I am not able to figure out how to determine the side chain assignment of Last C-terminal SERINE residue of my protein. I can determine CA, CB, CO, N,H values from HNCA, CBCANH, HNCACO. Can someone tell which experiment will give me the information of HA, HB2 and HB3
Hi, You need common side-chain specific experiments like : HC(C)NH, H(C)CH-TOCSY, (H)CCH-TOCSY and HBHANH.
The three first sequences are based on magnetization mixing by spin-lock on carbon frequency and the last one based on polarization transfert from proton to carbone followed by polarization transfert from CA/CB to NH.
H(C)CH-TOCSY and (H)CCH-TOCSY need some frequency to anchor side-chain assignments to backbone assignments. CA, CB, HA (find by common backbone assignment experiments) can be used as anchor-frequency. HC(C)NH and HBHANH correlate directly NH couple to side-chain frequency so assignment is straightforward.
hope that help. YM
answered Oct 10 '11 at 03:16
In addition to the experiments suggested by Yoan, a TOCSY-15N-HSQC experiment will correlate the Ha and Hb protons to the backbone amide.
Alternately, if you have all the other Ha, Hb, Ca, and Cb shifts in you protein assigned assigned, that region of a 13C-HMQC (or HSQC) is usually well resolved and you may be able to assign those protons using that spectrum.
answered Oct 11 '11 at 09:24