Quoting Jianzhong Liu <zhong.udel.edu>:
> My peptide looks like this HN(-)-CH2-CO-N(-)-CH2-CO-N(-)-CH2-COO(-).
So this means you have a total charges = -4! I hope you checked the pka value of
RCONHR/RCON(-)R since I think it is unlikely that the peptide bond is not
protonated in water at pH = 7.
> So we can see there are 3 deprotonated N(-) and one COO-. So I want to
> develop charge for these amino acid. I know RED I or RED II can develop it.
- R.E.D. I can derive RESP and ESP charges for the _whole_ molecule
HN(-)-CH2-CO-N(-)-CH2-CO-N(-)-CH2-COO(-) using multiple orientation RESP or ESP
fit in a single R.E.D. run
- R.E.D. II can derive RESP and ESP charges for the _whole_ molecule
HN(-)-CH2-CO-N(-)-CH2-CO-N(-)-CH2-COO(-) using multiple orientation && ||
multiple conformation RESP or ESP fit in a single R.E.D. run
- With R.E.D. III, the use of multiple molecules (each molecule with or without
multiple orientations && || multiple conformations) and the handling of intra-,
inter-molecular charge constraint and inter-molecular charge equivalencing has
been implemented. This allows to derive charge values for many different
molecule fragments.
> But I think these three glycines are different. And RED need structure
> optimization at first.
The user can proceed in two ways in R.E.D. I/II/III:
- She/He provides ONLY initial PDB file(s) as input(s) for R.E.D., and R.E.D. is
going to interface the three following steps: (i) the geom. opt. step (ii) the
MEP computation and (iii) fit
- Provides initial PDB file(s) and geom. opt. output(s) as input(s), and R.E.D.
is going to interface the two following steps: (i) the MEP computation and (ii)
fit
> So I want to know I need to use which structure to do
> optimization at first. Just one deprotonated glycine ( -N(-)-CH2-COO(-) or
> gly-gly-gly to do optimization at frst.
- If your molecule is 'simply' HN(-)-CH2-CO-N(-)-CH2-CO-N(-)-CH2-COO(-), you
might only consider the _whole_ molecule. Thus, using approaches developed in
R.E.D. II should be enough (moreover, the number of atoms is quite small for
keeping all of them in the same molecule).
- Now, if you have in mind to derive a whole set of charge values for the 20
aminoacids using 'your negatively charged peptide bond' (which would quite
interesting), you will need R.E.D. III to generate charge values for the
corresponding fragments. However, you can obviously use R.E.D. II and do some
works manually...
If you follow the Internet links to R.E.DD.B. (below), you get information to
derive charge values for (+)NH3-term, NH2-term, central, (-)OOC-term &
HOOC-term fragments:
N-terminal charged fragment of alpha-aminoisobutyric acid, AIB:
http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-7/info.html
N-terminal neutral fragment of AIB:
http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-15/info.html
Central fragment for AIB:
http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-1/info.html
C-terminal charged fragment of AIB:
http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-11/info.html
C-terminal neutral fragment of AIB:
http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-19/info.html
To get the all the corresponding RESP inputs and R.E.DD.B. projects/data, simply
use the "Download section" of R.E.DD.B. using the "--Molecule name" =
aminoisobutyric
Now, you can apply a similar method for your molecule. For instance, here is
what you could try:
-1- Central fragment: (-)NCH2CO
MeCO-NCH2CO-NHMe with 2 intra-mol. restraints = 0
(-)
-2- (-)NH-terminal fragment: (-)NHCH2CO
NH-Me + MeCO-NCH2CO-NHMe with 1 intra-mol. restraint = 0
(-) (-) with 1 inter-mol. restraint (11 atoms) = -1
-3- (-)OOC-terminal fragment: (-)NCH2COO(-)
MeCO-NCH2CO-NHMe + (-)OOC-Me with 1 intra-mol. restraint set = 0
(-) with 1 inter-mol. restraint set (12 atoms) = 0
Howerer, always check the RRMS since the intra-, inter- mol. restraints might
break your system: Indeed, the negative charge value is supposed to be strongly
delocalized in the peptide bond...
The latter approach would be quite interesting to test to see if it works ;-)
If you are interested, I could run R.E.D. III for you on this test case. In this
case, please contact me to my personal email.
Regards, Francois
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Received on Sun Mar 05 2006 - 06:10:21 PST
