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, 11:04 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,578
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 1H NMR assignment and secondary structure of the Ca2(+)-free form of the amino-termin

1H NMR assignment and secondary structure of the Ca2(+)-free form of the amino-terminal epidermal growth factor like domain in coagulation factor X.

Related Articles 1H NMR assignment and secondary structure of the Ca2(+)-free form of the amino-terminal epidermal growth factor like domain in coagulation factor X.

Biochemistry. 1990 Sep 4;29(35):8111-8

Authors: Selander M, Persson E, Stenflo J, Drakenberg T

Blood coagulation factor X is composed of discrete domains, two of which are homologous to the epidermal growth factor (EGF). The N-terminal EGF like domain in factor X (fX-EGFN), residues 45-86 of the intact protein, contains a beta-hydroxylated aspartic acid and has one Ca2(+)-binding site. Using 2D NMR techniques, we have made a full assignment of the 500-MHz 1H NMR spectrum of Ca2(+)-free fX-EGFN. On the basis of this assignment and complementary NOESY experiments, we have also determined the secondary structure of Ca2(+)-free fX-EGFN in water solution. Residues 45-49 are comparatively mobile, whereas residues 50-56 are constrained by two disulfide bonds to one side of an antiparallel beta-sheet involving residues 59-64 and 67-72. Another antiparallel beta-sheet involves residues 76-77 and 83-84. A small, parallel beta-sheet connects residues 80-81 and 55-56 and thereby orients the two antiparallel beta-sheets relative to each other. Four beta-turns are identified, involving residues 50-53, 56-59, 64-67, and 73-76. Residues 78-82 adopt an extended bend structure. On the basis of secondary structure and the location of the three disulfide bonds, we find that Asp 46, Asp 48, and Hya 63 are sufficiently close to each other to form a Ca2(+)-binding site. However, the amino terminus of the Ca2(+)-free form of fX-EGFN is not part of a triple-stranded beta-sheet as in other EGF like peptides. Differences and similarities between fX-EFGN and murine EGF with respect to secondary structure and conformational shifts are discussed.

PMID: 2261466 [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
VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy
VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy Abstract Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR...
nmrlearner Journal club 0 12-22-2011 06:50 AM
[NMR paper] Sequential 1H and 15N NMR resonance assignment and secondary structure of ferrocytoch
Sequential 1H and 15N NMR resonance assignment and secondary structure of ferrocytochrome c2 from Rhodobacter sphaeroides. Related Articles Sequential 1H and 15N NMR resonance assignment and secondary structure of ferrocytochrome c2 from Rhodobacter sphaeroides. J Biochem. 1996 Jun;119(6):1131-42 Authors: Gans P, Simorre JP, Caffrey M, Marion D, Richaud P, Verméglio A Sequence-specific 1H and 15N assignments have been made for the amino acids of the ferrocytochrome c2 from Rhodobacter sphaeroides. Initial assignments were made by analysis of...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] 1H and 15N assignment of NMR spectrum, secondary structure and global folding of the
1H and 15N assignment of NMR spectrum, secondary structure and global folding of the immunophilin-like domain of the 59-kDa FK506-binding protein. 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 and 15N assignment of NMR spectrum, secondary structure and global folding of the immunophilin-like domain of the 59-kDa FK506-binding protein. Eur J Biochem. 1995 Aug 1;231(3):761-72 Authors: Rouvière-Fourmy N, Craescu CT, Mispelter J, Lebeau MC,...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] Assignment of the backbone 1H,15N,13C NMR resonances and secondary structure of a dou
Assignment of the backbone 1H,15N,13C NMR resonances and secondary structure of a double-stranded RNA binding domain from the Drosophila protein staufen. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Assignment of the backbone 1H,15N,13C NMR resonances and secondary structure of a double-stranded RNA binding domain from the Drosophila protein staufen. FEBS Lett. 1995 Apr 10;362(3):333-6 Authors: Bycroft M, Proctor M, Freund SM, St Johnston D NMR spectroscopy has been...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Secondary structure and zinc ligation of human recombinant short-form stromelysin by
Secondary structure and zinc ligation of human recombinant short-form stromelysin by multidimensional heteronuclear NMR. Related Articles Secondary structure and zinc ligation of human recombinant short-form stromelysin by multidimensional heteronuclear NMR. Biochemistry. 1993 Dec 7;32(48):13098-108 Authors: Gooley PR, Johnson BA, Marcy AI, Cuca GC, Salowe SP, Hagmann WK, Esser CK, Springer JP Stromelysin-1, a member of the matrix metalloendoprotease family, is a zinc protease involved in the degradation of connective tissue in the...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] Assignment of the backbone 1H and 15N NMR resonances and secondary structure characte
Assignment of the backbone 1H and 15N NMR resonances and secondary structure characterization of barstar. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Assignment of the backbone 1H and 15N NMR resonances and secondary structure characterization of barstar. FEBS Lett. 1993 Oct 11;332(1-2):81-7 Authors: Lubienski MJ, Bycroft M, Jones DN, Fersht AR Barstar, a polypeptide inhibitor of ribonucleases, has been studied by 2D and 3D NMR techniques using uniformly...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] Assignment of the 1H NMR spectrum and secondary structure elucidation of the single-s
Assignment of the 1H NMR spectrum and secondary structure elucidation of the single-stranded DNA binding protein encoded by the filamentous bacteriophage IKe. Related Articles Assignment of the 1H NMR spectrum and secondary structure elucidation of the single-stranded DNA binding protein encoded by the filamentous bacteriophage IKe. Biochemistry. 1992 Feb 4;31(4):1254-62 Authors: van Duynhoven JP, Folkers PJ, Prinse CW, Harmsen BJ, Konings RN, Hilbers CW By means of 2D NMR techniques, all backbone resonances in the 1H NMR spectrum of the...
nmrlearner Journal club 0 08-21-2010 11:41 PM
[NMR paper] Complete assignment of the 1H NMR spectrum and secondary structure of the DNA binding
Complete assignment of the 1H NMR spectrum and secondary structure of the DNA binding domain of GAL4. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Complete assignment of the 1H NMR spectrum and secondary structure of the DNA binding domain of GAL4. FEBS Lett. 1990 Dec 10;276(1-2):49-53 Authors: Gadhavi PL, Raine AR, Alefounder PR, Laue ED Complete 1H NMR resonance assignments are presented for the cysteine rich region of the DNA binding domain of the yeast...
nmrlearner Journal club 0 08-21-2010 11:04 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 04:44 PM.


Map