Chemistry Reference
In-Depth Information
with a motif of about 60 residues is frequently found in proteins involved in
epigenetic regulation. Interestingly, NMR structure of human zf-CW domain and
PWWP domain containing proteins reveal a new fold in which a zinc is coordinated
tetrahedrally by four conserved Cys residues [
64
]. Such a structure partially
resembles the plant homeo domain (PHD) finger bound to the histone tail,
implicating a similar function of zf-CW domain [
64
]. This kind of Cys
4
motif is
widely found in other metalloproteins such as [NiFe] hydrogenases accessory
protein HypA. Solution structure of HypA from
H. pylori
(Fig.
2c
) showed that
zinc coordinated to four cysteines donated from loops and no apparent secondary
structure found in the zinc-domain [
15
]. The X-ray structure of HypA from
Thermococcus kodakaraensis KOD1
further confirmed such a zinc coordination
sphere [
65
].
2.2 Utilization of Chemical Shifts to Generate Structures
Protein NMR chemical shifts are highly sensitive to local structure and reflect
a wide array of structure factors including backbone and side-chain conformation,
secondary structure, hydrogen bonds, and the orientation/position of aromatic rings.
Chemical shift data can be used in conjunction with protein sequence information
and reasonable force field to generate 3D structure models using the method
of CHEMSHIRE or CS-ROSETTA [
66
-
68
]. The Chemical-Shift-ROSETTA
(CS-ROSETTA) is a robust protocol available for de novo protein structure gener-
ation. The method uses experimental chemical shifts of
13
C
a
,
13
C
b
,
13
C
0
,
15
N,
1
H
a
,
and
1
H
N
as an input to select polypeptide fragments in existing protein structures
(e.g., PDB data bank) in conjunction with the standard ROSETTA Monte Carlo
fragment assembly and energy minimization protocol [
67
,
68
]. The CS-ROSETTA
has been further combined with CYANA using unassigned NOESY data to direct
Rosetta trajectories toward the native structure and produces a more accurate models
than CS-ROSEAAR alone [
69
]. Moreover, chemical shifts have been further
extended in determination of protein-protein complex structures via the CamDock
method [
70
]. The method that utilizes chemical shifts to generate structures may
potentially provide a new direction for high-throughput NMR structure determination
of proteins including metalloproteins, although such a method has not yet been
applied in metalloproteins so far.
3
Identification of Metal Coordination
3.1 Homonuclear and Heteronuclear Metal NMR Spectroscopy
Metalloprotein functionality depends on subtle interaction between properties of
the metal ion, dictated by its coordination chemistry. Our present knowledge in
terms of structure-function of metalloproteins, in particular the role of metal ions
