structural biology
3capabilities at SPring-8, and is highly significant in view of the unique opportunities for using
advanced XFEL at SPring-8 in the near future. Based on Dr. Miyano’s past track record, enthusiasm
and collaborative nature in scientific work, there is little doubt that he will be unsuccessful in hisfuture research efforts.
With the completion of seven years’ service as Chief Scientist, and the ending of the Tanpaku3000project before advancing into new areas of research, now seems to be an excellent point in time for Dr.
Miyano to consider a sabbatical experience for a period of 3 to 6 months. During this refreshing period,
Dr. Miyano may want to devote 50% of his efforts towards exploring new collaborations andpossibilities, while also keeping the other 50% available for supervising his current research projects
remotely. This will likely add new insight and strength to the operations of the laboratory, which isalready highly innovative and productive.

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