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Structural Insight into the Molecular Mechanism of PET Degradation
A KAIST metabolic engineering research team has newly suggested a molecular mechanism showing superior degradability of poly ethylene terephthalate (PET).
This is the first report to simultaneously determine the 3D crystal structure of Ideonella sakaiensis PETase and develop the new variant with enhanced PET degradation.
Recently, diverse research projects are working to address the non-degradability of materials. A poly ethylene terephthalate (PET)-degrading bacterium called Ideonella sakaiensis was recently identified for the possible degradation and recycling of PET by Japanese team in Science journal (Yoshida et al., 2016). However, the detailed molecular mechanism of PET degradation has not been yet identified.
The team under Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering and the team under Professor Kyung-Jin Kim of the Department of Biotechnology at Kyungpook National University conducted this research. The findings were published in Nature Communications on January 26.
This research predicts a special molecular mechanism based on the docking simulation between PETase and a PET alternative mimic substrate. Furthermore, they succeeded in constructing the variant for IsPETase with enhanced PET-degrading activity using structural-based protein engineering.
It is expected that the new approaches taken in this research can be background for further study of other enzymes capable of degrading not only PET but other plastics as well.
PET is very important source in our daily lives. However, PET after use causes tremendous contamination issues to our environment due to its non-biodegradability, which has been a major advantage of PET. Conventionally, PET is disposed of in landfills, using incineration, and sometimes recycling using chemical methods, which induces additional environmental pollution. Therefore, a new development for highly-efficient PET degrading enzymes is essential to degrade PET using bio-based eco-friendly methods.
Recently, a new bacterial species, Ideonella sakaiensis, which can use PET as a carbon source, was isolated. The PETase of I. sakaiensis (IsPETase) can degrade PET with relatively higher success than other PET-degrading enzymes. However, the detailed enzyme mechanism has not been elucidated, hindering further studies.
The research teams investigated how the substrate binds to the enzyme and which differences in enzyme structure result in significantly higher PET degrading activity compared with other cutinases and esterases, which make IsPETase highly attractive for industrial applications toward PET waste recycling.
Based on the 3D structure and related biochemical studies, they successfully predicted the reasons for extraordinary PET degrading activity of IsPETase and suggested other enzymes that can degrade PET with a newly-classified phylogenetic tree. The team proposed that 4 MHET moieties are the most properly matched substrates due to a cleft on structure even with the 10-20-mers for PET. This is meaningful in that it is the first docking simulation between PETase and PET, not its monomer.
Furthermore, they succeeded in developing a new variant with much higher PET-degrading activity using a crystal structure of this variant to show that the changed structure is better to accommodate PET substrates than wild type PETase, which will lead to developing further superior enzymes and constructing platforms for microbial plastic recycling.
Professor Lee said, “Environmental pollution from plastics remains one of the greatest challenges worldwide with the increasing consumption of plastics. We successfully constructed a new superior PET-degrading variant with the determination of a crystal structure of PETase and its degrading molecular mechanism. This novel technology will help further studies to engineer more superior enzymes with high efficiency in degrading. This will be the subject of our team’s ongoing research projects to address the global environmental pollution problem for next generation.”
This work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries (NRF-2012M1A2A2026556 and NRF-2012M1A2A2026557) from the Ministry of Science and ICT through the National Research Foundation of Korea. Further Contact: Dr. Sang Yup Lee, Distinguished Professor, KAIST, Daejeon, Korea (leesy@kaist.ac.kr, +82-42-350-3930)
(Figure: Structural insight into the molecular mechanism of poly(ethylene terephthalate) degradation and the phylogenetic tree of possible PET degrading enzymes. This schematic diagram shows the overall conceptualization for structural insight into the molecular mechanism of poly (ethylene terephthalate) degradation and the phylogenetic tree of possible PET degrading enzymes.)
2018.01.31 View 9281 -
Harnessing the Strength of KAIST Alumni: New Head of KAA Inaugurated
KAIST alumni gathered in Seoul on January 13 to celebrate the New Year and the newly-elected leadership of the KAIST Alumni Association (KAA). More than 300 alumni, including President Sung-Chul Shin who is also an alumnus of KAIST, joined the gala event held at the Lotte Hotel.
Photo: Ki-Chul Cha(left) and Jung Sik Koh(right)
The KAA inaugurated its new president, Ki-Chul Cha, who was preceded by Jung Sik Koh, the former CEO at the Korea Resources Corporation. His term starts from January 2018 to December 2020.
Cha is the CEO of Inbody Co Ltd., a global company specializing in developing and selling medical instruments, such as a body composition analyzers, and medical solutions. He is also an adjunct professor in the Department of Mechanical Engineering at Yonsei University. Cha obtained a master’s degree in Mechanical Engineering at KAIST in 1980, and a Ph.D. in Bioengineering at the University of Utah, before finishing his post-doc fellowship at Harvard Medical School.
Cha plans to explore the idea that alumni engagement, saying, “KAIST stays as a home in the memories of 60,000 alumni. I will dedicate myself to stimulating the alumni association to make KAISTians proud.”
At the gala event, the KAA awarded the Alumni of the Year honor to six alumni who distinguished themselves in the areas of professional achievement, humanitarianism, and public service. They are the Director of Startup KAIST Professor Byoung Yoon Kim; President of LG Chem Ltd and Head of Battery Research and Development Myung Hwan Kim; Director of INNOX Advanced Materials Co., Ltd Kyung Ho Chang; Vice President of the Korea International Trade Association Jung-Kwan Kim; CEO of Samsung Electro-Mechanics Yun-Tae Lee; and CEO of ENF Technology Jinbae Jung.
Photo: President Shin(far right) poses with six awardees of the Distinguished Alumni Award and the former President of KAA, Koh(far left)
2018.01.16 View 10634 -
KAIST Students Invited to the BNL
Siheon Ryee and Taek Jung Kim, combined Masters and PhD students from the Department of Physics, have been invited to be visiting researchers at the Brookhaven National Laboratory (BNL).
The BNL, located in Long Island, New York, is one of the most esteemed institutes in the United States. Ryee and Kim received the invitation from the Center for Computational Design of Functional Strongly Correlated Materials and Theoretical Spectroscopy. This center was established by scholars who have been leading this field in the United States.
The two students will be participating in developing a methodology and code for calculating strongly correlated electronic materials, and a grant of 40,000 USD will be provided to each student. This amount of support is not often awarded to researchers outside of postdoctoral programs.
Moreover, they are guaranteed to continue their combined Masters and PhD program and write their dissertations under the supervision of their advisor, Professor Myung Joon Han from the Department of Physics.
Professor Han said, “I was impressed by how well-known scholars established the center in order to cooperate with each other to solve challenging problems. Also, I was surprised and happy that my students were invited to this outstanding institute.”
“I believe that doing research with leaders in their field will give valuable experience to the students. At the same time, my students will be a great help to the scholars of the institute,” he added.
2018.01.11 View 7991 -
Professor Jung Awarded the Pople Medal by the APATCC
(Professor Yousung Jung)
Professor Yousung Jung of the Graduate School of EEWS won the Pople Medal from the Asia-Pacific Association of Theoretical & Computational Chemists (APATCC).
The Pople Medal has been awarded annually since 2007 to recognize young scholars in the fields of theoretical/computational chemistry in honor of Sir John Anthony Pople, who passed away in 2004. Dr. Pople was a British theoretical chemist and a Nobel laureate in 1998 for his development of computational methods in quantum chemistry.
The Pople Medal is awarded to scientists at or under the age of 45 in the Asia-Pacific region who have distinguished themselves through pioneering and important contributions.
Professor Jung was honored for his outstanding contributions to developing efficient electronic structure methods and their applications to energy materials discovery. He has published more than 120 papers in prestigious academic journals. He also has an h-index of 44, and has been cited more than 8,000 times.
2018.01.10 View 7380 -
Meet the KAISTian of 2017, Professor YongKeun Park
Professor YongKeun Park from the Department of Physics is one of the star professors in KAIST. Rising to the academic stardom, Professor Park’s daily schedule is filled with series of business meetings in addition to lab meetings and lectures.
The year 2017 must have been special for him. During the year, he published numerous papers in international journals, such as Nature Photonics, Nature Communications and Science Advances. These high performances drew international attention from renowned media, including Newsweek and Forbes. Moreover, recognizing his research performance, he was elected as a fellow member of the Optical Society (OSA) in his mid-30s. Noting that the members’ age ranges from late 50s to early 60s, Professor Park’s case considered to be quite exceptional.
Adding to his academic achievement, he has launched two startups powered of his own technologies. One is called Tomocube, a company specialized in 3-D imaging microscope using holotomography technology. His company is currently exporting the products to multiple countries, including the United States and Japan. The other one is The.Wave.Talk which has technologies for examining pre-existing bacteria anywhere and anytime.
His research career and entrepreneurship are well deserved recipient of many honors. At the 2018 kick-off ceremony, Professor Park was awarded the KAISTian of 2017 in recognition of his developing holographic measure and control technology as well as founding a new field for technology application.
KAISTian of the Year, first presented in 2001, is an award to recognize the achievements and exemplary contribution of KAIST member who has put significant effort nationally and internationally, enhancing the value of KAIST.
While receiving the award, he thanked his colleagues and his students who have achieved this far together. He said, “I would like to thank KAIST for providing environment for young professors like me so that we can engage themselves in research. Also, I would like to mention that I am an idea seeder and my students do the most of the research. So, I appreciate my students for their hard works, and it is very pleasure to have them. Lastly, I thank the professors for teaching these outstanding students. I feel great responsibility over this title. I will dedicate myself to make further progress in commercializing technology in KAIST.”
Expecting his successful startup cases as a model and great inspiration to students as well as professors, KAIST interviewed Professor Park.
Q What made you decide to found your startups?
A I believed that my research areas could be further used. As a professor, I believe that it is a university’s role to create added value through commercializing technology and creating startups.
Q You have co-founded two startups. What is your role in each company?
A So, basically I have two full-time jobs, professor in KAIST and CTO in Tomocube. After transferring the technology, I hold the position of advisor in The.Wave.Talk.
(Holographic images captured by the product Professor Park developed)
Q Do your students also participate in your companies or can they?
A No, the school and companies are separate spaces; in other words, they are not participating in my companies. They have trained my employees when transferring the technologies, but they are not directly working for the companies.
However, they can participate if they want to. If there’s a need to develop a certain technology, an industry-academia contract can be made. According to the agreement, students can work for the companies.
Q Were there any hardships when preparing the startups?
A At the initial stage, I did not have a financial problem, thanks to support from Startup KAIST. Yet, inviting capital is the beginning, and I think every step I made to operate, generate revenue, and so on is not easy.
Q Do you believe KAIST is startup-friendly?
A Yes, there’s no school like KAIST in Korea and any other country. Besides various programs to support startup activities, Startup KAIST has many professors equipped with a great deal of experience. Therefore, I believe that KAIST provides an excellent environment for both students and professors to create startups.
Q Do you have any suggestion to KAIST institutionally?
A Well, I would like to make a comment to students and professors in KAIST. I strongly recommend them to challenge themselves by launching startups if they have good ideas. Many students wish to begin their jobs in government-funded research institutes or major corporates, but I believe that engaging in a startup company will also give them valuable and very productive experience.
Unlike before, startup institutions are well established, so attracting good capital is not so hard. There are various activities offered by Startup KAIST, so it’s worthwhile giving it a try.
Q What is your goal for 2018 as a professor and entrepreneur?
A I don’t have a grand plan, but I will work harder to produce good students with new topics in KAIST while adding power to my companies to grow bigger.
By Se Yi Kim from the PR Office
2018.01.03 View 11485 -
President Shin Reaffirms Innovation Initiatives in New Year Speech
(President Shin and representatives of faculty, students, staff celebrate the New Year in a reception held on January 2 at the auditorium.)
The KAIST community gathered to celebrate a fresh start for the year 2018. At the ceremony, held in the auditorium on January 2, members of KAIST community reaffirmed their commitment to be the trailblazers of Korea and beyond through unwavering innovations.
President Sung-Chul Shin presented his new vision and plan in his New Year speech, which focused on innovation for enhancing institutional competitiveness and global visibility. He said that as you are the future of KAIST, KAIST is the future of Korea. KAIST’s vision for a better future will have a significant impact on national progress and beyond. He stressed that innovation in the five pillars of education, research, technology commercialization, globalization, and future strategy will further advance the excellence of KAIST.
At the ceremony, President Shin also presented the award for ‘the KAISTian of the Year’ to Professor YongKeun Park of the Department of Physics. The annual award recognizes a distinguished professor whose academic accomplishments made the most significant impact.
In his New Year speech, President Shin said that the year 2018 will provide an opportunity to take a leap forward for becoming a ‘Global Value Creative, World-Leading University. The Vision 2031 Committee endorsed the five innovation initiatives to fulfill KAIST’s long-term vision and will open its recommendations to the public on March 20.
Educational innovation tops the initiatives. President Shin explained that the future of Korea is in the hands of talented individuals in science and technology, emphasizing the need to nurture creative, transdisciplinary talents with the capacity to enhance the social value of science and technology.
To this end, KAIST will establish a new undergraduate non-departmental program for transdisciplinary education. This plan will eventually provide students with more options in choosing their major, as well as help students build a strong foundation in basic science and engineering and encourage multidisciplinary approaches.
For creating an innovative institutional research infrastructure, KAIST plans to build a Network of Excellence for the Fourth Industrial Revolution (NExFire) for convergence research. The plan of ‘Cross-Generational Collaborative Labs,’ will bring out a new collaboration platform by pairing up senior and junior faculty. President Shin said it will be a stepping stone to extend the spectrum of knowledge without any cessation.
For technology commercialization, KAIST will maximize its intellectual property and economic value by stimulating technology-invested companies and startups. Close cooperation with venture capitalists at home and abroad will further accelerate the commercialization drive at KAIST.
Saying that the globalization is no long an option but a necessity, he stressed KAIST will strengthen its efforts to established a bilingual campus. “KAIST will make every effort to create a more welcoming and comfortable atmosphere for the international community and their families. We will expand benefits to our international community, such as access to the KAIST Child Care Center and collaboration with the Taejon Christian International School (TCIS),” he said. President Shin added he will further expand global networks and partnerships this year, participating in a diverse range of international events at home and abroad for increasing global visibility.
He also said that well-designed future strategies will complete innovation initiatives. The Future Strategy Research Center will serve as a think tank for identifying future agendas, establishing strategies and advocating for them.
In addition to the five innovation initiatives, President Shin emphasized a new organizational culture that embraces inclusiveness and mutual respect among all of the members of KAIST.
“So far, the ideal qualifications expected of KAISTians have included creativity and a challenging spirit. From now on, we will nurture talents with a focus on the 3Cs: Creativity, Challenge, and Caring. I would like to make a campus in which all members care for each other to help attain mutual growth with warmth and respect," he said.
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2018.01.02 View 9180 -
Expanding Gas Storage Capacity of Nanoporous Materials
A KAIST research team led by Professor Jihan Kim of the Department of Chemical and Biomolecular Engineering has successfully proposed a rational defect engineering methodology that can greatly enhance the gas storage capacity of nanoporous materials. The team conducted a high-throughput computational screening of a large experimental metal-organic framework database to identify 13 candidate materials that could experience significant methane uptake enhancement with only a small proportion of linker vacancy defects.
This research was published online on November 16 in Nature Communications, with M.S. candidate Sanggyu Chong from KAIST as the first author and post-doctorate researcher Günther Thiele from the Department of Chemistry at UC Berkeley as a contributing author.
Metal-organic frameworks, hereinafter MOF, are crystalline nanoporous materials that are comprised of metal clusters and organic linkers continuously bound together by coordination bonds. Due to their ultrahigh surface areas and pore volumes, they have been widely studied for various energy and environment applications.
Similar to other crystalline materials, MOFs are never perfectly crystalline and are likely to contain several different types of defects within their crystalline structures. Among these defects, linker vacancy defects, or the random absence of linker vacancies in their designated bonding positions, are known to be controllable by practicing careful control over the synthesis conditions.
The research team combined the concepts of rational defect engineering over the linker vacancy defects and the potential presence of inaccessible pores within MOFs to propose a methodology where controlled the introduction of linker vacancy defects could lead to a dramatic enhancement in gas adsorption and storage capacities.
The study utilized a Graphic Processing Unit (GPU) code developed by Professor Kim in a high-throughput computational screening of 12,000 experimentally synthesized MOFs to identify the structures with significant amounts of pores that were inaccessible for methane. In determining the presence of inaccessible pores, a flood-fill algorithm was performed over the energy-low regions of the structure, which is the same algorithm used for filling an area with color in Microsoft Paint.
For the MOFs with significant amounts of inaccessible pores, as determined from the screening, the research team emulated linker vacancy defects in their crystalline structures so that the previously inaccessible pores would be newly merged into the main adsorption channel with the introduction of defects for additional surface area and pore volume available for adsorption. The research team successfully identified 13 structures that would experience up to a 55.56% increase in their methane uptake with less than 8.33% of the linker vacancy defects.
The research team believes that this rational defect engineering scheme can be further utilized for many other applications in areas such as selective adsorption of an adsorbate from a gas mixture and the semi-permanent capture of gas molecules.
This research was conducted with the support of the Mid-career Research Program of the National Research Foundation of Korea.
Figure1. A diagram for flood fill algorithm and example of identification of inaccessible regions within the MOFs, using the flood fill algorithm
Figure2. Methane energy contours before and after detect introduction
2017.12.04 View 7986 -
Professor Je-Kyun Park, Awarded by The Korean BioChip Society
On November 9, Je-Kyun Park from the Department of Bio and Brain Engineering at KAIST received an award from the 2017 Fall Meeting of The Korean BioChip Society held in Paradise Hotel Busan, Korea. This year’s meeting recognized Professor Park for developing lab-on-a-chip and microfluidic analytical technologies.
The Korean BioChip Society is a corporation of biochip professional established in 2006 for the development of biochip technology. Every year, the Society selects a recipient based on the nominees’ academic achievements and contributions to bio-fusion industry.
Professor Park served on the international editorial boards of renowned international journals in related fields, including Biosensors and Bioelectronics and Lab on a Chip. He was also the Committee Chairman of MicroTas in 2015.
2017.11.22 View 8320 -
WEF-KAIST to Host a Forum Next April in Korea
(President Shin poses with Chairman Schwab at the meeting in Dubai)
President Sung-Chul Shin and Executive Chairman Klaus Schwab of the World Economic Forum agreed to co-host the Fourth Industrial Revolution Forum next April in Seoul during a meeting at the WEF Global Future Councils 2017 held in Dubai November 11-12.
Next April’s forum will be a follow-up event of the roundtable discussion KAIST and the WEF Center for the Fourth Industrial Revolution co-hosted in October in Seoul. The two hosted the roundtable discussion titled “Mastering the Fourth Industrial Revolution: The Future of Jobs and Inclusive Growth in Korea.”
During the annual meeting in Dubai, Chairman Schwab expressed his deep appreciation to President Shin for hosting the roundtable discussion and proposed a full-fledged forum in partnership with KAIST once again, which Chairman Schwab will be scheduled to attend.
Chairman Schwab emphasized once again that Korea, who has the world’s top high-end technologies such as 5G telecommunications and semiconductor memory, will be the best fit to realize the Fourth Industrial Revolution most rapidly. He also expressed his great interest in the city of Daejeon in which is being considered to become the Special City for the Fourth Industrial Revolution.
The Global Future Council of the WEF is the interdisciplinary knowledge network dedicated to promoting innovative thinking on the future. The annual council convenes in Dubai the most relevant and knowledgeable thought leaders from academia, government, business, and civil society to challenge conventional thinking and develop new insights and perspectives on key global systems, as well as the impact and governance of key emerging technologies. This year, more than 850 world-leading experts from 74 countries participated.
Under the theme of ‘Vision 2030,’ participants explored systematic changes in key areas such as energy, mobility, and infrastructure while reflecting on the impact of technological breakthroughs in artificial intelligence, biotechnology, and other areas related to the Fourth Industrial Revolution.
2017.11.13 View 9149 -
LG's Woo Jong Lee Named the Alumnus of College of Engineering
The College of Engineering at KAIST selected Woo Jong Lee, President and Head of the VC Business Division at LG Electronics Inc., as the 2017 Alumnus of the Year for the College of Engineering.
‘Alumnus of the Year’ is an award given to a distinguished alumnus who has contributed to the development of industrial technology or made outstanding academic achievements.
Lee graduated from KAIST with the master’s degrees in Industrial Engineering. He also worked at Daewoo Motors as an executive member in the development division. He has been a crucial human resource for LG since he joined the company in 2000.
While leading the VC business Division, which was established in 2013, Lee is recognized as a creative engineer as well as a leader in the automotive industry. Focusing on autonomous driving and eco-friendliness, he has been engaged in the production of major projects from the beginning to the end.
Since 2014, outstanding alumni whose achievements have represented KAIST at the highest level have received the award. The first recipient was Tae-Kyung Yoo, an executive at Lumens Co., Ltd., and the second recipient was Jung-Ju Kim, the founder of NXC. In 2016, the award was not given because an appropriate candidate could not be identified.
The award was held in the Industrial Engineering & Management Building (E2) on November 8. Faculty members including the dean of the College of Engineering Jong-Hwan Kim, the vice dean Hyochoong Bang, the head of Industrial & Systems Engineering Taesik Lee, and the dean of the KAIST Academy Tae-Eog Lee attended the ceremony.
After the ceremony, Lee delivered a lecture on ‘Auto-components Business of LG Electronics’ to KAIST students.
2017.11.09 View 8574 -
College of Business Honored with the WRDS-SSNR Innovation Award
(Professor Inmoo Lee (far left), Robert Zarazowski (WRDS), Gregg Gordon (SSRN) and Professor Jae Kyu Lee)
The KAIST College of Business received the WRDS (Wharton Research Data Services)-SSNR Innovation Award for the Asia-Pacific region on October 31 during the AACSB Asia-Pacific Conference in Seoul.
The WRDS-SSRN Innovation Award is intended to elevate the visibility of pioneering research across a broad range of financial and economic topics. Three winners are selected annually from across North America, Europe, and the Asia Pacific based on their ability to demonstrate innovation and research excellence.
The award was created through collaboration with SSRN, the world’s leading early-stage research platform and Elsevier, a global information analytics company specializing in science and health. It honors top business schools that produce exceptional data-driven research. A part of the Wharton School of the University of Pennsylvania, WRDS provides global corporations, universities, and regulatory agencies with the thought leadership, data access, and analytics needed to enable impactful research.
The Dean of the College of Business Youngbae Kim, said that KAIST has been taking the lead in responding to global trends, offering many innovative programs such as an MBA for Social Entrepreneurship and the Master Course for Green Growth Management. KAIST already has been selected as the Most Innovative University in the Asia-Pacific Region by Thomson Reuters for the last two years.
Robert Zarazowski, managing director of WRDS said they recognize and support the outstanding achievement taking place at KAIST as well as its commitment to growth and innovation in business education.
2017.11.03 View 7106 -
Scientist of November, Professor Hyung Jin Sung
Professor Hyung Jin Sung from the Department of Mechanical Engineering at KAIST received a ‘Science and Technology Award of the Month’ given by the Ministry of ICT and Science and the National Research Foundation of Korea for November 2017. He developed technology that can exquisitely control a micrometer-scaled liquid drop on a dime-sized lab-on-a-chip. With his work, he was recognized for reinforcing research capability on microfluidics.
Lab-on-a-chip is an emerging experiment and diagnostic technology in the form of a bio-microchip that facilitates complex and various experiments with only a minimal sample size required. This technology draws a lot of attention not only from medical and pharmaceutical areas, but also the health and environmental field. The biggest problem was that technology for the temperature control of a fluid sample, which is one of the core technologies in microfluidics, has low accuracy. This limit had to be overcome in order to use the lab-on-a-chip more widely.
Professor Sung developed an acoustic and thermal method which controls the temperature of a droplet quickly and meticulously by using sound and energy. This is a thermal method that uses heat generated during the absorption of an acoustic wave into viscoelastic substances. It facilitates a rapid heating rate and spatial-temporal temperature control, allowing heating in desired areas. In addition, Professor Sung applied his technology to polymerase chain reactions, which are used to amplify DNA.
Through this experiment, he successfully shortened the reaction time from 1-2 hours to only three minutes, making this a groundbreaking achievement.
Professor Sung said, “My research is significant for enhancing the applicability of microfluidics. I expect that it will lead to technological innovations in healthcare fields including biochemistry, medical checkups, and new medicine development.”
2017.11.03 View 9821