Aromatic side chain assignment with Aro-HCCH-COSY in XEASY: Difference between revisions
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== '''Aromatic Side-chain Resonance Assignment Using the Aromatic HCCHCOSY Spectrum''' == | |||
Aromatic (4,3)D HCCH shows signals for aromatic H-C-C-H moeties. See [[NESG:Aliphatic side-chain resonance assignment using the aliphatic HCCH COSY spectrum|aliphatic (4,3)D HCCH Analysis]] for comparison. | |||
* '''Phe, Tyr, His''' | |||
## In UBNMR, run <tt>makeAroPeaks</tt> and use the most recent version of bbsc.prot to generate starting lists <tt>hcchcosyaroI1.peaks</tt> and <tt>hcchcosyaroI1.prot</tt>. | |||
## In XEASY, use <tt>ns</tt> to load the three sub-spectra of aromatic (4,3)D HCCH; use <tt>ls</tt>, <tt>lp</tt> and <tt>lc</tt> to load, respectively, <tt>noe.seq</tt>, <tt>hcchcosyaroI1.peaks</tt> (with 1HD (QD) assigned in NOESY) and <tt>hcchcosyaroI1.prot</tt>; use <tt>se</tt> and <tt>gs</tt> to sort and display [w1(13C;1H);w3(1H)]-strips. | |||
## In XEASY, use <tt>pm</tt>, <tt>es</tt>, <tt>se</tt> and <tt>gs=( or =sf</tt>) to display [w1(13C;1H);w2(13C)]-planes, and sort and [w1(13C;1H);w2(13CD)]-planes; use <tt>mr</tt> to accurately adjust peak positions to assign 13CD chemical shifts; use <tt>pm</tt> and <tt>gs</tt> to re-display [w1(13C;1H); w3(1H)]-planes and [w1(13C;1H); w3(1H)]-strips; use <tt>mr</tt> to accurately adjust peak positions to confirm QD chemical shifts. The strips in the basic spectra are expected to exhibit peaks at 13CD, 13Main.CE, ..., 13CD±QD and 13CD±QE. Use <tt>mr</tt> to accurately position peaks along w1; use <tt>ac</tt>, <tt>wp</tt> and <tt>wc</tt> to save updated PeakList and AtomList. | |||
## In UBNMR, run <tt>updatacosyGFT</tt> to calculate SQ shifts from updated AtomList. | |||
## Repeat 1.- 3. and 4. for <tt>QE strips</tt> and assign HE. Note that for His, assignment is often complicated by the presence of strong signals from HIS-Tags introduced to facilitate protein purification. The QE strip in the basic spectra are expected to exhibit peaks at 13CD, 13Main.CE, 13CZ, ..., 13CD±QD, 13Main.CE±QE and possible 13CZ±1HZ (for Phe only). .See also: [[NESG:Side chain assignments using simultaneous 15N, 13C-resolved (1H,1H) NOESY|Assign Aromatic Side-chain Resonances using the NOESY and HCCH]]. | |||
* '''TRP''' | |||
## In XEASY, for residue Trp, repeat steps 1.-3. for strips in the order HH2 > HZ2 > HZ3 > HE3 (instead of the strip order QD > QE for Tyr and Phe). In HH2-strips, assign 13CH2±1HH2, and 13CZ2±1HZ2. In HZ2-strips assign 13CZ2± 1HH2, 13CZ2±1HZ2 and 13CZ3±1HZ3. In HZ3-strips, assign 13CZ3±1HZ3, 13CZ2±1HZ2 and 13CZ3±1HZ3. In HZ3 strip, assign 13CZ3±1HZ3, and 13CE3±1HE3. See also [[NESG:Side chain assignments using simultaneous 15N, 13C-resolved (1H,1H) NOESY|Assign Aromatic Side-chain Resonances using the NOESY and HCCH]]. | |||
## In XEASY, use <tt>ac</tt>, <tt>wp</tt> and <tt>wc</tt> to save the final PeakList and AtomList | |||
-- Main.GaohuaLiu - 01 Feb 2007 | |||
Revision as of 17:33, 9 October 2009
Aromatic Side-chain Resonance Assignment Using the Aromatic HCCHCOSY Spectrum
Aromatic (4,3)D HCCH shows signals for aromatic H-C-C-H moeties. See aliphatic (4,3)D HCCH Analysis for comparison.
- Phe, Tyr, His
- In UBNMR, run makeAroPeaks and use the most recent version of bbsc.prot to generate starting lists hcchcosyaroI1.peaks and hcchcosyaroI1.prot.
- In XEASY, use ns to load the three sub-spectra of aromatic (4,3)D HCCH; use ls, lp and lc to load, respectively, noe.seq, hcchcosyaroI1.peaks (with 1HD (QD) assigned in NOESY) and hcchcosyaroI1.prot; use se and gs to sort and display [w1(13C;1H);w3(1H)]-strips.
- In XEASY, use pm, es, se and gs=( or =sf) to display [w1(13C;1H);w2(13C)]-planes, and sort and [w1(13C;1H);w2(13CD)]-planes; use mr to accurately adjust peak positions to assign 13CD chemical shifts; use pm and gs to re-display [w1(13C;1H); w3(1H)]-planes and [w1(13C;1H); w3(1H)]-strips; use mr to accurately adjust peak positions to confirm QD chemical shifts. The strips in the basic spectra are expected to exhibit peaks at 13CD, 13Main.CE, ..., 13CD±QD and 13CD±QE. Use mr to accurately position peaks along w1; use ac, wp and wc to save updated PeakList and AtomList.
- In UBNMR, run updatacosyGFT to calculate SQ shifts from updated AtomList.
- Repeat 1.- 3. and 4. for QE strips and assign HE. Note that for His, assignment is often complicated by the presence of strong signals from HIS-Tags introduced to facilitate protein purification. The QE strip in the basic spectra are expected to exhibit peaks at 13CD, 13Main.CE, 13CZ, ..., 13CD±QD, 13Main.CE±QE and possible 13CZ±1HZ (for Phe only). .See also: Assign Aromatic Side-chain Resonances using the NOESY and HCCH.
- TRP
- In XEASY, for residue Trp, repeat steps 1.-3. for strips in the order HH2 > HZ2 > HZ3 > HE3 (instead of the strip order QD > QE for Tyr and Phe). In HH2-strips, assign 13CH2±1HH2, and 13CZ2±1HZ2. In HZ2-strips assign 13CZ2± 1HH2, 13CZ2±1HZ2 and 13CZ3±1HZ3. In HZ3-strips, assign 13CZ3±1HZ3, 13CZ2±1HZ2 and 13CZ3±1HZ3. In HZ3 strip, assign 13CZ3±1HZ3, and 13CE3±1HE3. See also Assign Aromatic Side-chain Resonances using the NOESY and HCCH.
- In XEASY, use ac, wp and wc to save the final PeakList and AtomList
-- Main.GaohuaLiu - 01 Feb 2007