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Hasan DeMirci

Email: 
Hasan_DeMirci@stanford.edu
Affiliation: 
Research Associate

Hasan DeMirci is a member of the Biosciences Division at SLAC National Accelerator Laboratory and also affiliated with Non-Periodic Imaging group at Stanford PULSE Institute. He completed his B.S. at Bosphorus University in 2002 and later obtained a Ph.D. in Molecular Biology, Cell Biology and Biochemistry at Brown University in 2007. 

ResearchMy research focuses on the structural biology of mutant prokaryotic ribosomes. I am interested in characterizing the function and dynamics of these mutants, with an eye toward answering questions in structure and dynamics of ribosomes which are resistant to some of today's commonly-used antibiotics. My current research efforts include methods development for ambient-temperature serial femtosecond X-ray crystallography (SFX) studies of ribosomes at next-generation lightsources like the Linac Coherent Light Source (LCLS) here at SLAC.

Recently, our latest work on a sample injector developed in-house by our group, the coMESH ("concentric microfluidic electric sample holder"), was published in Nature Methods. Using this method we were able to deliver microcrystals of 30S ribosomal subunits to the LCLS beam at ambient temperature, while kept in their native mother liquor. We solved the structure reported in the paper using several hundred (360) microliters of sample. In a previous preliminary paper (DeMirci et al., 2013), we used 10+ milliters of sample, and we had to choose between keeping my crystals in their unmodified mother liquor and using other sample delivery methods that had low flow rates. The emergence of coMESH meant we did not have to modify my crystals and we needed much less sample than before.

Based on our and others' additional experience using this sample injector, we are optimistic that we can use coMESH to deliver a wide variety of macromolecular crystals to an XFEL beam, meaning the features we benefited from can potentially place SFX within reach for many more biologists.

 


Diagram of the improved XFEL sample injector developed by Raymond Sierra and NPI (Sierra et al., 2015).
 


Diffraction pattern of T. thermophilus small (30S) ribosomal subunit taken at LCLS, illustrating potential for diffraction at high resolution at an XFEL (DeMirci et al., 2013).



Schematic of the original electrospin injection method ("MESH") for ambient-temperature SFX experiments at LCLS and other XFELs (Sierra et al., 2012).
 

We have also explored fixed-target femtosecond crystallography for mutant ribosomes, like this T. thermophilus ribosomal mutant missing the small Thx protein, at the LCLS using the goniometer based approach of Cohen et al. (2014).


T. thermophilus ribosome engineered by S. T. Gregory, H. DeMirci, et al. missing 26-aa Thx protein in the 30S subunit; ordinarily present in wild-type Tth (Dao et al., 2015).

Publications: A complete list of our publications is available at PubMed.

Media:

The Author File: Hasan DeMirci (Nature Methods)
Innovation Boosts Study of Fragile Biological Samples at SLAC's X-ray Laser (SLAC News)
Ribosome Research Takes Shape at SLAC (SLAC News)
SLAC Public Lecture Video: Mutant Ribosomes and the Action of Antibiotics
Science of SLAC Video: 'Dancing Ribosomes: The Dynamics of Decoding'

Team: I work with Ray Sierra (Mechanical Engineering/Sample Delivery/Microfluidics) and Han Dao (Biology/Crystallography). I also work with the new Biosciences Division at SLAC, applying crystallography and other methods of structural biology toward some of the current research questions being pursued there.

Collaborators: In addition to my own projects, I collaborate with the following investigators on a variety of projects:

  • Michael Levitt, Dept. of Structural Biology, Stanford School of Medicine
  • Jody Puglisi, Dept. of Structural Biology, Stanford School of Medicine
  • Tony Ricci and Alan Cheng, Dept. of Otolaryngology - Head and Neck Surgery, Stanford School of Medicine
  • Masami Otsuka, Faculty of Life Science, Kumamoto University
  • Paul F. Agris, The RNA Institute, University at Albany

Mentorship: I enjoy discussing the theory and practice behind my science and have had the opportunity to share my knowledge with some young, prospective scientists.

For summer 2017, the following students were in my lab:

  • Paul Mgbam
  • Aldis Petriceks
  • Yash Rao
  • Brandon Walker

In summer 2016, I hosted some new students, in addition to several returning students:

  • Trevor Obrinsky, Gonzaga University
  • Alex McGurk, Connecticut College
  • Returning students: Fulya Aksit, Halilibrahim Ciftci, Brandon Hayes, Paul Mgbam, Yash Rao

In summer 2015, I supervised the following students in my lab:

  • Halilibrahim Ciftci, Kumamoto University (Kumamoto, Japan)
  • Radman Ahmadi, San Jose State University
  • Lindsey Zhang, U.C. Berkeley
  • Yashas Rao, Cal. Poly. State University San Luis Obispo
  • Paul Mgbam, Santa Clara University
  • Fulya Aksit, Koç University (Istanbul, Turkey)

In summer 2014, I mentored Brandon Hayes (Cal. Poly. San Luis Obispo, class of 2016).

I welcome students interested in learning techniques in X-ray crystallography to spend a term in my lab, especially during the summer time. Please contact me via email to discuss potential arrangements.


NPI Group Summer 2015 (left to right): Halilibrahim Ciftci, Han Dao, Hasan DeMirci, Lindsey Zhang, Ray Sierra, Radman Ahmadi, Yash Rao, Paul Mgbam, Mark Hunter (LCLS)



NPI Group Summer 2015 & Mark Hunter (LCLS) Back: (left to right) Han Dao, Fulya Aksit, Paul Mgbam, That Mark Guy, Radman Ahmadi, Raymond Sierra, Halilibrahim Ciftci. Front: Hasan DeMirci, Yash Rao, Lindsey Zhang

2015 Summer Intern Mentorship:


Yash Rao (foreground) and Lindsey Zhang (background) observe crystals grown in microbatch wells using the stereoscope. (SLAC National Accelerator Laboratory)



Radman Ahmadi (left) and Paul Mgbam (right) perform crystallization screening in the lab. (SLAC National Accelerator Laboratory)


Han Dao examines a protein model built from crystallography data collected at SSRL. (SLAC National Accelerator Laboratory)

 


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