BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
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


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 08-21-2010, 11:16 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,751
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Conformation of MeAla6-cyclosporin A by NMR. Relationship of sidechain orientation of

Conformation of MeAla6-cyclosporin A by NMR. Relationship of sidechain orientation of the MeBmt-1, MeLeu-9, and MeLeu-10 residues to immunosuppressive activity.

Related Articles Conformation of MeAla6-cyclosporin A by NMR. Relationship of sidechain orientation of the MeBmt-1, MeLeu-9, and MeLeu-10 residues to immunosuppressive activity.

Int J Pept Protein Res. 1991 May;37(5):351-63

Authors: Gooley PR, Durette PL, Boger J, Armitage IM

MeAla6-cyclosporin A (MeAla6-CsA) is a unique CsA analog that shows weak immunosuppressive activity and yet binds strongly to the proposed cytosolic protein receptor, cyclophilin (CyP). Preliminary 1H NMR data showed significant chemical shift differences between spectra of MeAla6-CsA and CsA, suggesting different preferred conformations. A more detailed study, however, revealed that the backbone conformations of the two molecules are essentially identical, and that the differences can be accounted for, principally, by the sidechain motions of the MeBmt-1, MeLeu-9, and -10 residues. ROE and coupling constant data show that in MeAla6-CsA, the preferred chi 1 rotamers for MeLeu-9 and -10 are + 180 degrees (T), whereas in CsA there is a more even distribution of rotamer populations for MeLeu-10, and a preferred -60 degrees (G-) chi 1 rotamer for MeLeu-9. Similar data argue that the sidechain of MeBmt-1 is more restricted in its motion in MeAla-CsA than in CsA. Temperature studies suggest that these preferred rotamers for MeAla6-CsA may increase the stability of the hydrogen bond between NH(7) and CO(11), but prevent particular residues, especially the essential MeBmt-1 sidechain, from adopting orientations required to elicit immunosuppressive activity. The significant changes observed in the preferred orientations for the sidechains of the MeBmt-1, MeLeu-9, and MeLeu-10 residues in MeAla6-CsA argue that the particular orientations which they assume in CsA are not essential for cyclophilin binding.

PMID: 1917291 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[KPWU blog] [PyMOL] Sidechain helper in the cartoon view
Sidechain helper in the cartoon view Using cartoon view to present the protein secondary structures and tertiary structure is common and we also often see people present some sidechains of particular residues which may be important in some biological roles. In PyMOL, when sidechain atoms are presented in the “sticks mode” with the cartoon*scaffold, we always see the backbone atoms (e.g. http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=609&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.
nmrlearner News from NMR blogs 0 11-13-2011 04:51 AM
[NMR paper] Conformation and orientation of the retinyl chromophore in rhodopsin: a critical eval
Conformation and orientation of the retinyl chromophore in rhodopsin: a critical evaluation of recent NMR data on the basis of theoretical calculations results in a minimum energy structure consistent with all experimental data. Related Articles Conformation and orientation of the retinyl chromophore in rhodopsin: a critical evaluation of recent NMR data on the basis of theoretical calculations results in a minimum energy structure consistent with all experimental data. Biochemistry. 2001 Apr 10;40(14):4201-4 Authors: Singh D, Hudson BS, Middleton C,...
nmrlearner Journal club 0 11-19-2010 08:32 PM
Solution structural investigation and conformation-activity relationship of BAM8-22 b
Solution structural investigation and conformation-activity relationship of BAM8-22 by NMR and molecular dynamics simulations. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution structural investigation and conformation-activity relationship of BAM8-22 by NMR and molecular dynamics simulations. Bioorg Med Chem Lett. 2010 Feb 1;20(3):1260-2 Authors: Lv G, Dong S NMR spectroscopy and molecular dynamics simulations show that BAM8-22...
nmrlearner Journal club 0 09-22-2010 05:27 AM
[Question from NMRWiki Q&A forum] Aromatic sidechain assignment pulse sequences for Varian?
Aromatic sidechain assignment pulse sequences for Varian? Hi, someone asked a similar question before, but I'd like to know: Are there readily available varian pulse sequences that help assign aromatic side-chains? Maybe there is something like that in Biopack or elsewhere? Thanks a bunch! M.
nmrlearner News from other NMR forums 0 09-14-2010 03:44 AM
[NMR paper] NMR studies of [U-13C]cyclosporin A bound to cyclophilin: bound conformation and port
NMR studies of cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding. Related Articles NMR studies of cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding. Biochemistry. 1991 Jul 2;30(26):6574-83 Authors: Fesik SW, Gampe RT, Eaton HL, Gemmecker G, Olejniczak ET, Neri P, Holzman TF, Egan DA, Edalji R, Simmer R Cyclosporin A (CsA), a potent immunosuppressant, is known to bind with high specificity to cyclophilin (CyP), a 17.7 kDa protein with...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution.
The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution. Related Articles The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution. Biochemistry. 1991 Jul 2;30(26):6563-74 Authors: Weber C, Wider G, von Freyberg B, Traber R, Braun W, Widmer H, Wüthrich K Cyclosporin A bound to the presumed receptor protein cyclophilin was studied in aqueous solution at pH 6.0 by nuclear magnetic resonance spectroscopy using uniform 15N- or 13C-labeling of cyclosporin A and heteronuclear spectral editing techniques....
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] NMR studies of [U-13C]cyclosporin A bound to cyclophilin: bound conformation and port
NMR studies of cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding. Related Articles NMR studies of cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding. Biochemistry. 1991 Jul 2;30(26):6574-83 Authors: Fesik SW, Gampe RT, Eaton HL, Gemmecker G, Olejniczak ET, Neri P, Holzman TF, Egan DA, Edalji R, Simmer R Cyclosporin A (CsA), a potent immunosuppressant, is known to bind with high specificity to cyclophilin (CyP), a 17.7 kDa protein with...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution.
The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution. Related Articles The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution. Biochemistry. 1991 Jul 2;30(26):6563-74 Authors: Weber C, Wider G, von Freyberg B, Traber R, Braun W, Widmer H, Wüthrich K Cyclosporin A bound to the presumed receptor protein cyclophilin was studied in aqueous solution at pH 6.0 by nuclear magnetic resonance spectroscopy using uniform 15N- or 13C-labeling of cyclosporin A and heteronuclear spectral editing techniques....
nmrlearner Journal club 0 08-21-2010 11:12 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 10:20 AM.


Map