Subject: alpha-helix calculations (fwd)

From: Iraj Daizadeh <[email-masked]>
Date: Fri, 28 Jan 2000 23:10:07 -0500 (EST)

Hello. 

I have recently asked the pdb list ([email-masked]) the same question
concerning alpha-helix stability in water; the complete summary including
their replies is shown below.

Thanks again for the contributions and in general to those interested in
this question.

Iraj.

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Question:

On Sat, 22 Jan 2000, Iraj Daizadeh wrote:

> 
> Dear Members of the CCL:
> 
> Here are some questions that I have been interested in for some time; your
> thoughts would be appreciated.
> 
> Here's the general problem: Given a alpha helix cut out from a PDB
> protein, run md simulations to determine the folling:
> 
> 1. How can we ensure from md simulations that the alpha helix is stable in
> solution?  We solvate the alpha helix the run md simulations for how long?
> how much water [10 angstrom solvation shell?]? how many time steps? how
> long will the calculation take? and on what machine-- Cray?
> etc....details--details--details!
> 
> 2. References showing that results of the above calculation have been
> verified by experiment? References describing results of the above
> calculations on such small subsets of PDB data?
> 
> I ( as usual ) will post a summary of your responses.
> 
> Thanks, Iraj.
> 
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Quite a feq MD simulations have been done on alpha-helices. I will point
you to my own older work that has all the references:

@Article{Spoel96a,
  author =       {David van der Spoel and Bert L. de
                  Groot and Steven Hayward and Herman J. C. Berendsen
                  and Hans J. Vogel},
  title =        {Bending of the Calmodulin Central Helix: A
                  Theoretical Study},
journal =        "Prot. Sci.",
year    =        1996,
volume = 5,
pages = {2044-2053}              
}

@Article{Spoel96b,
  author =       {David van der Spoel and Hans J. Vogel and Herman
                  J. C. Berendsen},
  title =        {Molecular Dynamics Simulations of {N}-terminal Peptides from a Nucleotide Binding Protein},
  journal =      "Proteins",
  year =         1996,
  volume =       24,
  pages =        {450-466}
}
Especially this latter has a systematic search of peptides to test for 
stability.

If you want to do calculations yourself: just get a couple of Pentium IIs, 
you can certainly do 1 or 2 ns a week per processor.
You should not use a plastic bag (sphere) with water,
since your helices will unfold and occupy a large volume. Use normal PBC, with
a cubic or truncated octahedron box.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel         Biomedical center, Dept. of Biochemistry
s-mail: Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]    www: http://zorn.bmc.uu.se/~spoel
phone:  46 18 471 4205          fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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On Sat, 22 Jan 2000, Iraj Daizadeh wrote:
> Here's the general problem: Given a alpha helix cut out from a PDB
> protein, run md simulations to determine the folling:
> 
> 1. How can we ensure from md simulations that the alpha helix is stable in
> solution?  

I'd say you can't, not with 100% certainty; but with a good deal of work
you might be able to develop a protocol with some degree of reliability,
enough to be useful.

One of the dilemmas in this area is evaluating the free energy of the
folded state vs. the unfolded state, in large part because there are so
many possible unfolded states.

> We solvate the alpha helix the run md simulations for how long?

Many nanoseconds, at least.  You may need to determine that yourself, by
testing against cases with known results, e.g. a couple cases where the
helix is stable in water in expt, and a couple cases where it isn't. 

You should probably also deliberately refold the peptide into random
coil configs (molten globule?) and subject it to the same protocol.

> how much water [10 angstrom solvation shell?]? 

I recommend constant P,T methods in a periodic cell, with at least 12 A
(typical nonbond cutoff) from the solute (protein) to the closest cell
face.  I wouldn't recommend using a sphere of water in general, and
certainly not without employing e.g. a reaction field method.

> how many time steps? 

Probably at least 10 ns per sim, but you should run sims of helices
which are unstable when excised to determine that.

> how long will the calculation take? 

A good Ph.D. project, or a very talented postdoc

> and on what machine-- Cray?

Whatever you can get access to-- considerable CPU time will be needed.
Cray if you have the dollars or grant writing skills needed, but CHARMM
on a Linux cluster would work for this as well.  

> 2. References showing that results of the above calculation have been
> verified by experiment? References describing results of the above
> calculations on such small subsets of PDB data?

I know this has been done for paired helices, esp. the leucine zipper
motif; the peptide GCN4-p1, 33 AA from the GCN4 protein, has been
studied extensively by expt (X-ray crystal, NMR) and MD/MC techniques. 

> how long will the calculation take? 

A good Ph.D. project, or a very talented postdoc

> and on what machine-- Cray?

Whatever you can get access to-- considerable CPU time will be needed.
Cray if you have the dollars or grant writing skills needed, but CHARMM
on a Linux cluster would work for this as well.  

> 2. References showing that results of the above calculation have been
> verified by experiment? References describing results of the above
> calculations on such small subsets of PDB data?

I know this has been done for paired helices, esp. the leucine zipper
motif; the peptide GCN4-p1, 33 AA from the GCN4 protein, has been
studied extensively by expt (X-ray crystal, NMR) and MD/MC techniques. 

Another area studied extensively by both expt and simulation techniques
is helix bundles, including some with designed helices.

I'm not as aware of the work on single, isolated helices; however, some
of the dimer or bundle literature may have refs to single helix work.

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]          |    \  /  |=|    position of the FDA; for that,
http://www.erols.com/rvenable       \/   |=|    see   http://www.fda.gov  )

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Dear Iraj,

I cannot answer all your questions, but can give input on a couple.

>1. How can we ensure from md simulations that the alpha helix is stable in
>solution?
>
First of all, in general, I expect a free alpha helix NOT to be stable in
aqueous solution - my argument is that the main-chain H-bonds should be
able to form lower energy hydrogen bonds with water instead of its own
chain elements if totally unconstrained.  I suppose you could do a quick
assessment by doing mechanics calc in water at various degrees of helix
opening to assess energy changes to specifically address this.

>how much water [10 angstrom solvation shell?]?

Unfortunately, I think a stand alone solvation shell will only simulate a
shell of water in a vacuum, which will be very different than in bulk
water.  I believe you need to use repeat boundary conditions with full
hydration if you wish to simuate behavior in an aqueous environment.

Best wishes,
Bob Latour

===========================================

Robert A. Latour Jr., Ph.D.
Associate Professor of Bioengineering
   and Materials Science & Engineering
501 Rhodes Research Center
Clemson University, Clemson, SC 29634
[email-masked]
tel: (864) 656 -5552 / fax: (864) 656-4466

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Dear Iraj,

Yesterday I emailed you my opinion about your questions on alpha helix
modeling and stability.  The best reference that I have found on this is
cited below - this paper does directly address alpha-helix stability and
dynamics modeling in aqueous solution.

M.J. Bodkin and J.M. Goodfellow, Competing interactions contributing to
a-helical stability in aqueous solution, Protein Science, 4: 603-612 (1995).

Regards,
Bob Latour

===========================================

Robert A. Latour Jr., Ph.D.
Associate Professor of Bioengineering
   and Materials Science & Engineering
501 Rhodes Research Center
Clemson University, Clemson, SC 29634
[email-masked]
tel: (864) 656 -5552 / fax: (864) 656-4466

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>from pdb list:

Dear Iraj Daizadzeh,

You might try a medline search for the work of Louis Serrano and
collaborators. They publish their opinion, that their AGADIR
(Biopolymers 1997 Apr 15;41(5):495-509) formalism is quite well suited
to estimate sequence-stability relationships in helices. Perhaps you do
not really need an explicit simulation for your question.

You should also be aware of the excellent work Barry Honig has
contributed to the subject (e.g. J Mol Biol. 1995 Sep 22;252(3):351-65. ).

For me, the acid test of whether a model or simulation is worth one's
time is the question of whether the result can be experimentally
verified. Very few explicit MD simulations score well on this criterion.

Sincerely,

Boris Steipe

  +---Dr. Boris Steipe------------<[email-masked]>---+
  |   Genzentrum                                                 |
  |   Feodor-Lynen Str. 25            Tel +49 (0)89 2180-6987    |
  |   81377 Muenchen, Germany         Fax               -6999    |
  +---<http://www.LMB.uni-muenchen.de/users/steipe/boris.html>---+

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Hi Iraj, 

I think your question is quite interesting. People have done MD
simulations of alpha helices taking them out from proteins. 
For example, All the seven helices of bacteriorhodospin 
 have been simulated. The simulations have been carried out on 
single helices. There are reports on molecular 
dynamics simulations on proline containing helices as well. 
I would probably search Medline on these to find protocols. 
Several helix bundles and leucine zippers have been simulated 
as well. I think quite a work has been done along these lines as it 
directly relates to secondary structure formation and protein folding.

Warm regards,
Sandeep

                    Sandeep Kumar, Ph.D.
                    Laboratory of Experimental and
                    Computational Biology,
                    NCI - FCRDC, 
                    Bldg. 469, Room 151,
                    Frederick, MD 21702,
                    USA. 
                    Phone: 301 846 6542 (Work)
                    FAX  : 301 846 5598
                    Email: [email-masked]
                    URL  : http://www-lecb.ncifcrf.gov/~kumarsan

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In addition to the references listed you may want to take a look at the
work of Tirado-Rives and Jorgensen (Biochemistry late 80's or early 90's),
Daggett and Levitt (JMB about the same time). C. Brooks also published on
this a bit later in JMB.

Regarding experimental systems, perhaps the most convenient is the "AQ"
peptide studied by Baldwin and coworkers (JACS late 80's early 90's), this
is a 13- or 14-mer with no formal charges.  The same group studied a
similar "AK" peptide (Marqusee & Baldwin PNAS 88 or 89), but this may be
harder to study computationally.

There is also some work by an Austrian or German group in JMB looking at
the effect of cut-offs and electrostatics treatment in simulations of
alpha-helices, worth tracking down.  This paper anticipated some of the
recent excitement on the use of rapid schemes for treatment of Ewald sums
(Darden) for simulations of proteins and DNA.

More recently, look at the work of S. Wang of Georgetown U. on several
versions of simulations on the aforementioned "AQ" peptide (and early work
by Wang and Sung).  A 98 or 99 paper in J. Phys. Chem. used a modified
version of CHARMM to study the peptide in a water box.

Best regards,

Max

***********************************
Max Vasquez, PhD
Protein Design Labs, Inc.
34801 Campus Drive
Fremont, CA 94555

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