Nanoscale Biomechanics

PI: Prof. Piotr Marszalek

Duke University

Overview

Our research has focused on investigating relationships between structural, functional, and mechanical properties of biopolymers such as polysaccharides, DNA, and proteins. We study these molecules at a single molecule level using single-molecule force spectroscopy techniques and computational methods involving Molecular Dynamics simulations and ab initio quantum mechanical calculations.

Currently, we are particularly interested in folding pathways of large multidomain proteins during their spontaneous and chaperone-assisted refolding that we examine using atomic force microscopy (AFM) and magnetic Tweezers (MT). We also plan to use single-particle cryogenic electron microscopy (SP-cryo-EM) for structural studies of large proteins and their interactions with chaperones using state of the art cryo-EM instrumentation in the vicinity of our lab at Duke University.

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:

Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations, Methods, 2022
Progress and Prospects of Single-Molecule Force Spectroscopy in Biological and Chemical Sciences, Journal of Cell Science, 2020
Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope, JoVE, 2019
Nanomechanics of biomacromolecules, Handbook of Nanomaterials Proper., 2014
Single molecule mechanical manipulation for studying proteins, DNA, and sugars, Wiley Interdis. Reviews, 2013
Stretching polysaccharides and proteins, Chem. Soc. Rev., 2012

Projects

cryo-em

Applications of Single-Particle Cryogenic Electron Microscopy to examine spontaneous and chaperone assisted folding of large proteins

APPLY

olfaction

Exploring the Quantum-Mechanical Basis of Odorant Detection by Olfactory Receptors

APPLY DEDICATED PAGE

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

SMFS Workshop at Duke University

August 2019 article, publications

In August 2019, Piotr together with Andres Oberhauser organized a NSF-sponsored workshop “Progress and Prospects of Single-Molecule Force Spectroscopy in Biological and Chemical Sciences”.”.

MEMS feature story

Mon, Aug 8, 2016 article, publications

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”.

Zack won 2014 SRAA

Sun, Feb 16, 2014 academic, awards

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.”

ChemComm cover

Fri, Dec 14, 2012 cover, publications

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”.