capping is important if the residues, which are close to the place of truncation (consequently to the capping), have a non-negligible effect on the property you are interested in. Non-appropriate capping groups can generate artificial interactions which would not be present in the native, non-truncated protein and cover-up what really happens in the native peptide region.
You might want to read the following paper about different capping options.
Abstract: The accuracy of the determination of the energy of interaction between Phe20 and the Pro5-Thr6-Tyr7-Pro8 complex inside the hydrophobic core of avian pancreatic polypeptide was investigated using three capping strategies for molecular fractionation with conjugated caps and DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory. The most accurate determination resulted from acetylation of the a-amino group combined with methyl amidation of the a-carbonyl group, with relative deviations less than 10%. Combinations of hydrogenation of the a-amino group with the replacement of the a-carbonyl group with a hydrogen and the hydrogenation of the a-amino group with methylation of the a-carbonyl group were less accurate, leading to relative deviations up to 35%. Choice of capping methods depends on the structural features of the polypeptide system, the desired accuracy, and the available computational resources.
On 09/16/2010 09:16 AM, Maura Mooney mmooney05,+,qub.ac.uk wrote:
Sent to CCL by: "Maura Mooney" [mmooney05%a%qub.ac.uk] Hi, My question regards peptide caps. I have a few proteins (~25kDa) in which the first and last few residues are truncated. In what circumstances should I cap the protein termini, and apart from stability in small alpha helices, why should we cap protein termini? Thanx,E-mail to subscribers: CHEMISTRY++ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST++ccl.net or use http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/