|
Research Objectives Since 2004
we have been discussing on the possibilities of extending the objectives of
our surface-scientific instrumentation towards biological molecules. Our surface-scientific technology has
been primarily used for nanometer-scale studies of solid materials. Together with biologists of RIKEN, we
made consideration how to what extent the biological entities can conform with such physical methods, and actually repeated
elementary experiments to realize this collaboration. Then, we
had chances to communicate with researchers with similar collaborative
ideas, in Japan and in the world. In
2005, we participated a newly build research organization named “Molecular-informational Life Science”,
a trans-Japan network-basis group of research institutes/universities. In conducting our biological researches,
we owe principle ideas in many aspects from this research community. We now aim to reveal
dynamic processes within biomolecules as well as
within assortments of molecules, by directly looking at the biomolecules actually moving and performing
physiological functions. Scanning
probe methods and other spectroscopic tools are our usual tools to cope
with these problems. Background Kawai Surface
Chemistry Laboratory has been originally interested in the chemistry and
dynamic processes on solid surfaces in the angstrom scale. Our efforts have been concentrated on the
methodological development to study the molecular processes specific to the
surface.
Recently, the ultra-low
temperature scanning tunneling microscopy (LTSTM) has been applied for the
study of chemistry and physics of single isolated molecules on the basis of
electronic and vibrational processes. By this approach for classical
molecule/surface systems, a series of basic studies has been accomplished,
representing one of the great achievements of RIKEN today. When you look at a
molecule on a surface of solid in a physical sense, it is a cross section
of a crystal with the continuum of electronic structure, baring molecules
with discrete electronic levels. As the place of mixing these two types of "approximations",
the solid surface adsorption system is an awkward object to give a concise
description in physics. Also for
experimentalists, there have been all sorts of difficulties to handle
surface systems. Surface science has
been, until recently, a field for us to pursue with patience and
frustration. However,
today, observational techniques for solid surfaces, such as scanning probe
methods, have been adequately developed, and complete sets of apparatuses
became commercially available. As
long as resources for your research last, you are able to perform detailed
physical observation on the basis of solid-state physics. You can jump into the world of nanometer
without much technological hindrance.
(I think, as mentioned above, the theoretical difficulties on solid
surfaces have not been satisfactorily solved.) Surface
science has history for more than a half century, and most of us subtly
feel that the related fields have been matured as basic disciplines,
especially when we participate social occasions of such communities. More explicitly, in the US for example,
people think it rather outdated to take on the first-generation basic
surface science founded on ultrahigh vacuum technology. For instance, when a candidate is
selected for your institute’s project-leader position, the criterion of
“matured surface science into practice” is not negligible any more. Practical application is always a vague
idea, but anyway, the general trend expects application of present surface
science into all sorts of novel research fields and synergy effects between
them. We RIKEN
now have as many as 3,000 research scientists, and 70% of them are related
to biological science. Our research
group, as solid-state chemists/physicists, became a sort of minority. As a result, we, regardless we like or
not, are daily exposed to plenty of information from advanced biological
sciences. Yamada group naturally
determined to study biological molecules within an environment with many
friendly RIKEN biologists. Physiological
phenomena have origins in the microscopic dynamic processes of large
molecules in general. Physically
speaking, large molecules are a bunch of fine discrete levels. Physical understanding of such objects
will be harder when combined with the above-mentioned difficulty of
molecular contact with solids.
Experimentally, the biological entities in general work within
aqueous media at regular temperature and pressure. This is a discontinuity from the
ultrahigh-vacuum low-temperature condition that has been taken in the
advanced surface science so far. Our
past Research Achievements 1. EC-STM observation on
electrochemical response of fluidic phospholipid
monolayer on Au(111) modified with 1-octanethiol S. Matsunaga, R. Yokomori, D. Ino, T. Yamada, M. Kawai, T.
Kobayashi; Electrochem. Commn. 9 (2007) 645-648. Electrochemical
scanning tunneling microscopy (EC-STM) was applied to observe phospholipid layers over thiol-modified
gold substrates as a model biological cell membrane. On a monolayer of
1-octanethiol on Au (111), a synthetic lipid, 1,2-dihexanoyl-sn-glycero-3- phosphocholine,
was introduced in a neutral 0.05 M NH4ClO4 buffer
solution. The lipid molecules formed a fluidic layer at 0.0 V vs. RHE of
the substrate electrode potential. By cycling the electrode potential
between +0.2 V and -0.2 V, the lipid layer reversibly changed over between the
fluidic phase and a striped/grainy structure. This structural change might
involve partial decomposition and oligomerization
of phospholipids. This method will contribute for molecular biology by
revealing the nanometer-scale structure of cell membrane. 2. Geometrical characterization
of adenine and guanine on Cu(110) by NEXAFS, XPS, and DFT calculation M. Furukawa, T. Yamada, S. Katano, M. Kawai, H. Ogasawara, A.
Nilsson; Surf. Sci. 601 (2007) 5433-5440. 601 Adsorption of purine DNA bases
(guanine and adenine) on Cu(110) was studied by
X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption
fine-structure spectroscopy (NEXAFS), and density-functional theory (DFT)
calculation. At coverages near 0.2 monolayers, Angular-resolved NEXAFS analysis revealed
that adenine adsorbates lie almost flat and that
guanine adsorbates are tilted up on the surface
with the purine ring parallel to the atom rows of
Cu(110). Referring to the previous studies on pyrimidine DNA bases, the isomerization
of DNA bases on Cu(110) was found to play an
important role in the adsorption geometry. Guanine, thymine and cytosine
adsorption have an amine-type nitrogen next to a carbonyl group, which is
dehydrogenated into imine nitrogen on Cu(110). These bases are bonded by the inherent portion
of –NH–CO– altered by conversion into enolic form
and dehydrogenation. Adenine contains no CO group and is bonded to Cu(110) by participation of the inherent amine parts,
resulting in nearly flatly-lying position. 3. Luminescence from
3,4,9,10-perylenetetracarboxylic dianhydride on Ag
(111) surface excited by tunneling electrons in scanning tunneling
microscopy D. Ino, T. Yamada, Maki Kawai; J. Chem. Phys. 129 (2008) 014701 (1-5). The electronic excitations
induced with tunneling electrons into adlayers of
3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) on Ag(111) have been investigated
by in situ fluorescence spectroscopy in scanning tunneling microscopy
(STM). A minute area of the surface is excited by an electron tunneling
process in STM. Fluorescence spectra strongly depend on the coverage of
PTCDA on Ag(111). The adsorption of the first
PTCDA layer quenches the intrinsic surface plasmon
originated from the clean Ag(111). When the second
layer is formed, fluorescence spectra are dominated by the signals from
PTCDA, which are interpreted as the radiative
decay from the manifold of first singlet excited state (S1) of adsorbed
PTCDA. The fluorescence of PTCDA is independent of the bias polarity. In
addition, the fluorescence excitation spectrum agrees with that by optical
excitation. Both results indicate that S1 is directly excited by the
inelastic impact scattering of electrons tunneling within the PTCDA
adlayer. 4. Observation
of Photoactive Yellow Protein Anchored to Modified Au (111) Surfaces by
Scanning Tunneling Microscopy II Rzeźnicka,
GWH Wurpel, M. Bonn, MA van der Horst, K. Hellingwerf, S., Matsunaga, T. Yamada, M. Kawai; Chem. Phys. Lett.
472 (2009) 113-117. The adsorption of photoactive
yellow protein (PYP) on a Au(111) surface and its
fluorescence activity have been studied by electrochemical scanning
tunneling microscopy (EC-STM) and fluorescence photometry. A stable,
densely packed protein layer was observed after protein immobilization onto
a Au(111) surface modified with a mixture of
3-mercaptopropanoic acid (3-MPA) and 11-mercaptoundecanoic acid (11-MUA)
and subsequent formation of the amide bond with the use of N-hydroxysuccinimide and carbodiimide.
Fluorescence photometry data indicate that covalent binding of PYP to the
functionalized Au(111) surface does not interfere
with the fluorescence properties of the native protein. 5. Visualization of phospholipid particle fusion induced by duramycin S. Matsunaga, T. Matsunaga, K. Iwamoto, T.
Yamada, M. Shibayama, M. Kawai, T. Kobayashi; Langmuir 25 (2009) 8200-8207. We visualized nanometer-scale phospholipid particle fusion by scanning tunneling
microscopy (STM) on an alkanethiol-modified gold
substrate, induced by duramycin, a tetracyclic antibiotic peptide with 19 amino residues.
Ultrasonic homogenization generated a suspension mainly consisting of
minimal lipid particles (MLP) from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
(POPC), and 1-palmitoyl-2- oleoyl-sn-glycero-3-phosphoethanolamine (POPE)
in a phosphate buffer solution, confirmed by dynamic light scattering
(DLS). In situ STM discerned individualMLPas
particles (diameter∼8 nm) spread on Au(111), modified
with alkanethiol, within the suspension. The MLP
became fragile by the presence of duramycin, and
the MLP were easily scratched by the scanning tip into multilayers
along the surface. This process of particle fusion on the gold surface
coincides with the aggregation of MLP in the suspension, observed by DLS.
It was demonstrated that STM is capable of discerning and monitoring the
nanometer-scale features of phospholipid
particles altered by antibiotics with biochemical impact. STM might allow
in situ, real-space, nanometer-scale observations of minute particles
composed of phospholipids within the real cells with the highest
magnification ratio 6. Antimicrobial Destabilization of Phosopholipid Monolayer Spread along Aqueous
Surface" I.I. Rzeźnicka, M.
Sovago, M. Bonn, T. Kobayashi, T. Yamada, M. Kawai; Submitted
to Biophys. J. Inspired by previous
research, we applied laser nonlinear vibration spectroscopy "SFG"
to observe the molecular interaction of phospholipid
and duramycin layers formed at gas-liquid interface.
Both pure POPE and pure duramycin formed a single-orientation monolayer for
each. When duramycin
was injected below a POPE monolayer, the SFG spectrum was almost a linear
combination of the spectra of two pure monolayers,
except the O-H (O-D) stretching region of water. Most parts of POPE and duramycin did not substantially change, and the
interfacial water molecules seemed to lose hydrogen-bonding network. As a result, the entire membrane system
becomes unstable, leading to disintegration of the membrane. For DOPC+duramycin
system, duramycin did not appear in SFG. A very sharp selectivity of duramycin towards phospholipids has been demonstrated. |
|
Dr.
Taro Yamada |
|
|
|