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Re: WSN: the solvent accessibility to proteins (fwd)
Sender: raman@bioc01.uthscsa.edu (C.S.RAMAN)
Subject: Re: WSN: the solvent accessibility to proteins
Pornthep:
> Could anybody suggest me the references about the accessibility of
> solvents (especially H2O) to the proteins?
Your posting was not specific about what aspect of solvent accessibility
of proteins you were interested in. Here are some pointers:
(1) As early as 1933 John Edsall found a correlation between solvent
accessible surface areas of non-polar groups and heat capacity changes.
This correlation has been extended to the understanding of the
energetics of protein folding during the past decade by the following
groups: Tom Record (U. Wisc), Peter Privalov (Johns Hopkins), Julian
Sturtevant (Yale), B.K. Lee (NIH), Buzz Baldwin (Stanford), Cy Chothia,
Arthur Lesk (MRC, UK), David Eisenberg (UCLA), Barry Honig (Columbia),
Arieh Ben-Naim (HUJI, Israel), Ernesto Friere (Johns Hopkins).
This is not a complete list and I am going from memory. A literature
search using these authors should provide you plenty of material to go
on.
(2) Re - software for calculating accessible surface area of proteins,
ther are different versions floating around. The best one in my opinion
is ACCESS from Fred Richards' group at Yale (contact Art Perlo,
perlo@hhvms8.csb.yale.edu). Richards' group also supplies a nice
companion program VOLUME to calculate the volume of a surface. Both
programs are free for academia. Mike Connolly (of the Connolly surface
fame) distributes a package called MSP which is great for doing numerous
surface related calculations (contact connolly@netcom.com). If you are
interested in the most spectacular representation of molecular surfaces
in 3D, then consider getting GRASP (contact Anthony Nicholls,
nicholls@cuhhca.hhmi.columbia.edu). ACCESS from Richards' group is
written in FORTRAN. A C version of a slightly different algorithm is
available from Scott Presnell at UCSF. There are also some
modified versions of ACCESS available from George Rose at Johns Hopkins.
Although a default probe of radius 1.4 A is used by these programs, it
can be changed to any user selected value.
There are a lot of interesting things to discuss on the topic of solvent
accessibility and if you need something specific let me know.
Cheers
-raman
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