From owner-chemistry: at :ccl.net Fri Sep 17 08:25:00 2010 From: "Jozsef Csontos jcsontos.lists],[gmail.com" To: CCL Subject: CCL: Capping termini - protein modeling Message-Id: <-42782-100917051429-9841-v7BNGxGL3Ap5YFxaW15iGQ!A!server.ccl.net> X-Original-From: Jozsef Csontos Content-Type: multipart/alternative; boundary="------------090707060609000700010802" Date: Fri, 17 Sep 2010 11:14:15 +0200 MIME-Version: 1.0 Sent to CCL by: Jozsef Csontos [jcsontos.lists===gmail.com] This is a multi-part message in MIME format. --------------090707060609000700010802 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Maura, 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. http://dx.doi.org/10.1002/qua.21553 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. Best, Jozsef 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,> > > --------------090707060609000700010802 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit Maura,

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.

http://dx.doi.org/10.1002/qua.21553

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.

Best,
Jozsef

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?

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