Research

The invention of the atomic force microscope (AFM) in 1986 by Binnig, Quate and Gerber (Phys. Rev. Lett. 56, 930) started a revolution in many branches of science by realizing an unprecedented possibility to visualize and manipulate individual molecules under ambient conditions including water, which is critical for most studies involving bio-molecules. Biomolecular studies are therefore, in my opinion one of the main beneficiaries of this seminal invention. I was very fortunate to start my AFM research in 1997, the year, which marked great progress in AFM-based single-molecule force spectroscopy of proteins and polysaccharides. From the very beginning of my AFM work I experienced a particular appeal to polysaccharides research. This is because the wealth of information contained in their AFM measured force-extension relationships with totally unanticipated deviations from the entropic elasticity of simple polymers prompted me to believe that many interesting and quite fundamental observations can soon be made by studying polysaccharides elasticity. Protein mechanics is, in my opinion, another area of great potential because investigating the elastic properties of individual proteins promises to make significant contributions to the understanding of elasticity of various intra- and extra-cellular structures and of adhesion and mechanotransduction. In addition, investigating mechanical unfolding and refolding reactions of individual proteins under “vectorial” condition can contribute to elucidating the mechanism of protein folding in vitro and in vivo (co-translational folding), which is fundamental to all biology.

More recently we initiated a new area of research by applying the AFM-based technology to study DNA mechanics, damage and repair. While the polysaccharide and protein research is extremely rewarding by continuously offering quite fundamental observations and discoveries to be made, the DNA research promises, in addition, even a greater scientific fulfillment through its possible contributions to medicine and human health. This new “DNA direction” has already proved quite successful. Our (Ke, Humeniuk, S-Gracz, Marszalek) 2007 paper in Physical Review Letters “Direct Measurements of Base Stacking Interactions in DNA by Single Molecule Atomic Force Spectroscopy” was selected by APS News, a publication of the American Physical Society, as one of the 36 most interesting works in Physics in 2007.

For an overview of our research and research in the field, see our recently published reviews:

Projects

AFM design

Improvement of hardware and software for AFM

DNA Damage and Repair

Determining the mechanistic interactions between DNA damage and repair proteins

DNA Mechanics

Revealing the inherent mechanical properties of DNA

Mechanics of polysaccharides

AFM reveals the mechanical complexity of simple sugars

Nanomechanics of repeat proteins

Repeat proteins have many nice properties.

Protein folding

Repeat proteins have many nice properties.

News

Our recent work on Protein S has been highlighted in a feature article in the Duke Mehcanical Engineering and Materials Science, entitled “Slowly Pulling Proteins Apart Reveals Unexpected Path to Stability”.

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Congratulations to Zack Scholl who won the 2014 Student Research Achievement Award for his outstanding poster presentation at the National Biophysical Society 58th Annual Meeting in San Francisco, California. His research in molecular biophysics was titled “N-terminal domain of Luciferase prevents folding pathway from falling into kinetic traps.”

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Congratulations to Dr. Anna Lokstejn and Zack Scholl for getting the outside cover of Chemical Communications with their manuscript entitled “Atomic force microscopy captures folded ribosome bound nascent chains”.

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People

Current group members:

Prof. Piotr Marszalek

Principal investigator
pemar@duke.edu

Dr. Eric Josephs

Post-doc
eric.josephs@duke.edu

Dr. Zackary Scholl

Post-doc
zns@duke.edu

Qing Li

Grad student
ql29@duke.edu

David Wang

Undergraduate researcher
david.wang3@duke.edu

Dhananjay Dhruva (DJ)

Masters student
dhananjay.dhruva@duke.edu

Previous group members:

Lilly Zheng

Lab tech, 2013-2015

Morgan Goodwin

Masters student, 2013-2015

Steve Kusnetsov

Undergradute researcher, 2013-2014

Mark Qi

Undergradute researcher, 2012-2013

Dr. Anna Loksztejn

Post-doc, 2009-2012

Dr. Minkyu Kim

Grad student 2006-2011 and Post-doc 2011-2012

Dr. Whasil Lee

Grad student 2006-2011 and Post-doc 2011-2012

Ye Yang

Graduate Student 2006-2011, currently C/C++ Senior Software Engineer at The MathWorks

Mahir Rabbi

Graduate Student 2006-2011, currently: Networking Solutions Engineer at Sirius Computer Solutions

Julia Weidner

Pratt fellow, 2011

Chien-chung Wang

Visiting graduate student, currently Post-doc at Harvard

Laura Mason

Pratt fellow, 2009-2011

Kristina Rotolo

Pratt fellow, 2009-2011. Currently Manufacturing Project Lead at Abbott Vascular Structural Heart.

Justyna Jaroniec

Visiting graduate student

Michael Sarna

Visiting graduate student

Janusz Strzelecki

Post-doc, currently Associate in Research at Nicolaus Copernicus University

Changhong Ke

Post-doc, currently Associate Professor at the Binghamton University

Qingmin Zhang

Post-doc

Michael Humenium

Undergraduate student, 2006-2007

Tiziana Svaldo-Lanero

Post-doc, 2006-2007. Currently, University of Li├Ęge.

Yong Jiang

Post-doc

Gwangrog Lee

Graduate student, 2002-2006. Currently Associate Professor Gwangju Institute of Science and Technology.

Collaborators

Protein mechanics

Computational Modeling

Polysaccharide Mechanics

Nuclear Magnetic Resonance

Nanoscale Aging of Materials

Contact

  • pemar@duke.edu
  • 919-660-5381
  • Duke University, Pratt School of Engineering, MEMS Department, 144 Hudson Hall, Box 90300, Durham, NC 27708