[RASMB] Partial specific volume of nucleotides

[Urbanke.Claus at MH-Hannover.DE]

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 <mattia.rocco at istge.it>:

> 
> 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: mattia.rocco at istge.it
> 
> 
> 
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