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

Go Back   BioNMR > NMR community > News from NMR blogs
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 10-24-2010, 08:03 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 21,379
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 Conformational analysis of cyclic compounds using Mspin and RDCs

Conformational analysis of cyclic compounds using Mspin and RDCs

On the occasion of the release of a new version of Mspin (BTW, this is the very first multiplatform version of Mspin: it works now in Windows, Mac OS X and Linux), I would like to bring into your attention one of the many applications where this software plays an instrumental role: The application of Mspin to the study of seven-membered rings compounds by NMR.



The NMR study of seven-membered ring compounds is a classical problem in conformational analysis. They are commonly studied by means of NOE-based experiments or 3J coupling analysis using Karplus-Altona relationships. In a recent work, recently published in Chemical Communications, [ Chem. Commun. , 2010, 46, 5879Ė5881 ]from the groups of Roberto Gil (Carnegie Mellon University) and Navarro-VŠzquez ( Universidade de Vigo ) have demonstrated that the conformation of a 3-benzazepine compound can be completely determined by using 1DCH residual dipolar couplings (RDCs). These RDCs were easily obtained by performing HSQC experiments coupled in the direct dimension using a polydimethylsiloxane gel as oriented medium



Conformational search indicated the presence of 11 possible conformations for this molecule. In agreement with computed DFT energies for these conformers, as well as observed 3J couplings, chemical shifts, and NOE's RDC analysis shows the preference of the system for a crown-chair conformation with equatorial disposition of the substituents.

Here you can download the rdc data file ( click here ) in the MSpin format and a multiconformer XYZ file with the DFT optimized conformations (click here) . Load them into the RDC module of Mspin, select the singular value decomposition method (SVD), just click the calculate button and see how convenient is to perform the RDC analysis with Mspin






More...

Source: NMR-analysis blog
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[Question from NMRWiki Q&A forum] RDCs di-Methyl lysine
RDCs di-Methyl lysine We are interested in studying di-methyl lysine, given that in most cases the two methyl groups are equivalent and each have the three protons, how much and if so what, information could you realistically get from RDCs on the Di- methyl signals? Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 03-30-2011 09:11 PM
[NMR paper] Conformational analysis by NMR and distance geometry techniques of a peptide mimetic
Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain. Related Articles Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain. J Pept Res. 2005 Feb;65(2):200-8 Authors: Saviano M, Isernia C, Bassarello C, Di Lello P, Galdiero S, Mierke DF, Benedetti E, Pedone C The Antennapedia homeodomain structure consists of four helices. The helices II and III are connected by a tripeptide that...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] NMR-based determination of the binding epitope and conformational analysis of MUC-1 g
NMR-based determination of the binding epitope and conformational analysis of MUC-1 glycopeptides and peptides bound to the breast cancer-selective monoclonal antibody SM3. Related Articles NMR-based determination of the binding epitope and conformational analysis of MUC-1 glycopeptides and peptides bound to the breast cancer-selective monoclonal antibody SM3. Eur J Biochem. 2002 Mar;269(5):1444-55 Authors: MŲller H, Serttas N, Paulsen H, Burchell JM, Taylor-Papadimitriou J, Mucin glycoproteins on breast cancer cells carry shortened...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Analysis of stress in the active site of myosin accompanied by conformational changes
Analysis of stress in the active site of myosin accompanied by conformational changes in transient state intermediate complexes using photoaffinity labeling and 19F-NMR spectroscopy. Related Articles Analysis of stress in the active site of myosin accompanied by conformational changes in transient state intermediate complexes using photoaffinity labeling and 19F-NMR spectroscopy. Eur J Biochem. 1998 Mar 15;252(3):520-9 Authors: Maruta S, Henry GD, Ohki T, Kambara T, Sykes BD, Ikebe M Myosin forms stable ternary complexes with ADP and the...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics sim
Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide Related Articles Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide J Comput Aided Mol Des. 1996 Jun;10(3):213-32 Authors: Buono RA, Kucharczyk N, Neuenschwander M, Kemmink J, Hwang LY, Fauchère JL, Venanzi CA The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] Conformational analysis of protein structures derived from NMR data.
Conformational analysis of protein structures derived from NMR data. Related Articles Conformational analysis of protein structures derived from NMR data. Proteins. 1993 Nov;17(3):232-51 Authors: MacArthur MW, Thornton JM A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] Conformational analysis of a mitochondrial presequence derived from the F1-ATPase bet
Conformational analysis of a mitochondrial presequence derived from the F1-ATPase beta-subunit by CD and NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Conformational analysis of a mitochondrial presequence derived from the F1-ATPase beta-subunit by CD and NMR spectroscopy. Biochim Biophys Acta. 1992 Sep 4;1159(1):81-93 Authors: Bruch MD, Hoyt DW Previous studies on mitochondrial targeting presequences have indicated that formation of an amphiphillic...
nmrlearner Journal club 0 08-21-2010 11:45 PM
[NMR analysis blog] Mspin, RDCís and efficient use of freely rotating groups
Mspin, RDCís and efficient use of freely rotating groups http://4.bp.blogspot.com/_-MfflvAgRls/ShKZ8q7lHcI/AAAAAAAAAZU/9I126hQPTBo/s400/mspin.jpg In the last ten years, Residual Dipolar Couplings (RDC) have come to occupy a very important place in the structure determination of proteins, nucleic acids and carbohydrates in liquid state. Although RDCs were originally discovered and theoretically explained for small molecules in liquid crystal solvents by A. Saupe in 1968 (Angew. Chem. Int. Ed. Engl. 1968, 7, 97) the spectra were too complex for a practical use in structure determination....
nmrlearner News from NMR blogs 0 08-21-2010 09:12 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 Off
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 - 2021, 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 07:27 PM.


Map