I have carefully examined all the five structures, the following is my
summary:
BAL2 (7aa): contains an additional sp3 carbon in mainchain. The measured
CT-N-C-CT angles are: -170.8, 175.0, -177.6, -176.1, 177.0, 178.8, -172.8
cR9 (9aa): the only peptide has natural AAs, it has two structures
(I): 177.8, 176.7, -179.1, -173.5, -157.6, -91.5, 139.9, -177.0,
161.8
(II): -172.7 164.3, 176.5, 175.8, 178.7, -172.2, -164.2, 88.2,
143.0
PMB (7aa): contains an additional sp3 carbon in mainchain. -3.1, 178.5,
-177.6, 178.3, -178.0, -179.0, -179.2
Tat2 (15aa): -179.5, 178.5, 179.5, 179.6, 179.7, 179.4, -179.4, 179.6,
179.5, 179.8, -180.0, -179.4, 178.9, -179.3, 178.9
PMB2 (7aa): contains an additional sp3 carbon in mainchain. 179.9, 179.9,
179.5, 179.9, 179.9, 179.9, 179.9
Clearly, Tat2 is a special case, as it has 15 AA residues and the
ring-formation pressure is low. For others small ring peptides, introducing
one additional sp3 carbon (other than CA) in the main chain can lower the
ring-formation pressure (such as BAL2, PMB, PMB2). If all natural aa are
used, such as cR9, some torsional angles are not close to 180 anymore due
to the ring-formation pressure. My conclusion is that some torsional angles
deviate from 180 degree because of ring-formation pressure.
Best
Junmei
On Thu, Apr 30, 2020 at 4:27 AM Arnaud Bondon <arnaud.bondon.univ-rennes1.fr>
wrote:
> Hi,
>
> Please find attached five pdb, the more relevant are PMB and PMB2 or
> polymixin B closely related to our peptide.
>
> Some pdb are from large complexes with protein partners and accessible
> on the pdb. For clarity I kept only the peptides
>
> Thanks again
>
> arnuad
>
> Le 30/04/2020 à 06:45, Junmei Wang a écrit :
> > For the residue topology file generated by you, testsirus.prepin, many
> > torsional angles of CT-C-N-CT have values around 150 to 160 or -160 to
> > -150. If you know NMR structures of cyclic peptides that have similar
> > number of residues, could you list the PDB ids?
> >
> > Thanks
> > Junmei
> >
> > On Wed, Apr 29, 2020 at 12:51 PM Arnaud Bondon <
> > arnaud.bondon.univ-rennes1.fr> wrote:
> >
> >> Sorry again for the angles I wanted to write
> >> Calpha-1 - C - N - Calpha of 148 and 150° respectively.
> >> As you mentionned the standard O=C-N-H are pretty close to 180° and
> >> Calpha-1 - C - N - Calpha should also be 180°. The differences are only
> >> associated with the pyramidal character of the nitrogen atoms.
> >>
> >> I looked for many cyclic peptide structures solved by NMR or X-Ray and I
> >> did not find examples of such distorsions, so I am still in trouble.
> >>
> >>
> >> arnaud
> >> Le 29/04/2020 à 17:22, Arnaud Bondon a écrit :
> >>> Sorry the angles were
> >>>
> >>> *C**a**_- *_1 -C*_-1 -N-C**a***
> >>>
> >>>
> >>>
> >>> Le 29/04/2020 à 17:13, Arnaud Bondon a écrit :
> >>>> I reproduced your minimization and I have hopefully the same pdb,
> which
> >>>> correponds to the distorted N3 and N1 and dihedral omega angles of
> 148
> >>>> and 150° respectively.
> >>>>
> >>>> I believed these values were out of range even for cyclic peptide but
> if
> >>>> you say that it is consistent with reality I have to trust you.
> >>>> Many thanks again
> >>>>
> >>>> arnuad
> >>>>
> >>>> Le 29/04/2020 à 17:09, Junmei Wang a écrit :
> >>>>> The N1 and N13 are almost planar (torsional angles of O=C-N-H are 177
> >> and
> >>>>> 179 degrees). I don't think they are like pyramidal nitrogen in
> >> amines. I
> >>>>> think the slightly deviation from the ideal geometry is because your
> >>>>> molecule is cyclic peptide.
> >>>>>
> >>>>> Best
> >>>>>
> >>>>> Junmei
> >>>>>
> >>>>>
> >>>>> On Wed, Apr 29, 2020 at 10:52 AM Arnaud Bondon <
> >>>>> arnaud.bondon.univ-rennes1.fr> wrote:
> >>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> I looked at your min.pdb and for me the N13 displays a pyramidal
> >>>>>> character and also the N1 a little
> >>>>>>
> >>>>>> May be less pronounced that my previous pdb but not really planar
> >>>>>>
> >>>>>> I start the same command, I'll tell you
> >>>>>>
> >>>>>> thanks
> >>>>>>
> >>>>>> arnaud
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Le 29/04/2020 à 16:12, Junmei Wang a écrit :
> >>>>>>> I have tested your molecule using your prepin and frcmod files. I
> >> also
> >>>>>> did
> >>>>>>> igb=1 minimization for 10,000 steps. I did not observe weird
> >> behavior of
> >>>>>>> amide groups. Please check if you can reproduce my result.
> >>>>>>>
> >>>>>>> All the best
> >>>>>>>
> >>>>>>> Junmei
> >>>>>>>
> >>>>>>> On Wed, Apr 29, 2020 at 4:44 AM Arnaud Bondon <
> >>>>>> arnaud.bondon.univ-rennes1.fr>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> Thanks for the two responses.
> >>>>>>>>
> >>>>>>>> About solvent I only used igb=1 when performing simulated
> annealing
> >>>>>>>> under NMR restraints (sa.in)
> >>>>>>>>
> >>>>>>>> The prep directory is attached.
> >>>>>>>>
> >>>>>>>> Many thanks for your help
> >>>>>>>>
> >>>>>>>> sincerely
> >>>>>>>>
> >>>>>>>> arnaud
> >>>>>>>>
> >>>>>>>> Le 28/04/2020 à 23:02, Junmei Wang a écrit :
> >>>>>>>>> Gaff adopted the good parameters from amber biomolecular force
> >> field.
> >>>>>> So
> >>>>>>>>> the peptide-like parameters should be similar. For you
> >> minimization,
> >>>>>> did
> >>>>>>>>> you consider solvent effect? If you send me your prep file, I
> will
> >>>>>> check
> >>>>>>>> if
> >>>>>>>>> it is a force field issue or not.
> >>>>>>>>>
> >>>>>>>>> Best
> >>>>>>>>>
> >>>>>>>>> Junmei
> >>>>>>>>>
> >>>>>>>>> On Fri, Apr 24, 2020 at 11:02 AM David A Case <
> >> david.case.rutgers.edu>
> >>>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>>> On Fri, Apr 24, 2020, Arnaud Bondon wrote:
> >>>>>>>>>>
> >>>>>>>>>>> ). Clearly the N10 amide nitrogen
> >>>>>>>>>>> has an pyramidal character. And the omega dihedral angles are
> not
> >>>>>> good
> >>>>>>>>>>> The molecule was prepared as a mol2 file Nitrogen are N.am
> >>>>>>>>>> The input atoms types don't matter: you should look at the
> output
> >>>>>> types
> >>>>>>>>>> in the prep file. If this is a peptide-like molecule, it may be
> >> that
> >>>>>>>>>> the gaff types don't do as well as the tuned Amber atom types.
> >>>>>>>>>> You might want to see what happens if you request Amber atom
> >> types.
> >>>>>>>>>> I'm not sure whether GAFF has types that are specifically tuned
> >> for
> >>>>>>>>>> peptide bonds or not...cc-ing Junmei here.
> >>>>>>>>>>
> >>>>>>>>>> ...good luck...dac
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> _______________________________________________
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> >>>>>>>>>>
> >>>>>>>>> _______________________________________________
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> >>>>>>>> --
> >>>>>>>> POUR UNE RECONNAISSANCE DE LA PALESTINE DANS LES FRONTIERES DE
> 1967
> >>>>>>>> OU UN ETAT COMMUN
> >>>>>>>>
> >>>>>>>> Arnaud BONDON
> >>>>>>>> Equipe CORINT, UMR CNRS 6226
> >>>>>>>> PRISM
> >>>>>>>> CS 34317
> >>>>>>>> Campus de villejean
> >>>>>>>> Université de Rennes 1
> >>>>>>>> 35043 RENNES Cedex France
> >>>>>>>> tel: (0)2 23 23 65 61
> >>>>>>>> arnaud.bondon.univ-rennes1.fr
> >>>>>>>> http://iscr.univ-rennes1.fr
> >>>>>>>>
> >>>>>>>> _______________________________________________
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> >>>>>>>>
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> >>>>>> POUR UNE RECONNAISSANCE DE LA PALESTINE DANS LES FRONTIERES DE 1967
> >>>>>> OU UN ETAT COMMUN
> >>>>>>
> >>>>>> Arnaud BONDON
> >>>>>> Equipe CORINT, UMR CNRS 6226
> >>>>>> PRISM
> >>>>>> CS 34317
> >>>>>> Campus de villejean
> >>>>>> Université de Rennes 1
> >>>>>> 35043 RENNES Cedex France
> >>>>>> tel: (0)2 23 23 65 61
> >>>>>> arnaud.bondon.univ-rennes1.fr
> >>>>>> http://iscr.univ-rennes1.fr
> >>>>>>
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> >> --
> >> POUR UNE RECONNAISSANCE DE LA PALESTINE DANS LES FRONTIERES DE 1967
> >> OU UN ETAT COMMUN
> >>
> >> Arnaud BONDON
> >> Equipe CORINT, UMR CNRS 6226
> >> PRISM
> >> CS 34317
> >> Campus de villejean
> >> Université de Rennes 1
> >> 35043 RENNES Cedex France
> >> tel: (0)2 23 23 65 61
> >> arnaud.bondon.univ-rennes1.fr
> >> http://iscr.univ-rennes1.fr
> >>
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> --
> POUR UNE RECONNAISSANCE DE LA PALESTINE DANS LES FRONTIERES DE 1967
> OU UN ETAT COMMUN
>
> Arnaud BONDON
> Equipe CORINT, UMR CNRS 6226
> PRISM
> CS 34317
> Campus de villejean
> Université de Rennes 1
> 35043 RENNES Cedex France
> tel: (0)2 23 23 65 61
> arnaud.bondon.univ-rennes1.fr
> http://iscr.univ-rennes1.fr
>
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Received on Thu Apr 30 2020 - 20:30:02 PDT
