Subject: SUMMARY disulfide bonds

From: [email-masked] (Peter Grootenhuis)
Date: Wed, 4 Jan 95 09:27:02 GMT

My question was:
Netters, i want to design some additional disulfide bonds in a protein
structure and i am wondering whether there is software that will help
you to locate optimal positions for the corresponding point mutations.

The answers (in order of arrival): 

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1) Leif Norskov, Novo Nordisk A/S, Copenhagen, Denmark, [email-masked]

... Your fellow countryman Dijke Baukstra developed a program some years ago
to do exactly that.  I don't have it, but I may be able to dig up a
reference if you cannot ask him directly. ...
[After contacting Prof Bauke Dijkstra, [email-masked], I obtained
a copy of his program.]
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2) J. Bruce Pitner, Molecular Biology Department, Becton Dickinson 
Research Center, Research Triangle Park, NC 27709, [email-masked]

You might take a look at:
1.  Pabo and Suchanek, Biochemistry, vol. 25, pp. 5987-5991 (1986)
2.  Glockshuber, et al, Biochemistry, vol. 29, pp. 1362-1367 (1990)
The second paper describes stabilization of an antibody Fv fragment
by site-directed mutagenesis incorporating inter-chain disulfide bonds.
They used a database of protein disulfide bond geometries created by
the first paper's method.
We've used a similar approach to stabilizing single chain antibodies but
with an even simpler model.  We compared the distances between the
respective alpha and beta carbons of each pair of residues against a
database of disulfides in similar environments.  This gave a pretty short
list of potential sites for linking the two separate chains, once you
throw out pairs too close to the binding site.
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3) David Mosenkis, Tripos, [email-masked]
P. Balaram's group in Bangalore, India developed a program called MODIP to
select appropriate sites for engineering disulfide bonds into protein
structures.  Their method is described in Protein Engineering vol.3, no.2,
pp. 95-103, 1989.  You can reach one of the authors, N. Srinivasan, at
[email-masked].
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4) Steve Muskal, [email-masked]
We used neural network models to predict a cysteine's disulfide bonding 
state given its local sequence context. The prediction accuracy was quite 
good. 
Ref: Muskal, S., Holbrook, S., Kim, S.H. Protein Eng. 3, 667-72 (1990)
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5) N.Srinivasan, [email-masked]
The program MODIP selects sites
in a protein of known 3D structure, wherein if Cys residues are
introduced, a potential unstrained disulphide can be formed.
Fuller details are available in:
R.Sowdhamini, N.Srinivasan, B.Shoichet, D.V.Santi, C.Ramakrishnan
and P.Balaram (1989) Prot. Engng. 3, 95-103.

We have a version running in Silicon Graphics machine with f77
compiler (although it is not a graphics program). The object code
can be distributed to any academic institution free of charge
with the understanding that the program will not be used for
any commercial purpose. We would like to have this agreement,
because this program is likely to be commercialised with Tripos
Inc. 
If you are interested in getting MODIP, please send me or
Dr.Sowdhamini (both currently at Birkbeck college, London)
a high density tape cartridge (DC 6150 - 150 Mbytes).
We would then send you the program along with help files for
installation and running the program.
DIP contact in London:

 Dr.R.Sowdhamini or Dr.N.Srinivasan
 ICRF unit
 Department of Crystallography
 Birkbeck College
 Malet Street
 London WC1E 7HX
 U.K.
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6) Johan Postma,EMBL,Heidelberg,FRG,[email-masked]
... We have an efficient data-access mechanism for PDB data files.
Recently I performed an analysis that may answer your questions.
Distribution of CA-CA/CB-C (and CA-CA/CHI3; CB-CB/CHI3) from SS-bonded
cysteins. The distribution of CACA-CBCB suggests that the "best"
SS-bonds are observed when CACA(3.9)-CBCB(5.2);CACA(3.8)-CBCB(5.8);
CACA(3.7)-CBCB(6.2) ....                 (translated by PG)
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7) Andy King, [email-masked]
It sounds like Cameleon would be ideal for your application.  
Cameleon provides an interactive graphical bridge between the sequence of 
a protein and its 3-dimensional structure.
Cameleon allows users to work with multiple representations of the 
proteins, including a variety of property profiles, secondary structure 
predictions, alignments and homologous structures.  Clicking on a residue 
in one display highlights that residue in all the other displays allowing 
easy tracking of regions of interest across all representations
Cameleon is an ideal guide for the location of optimal sites for a variety 
of modelling operations, including additional disulphide bridge insertion, 
an example of which is actually included in the manual.....
Let me know if you are interested or if you need more information about 
Cameleon before making a decision.
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8) Carlos Faerman, [email-masked]
There may be a specific program to do this but the simples idea you
can try is:
1) to write a program that will explore either Calpha-Calpha distances
or Cbeta-Cbeta distances and get a general idea about the residues that
are at least somewhat close to each other. This preliminary test which
you may have already done will give some useful hints. The major
disadvantage is that you are not taking into account possible
conformational changes...
Anyhow this is what we attempted before actually preparing a XCYS X'CYS 
double mutant....
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Thanks a lot for your responses !
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Dr. Peter D.J. Grootenhuis --- CMC dept. RK2330 --- N.V. Organon
P.O. Box 20 --- 5340 BH Oss --- The Netherlands
Phone: 31-4120-61920 --- Fax: 31-4120-62539
E-mail: [email-masked]
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