Hi Chitra, Sometimes disorder ‘is’ the functional state of a peptide segment, and in those cases, if you see the segment ordered in your crystal structure, it is not physiologically relevant; rather it is a result of crystal packing. Sometimes disordered segments undergo a folding when they bind a ligand, or they are targets for post-translational modifications, and in some cases they can actually generate an entropic force which can modify the structural ensemble of the protein (https://www.nature.com/articles/s41586-018-0699-5). In the latter case, the protein had a disordered 30 residue C-terminus that used entropic force to change the structure of the folded portion of the protein to enhance ligand affinity.
Best regards, Z *********************************************** Zachary A. Wood, Ph.D. Associate Professor and Graduate Coordinator Department of Biochemistry & Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *********************************************** From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Debanu Das <debanu....@gmail.com> Reply-To: "debanu....@gmail.com" <debanu....@gmail.com> Date: Thursday, March 12, 2020 at 12:53 PM To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Flexible C terminus [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Chitra, To add to the discussion, I can offer an example about obtaining the structure of a flexible/disordered N-term of a membrane protein. Previous structures of the full-length multidrug efflux transporter AcrB (12 TM helices in each protein ~1000 residues, forms a trimer, so 36 TM helices) were missing the first 6 residues in the N-term in the cytoplasm but we could determine this structure and look at some interesting sequence-structure implications of these first 6 residues in our structure: "Crystal structure of the multidrug efflux transporter AcrB at 3.1 Å resolution reveals the N-terminal region with conserved amino acids Debanu Das,* Qian Steven Xu,* Jonas Y. Lee, Irina Ankoudinova, Candice Huang, Yun Lou, Andy DeGiovanni, Rosalind Kim, and Sung-Hou Kim" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2023878/ I think there should also be examples of C-term or N-term expression/purification tags that are ordered in some crystal forms of a target but disordered in other crystal forms/structures of the same target/homologs. Best, Debanu -- Debanu Das On Thu, Mar 12, 2020 at 5:02 AM chitra latka <chitra.la...@gmail.com<mailto:chitra.la...@gmail.com>> wrote: Dear Klemens, I am going to setup the crystallisation of the entire protein anyhow. I hope I get lucky :) Thanks Chitra On Thu, Mar 12, 2020 at 5:12 PM Klemens Wild <klemens.w...@bzh.uni-heidelberg.de<mailto:klemens.w...@bzh.uni-heidelberg.de>> wrote: On 12.03.20 08:53, chitra latka wrote: Dear All, I am working on a protein that has flexible C terminus. None of the available structures even in homologs have density for C term region (around 20 odd residues). All the available pdb entries have missing density for these 20 residues at C terminus. I am going to try my luck crystallising the entire protein in hope of getting density for C term residues as well (Fingers crossed). Has anyone faced a similar problem where they have managed to get density for a flexible terminus successfully? Any suggestions would be appreciated. Cheers ! Chitra Latka ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 Dear Chitra I would nevertheless try. Sometimes flexible termini fold back either in cis or in trans (crystal packing, a case I just had Yesterday) and you might learn sth important for biological regulation if you are lucky. At the same time I would truncate the terminus and crystallize the globular domain in parallel. Good luck Klemens -- Regards Chitra ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
