Current
Chemical Biology
ISSN: 1872-3136
Current Chemical Biology
Volume 1, Number 2, May 2007
Contents
Methionine-Independent Translation Initiation
from Naturally Occurring Non-AUG Codons
Pp. 129-139
Péter Medveczky, Attila Németh, László
Gráf and László Szilágyi
[Abstract]
Recent Developments in Boron Neutron Capture Therapy
(BNCT) Driven by Nanotechnology Pp. 141-149
Zhu Yinghuai, Koh Cheng Yan, John A. Maguire and Narayan
S. Hosmane
[Abstract]
New Insights into the Roles of XPA and RPA in
DNA Repair and Damage Responses Pp. 151-160
Yiyong Liu and Yue Zou
[Abstract]
Lipid Modifications During Membrane Fusion in Regulated
Exocytosis Pp. 161-166
Maria Zeniou-Meyer, Aurélie Begle and Nicolas Vitale
[Abstract]
Quantum Dot Nanocrystals and Supramolecular Lanthanide
Complexes – Energy Transfer Systems for Sensitive In
Vitro Diagnostics and High Throughput Screening in Chemical
Biology Pp. 167-186
Niko Hildebrandt and Hans-Gerd Löhmannsröben
[Abstract]
Carbohydrate Microarray Technology for Functional
Glycomics Pp. 187-199
Injae Shin, Jinsung Tae and Sungjin Park
[Abstract]
pH-Sensitive Inorganic Nano-Particles and Their Precise
Cell Targetibility: An Efficient Gene Delivery and Expression
System Pp. 201-213
Ezharul Hoque Chowdhury and Toshihiro Akaike
[Abstract]
Affinity Can have Many Faces: Thermodynamic and Kinetic
Properties of Ras-Effector Complex Formation Pp.
215-225
Christina Kiel and Luis Serrano
[Abstract]
The Wnt Pathway as a Target for Small Synthetic Anti-Cancer
Molecules Pp. 227-239
Sonja Röhrs and Oliver Müller
[Abstract]
Abstracts
[Back to top]
Methionine-Independent Translation Initiation
from Naturally Occurring Non-AUG Codons
Péter Medveczky, Attila Németh, László
Gráf and László Szilágyi
Translational initiation sites in eukaryotic mRNAs are
reached via a scanning mechanism which predicts that
translation should start at the AUG codon nearest the 5’
end of the mRNA. During the translational initiation in eukaryotic
cell, the small (40S) ribosomal subunit binds to the 5' end
of the mRNA. The 40S ribosomal subunit, carrying Met-tRNAi*
eIF2*GTP complex and other factors, then migrates through
the 5' UTR until it encounters the first AUG codon, which
is recognized by base pairing with the anticodon in Met-tRNAi.
Recently interest has focused on mechanisms that occasionally
allow escape from this first-AUG rule. Approximately 10% of
eukaryotic mRNAs skip this first AUG if it is in an unfavorable
sequence context, and translation starts from the second or
any downstream AUG codon. Furthermore, there is an increasing
number of evidence to show that scanning translational initiation
may start from a non-AUG codon that precedes or follow the
first AUG codon in the mRNA. The initiation from non-AUG codons
was discovered among viral genes, but newly reported examples
include eukaryotic genes like those for some proto-oncogenes,
transcription factor kinases and growth factors. Previously
it was shown that regardless of the initiation codon used,
methionine appears to be the initiating residue in all examples
that have been investigated in eukaryotes. Recently few published
results and our experiments showed that leucine can be translated
as an initiator amino acid using CUG codon. Genome analysis
generally considers the first AUG triplet in the open reading
frame as the translation initiation codon. However the recent
results indicate that non-AUG translation initiation may be
operable more often than has been anticipated. This may have
a great impact on the analysis of gene function based on genome
information.
[Back to top]
Recent Developments in Boron Neutron Capture Therapy
(BNCT) Driven by Nanotechnology
Zhu Yinghuai, Koh Cheng Yan, John A. Maguire and Narayan
S. Hosmane
Boron neutron capture therapy (BNCT) is a promising treatment
for malignant brain tumors as well as other cancers. Current
research centers on both the design and synthesis of high
boron containing compounds as BNCT agents, and the search
for more effective delivery vehicles. This review discusses
recent work on the development of nanomaterial based BNCT
agents.
[Back to top]
New Insights into the Roles of XPA and RPA in
DNA Repair and Damage Responses
Yiyong Liu and Yue Zou
Xeroderma pigmentosum group A (XPA) and replication protein
A (RPA) are two essential proteins for nucleotide excision
repair (NER), a DNA repair pathway that removes a large variety
of bulky DNA lesions in cells. In addition to its role in
NER, RPA also is required for almost all other cellular DNA
metabolic pathways, such as DNA replication, recombination,
and other repair pathways. Although both proteins have been
extensively studied for more than a decade, efforts have been
focused mostly on their roles in DNA damage recognition in
NER and/or single-stranded DNA binding. Recent advance in
understanding the cellular functions of XPA and RPA reveals
novel activities of the proteins in DNA damage responses.
Briefly, XPA was found to be recruited to a DNA damage site
for repair after TFIIH binds. The protein is also able to
recognize specific structures of undamaged DNA. In addition,
a nuclear import of XPA occurs upon DNA damage and in an ataxia-telangiectasia
mutated and Rad3-related (ATR)-dependent manner. Furthermore,
XPA undergoes phosphorylation by ATR checkpoint, promoting
cell survival in response to UV irradiation. For RPA, the
protein was found to play a role in activation of DNA damage
checkpoint apparatuses ATR and the Rad9/Rad1/Hus1 complex.
RPA also undergoes hyperphosphorylation upon DNA damage, which
induces structural changes of the protein. Finally the hyperphosphorylation
appears to be involved in modulating the activities of RPA
and, thus, the cellular processes in which it participates.
Here the molecular mechanisms by which XPA and RPA function
in DNA damage responses are discussed in light of our recent
understandings.
[Back to top]
Lipid Modifications During Membrane Fusion in Regulated
Exocytosis
Maria Zeniou-Meyer, Aurélie Begle and Nicolas Vitale
Cells have evolved specific intracellular compartments that
permit local concentration of macromolecules. These macromolecules
are transported from one part of the cell to another and eventually
released into the extracellular space to participate in cell-to-cell
communication. Neurons and neuroendocrine cells secrete neurotransmitters
and hormones by exocytosis, a highly regulated process in
which secretory vesicles fuse with the plasma membrane to
release their contents in response to a calcium trigger. To
date, many proteins that catalyze the formation, targeting
and fusion of secretory vesicles have been identified. However,
the lipid composition of vesicles and their target membrane
is also critical and lipid modifications may be required at
several stages of the exocytotic pathway. In this review,
we will discuss the latest results suggesting important functions
for cholesterol, phosphatidic acid (PA) and phosphatidylinositol
4,5-bisphosphate (PIP2) in the membrane merging process. We
propose that exocytotic sites are determined by the local
formation of lipid micro-domains, which are potentially important
to allow structural and spatial organization of the exocytotic
machinery. Among the lipid candidates, our results show that
PA plays a decisive role in the late stages of exocytosis,
most likely by changing the membrane curvature that may be
required for membrane fusion to occur. The spatial and temporal
coordination of the various players to form an efficient machinery
for secretion now needs to be determined.
[Back to top]
Quantum Dot Nanocrystals and Supramolecular Lanthanide
Complexes – Energy Transfer Systems for Sensitive In
Vitro Diagnostics and High Throughput Screening in Chemical
Biology
Niko Hildebrandt and Hans-Gerd Löhmannsröben
Resonance Energy Transfer (RET) plays an important role, both
scientifically and commercially, in diagnostics and high throughput
screening. For qualitative and quantitative analysis, RET
systems are usually assembled through molecular recognition
of biomolecules labeled with donor and acceptor luminophores.
Lanthanide complexes, as well as quantum dot nanocrystals
(QD), possess unique photophysical properties that make them
especially suitable for applied RET systems in chemical biology.
This review deals with the RET theory, and advantages are
compared to conventional systems (using optical and other
detection techniques). Different molecular recognition processes,
as well as labeling techniques yielding biocompatibility are
described. The photophysics of Ln complexes (e.g. millisecond
luminescence decay times, line-shaped emission spectra, antenna
effect of the ligand) and of QD (e.g. high extinction coefficients,
size-tunable emission spectra, chemical stability) as well
as their RET properties are described in detail.
We give an overview of biochemical applications using lanthanide
complexes and QD, e.g. immunoassays, DNA analysis and nanometer
distance measurements (spectroscopic ruler) and some selected
results are outlined. In particular, the recent scientific
progress in biocompatible QD RET systems with the use of QD
as energy donors as well as acceptors together with Ln complexes
as donors is highlighted. The worldwide economic and scientific
interests, as well as potentials for in vitro diagnostics
(IVD) are addressed and the benefits regarding high throughput
techniques, ultrahigh sensitivity, multiplexing measurements
and miniaturization are discussed.
[Back to top]
Carbohydrate Microarray Technology for Functional
Glycomics
Injae Shin, Jinsung Tae and Sungjin Park
Carbohydrates in living cells and organisms are involved in
various physiological and pathogenic processes through specific
interactions with proteins. As a result, studies of carbohydrate-protein
interactions not only provide valuable information for the
understanding of biological phenomena but they also have the
potential of leading to the development of novel carbohydrate-based
pharmaceutical agents. The significance of these biomolecular
interactions has stimulated exploitation for new technologies
to rapidly analyze carbohydrate-mediated biological processes.
In recent years, much effort has been made to develop carbohydrate
microarrays which can be used for this purpose. The advancements
made in this area have extended the scope of biological and
biomedical research on carbohydrate-mediated molecular interactions.
In this review, we describe progress that has been made in
fabrication of carbohydrate microarrays, as well as in various
applications of this technique to functional glycomics. In
addition, recent progress of lectin microarrays for uses in
glycoprofiling of glycoproteins, cells and pathogens is also
described.
[Back to top]
pH-Sensitive Inorganic Nano-Particles and Their Precise
Cell Targetibility: An Efficient Gene Delivery and Expression
System
Ezharul Hoque Chowdhury and Toshihiro Akaike
The completion of whole human genome sequencing encourages
the development of a powerful gene delivery technology for
elucidating structure, regulation and function of genes and
proteins in addition to the emerging biomedical applications,
such as industry-based productions of therapeutic proteins
and ‘gene therapy’. Due to some major limitations
of viral-mediated delivery, non-viral synthetic systems have
become increasingly desirable. However, synthetic systems
are notably inefficient compared to the viral ones in gene
delivery and expression. We have recently developed the simplest,
but highly efficient gene delivery device based on generated
carbonate apatite nano-crystals having high affinity for DNA
but fast dissolution kinetics for effective release of DNA
during vesicular acidification and thus resulting in 5 to
100-fold higher transgene expression than the existing ones.
Since like carbonate, Mg2+ incorporation into apatite
could regulate particle size and solubility, we have also
successfully designed nano-precipitates of Ca-Mg phosphate
as much more efficient carriers of genetic materials than
classical Ca phosphate precipitation method. Moreover, for
cell-specific and more efficient transgene delivery, we successfully
assembled a desirable cell-recognizable protein in the flexible
manner and a highly hydrophilic protein onto the DNA/crystal
surfaces, thereby creating dual surface properties, one facilitating
cell-specific delivery and the other blocking non-specific
interactions. Thus, considering the efficiency, cell-targetability,
biodegradability and simplicity, this newly developed gene
delivery technology would emerge as a superior tool over the
other existing ones for both basic research laboratories and
clinical medicine and additionally, would enable to develop
a new era for inorganic crystal-based therapeutic delivery.
[Back to top]
Affinity Can have Many Faces: Thermodynamic and Kinetic
Properties of Ras-Effector Complex Formation
Christina Kiel and Luis Serrano
Ras proteins belong to the superfamily of small GTP-binding
proteins which have the ability to recognize and bind to several
sets of effector proteins, thereby communicating signals into
different pathways. Although the Ras proteins have almost
identical amino acid residues in the effector binding region,
and the Ras binding domains have a similar ubiquitin-like
topology, the affinity constants span three orders of magnitude.
Moreover, large differences in the individual enthalpic and
entropic contributions are observed. Another important feature
of Ras-effector interactions is the charge complementarity
found between the proteins in the complex. As a result, the
association rate constant is very high and contributes significantly
to the affinity of the complex. Differences in binding affinities
are mainly due to changes in the association rate constants
with the dissociation rate constants being at a similar range.
Here, we discuss the importance of understanding protein complex
formation in signal transduction pathways on a molecular level,
both, thermodynamically and kinetically. Although the focus
is mainly on Ras-effector interactions, comparisons of different
binding modes, thermodynamics and electrostatics of various
effectors in complex with members of the Rho, Rab, Arf, and
Ran families will also be considered. This information could
be important to understand the specificity in different pathways
and for a rational design of compounds which block specific
pathways.
[Back to top]
The Wnt Pathway as a Target for Small Synthetic Anti-Cancer
Molecules
Sonja Röhrs and Oliver Müller
The Wnt signaling pathway regulates embryonic development,
cell proliferation and cellular morphology. Deregulation and
inappropriate activation of the pathway are associated with
several diseases including cancer as well as bone and cartilage
diseases such as arthritis. The high medical relevance of
the Wnt pathway turns it into a tempting target for drug intervention.
In this review we will summarize the major functions of the
classical Wnt pathway with focus on its role in tumorigenesis.
The proto-oncoproteins and tumor suppressor proteins of the
Wnt pathway, which might serve as targets for therapeutic
intervention, will be introduced. Despite many difficulties,
a few promising achievements have been made over the last
few years. Remarkable technical developments allowed the screening
for compounds, which interfere with components and the activity
of the Wnt pathway. We will describe several small synthetic
compounds with inhibitory effects on the Wnt pathway and their
effectiveness in biochemical and cell biological assays will
be summarized.
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