Biology Reference
In-Depth Information
number of papers in the journal
Biochemistry
at that time were entitled 'purifi-
cation and properties of <some enzyme>'), and we need these times to return to
biology, with concomitant modernization of the way in which and the scale at
which the experiments are done. Indeed, in an account of what needs to be done
by bottom up systems biology, one finds many 'old-fashioned' looking terms
(cf. Table 1).
4.3.5. Strategies for determining binding and kinetic constants for
individual proteins
In the spirit of Mrs Beeton (Beeton, 2000), 'first get your protein'. While these
will still require purification, often via dual affinity tags, they will normally
Table 1
Some methodologies of significance for 'bottom-up' systems biology
Stages
Methodologies
Comments
Selected
references
'First get your
protein'
Cloning,
expression and
purification
Choice of
hosts and
vectors, tags,
growth media,
glycosylation
and refolding
Qualitative
binding assays
Mass
spectrometry and
FTIR
Allows
production of a
structural model.
The binding of
some elements
may depend on
that of others.
(Muckenschnabel
et al., 2004;
Wharton, 2000;
Zehender et al.,
2004)
Quantitative
binding assays
Mass
spectrometry
High-resolution
methods such as
FTICR are
useful
(Last &
Robinson,
1999)
High-throughput
kinetic methods
Optical, mass
spectrometry and
calorimetry
(Shen et al.,
2004; Ward
& Holdgate, 2001)
Omics
measurements
Microarrays
and mass
spectrometry
(Aebersold &
Mann, 2003;
Goodacre et al.,
2004; Schena,
2000)
Bottom-up
model
ODE modelling
(Mendes & Kell,
1998)
