NMR analysis blog Conformational analysis of cyclic compounds using Mspin and RDCs

		BioNMR > NMR community > News from NMR blogs
[NMR analysis blog] Conformational analysis of cyclic compounds using Mspin and RDCs

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

10-24-2010, 08:03 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,174

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

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, 5879–5881 ]from the groups of Roberto Gil (Carnegie Mellon University) and Navarro-Vázquez ( 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

Did you find this post helpful?

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: Möller 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, FauchÃ¨re 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, RDC’s and efficient use of freely rotating groups Mspin, RDC’s 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

« Previous Thread | Next 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