| Current
Nanoscience
ISSN: 1573-4137
Current Nanoscience
Volume 3, Number 1, January 2007
Contents
Nanomechanics
Guest Editors: Atsushi Ikai, Alastair Smith and Masaru
Tsukada
Editorial Pp. 1
Force Denaturation of Proteins – an Unfolding
Story Pp. 3-15
David J. Brockwell
[Abstract] [Full
text article]
Pulling and Pushing Protein Molecules by AFM
Pp. 17-29
Atsushi Ikai, Rehana Afrin and Hiroshi Sekiguchi
[Abstract] [Full
text article]
Toward Atom-by-Atom Assembly of Compound Semiconductor
Nano-structures: Mechanical Atomic Discrimination and Atomic
Manipulation at Room Temperature Pp. 31-40
Seizo Morita, Yoshiaki Sugimoto and Masayuki Abe
[Abstract] [Full
text article]
Counting and Breaking Individual Biological Bonds:
Force Spectroscopy of Tethered Ligand-Receptor Pairs
Pp. 41-48
Raymond W. Friddle, Todd A. Sulchek, Huguette Albrecht,
Sally J. De Nardo and Aleksandr Noy
[Abstract] [Full
text article]
Single Molecule Force Microscopy on Cells and Biological
Membranes Pp. 49-56
Andreas Ebner, Josef Madl, Ferry Kienberger, Lilia A.
Chtcheglova, Theeraporn Puntheeranurak, Rong Zhu, Jilin Tang,
Hermann J. Gruber, Gerhard J. Schütz and Peter Hinterdorfer
[Abstract] [Full
text article]
Theoretical Simulations of Scanning Probe Microscopy
for Organic and Inorganic Materials Pp. 57-62
M. Tsukada, K. Tagami, Q. Gao and N. Watanabe
[Abstract] [Full
text article]
Understanding the Counterintuitive Phenomenon of Catch
Bonds Pp. 63-77
Wendy E. Thomas
[Abstract] [Full
text article]
Techniques for Measuring Microtubule Stiffness
Pp. 79-96
S. Kasas and G. Dietler
[Abstract] [Full
text article]
Imaging Mechanical Properties of Living Cells by Scanning
Probe Microscopy Pp. 97-103
Hisashi Haga, Masafumi Nagayama and Kazushige Kawabata
[Abstract] [Full
text article]
Nanomechanical Studies of Superlubricity
Pp. 105-115
Naruo Sasaki, Noriaki Itamura, Daisuke Tsuda and Kouji
Miura
[Abstract] [Full
text article]
Abstracts
[Back to top]
Editorial
Nanomechanics
In this special issue of Current Nanoscience, ten invited
reviews on nanomechanics of atomic and molecular systems written
by expert scholars in respective fields are presented. Driven
by rapid advancement both on experimental and theoretical
fronts, the interest of nano-oriented scientists and engineers
is now focused on elucidating precise mechanisms of the rate
altering effect of externally applied force on the atomic
and molecular processes which are otherwise very slow or very
rare. Acceleration or deceleration of such processes in bulk
materials can be achieved by changing the external parameters
such as temperature or pressure but a prominent aspect of
the new nanoscience is in the manipulation of individual atoms
and molecules by human hands through application of force.
The development of instruments such as probe microscopes and
laser tweezers, among others, has enabled us to perform such
experiments with unprecedented levels of precision reaching
sub-nanometers and sub-nanonewtons in many cases. With these
instruments and at these analytical scales, there is a commonality
of language between researchers in different disciplines of
science and engineering and many are now starting to understand
the problems and achievements in otherwise distantly related
fields, and importing new terminology in a much easier manner
than before. Our attempt to collate expert reviews on nanoscience
from diverse disciplines covering theoretical, physical, chemical
and biological problems is now, therefore, made possible and
it will hopefully provide a useful resource for researchers
and students in a wide range of disciplines. It is the wish
of the guest editors that this special issue be a catalyst
for understanding the contributions made by a wide range of
disciplines to the study of nanomechanics of atoms and molecules.
Guest Editors
Atsushi Ikai
Alastair Smith
Masaru Tsukada
[Back to top]
Force Denaturation of Proteins – an Unfolding Story
David J. Brockwell
[Full
text article]
Many proteins react or respond to mechanical force as part
of their function. Until recently the mechanical properties
of proteins on the nanoscale were unknown as techniques that
allowed their manipulation and measurement were not available.
Over the last decade, development of robust instruments capable
of picoNewton force sensitivity and sub-nanometre positional
accuracy has allowed such experiments to be routinely undertaken.
These experimental data, in conjunction with computational
simulation methods and the development of an underpinning
theoretical framework, have resulted in a greater understanding
of the effects of a mechanical perturbation on biomolecules.
The aim of this review is to describe how mechanical extension
is thought to denature proteins, how this process differs
to the intrinsic unfolding pathway and, by reference to examples,
to rationalise the wide range of mechanical responses that
have been observed, sometimes in proteins with very similar
structures.
[Back to top]
Pulling and Pushing Protein Molecules by AFM
Atsushi Ikai, Rehana Afrin and Hiroshi Sekiguchi
[Full
text article]
This paper reviews a recent progress of molecular level studies
on the rigidity of surface immobilized as well as membrane
bound proteins embedded in the lipid bilayer. Some details
and emphasis are given to the work done in our laboratory
in the last few years. Immobilization of protein molecules
on a solid surface through covalent crosslinkers on one side
and to the probe of the atomic force microscope on the other
enabled us to pull or push a single protein molecule to specified
directions. On pulling, the internal structure of the protein
molecule is mechanically opened up and, on pushing, it is
compressively deformed until it is flattened out. Such experiments
reveal the mechanical rigidity of the folded structure of
a protein molecule in two different ways. In the field of
ligand-protein interaction, some merits and problems of newly
introduced compression free method are discussed. When a protein
molecule is embedded in a lipid membrane, information on its
anchoring force to the membrane can be obtained by pulling
it out from the membrane. Experiments have been done either
on a lipid bilayer formed on a solid surface, or on the surface
of live cells. The extraction process of membrane proteins
is often accompanied by extrusion of a thin lipid tether trailing
behind the target protein of the tensile force. A short review
of the tether forming process from the red cell membrane surface
will be given.
[Back to top]
Toward Atom-by-Atom Assembly of Compound Semiconductor
Nano-structures: Mechanical Atomic Discrimination and Atomic
Manipulation at Room Temperature
Seizo Morita, Yoshiaki Sugimoto and Masayuki Abe
[Full
text article]
An atomic force microscope (AFM) under noncontact and nearcontact
regions operated at room-temperature (RT) in ultrahigh vacuum,
is used as a tool for topography-based atomic discrimination
and lateral atomic manipulations of two intermixed atomic
species on semiconductor surfaces. Noncontact AFM topography
can give height difference between two intermixed atomic species.
Therefore, noncontact AFM topography is a kind of atom selective
image and hence can serve for atomic discrimination in simple
cases. Besides, site-specific force curves provide the chemical
covalent bonding forces between the tip apex and the atoms
at the surface. Here, we introduced both examples related
to topography-based atomic discrimination using selected Sn
and Si adatoms in Sn/Si(111)-(√3Χ√3)
surface. Recently, under nearcontact region, we found a lateral
atom-interchange manipulation phenomenon at RT in Sn/Ge(111)-c(2Χ8)
intermixed sample. This phenomenon can interchange an embedded
Sn atom with a neighbor Ge atom at RT. Using the vector scan
method under nearcontact region, we constructed “Atom
Inlay”, that is, atom letters “Sn” consisted
of 19 Sn atoms embedded in Ge(111)-c(2Χ8)
substrate. Using these methods, now we can assemble compound
semiconductor nanostructures atom-by-atom.
[Back to top]
Counting and Breaking Individual Biological Bonds:
Force Spectroscopy of Tethered Ligand-Receptor Pairs
Raymond W. Friddle, Todd A. Sulchek, Huguette Albrecht,
Sally J. De Nardo and Aleksandr Noy
[Full
text article]
Force spectroscopy provides a direct approach for probing
biological interactions at the single-molecule level. Tethered
systems, in which flexible polymer linkers connect the interacting
molecules to the surfaces of the atomic force microscope probe
and sample, provide a particularly attractive platform for
studying such interactions. We will review the basic physical
principles of force spectroscopy measurements in these systems,
and show that mechanical properties of the tether linkages
allow independent determination of the bond rupture forces
and the number of ruptured bonds. Forces measured in these
systems obey the predictions of a Markovian model for the
strength of multiple parallel bonds. Finally, we discuss the
use of the dynamic force spectra of single and multiple protein-ligand
bonds for determination of kinetic parameters for multivalent
interactions.
[Back to top]
Single Molecule Force Microscopy on Cells and Biological
Membranes
Andreas Ebner, Josef Madl, Ferry Kienberger, Lilia A.
Chtcheglova, Theeraporn Puntheeranurak, Rong Zhu, Jilin Tang,
Hermann J. Gruber, Gerhard J. Schütz and Peter Hinterdorfer
[Full
text article]
Atomic force microscopy (AFM) enables high resolution topographic
imaging of biological samples under near-physiological conditions.
Therefore, the AFM is optimally suited for investigation of
biological membranes and cell surfaces, as exemplified by
studies on bacterial S-layers, purple membranes and cultured
living cells. Topographic imaging allows visualizing single
proteins and protein assemblies in native membranes, as well
as substructures of live cells, such as cytoskeletal architecture.
In addition to high-resolution imaging, the measurement of
mechanical forces yields detailed insight into structure-function
relationships of molecular processes in their native environment.
In molecular recognition force microscopy, interaction forces
between tip-bound ligands and membrane-embedded receptors
can be studied under well-controlled buffer conditions and
effector’s concentrations. In case of low lateral density
and inhomogeneous distribution of the target molecules in
a cell membrane, fluorescence microscopy can help to guide
the AFM tip to the membrane proteins of interest, which can
subsequently be investigated by molecular recognition force
microscopy.
[Back to top]
Theoretical Simulations of Scanning Probe Microscopy
for Organic and Inorganic Materials
M. Tsukada, K. Tagami, Q. Gao and N. Watanabe
[Full
text article]
Current topics are introduced from the results for the JST
(Japan Science and Technology Agency) project for the development
of the theoretical simulator of scanning probe microscopy.
In spite of the crucial role played by the theoretical simulation
for understanding experimental results, the theoretical calculations
so far tried have been computationally very demanding. Thus
one of the aim of this project is the development of efficient
methods for the simulation of STM(Scanning Tunneling Microscopy),
AFM(Atomic Force Microscopy) and KFM(Kelvin Force Microscopy)
and their spectroscopy. Toward this purpose the simplified
and efficient calculation program, as well as user friendly
GUI tools for the wide range users are aimed in the JST SPM
project. Another targets of the project are the development
of a new frontier of the SPM simulation, in particular, for
supporting experiments on biological and organic molecular
systems, and for the measurement in liquids.
We will discuss for the STM simulation the inelastic tunneling
processes and decorated tip model. As for the AFM, we consider
how to treat the dynamic cantilever motion in liquids, and
the theoretical simulation for some of the protein molecules.
[Back to top]
Understanding the Counterintuitive Phenomenon of Catch
Bonds
Wendy E. Thomas
[Full
text article]
Cells bind to each other and to surfaces using complementary
receptor-ligand pairs as an essential part of their function.
The mechanical forces that build up on these bonds was assumed
to weaken them until three receptor-ligand complexes were
shown to form catch bonds that are instead strengthened by
mechanical force. This review analyzes the experimental data
for these complexes to better understand this counterintuitive
effect. Models of how force affects the energy landscapes
of bonds are related to the behavior of various catch bonds
when subjected to force. Structural explanations of how force
affects molecular structure and function are also presented
and related to simulations of the effect of force on structure
and to the effect of point mutations on bond function. It
can be concluded that catch bonds arise when force changes
the angle or distance between two domains in a way that leads
to enhanced binding. However, their mechanism through which
the interdomain region can influence the lifetime of the distant
binding site remains unsolved since more than one proposed
mechanism can explain the data. It remains possible that different
catch bonds work differently or even that multiple mechanism
act in the same protein.
[Back to top]
Techniques for Measuring Microtubule Stiffness
S. Kasas and G. Dietler
[Full
text article]
Studies conducted during the past few decades have revealed
the existence of a close connection between the mechanical
responses of biological structures to stimuli and the functions
of different cells, tissues and organs. The cornerstone to
understanding this chain of reactions lies in a knowledge
of the mechanical properties of the structures implicated
in the transduction of mechanical signals. A progress in this
direction has evolved rapidly in recent years, owing to innovations
in the techniques used for measuring forces in the piconewton
range and displacements smaller than a nanometer. In this
short review, we survey the technologies that have been applied
to measure the mechanical properties of one cytoskeletal component:
the microtubules.
[Back to top]
Imaging Mechanical Properties of Living Cells by Scanning
Probe Microscopy
Hisashi Haga, Masafumi Nagayama and Kazushige Kawabata
[Full
text article]
Scanning probe microscope (SPM) has been developed as a powerful
tool for obtaining high resolution topographic images of biological
samples in their natural aqueous environment. SPM can also
be used to evaluate mechanical properties because its probe
is physically in contact with the samples during measurement.
To obtain cellular stiffness with SPM, we have proposed two
methods: a force modulation mode and a force mapping mode.
Considering the influence of the drag force of liquids, we
have successfully improved the quantitative evaluation of
cellular stiffness by using the force modulation mode. Experiments
performed using the two methods revealed that the local stiffness
of fibroblasts was not homogeneous on the cell surface but
largely varied from point to point. It was revealed that spatial
and temporal distributions of cellular stiffness originate
in cytoskeletal distribution, mode of cellular migration,
and intracellular contractile force.
[Back to top]
Nanomechanical Studies of Superlubricity
Naruo Sasaki, Noriaki Itamura, Daisuke Tsuda and Kouji
Miura
[Full
text article]
We briefly review the nanomechanical studies of ultralow friction
in the following carbon hybrid systems: atomic force microscopy
(AFM) tip on graphite surface, AFM tip on C60/graphite,
graphite on graphite surface, graphite/C60/graphite,
and C60 intercalated graphite. For the atomic and
flake frictions, frictional force maps are compared between
simulations and experiments, which can be explained by stick-slip
motion of the tip apex atom and flake. For the graphite/C60/graphite
system, superlubricity appears, where the maximum static frictional
forces have finite values but denote that dynamical frictional
forces are zero within the resolution of the experiment. Furthermore,
for the C60 intercalated graphite system, greater
superlubricity appears. It is clarified that fullerene intercalated
graphite films exhibit ultralow average friction force, and
excellent friction coefficients μ<
0.001. Our results propose one of the simple guidelines of
designing a practical superlubric system – reduction
of the contact area between intercalated C60 and
graphite sheet to the point contact. Clearly, the C60
intercalated graphite system will contribute to solving energy
and environmental problems in the future.
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