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NMR processing:
MDD
NMR assignment:
Backbone:
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MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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  #1  
Unread 02-25-2011, 04:10 PM
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Question Unanswered: αH(i,i+1) NOEs in helical peptide, can this be present continuously...

Hi,

I have observed some interesting NOEs for my peptide (5 kDa) in my 2D NOESY spectrum recorded at 900 MHz. I see NOEs that forms an α-helical pattern between 12-24 residues and N&C-terminus of my peptide is unstructured and does not have any secondary structure. The interesting part is, apart from seeing helical NOE patterns, such as αN(i,i+3)and αβ(i,i+3) for the residues between 12 & 24, I see in the alpha proton chemical shift regions of my 2D NOESY spectrum, a continuous αH(i,i+1) NOEs for the residues where I have helical secondary structural region (12-24 aa). That is, I see NOE patterns like 12Hα -13Hα, 13Hα to 14Hα, 14Hα-15Hα, 15Hα to 16Hα, 17Hα-18Hα, 19Hα to 20 Hα and so on until 24th residue. In general, I have never seen in any literature reported this type of NOE patterns for the α-helical peptide. The mixing time that I used for my NOE is 300 ms. Did any of you have observed this type of Hα(i)-Hα(i+1) NOEs for α-helical regions of peptide? I would appreciate your answers and thanks a lot.
- Vivek

Last edited by Vivekanandan Subramanian; 02-25-2011 at 04:17 PM.
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  #2  
Unread 11-15-2011, 12:00 PM
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Default alpha- alpha NOE

Hi,

If you are observing alpha-alpha NOEs continuously it must be beta sheet structure. In alpha helix you should observe continuous NH-NH NOEs. If both are present then your molecule must be existing in two conformations.

cheers, krishna.
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  #3  
Unread 05-06-2013, 02:31 PM
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Default

how do the ha to ha noe's compare to the hn to hn Noe's for the same residues.

300ms is pretty long for a 5kda peptide - it wouldn't be surprising to see spin diffusion errors.
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