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Hi-<br>
I believe there are several values in the RASMB archives. The ion-type
dependence and assembly state dependence (ss, ds, qs) is significant,
and points out one of the limitations of calculating the buoyancy from
vbar estimates.<br>
Best wishes,<br>
Tom<br>
<br>
<a class="moz-txt-link-abbreviated" href="mailto:Urbanke.Claus@MH-Hannover.DE">Urbanke.Claus@MH-Hannover.DE</a> wrote:
<blockquote
cite="mid:1232011064.496eff38279a4@webmail.bpc.mh-hannover.de"
type="cite">
<pre wrap="">Hello Mattia and all others,
some data of DNA are given in the book "physical chemistry of nucleic acids, V.
Bloomfield, I Tinoco and D. Crothers on page 223. They cite G.Cohen and H.
Eisenberg, Biopolymers 6, 1077 (1968). The psv of nucleic acids depends on the
ionic envirónment much stronger than that of amino acids.
You might also consult the compilation of Durchschlag, Thermodynamic Data for
Biochemistry and Biotechnology, H.J. Hinz ed. , Springer, NewYork, 1986, ch.3.
Best wishes
Claus
Zitat von Mattia Rocco <a class="moz-txt-link-rfc2396E" href="mailto:mattia.rocco@istge.it"><mattia.rocco@istge.it></a>:
</pre>
<blockquote type="cite">
<pre wrap="">Hello everybody,
as you might know, together with Bo Demeler and Emre Brookes we are
preparing the beta-version release of the UltraScan-SOMO software package
for biomacromolecular bead modeling starting from high-resolution
structures. Together with the program we will distribute user-editable
tables containing the definition of residues found in PDB files, tables
that are needed for proper SOMO operation. One of the fields in the
residues definition table is the partial specific volume, used to compute
the psv of the structure under examination (which can nevertheless be
overridden by entering, say, an experimental value).
While the values for amino acids and carbohydrate residues, for instance,
are well defined, this is apparently not the case for ribo and
deoxyribonucleic acids. Nevertheless, we would like to enter a reasonable
value for each of the standard four ribonucleosides and ribonucleotides
(that is, without and with the phosphate) and they deoxy counterparts.
We would therefore appreciate if you could either provide such psv values
to me (with proper references, please), or indicate to me where to find
such information.
Many thanks in advance, and happy 2009!
Mattia
Dr. Mattia Rocco
Biopolimeri e Proteomica
Istituto Nazionale per la Ricerca sul Cancro (IST)
c/o Centro per le Biotecnologie Avanzate (CBA)
IST c/o CBA, Largo Rosanna Benzi 10
I-16132 Genova, Italy
Phone: +39-0105737-310
Fax: +39-0105737-325
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:mattia.rocco@istge.it">mattia.rocco@istge.it</a>
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</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Department of Biochemistry and Molecular Biology
University of New Hampshire
Rudman Hall 379
46 College Road
Durham, NH 03824-3544
Phone: 603-862-2459
FAX: 603-862-0031
<a class="moz-txt-link-abbreviated" href="http://www.camis.unh.edu">www.camis.unh.edu</a>
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