Current Proteomics
ISSN: 1570-1646
Current Proteomics
Volume 3 Number 3, October 2006
Contents
Cardiovascular Proteomics Pp. 147-170
F. Vivanco, V.M. Dardé, F. De la Cuesta and M.G. Barderas
[Abstract]
The Concept of Protein Mosaics: Physiological
Role and Relevance for Prion Disease Pp. 171-179
L.F. Agnati, S. Genedani, C. Carone, G. Leo and K. Fuxe
[Abstract]
Computational Tools for Modeling Protein Networks
Pp. 181-197
F.T. Bergmann, R.R. Vallabhajosyula and H.M. Sauro
[Abstract]
Recent Progress and Future Prospects in Protein Display
Technologies as Tools for Proteomics Pp. 199-215
N. Matsumura, N. Doi and H. Yanagawa
[Abstract]
Abstracts
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Cardiovascular Proteomics
F. Vivanco, V.M. Dardé, F. De la Cuesta and M.G. Barderas
Cardiovascular diseases are among the leading cause of
morbidity and mortality in Western societies and developing
countries. The ability to investigate the complete proteome
provides a critical tool toward elucidating the complex and
multifactorial basis of cardiovascular biology, especially
disease processes. In recent years the proteome (and secretome)
of the most relevant cellular elements (myocytes, endothelial
cells, smooth muscle cells, foam cells, circulating monocytes,
platelets) of the cardiovascular system has begun to be depicted
with the construction of two dimensional gel electrophoresis
maps and databases. The development of differential proteomics
allows examination of global alterations in protein expression
in the cardiovascular diseases and identifies new potential
proteins implicated in the genesis of myocardial infarction,
heart failure, stroke, and peripheral arterial disease. Moreover,
different strategies have been used to discover novel potential
biomarkers that could be related with cardiovascular risk.
The multi-factorial nature of cardiovascular diseases necessitates
the use of biomarkers for early detection, for monitoring
the response to therapy and to predict clinical outcome. In
this review we summarize the current status of different proteomic
technologies and recent findings that can help to understand
the mechanisms implicated in the cardiovascular diseases.
The application of proteomics to cardiovascular disease holds
great promise and offer exciting advances toward predictive,
preventive, and personalized medicine.
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The Concept of Protein Mosaics: Physiological
Role and Relevance for Prion Disease
L.F. Agnati, S. Genedani, C. Carone, G. Leo and K. Fuxe
The tendency of the proteins to aggregate (i.e., their so-called
Lego property) is viewed as a necessary feature of proteins
to build up molecular networks, which are the informational
substrate that allows integrative actions of cells and hence
of tissues. Thus, the concept of physiological protein mosaics
is discussed not only as the basis for the formation of structural
elements of the cell and of the extra-cellular matrix, but
also as the main component of molecular networks. Against
this background, the hypothesis is introduced that prion-like
properties of some proteins have a possible physiological
meaning for the formation of physiological protein mosaics
and hence of complex molecular networks. Protein misfolding
and the Lego property can favour the formation of unwanted
protein aggregates. On this basis, the concept of pathological
mosaics is introduced as the most frequent consequence of
alterations in the three dimensional structures of proteins,
thus representing a feature characterising the conformational
protein diseases.
It is postulated that pathological protein mosaics affect
the structure and function of the global molecular network
enmeshing the whole central nervous system leading to neurodegenerative
disease, the most clear cut example being Prion disease.
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Computational Tools for Modeling Protein Networks
F.T. Bergmann, R.R. Vallabhajosyula and H.M. Sauro
There are a large number of software packages available, both
commercial and academic, to assist researchers in modeling
protein networks. In this paper, we briefly review some of
the more commonly used tools and focus on the current state
of the Systems Biology Workbench (SBW), a modular framework
that connects modeling and analysis applications, enabling
tools to reuse each other’s capabilities. We describe
how users and developers perceive SBW and then describe the
currently available SBW modules.
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Recent Progress and Future Prospects in Protein Display
Technologies as Tools for Proteomics
N. Matsumura, N. Doi and H. Yanagawa
Studies of protein–protein interaction networks provide
a valuable framework for understanding the functional processes
of living systems, because many biological processes are triggered
by the interaction or binding of molecules. Display technologies
are powerful tools, both for selecting and engineering polypeptides
or proteins with novel functions and for analyzing protein
interactions. Display technologies can be divided into two
types: cell (or viral)-based display, and cell-free display.
These display systems permit multiple rounds of affinity selection,
and finally the amino acid sequence of the displayed protein
can be determined by sequencing the corresponding DNA (or
RNA). Display technologies are currently applied to select
antibodies, peptides, enzymes, and biologically interacting
partners. Because each display technology has various advantages
and limitations, both in theory and in practice, one should
adapt an appropriate method for a particular purpose. In this
review, we summarize recent advances in and prospects for
display technologies.
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