[gmx-users] Re: The N and C termini of peptides

[Justin A. Lemkul]

errabah fatima ezzahra wrote:
 two trimers , the first that has three peptides , first pepetide goes 
from N to C terminus and the other are antiparallel with it they go from 
C to N  so if you look at the end of peptides on one side of the first 
trimer you see LEU GLU GLU

then the other trimer that is one goes from   N-terminus to C-terminus 
and next two that goes from  C-terminus to N-terminus so you see at the 
end LEU GLU LEU.



Sidedness is not a helpful description, since it doesn't exist in protein 
sequencing.  All peptide sequences should be read from N- to C-terminus.  There 
is no C-to-N sequencing, so it's hard to visualize what you're talking about.

so i was thinking that if they are LEU GLU LEU then GLU LEU GLU would be 
better for self assembly than leu glu glu leu glu leu. am i wrong ??and 
if not is there any way to orient them. will capping solve the problem 
with the order of the side chains??

Capping is irrelevant probably in this discussion, since, as I said before, 
acetylation of N- and/or C-termini have nothing to do with sidechains.  Please 
see my previous message for an explanation of when capping might be necessary.


please thanks for your help and sorry if i bugged you alot with this topic


The present descriptions make it difficult if not impossible to help you. 
Please mind conventions when discussion peptide sequences and not some invented 
representation based on what you see (since no one else can see what you're 
looking at).  If you want to discuss sequences and orientations, please use 
something like: Nt-LQQ-Ct for a peptide of N-terminus-Leu-Glu-Glu-C-terminus. 
That way, you can diagram assemblies with different orientations, e.g.:

Nt-LQQ-Ct
Ct-QQL-Nt

etc.  As it stands, I can't make sense of what you're describing.

-Justin

thank you
fz

------------------------------------------------------------------------
*De :* Justin A. Lemkul <jalem...@vt.edu>
*À :* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Envoyé le :* Vendredi 8 Juillet 2011 14h40
*Objet :* Re: Re : Re : Re : Re : Re : [gmx-users] Re: Hexamer problem/ 
The N and C termini of peptides



errabah fatima ezzahra wrote:
 > Hi All
 >
 > I am using course grained model where i have the whole glutamic acid 
as a sphere , and the other end is Lucine (hydrophobic) , do i need to 
still worry about capping the residue to evoid the negative charge in 
GLU from repelling other GLU .
 >

Capping groups are applied to N- and C-termini to compensate for the 
charges on the termini themselves, not the side chains.

 > Also is it possible to control the orientation of the peptides like 
to have them assembeled where it GLU LEU GLU LEU GLU LEU on one side of 
the  trminis and the other side trmini LEU GLU LEU GLU LEU GLU because i 
was thinking  that if it GLU GLU GLU than they will repel each other and 
that is my be causing the problem
 >

I don't fully understand your question.  How can you have one or the 
other side of a terminus?  A peptide always goes from N-terminus 
(positively charged at neutral pH) to C-terminus (negative at neutral 
pH) with the amino acids in sequence within.

The sequence you model should be based on whatever it is you're trying 
to model.  Certainly any sequence of Glu-Glu-Glu will repel a like 
sequence, but if you're trying to hack that apart to make something else 
work, it sounds like a whole bunch of nonsense.  Perhaps you can provide 
some more detail on what it is you're modeling.  Right now it sounds 
like you're trying to randomly alter a peptide sequence to make them 
stick together.

-Justin

 > fatima ezzahra
 >
 > ------------------------------------------------------------------------
 > *De :* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
 > *À :* Discussion list for GROMACS users <gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org>>
 > *Envoyé le :* Jeudi 7 Juillet 2011 17h03
 > *Objet :* Re: Re : Re : Re : Re : [gmx-users] Re: Hexamer problem/ 
The N and C termini of peptides
 >
 >
 >
 > errabah fatima ezzahra wrote:
 >  > Thank you so much for your help , my pdb file says that gen_seed = 
473529 so i will change it to different numbers , but i saw online that
 > Your .mdp file, you mean?
 >
 >  > some gen_seed = -1 and that to generate random seed is that correct ??
 >
 > Yes, with -1 you will get a random number based on the process ID.
 >
 >  > also please  how i can control the starting initial states so that 
i can have starting from more one initial states??  tried looking it up 
on line but did not find that much information.
 >  >
 > If you generate different velocities, then that is a different 
state.  If you want to control what the velocities are (to some degree), 
then set gen_seed explicitly.  If you want to start from a different 
configuration, build a new starting structure.
 >
 > -Justin
 >
 >  > Thank you so much
 >  >
 >  > fatima ezahra
 >  >
 >  >
 >  >
 >  > 
------------------------------------------------------------------------
 >  > *De :* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu> 
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
 >  > *À :* Discussion list for GROMACS users <gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org>>>
 >  > *Envoyé le :* Jeudi 7 Juillet 2011 15h55
 >  > *Objet :* Re: Re : Re : Re : [gmx-users] Re: Hexamer problem/ The 
N and C termini of peptides
 >  >
 >  >
 >  >
 >  > errabah fatima ezzahra wrote:
 >  >  > I am sorry to be asking you again but do you start with 
different velocities  by changing the temperature that will lead to 
change in velocities, i ma new to Gromacs so i dont know where to change 
he velocities, i checked the  mdp file and i didn't see any velocity
 >  >  >
 >  >
 >  > Keep the temperature the same and change gen_seed.
 >  >
 >  > -Justin
 >  >
 >  >  > thank you
 >  >  >
 >  >  > Fatima ezzahra
 >  >  >
 >  >  > 
------------------------------------------------------------------------
 >  >  > *De :* Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu 
<mailto:jalem...@vt.edu>> <mailto:jalem...@vt.edu 
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>
 >  >  > *À :* Discussion list for GROMACS users <gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org>> <mailto:gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org>>>>
 >  >  > *Envoyé le :* Jeudi 7 Juillet 2011 14h55
 >  >  > *Objet :* Re: Re : Re : [gmx-users] Re: Hexamer problem/ The N 
and C termini of peptides
 >  >  >
 >  >  >
 >  >  >
 >  >  > errabah fatima ezzahra wrote:
 >  >  >  > *
 >  >  >  >
 >  >  >  > hello
 >  >  >  > Does anybody knows why The N and C termini of peptides can 
be neutralized before running simulation of peptides  ?? i read this 
some where in a research paper , they dont say why but they do that 
using acetyl amine groops. Probably to evoid the repulsive interactions 
between the end of the peptides , please correct if i am wrong as my 
chemistry is not good, my one trimer is  made of 3 peptides that ends 
with GLU LEU LEU and the other trimer ends with is LEU GLU LEU , should 
i worry about neutralizing the c and N termini
 >  >  >  >
 >  >  >
 >  >  > Capping groups can be added to termini using different software 
programs.  There is no utility in Gromacs to do so.  Once built, choose 
'None' for the termini when running pdb2gmx to build a normal peptide 
bond between the terminal residue(s) and capping group(s).
 >  >  >
 >  >  > Such groups are often added (1) if artificial terminal 
attraction or repulsion should be avoided or (2) if the modeled peptide 
is a segment of a longer polypeptide or protein, in which case such 
integral charges are an incorrect representation of reality.
 >  >  >
 >  >  >  >  Also what the important of running 20 simulations  of the 
same 6 peptides ???. is that to compare the 20 simulation results and 
see **** which give better simulation sorry if my question are something 
i should know. i am trying to find how to get six peptides to self 
assemble to a hexamer  . i will really appreciate your answers.
 >  >  >  >
 >  >  >
 >  >  > Running multiple simulations of a given configuration (using 
different starting velocities) gives better sampling.  You can't 
conclude anything from a single trajectory.  Just as you wouldn't run a 
single experiment on the bench and call it conclusive, so too is it true 
of simulations - if you run just one simulation, how do you know you're 
not seeing the one outlier in the data set?
 >  >  >
 >  >  > -Justin
 >  >  >
 >  >  > -- ========================================
 >  >  >
 >  >  > Justin A. Lemkul
 >  >  > Ph.D. Candidate
 >  >  > ICTAS Doctoral Scholar
 >  >  > MILES-IGERT Trainee
 >  >  > Department of Biochemistry
 >  >  > Virginia Tech
 >  >  > Blacksburg, VA
 >  >  > jalemkul[at]vt.edu | (540) 231-9080
 >  >  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >  >  >
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 >  >
 >  > -- ========================================
 >  >
 >  > Justin A. Lemkul
 >  > Ph.D. Candidate
 >  > ICTAS Doctoral Scholar
 >  > MILES-IGERT Trainee
 >  > Department of Biochemistry
 >  > Virginia Tech
 >  > Blacksburg, VA
 >  > jalemkul[at]vt.edu | (540) 231-9080
 >  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >  >
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 > -- ========================================
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > MILES-IGERT Trainee
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
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-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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