Subject: Summary: modelling protein under point mutation

From: Jeremy R Greenwood <[email-masked]>
Date: Thu, 23 Feb 1995 14:11:03 +1100 (EST)

Thanks to all who responded to my request for information about
protein structure determination under point mutation. There are some
excellent suggestions.

Jeremy

Original request:
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Greetings to all,

I have just been approached with a project concerning the modelling of
the changes in structure and function of a protein under various
point mutations. The X-ray crystal structure is known, as are all the 
different inherited single point mutations which lead to a particular 
pathology. Not being a protein modeller by trade, I'm asking for some 
preliminary qualitative advice:

* Roughly how hard is it to model changes in structure or binding 
resulting from a single point mutation? (apparantly many such typical
mutations are from charged to uncharged residues). Is it feasible to 
obtain meaningful results, given the state of the art? (obviously this 
will depend on the given system, but perhaps some out there have 
attempted this kind of problem previously.)

* What kinds of tools are necessary or useful? (e.g. AMBER, MD, MC, 
simulated annealing, semi-empirical calculations on local regions with 
substrate binding, etc.) Which software packages are recommended
(anything cheaper than Biosym?) and what level of hardware?

* Any other advice for the neophyte protein modeller? Recommended
texts?

Summary to follow, as per usual.

Naively,
	Jeremy
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>From [email-masked] Fri Feb 17 19:07:53 1995

I would recommend to use the comprehensive protein modelling software
WHATIF, developed by Gert Vriend at EMBL Heidelberg. WHATIF was developed
to answer such questions as "WHAT happens IF I do this or that mutation
to my protein?". Although it is not very easy to use, compared to some
glossy commercial software, it is extremely powerful, and cheap.
Contact Gert at [email-masked], if you are interested in this
software.

Good luck,
- Friedrich -

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>From [email-masked] Fri Feb 17 06:10:33 1995

Jeremy,

Could you check out this reference and see if it is of any
use to you? I'd be interested to know what you think. The
authors have in fact offered to make available a 
program. 

P Koehl & M Delarue, "Polar and Nonpolar Atomic Environments
in the Protein Core: Implications for Folding and Binding",
PROTEINS: Structure, Function and Genetics 20:264-278 (1994).

You should also hear from people working in site directed
mutagensis, I understand they have other programs too.

-- 

Harold Cox | [email-masked]
           | 510 231 1008  

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>From [email-masked] Fri Feb 17 05:17:23 1995

In theory, you could do a perturbation of one residue to
another; AMBER's free energy program does this. Since
sampling is a big issue, there is a bit of art in doing
this, so I'd advise reading papers on it.. no refs handy.
the good news is that AMBER is pretty cheap, and the next
release which is due 'any week' will have some graphics
for setting up the molecule files. See 

  http://www.amber.ucsf.edu

Bill Ross
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>From [email-masked] Fri Feb 17 03:57:22 1995

Hi, Jeremy.
 
> * Roughly how hard is it to model changes in structure or binding 
> resulting from a single point mutation? (apparantly many such typical
> mutations are from charged to uncharged residues). Is it feasible to 
> obtain meaningful results, given the state of the art? (obviously this 
> will depend on the given system, but perhaps some out there have 
> attempted this kind of problem previously.)

Our HyperChem software trivially allows single-point mutations of
proteins, and allows specific control over secondary-conformation
details.  The Sequence Editor module of the ChemPlus enhancements
package is convenient for editing or generating proteins on a more
abstract level, and then the resulting sequence can be returned to
HyperChem.
 
> * What kinds of tools are necessary or useful? (e.g. AMBER, MD, MC, 
> simulated annealing, semi-empirical calculations on local regions with 
> substrate binding, etc.) Which software packages are recommended
> (anything cheaper than Biosym?) and what level of hardware?

HyperChem will do all of the above except MC, with annealing being 
done via scripts or an external controller such as Visual Basic or 
Excel.  The suggested retail price for HyperChem is US$1995 commercial/
$995 academic.  Hardware requirements are a 386-or-better PC 
with math coprocessor, minimum 4MB RAM (it would be better to have 
considerably more RAM for macromolecule work), Windows 3.1, and the 
sorts of display, etc. that are standard with a system of that level.

Regards,
Joel
 
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Email to: [email-masked] 

Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: [email-masked]    Support questions to: [email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]

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>From [email-masked] Fri Feb 17 03:03:19 1995

Jeremy,

You could try QUANTA/MODELER/CHARMm etc...
try http://www.msi.com/ or
[email-masked]

to find out more.

Sincerely,

Ryszard Czerminski
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>From [email-masked] Fri Feb 17 00:18:57 1995

Dear Jeremy,

We have attempted modeling a mutant HIV-1 protease N88Q.  This single mutation
is known to prevent dimerization of the protease subunits.  We were able to
observe a destablization of the dimer interface by studying the MD trajectory
for 100ps.  We used WESDYN an MD package developed at Wesleyan University by S.
Swaminathan.  Our results were published in J. Am. Chem. Soc. (1993) 115,
1231-1234.

Hope this helps.

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>From [email-masked] Thu Feb 16 21:22:49 1995

Jeremy:

   One particularily interesting reference that relates to the problem of
predicting changes in structure and binding properties of mutant proteins is
by Wilson et al.[1]  Using molecular mechanics with a solvent correction plus
a protein side-chain rotamer library, these authors were able to design a
mutant enzyme with altered substrate specificity and good selectivity. 

   As Wilson et al. have done, you will probably need to consider alternative
sied-chain conformations of the residue that has mutated as well as the
immediately surounding residues.  This is especially true of surface residues.
For this purpose, the rotamer library of Dunbrack and Karplus is the most
up-to-date.[2] 

    This library along with a Fortran program for reading it are available
directly from the author ([email-masked]) or from anonymous ftp
(babar.ucsf.edu).  Finally, if you have access to Sybyl, I have written an SPL
for assignment of sidechain conformation, given the coordinates of the
backbone based on the Dunbrack and Karplus rotamer library.  This is available
via anonymous ftp (extreme.chem.rpi.edu), and the file is
/pub/sybyl/spl/sarl.spl.Z.  where SARL stands for Sidechain Assignment by
Rotatmer Library.  This script iteratively explores sidechain conformations
taken from the rotamer library which minimize the number of bad contacts.  The
script also allows you to restrict the conformer search to a subset of
residues. 

[1]  Wilson, C.; Mace, J. E.; Agard, D. A. Computational method for the design
     of enzymes with altered substrate specificity.  J. Mol. Biol. 1991, 220,
     495-506. 
[2]  Dunbrack, R. L., Jr.; Karplus, M. Backbone-dependent rotamer library for
     proteins.  Application to side-chain prediction.  J. Mol. Biol.  1993,
     230, 543-574. 

   I hope you find these references helpful.

   Ciao,

Konrad

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>From [email-masked] Thu Feb 16 20:56:59 1995

Hi Jeremy,
You can mutate with AMBER during a MD simulation from one amino acid
into another.  I am doing such a mutation but with CHARMM but I'm not
sure if you have this package.  If this is what you looking for then
I can mail you some references for AMBER or give you some advice about
CHARMM.  Mail me if I can help.

regards
Matthew McCarron
e-mail:  [email-masked]

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>From [email-masked] Thu Feb 16 20:09:42 1995

i am currently doing something similar to what you are suggesting and I find that Amber is quit capable of dealing with these mutations

It is possible to change single residues in the link stage ie remove charge etc

or even mutate the residue using WHATIF see Gert Vriend Heidleberg EMBL

I do not have a full set of results yet but they look promising

So in answer to your question Amber MD is quite sufficient
Please mail me if you have any other ideas/questions 
[email-masked]

byee
Paul

>From [email-masked] Thu Feb 16 19:28:29 1995
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Received: from sentry.novo.dk (sentio.novo.dk [130.227.249.6])
From: [email-masked] (Robert Bywater)
Message-Id: <[email-masked]>
To: [email-masked]
Status: OR

Dear Jeremy

You will find all the tools to do just what you want in the program
package WHAT IF. This will enable you to do mutations, refinements of th e
mutated protein(s) and a lot else besides. You will also need to do some
MD, then you should get the program GROMOS. WHAT IF has an excellent
interface to GROMOS.

WHAT IF is available ( at close to zero cost ) from :

Dr. Gert Vriend
EMBL
Heidelberg
Germany

email: [email-masked]

Very likely, you can get it by 'ftp' transfer, but he will arrange
all that for you.

WHAT IF is very easy to use, but it does take some practice, just like
any program, in some ways more so, because of the ENORMOUS number of
options. Oh, and you better make sure you have at least 1 Gb disk free
for this program.

I may be in OZ in August this year, and if so, could help you with a
tutorial, as by now, I am one of the seasoned users. But maybe Gert
wants to come to OZ. Anyway he will decide.

Please tell hime I recommended WHAT IF to you.

best regrds

Robert Bywater

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