Hi Carlos,
Many thanks for your reply.
The initial 3D structure of enzyme was
generated by homology modeling based on
the known aa sequence. Then the structure of free enzyme
was relaxed by amber ff14sb in water box at about 300 ns productive
MD simulation until RMSD convergence of the backbone was achieved.
It is serine protease where catalytic Ser nucleophile is activated by
His general base catalysis. In the Michaelis complex of serine protease
N eps His and O gamma Ser form H-bond (the ultimate condition of
proton transfer), so I used 2.8 A restraint of this interatomic distance.
The second restraint is between attacking Ser O gamma atom and peptide substrate
amide carbonyl carbon atom (electrophilic center). This distance was restraint
at 3.0 A in the MD simulated Michaelis complex (MC). The mentioned distances restraint
is what I called as "biochemically reasonable". I used the restraints
because without them the ff14sb didn't keep the mentioned critical for catalysis
distances at reasonable values considerably increasing them.
I have been planning to relax by unrestrained MD the MC structure when previous conditional
restraint MD simulation would satisfy RMSD. Unfortunately, as I wrote I faced cis
isomerization of peptide bond in restrained MD.
I still need your expertize of my script files attached to previous email.
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il
________________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Sunday, July 26, 2015 7:43 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MD simulation: cis isomer of peptide bond
the barrier for this is fairly large so I would not expect it unless you
have some other problem in your structure, or the cis isomer is strongly
stabilized during/after the transition. I would look to see what's going on
right before it happens. using a restraint may just cover up the larger
problem. it might be in the initial structure (you didn't say how you
obtained it) or perhaps in the distance restraints that you applied. what
do you mean by "biochemically reasonable"? look at the energies and force
in your minimizations prior to MD.
On Sun, Jul 26, 2015 at 12:07 PM, Michael Shokhen <michael.shokhen.biu.ac.il
> wrote:
> Dear Amber List members,
>
> I have been running production MD simulation of non-covalent enzyme
> –peptide
> substrate (SVLAKEL) complex by Amber14 with ff14sb force field in periodic
> water box.
> I used restraints on two interatomic distances (RST.dist file) in order to
> keep
> biochemically reasonable position of catalytic residues and substrate.
> Suddenly,
> at 31 ns snapshot I have observed irrelevant isomerization at the A-K
> (Ala-Lys)
> amide bond of peptide substrate backbone where carbonyl bond of Ala became
> in cis position to N-H amide bond of Lys.
>
> In order to fix the problem I have added torsional restraint on the
> problematic
> amide bond (rst.bb file) and restarted MD from 30 ns snapshot with correct
> trans isomer of the target amide bond. Unfortunately, I found again
> incorrect cis
> isomer at 31 ns on this amide bond.
> It seems that there is an error in my md3.in and rst.bb files.
> See below listings of the files.
>
> I would appreciate your help.
>
> Thank you,
>
> Michael
>
> *md4.in <http://md4.in>*
>
> 30 ns production phase MD
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 1.0,
> cut = 10.0, ntr = 0, iwrap = 1,
> ntc = 2, ntf = 2,
> tempi = 310.0, temp0 = 310.0,
> ntt = 3, gamma_ln = 0.5,
> nstlim = 15000000, dt = 0.002,
> ntpr = 5000, ntwx = 5000, ntwr = 5000, ig = -1,
> nmropt=1,
> /
> &wt type='END' /
> DISANG= ../RST.dist
> LISTOUT=POUT
> /
> DISANG1= ../rst.bb
> LISTOUT=POUT
> /
>
>
> *RST.dist*
>
> &rst
> ixpk= 0, nxpk= 0, iat=1030,1692, r1= 1.30, r2= 1.80, r3= 2.80, r4= 3.30,
> rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
> &end
> &rst
> ixpk= 0, nxpk= 0, iat=1030,61, r1= 1.30, r2= 1.80, r3= 3.00, r4= 3.50,
> rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
> &end
>
>
> *rst.bb <http://rst.bb>*
>
> &rst
> iat=36,51,53,55, r1=0., r2=180., r3=180., r4=360.,
> rk2 = 35., rk3 = 35., /
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: michael.shokhen.gmail.com
> email: shokhen.mail.biu.ac.il
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jul 26 2015 - 11:00:03 PDT
