Chemistry Reference
In-Depth Information
Contents
1 Introduction ................................................................................... 36
1.1 Chemical Shift Perturbation Mapping ................................................. 37
1.2 Nuclear Overhauser Effect . ............................................................ 38
1.3 Residual Dipolar Couplings ............................................................ 40
1.4 Paramagnetic NMR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
2 Conclusions ................................................................................... 43
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
1
Introduction
Living organisms are very complex, highly structured, tightly regulated systems with
precisely orchestrated communications at every level of organizational hierarchy.
These communications are largely mediated by protein-protein interactions (PPIs).
The complete genome sequencing now reveals that there are thousands of potential
PPIs that may function as building blocks for these communication networks [
1
,
2
].
PPIs can be classified based upon the strength of interaction, which is often rendered
by the equilibrium dissociation constant (
K
d
)equalto
k
off
/
k
on
,where
k
off
is the rate
constant of the complex dissociation reaction and
k
on
is the rate constant of the
association reaction. The window of biologically relevant
K
d
values is extremely
wide and can cover 12 orders of magnitude [
3
]. PPIs can be very loosely divided into
three major subclasses [
4
]: (1) strong, with
K
d
<
10
9
M, and permanent association,
(2) strong and transient, where the change in the quaternary state can be triggered, for
example, by ligand binding, and (3) weak, with
K
d
>
10
4
M, and transient association
with
k
off
rates of up to 10
4
s
1
, which results in lifetimes as short as 100
s[
5
]. Decades
of extensive studies have illuminated structural and functional features for the PPIs
from the first two subclasses characterized by strong binding with
K
d
<
m
10
6
M, which
are summarized in numerous reviews [
6
-
8
]. The weak PPIs and their physiological
importance (wPPIs, with
K
d
>
10
4
M), on the other hand, are less well under-
stood. This could be attributed in part to the technical difficulties encountered
during attempts to characterize them directly in vitro or in vivo. The other reason
relates to a common prejudice that wPPIs might not be found in living
cells, especially considering low (
10
7
M) protein concentrations estimated by
the whole cell volumes. However, it is now being increasingly appreciated that
wPPIs are crucial for promoting diverse biologically important processes such as
reversible cell-cell contacts, transient assembly and/or disassembly of large signal-
ing complexes, and dynamic regulation of enzymes [
9
]. Figure
1
provides three
possible scenarios of wPPIs: (1) wPPI between two intact proteins, (2) wPPI as part of
multi-domain interactions between two intact proteins, and (3) wPPI as part of a
multi-protein complex. Conventional methods such as X-ray crystallography, surface
Plasmon resonance (SPR), and isothermal titration calorimetry (ITC) often fail to
study these wPPIs accurately. In contrast, nuclear magnetic resonance (NMR) has
been proven as a particularly powerful tool to examine them at atomic level resolution
<
