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 08-22-2010, 03:29 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,586
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 Sequential 1H, 13C, and 15N NMR assignments and solution conformation of apokedarcidi

Sequential 1H, 13C, and 15N NMR assignments and solution conformation of apokedarcidin.

Related Articles Sequential 1H, 13C, and 15N NMR assignments and solution conformation of apokedarcidin.

Biochemistry. 1994 Sep 27;33(38):11438-52

Authors: Constantine KL, Colson KL, Wittekind M, Friedrichs MS, Zein N, Tuttle J, Langley DR, Leet JE, Schroeder DR, Lam KS

Kedarcidin is a recently discovered antitumor antibiotic chromoprotein. The solution conformation of the kedarcidin apoprotein (114 residues) has been characterized by heteronuclear multidimensional NMR spectroscopy. Sequence-specific backbone atom resonance assignments were obtained for a uniformly 13C/15N-enriched sample of apokedarcidin via a semiautomated analysis of 3D HNCACB, 3D CBCA-(CO)NH, 4D HNCAHA, 4D HN(CO)CAHA, 3D HBHA(CO)NH, and 3D HNHA(Gly) spectra. Side-chain assignments were subsequently obtained by analysis of (primarily) 3D HCCH-TOCSY and HCCH-COSY spectra. A qualitative analysis of the secondary structure is presented on the basis of 3J alpha NH coupling constants, deviations of 13C alpha and 13C beta chemical shifts from random coil values, and NOEs observed in 3D 15N- and 13C-edited NOESY-HSQC spectra. This analysis revealed a four-stranded antiparallel beta-sheet, a three-stranded antiparallel beta-sheet, and two two-standed antiparallel beta-sheets. The assignments of cross-peaks in the 3D NOESY spectra were assisted by reference to a preliminary model of apokedarcidin built using the program CONGEN starting from the X-ray structure of the homologous protein aponeocarzinostatin. An ensemble of 15 apokedarcidin solution structures has been generated by variable target function minimization (DIANA program) and refined by simulated annealing (X-PLOR program). The average backbone atom root-mean-square difference between the individual structures and the mean coordinates is 0.68 +/- 0.08 A. The overall fold of apokedarcidin is well-defined; it is composed of an immunoglobulin-like seven-stranded antiparallel beta-barrel and a subdomain containing two antiparallel beta-ribbons. Highly similar tertiary structures have been previously reported for the related proteins neocarzinostatin, macromomycin, and actinoxanthin. Important structural features are revealed, including the dimensions of the chromophore-binding pocket and the locations of side chains that are likely to be involved in chromophore stabilization.

PMID: 7918358 [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
Solid-state NMR sequential assignments of ?-synuclein.
Solid-state NMR sequential assignments of ?-synuclein. Solid-state NMR sequential assignments of ?-synuclein. Biomol NMR Assign. 2011 Jul 9; Authors: Gath J, Habenstein B, Bousset L, Melki R, Meier BH, Böckmann A Parkinson's disease is amongst the most frequent and most devastating neurodegenerative diseases. It is tightly associated with the assembly of proteins into high-molecular weight protein species, which propagate between neurons in the central nervous system. The principal protein involved in this process is ?-synuclein which is a...
nmrlearner Journal club 0 07-12-2011 06:23 PM
[NMR paper] Proton NMR assignments and solution conformation of RANTES, a chemokine of the C-C ty
Proton NMR assignments and solution conformation of RANTES, a chemokine of the C-C type. Related Articles Proton NMR assignments and solution conformation of RANTES, a chemokine of the C-C type. Biochemistry. 1995 Apr 25;34(16):5329-42 Authors: Skelton NJ, Aspiras F, Ogez J, Schall TJ 1H NMR has been used to investigate the structural properties of RANTES, a protein from the C-C branch of the chemotactic cytokine family that has a strong chemoattractive effect on monocytes, lymphocytes, and eosinophils. Titration of pH from 5.0 to 2.5...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] NMR sequential assignments and solution structure of chlorotoxin, a small scorpion to
NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels. Related Articles NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels. Biochemistry. 1995 Jan 10;34(1):13-21 Authors: Lippens G, Najib J, Wodak SJ, Tartar A The solution structure of chlorotoxin, a small toxin purified from the venom of the Leiurus quinquestriatus scorpion, has been determined using 2D 1H NMR spectroscopy. Analysis of the NMR data shows that...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Sequential 1H and 15N NMR assignments and secondary structure of a recombinant anti-d
Sequential 1H and 15N NMR assignments and secondary structure of a recombinant anti-digoxin antibody VL domain. Related Articles Sequential 1H and 15N NMR assignments and secondary structure of a recombinant anti-digoxin antibody VL domain. Biochemistry. 1992 Jun 2;31(21):5033-43 Authors: Constantine KL, Goldfarb V, Wittekind M, Anthony J, Ng SC, Mueller L A uniformly 15N-labeled recombinant light-chain variable (VL) domain from the anti-digoxin antibody 26-10 has been investigated by heteronuclear two-dimensional (2D) and three-dimensional...
nmrlearner Journal club 0 08-21-2010 11:41 PM
[NMR paper] 1H NMR sequential assignments and identification of secondary structural elements in
1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas. Related Articles 1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas. Biochemistry. 1992 Feb 25;31(7):1961-8 Authors: Ye XM, Pochapsky TC, Pochapsky SS Sequential 1H resonance assignments and secondary structural features of putidaredoxin (Pdx), a 106-residue globular protein consisting of...
nmrlearner Journal club 0 08-21-2010 11:41 PM
[NMR paper] Dihydrofolate reductase: sequential resonance assignments using 2D and 3D NMR and sec
Dihydrofolate reductase: sequential resonance assignments using 2D and 3D NMR and secondary structure determination in solution. Related Articles Dihydrofolate reductase: sequential resonance assignments using 2D and 3D NMR and secondary structure determination in solution. Biochemistry. 1991 Jun 25;30(25):6330-41 Authors: Carr MD, Birdsall B, Frenkiel TA, Bauer CJ, Jimenez-Barbero J, Polshakov VI, McCormick JE, Roberts GC, Feeney J Three-dimensional (3D) heteronuclear NMR techniques have been used to make sequential 1H and 15N resonance...
nmrlearner Journal club 0 08-21-2010 11:16 PM
[NMR paper] 1H NMR studies of echistatin in solution. Sequential resonance assignments and second
1H NMR studies of echistatin in solution. Sequential resonance assignments and secondary structure. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles 1H NMR studies of echistatin in solution. Sequential resonance assignments and secondary structure. Eur J Biochem. 1991 Dec 5;202(2):315-21 Authors: Dalvit C, Widmer H, Bovermann G, Breckenridge R, Metternich R Two-dimensional 1H-NMR methods have been used to obtain complete proton...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] 1H NMR studies of echistatin in solution. Sequential resonance assignments and second
1H NMR studies of echistatin in solution. Sequential resonance assignments and secondary structure. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles 1H NMR studies of echistatin in solution. Sequential resonance assignments and secondary structure. Eur J Biochem. 1991 Dec 5;202(2):315-21 Authors: Dalvit C, Widmer H, Bovermann G, Breckenridge R, Metternich R Two-dimensional 1H-NMR methods have been used to obtain complete proton...
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 - 2017, 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 03:59 PM.


Map