Creating the Backbone for the Virtual Cell: Cell Mapping Projects on the Run
The ability to identify proteins with mass spectrometry has a profound
impact on biological research. Its long term effects can only be compared
with the significance the PCR enzyme had for the advancement of biological
science.
Suddenly proteins can be identified having only minute quantities
available. The efforts invested into the technology lead to a constant
increase in throughput - comparable to the development of DNA sequencing
technology.
Biological mechanisms can be studied directly on the protein level. There
are two research directions: protein expression based proteomics and cell
mapping or functional proteomics.
Protein expression based proteomics is focussing on the understanding of
cellular states by analyzing the protein expression level of as many
proteins as possible. In cell mapping experiments the protein - protein
interaction network within a cell is analyzed.
At the EMBL a protein complex purification technique, called tandem
affinity purification (TAP), was developed which allows to rapidly purify
very specifically non covalently interacting proteins which can be
subsequently analyzed with mass spectrometry (cell mapping approach). The
complexes assemble in vivo, are purified as such and characterized. The
technique had been developed in yeast and efforts are under way to
establish similar methods in higher eukaryotes. The comparison of this
technique with similar experiments based on two hybrid screens demonstrate
that the protein based approach is more specific and functional data
suggest that it is more complete. This may be due to the fact that the
complexes assemble first in their native environment and are then pulled
out for characterization.
The organization of all the proteins into groups of physically interacting
proteins is an important step towards understanding their functional role
within a cell. To a large degree cellular processes organize themselves
based on the non-covalent affinity of proteins. Protein based approaches as
exemplified by the tandem affinity purification method in conjunction with
mass spectrometry are very important in analyzing this functional infra
structure. The identification of all the proteins involved in a particular
biological mechanism and the characterization of their interaction
constants may provide the physical data to simulate the process by a
computer.