Thanks
Victor, Dale and John for inputs concerning this question. Yes,
always to check the cif files. I will look carefully at the
hydrogen bond network, though both conformations might be
possible; right now I am testing both and I will check better
for B-factor differences for two glutamines nearby.
Yours,
Jorge
On 05/19/2017 07:23 AM, Victor Lamzin
wrote:
There are theories that the NAD carboxamide group in
an enzyme active site should be out of the nicotine plane by 20-30
degrees, to help develop a partial positive charge on the C4 atom.
This also helps distorting the planarity of the nicotine ring to
ease the catalytic transformation of NAD to NADH. A while ago we
published a paper on a related topic, the enzymatic activation of
NADH: Meijers et al https://www.ncbi.nlm.nih.gov/pubmed/11134046
Victor Lamzin
On 19/05/2017 00:44, Dale Tronrud wrote:
I have looked over a number of high
resolution models with NAD+ and
NADH in the PDB as well as small molecule structures. I also
have some
familiarity with similar chemistry in the decorations on the
edge of
bacteriochlorophyll-a molecules. The CONH2 group does flip over
when
the hydrogen bonding environment calls for it. It is very hard
to tell
the difference between the oxygen atom and the nitrogen atom
from the
appearance of the electron density so you always have to check
the
hydrogen bonding environment when building an NAD? model.
I have seen one case where a Ser -> Ala mutation in the
protein
caused the group to flip with interesting consequences on the
far side
of the co-factor. My go-to QM person tells me that flipping
this group
will change the energies of the molecular orbitals and therefor
the
redox potential of the NAD? molecule so this conformational
change may
be important to the action of your catalysis.
I have also seen a number of NAD? models in the PDB where
this group
is clearly misorientated.
As you note, the torsion angle should be close to zero or
180.
However it is unlikely to have exactly those values because
there are
non-bonded clashes when everything is in one plane. Some
restraint
libraries inappropriately restrain this group to be co-planar
with the
six-membered ring. As always, check you CIF!
Dale Tronrud
On 5/17/2017 12:46 PM, Jorge Iulek wrote:
Dear all,
I came across some difficulty to refine a NAD molecule in
a
structure, specially its amide of the nicotinamide moiety.
A (very) brief search in deposited structures seems to
point that
not so ever the C2N-C3N-C7N-N7N dihedral is close to either 0
or 180
degrees, but in most cases it is to one of these, with a
preference
towards 0 degrees. Another search in the literature, and I
could not
find any study on either NAD or even the nicotinamide alone to
calculate
the energy barrier to rotate around this bond (in vacuum, eg).
My data quality and resolution do not put much confidence
on
B-factor differences, but they seem to indicate that the cited
dihedral
angle should be close to 180 degrees, id est, O7N is "closer"
to C2N
(and, consequently, to N1N) than N7N is. In fact, I have a
glutamine
nearby whose terminal amide is interacting with the
nicotinamide amide,
so my idea is to make one's nitrogen to interact with other's
oxygen.
Concerning b-factor differences for this glutamine, they favor
its NE2
to point to nicotinamide amide, what would imply that the
C2N-C3N-C7N-N7N dihedral to would be close to 180 degrees
rather than 0
degree.
Is there any wide study on NAD nicotinamide amide
conformation?
Specially, bound to protein structures?
Thanks,
Jorge
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