for an experimental way to determine soluble domains see the following paper: ESPRIT: an automated, library-based method for mapping and soluble expression of protein domains from challenging targets. Yumerefendi H, Tarendeau F, Mas PJ, Hart DJ. J Struct Biol. 2010 Oct;172(1):66-74. Epub 2010 Mar 4. Review. PMID: 20206698 [PubMed - indexed for MEDLINE]
Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1 On 7 Mar 2011, at 19:18, gauri misra wrote: > Hi, > To start with it would be great if you look in to the secondary structure > prediction of the sequence using any of the standard servers like PSIPRED, > JPRED etc. Many more available at expasy site http://ca.expasy.org/tools/. > Whatever construct you finally choose to make just remember the standard rule > that we generally follow is to avoid deleting the alpha helices and beta > sheets. You can design your initial primers so as to obtain the complete > amplification of these secondary structures from any part within the protein. > You can even use the various modules of the following online available server > http://scratch.proteomics.ics.uci.edu/ > to have an idea of the intrinsically disordered regions in the protein, > transmemebrane regions and disulfide bonds that would certainly help you in > initiating in the right direction. > > Best wishes > Gauri > > On Mon, Mar 7, 2011 at 4:10 AM, Xianhui Wu <wuxian...@gmail.com> wrote: > Dear all, > > Before we try to study the crystal structure of an unknown protein, we need > to determine the sequence that can fold into a compact and stable 3D domain. > What kinds of methods can we choose? > > -- > Best regards, > XH Wu >
