Dr. Chalermpol Kanchanawarin's Theoretical and Computational Biophysics Group

Lab Location

Laboratory of Theoretical and Computational Biophysics

Room 451, 4th Floor, Physical Science (Sci 45 years) Building,

Department of Physics, Faculty of Science. 

Research Interests

My research group aims to understand how proteins work as nano-machines at atomic level. In particular, we use molecular dynamics simulations in combination with theoratical physics and data analysis from biochemical/ biophysical experiments to investigate biomolecular motion and functions.  Our current research topics are

• Ion conduction and pore formation by bacterial protein toxins
• Behaviours of water molecules around proteins and membranes
• Cytoskeletal polymerization of actin and actin like proteins
• Rotary mechanism and proton transport in biomolecular motors such as ATP synthase and Flagellar motors
• Calcium-dependent membrane binding proteins (Annexin A5)

Figure 1 shows 3D structure of a pore-forming protein (side and top view)

Group Members and Collaborations

Most of my research students whom I have been working with have personal interests in biology in some ways. They are not just physics students but also those from various other departments such as chemistry, biochemistry, medical technology, medicine, biology, and genetics etc. I am interested in taking some more research students. If you are interested in learning biophysics and are keen to learn how chemistry, physics, maths and computer are used to study biology then please come to talk to me.

Principal Investigator

Asst. Prof. Chalermpol Kanchanawarin (Ph.D. in physics, University of Illinois at Urbana-Champaign, USA; M.Phys. in physics, University of Oxford, UK)

For more info about me please see My home page.

Current students

• 2013-Present   Ms. Chattip Kurehong (Ph.D. in Molecular Genetics and Genetics Engineering, Mahidol University)
• 2014-Present   Mr. Kanpong Boonthaworn (Ph.D. in Biology, Mahidol University)
• 2014-Present   Ms. Aunyamanee Preuksachonlatharn (B.S. in Physics, Kasetsart University)
• 2014-Present   Mr. Somsak Mongkon (B.S. in Physics, Kasetsart University)
• 2014-Present   Ms. Intuon Chatratin (B.S. in Physics, Kasetsart University)
• 2015-Present   Ms. Worachapar Bunyongkid (B.S. in Physics, Kasetsart University)

Previous students

• 2010-2014       Dr. Chompounoot Imtong (Ph.D. in Molecular Genetics and Genetics Engineering, Mahidol University; Currently teaching in a university in Northern part of Thailand)
• 2010-2013       Mr. Somyot Srikongrak (M.S. in Physics, Kasetsart University; Currently a lecturer at Rumpaipannee Rachapat University, Chantabury)
• 2007-2010       Dr. Taveechai Taveechareonkool (M.D. Ph.D., Mahidol University and  Siriraj Hospital; currently freelance medical doctor) 
• 2007-2010       Mr. Witchukorn Phuthong (B.S. in Physics, Kasetsart University; currently a Ph.D. student doing Biophysics in Department of Materials at Stanford university, US)
• 2008-2010       Ms. Pattama Wapeesittipan (M.S. in Chemistry, Chulalongkorn University; B.S. in Chemistry, Mahidol University; currently doing D.Phil. in chemistry at Edinburgh University, UK)

Collaborations

I belief that one of the best ways to solve a biophysics problem is to work closely with experimentalists who work on that problem. Over the past several years, I have had a great pleasure working with the following people. We have learned a lot from each other.

• Prof. Chanan Angsuthanasombat (experimental biochemist and biophysicist), Institute of Molecular Biosciences, Mahidol university (Salaya campus), Nakorn Pratom, Thailand.
• Dr. Puey Ounjai (Experimental Biophysicist), Department of Biology, Mahidol university, Bangkok, Thailand.

Publications

• Kurehong, C., Kanchanawarin, C., Powthongchin, B., Katzenmeier, G., and Angsuthanasombat, C. (2015) Membrane-pore formation characteristics of the Bordetella pertussis CyaA-Hymolysin Domain, Toxins, 7(5) p1486-96. [IF=2.48]
• Imtong, C., Kanchanawarin, C., Katzenmeier, G., and Angsuthanasombat, C. (2014) Bacillusthuringiensis Cry4Aa insecticidal protein: functional importance of intrinsic stability of the unqique α4–α5 loop comprising the Pro-rich sequence. BBA Proteins and Proteomics, 1844(6) p.1111-8. [IF=3.19]
• Juntadech, T., Kanintronkul, C., Kanchanawarin, C., Katzenmeier, G.,  and Angsuthanasombat, C. (2014). Importance of polarity of the α4–α5 loop residue - Asn166 in the pore-forming domain of the Bacillus thuringiensis Cry4Ba toxin: Implication for ion premeation and pore opening. BBA Biomembranes, 1838(1), p.319-327. [IF=3.43]
• Taveecharoenkool, T, Angsuthanasombat C, Kanchanawarin C.  (2010)  Combined molecular dynamics and continuum solvent studies of the pre-pore Cry4Aa trimer suggest its stability in solution and how it may form pore. PMC Biophysics. 3(10). [IF=2.18]

Research Facilities

We have a high performance computing facility. Together with Asst. Prof. Jiraroj T-Tienprasert, we have designed, built, managed the following computer systems

• a Rocks computer cluster consisting of 16 blade servers each with dual quad-core Opteron CPUs running NAMD programs for doing large scale molecular dynamics simulations (upto about one million atoms).
• two visualization Linux workstations consisting of dual quad-core Xeon CPUs with high-end graphics, stereographics glasses and large memory for analysis of large trajectories of MD data using VMD program.

Note: These machines will not be possible without the support from the following research grants and agencies; 1) Kasetsart University Research and Development Institute (KURDI) Grants for Dr. Chalermpol (# Wor-Tor(Dor)27.51) and  KURDI Grant for Dr. Wiwat, 2) Thailand Research Fund (TRF) Grant No. MRG5180355 for Dr. Chalermpol and TRF Grant for Dr. Palawan, 3) Science Research Fund (ScRF) Grant No. SCRF-E10/2551 from the faculty of science at Kasetsart University, 4) Some funding from a research grant of Dr. Chanan at Mahidol University, 5) Funding from Physics Department, Kasetsart University, 6) Help from technicians from the faculty of science, Kasetsart university.

Funding Resources

Previously, our research group was funded by the following funding agencies.

1. KURDI (Kasetsart University Research and Development Institute

2. TRF (Thailand Research Fund)

3. Faculty of Science, Kasetsart University

4. ThEP Center (Thailand Center of Excellence in Physics)

5. Department of Physics, Kasetsart University

More info about biophysics