NMR paper 1H NMR sequential assignments and identification of secondary structural elements in

		BioNMR > Educational resources > Journal club
[NMR paper] 1H NMR sequential assignments and identification of secondary structural elements in

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

08-21-2010, 11:41 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

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 a single polypeptide chain and a [2Fe-2S] cluster, are reported. No crystal structure has been obtained for Pdx or for any closely homologous protein. The sequentially assigned resonances represent ca. 83% of all the protons in Pdx and a large majority of those protons which are unaffected by the paramagnetism of the iron-sulfur cluster. A total of three alpha-helices, two beta-sheets, and two type I beta-turns have been identified from NOE (nuclear Overhauser effect) patterns. Besides the extensive beta-sheet described previously, a second sheet is identified, consisting of two short antiparallel strands (Ile 89-Thr 91 and Val 21-Leu 23), one of which ends in a tight type I turn (Thr 91-Pro 92-Glu 93-Leu 94). One short helix (Ala 26-Gly 31) and a second longer helical region (Glu 54-Cys 73) are present. This second helical region is discontinuous, breaking at Pro 61, resuming at Glu 65, and ending at Cys 73. The functionally important C-terminal tryptophan residue has been identified, and some structural constraints on this residue are described. Previously reported functional data concerning Pdx are discussed in light of present structural information. Finally, approaches to the determination of a high-resolution solution structure of the protein are discussed.

PMID: 1536837 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] An NMR view of the unfolding process of rusticyanin: Structural elements that maintain the architecture of a beta-barrel metalloprotein. An NMR view of the unfolding process of rusticyanin: Structural elements that maintain the architecture of a beta-barrel metalloprotein. Related Articles An NMR view of the unfolding process of rusticyanin: Structural elements that maintain the architecture of a beta-barrel metalloprotein. Protein Sci. 2005 Jul;14(7):1710-22 Authors: Alcaraz LA, Jiménez B, Moratal JM, Donaire A The unfolding process of the blue copper protein rusticyanin (Rc) as well as its dynamic and D(2)O/H(2)O exchange properties in an incipient unfolded state have been...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
NMR assignments and the identification of the secondary structure of the anti-retrovi NMR assignments and the identification of the secondary structure of the anti-retroviral cytidine deaminase. Related Articles NMR assignments and the identification of the secondary structure of the anti-retroviral cytidine deaminase. Nucleic Acids Symp Ser (Oxf). 2008;(52):183-4 Authors: Furukawa A, Nagata T, Habu Y, Sugiyama R, Hayashi F, Yokoyama S, Takaku H, Katahira M APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G) is known to have a role in intrinsic cellular immunity against human immunodeficiency virus type1...	nmrlearner	Journal club	0	11-17-2010 05:49 PM
[NMR paper] Sequential assignments and identification of secondary structure elements of the coli Sequential assignments and identification of secondary structure elements of the colicin E9 immunity protein in solution by homonuclear and heteronuclear NMR. Related Articles Sequential assignments and identification of secondary structure elements of the colicin E9 immunity protein in solution by homonuclear and heteronuclear NMR. Biochemistry. 1994 Oct 18;33(41):12347-55 Authors: Osborne MJ, Lian LY, Wallis R, Reilly A, James R, Kleanthous C, Moore GR 1H-1H, 1H-15N, and 1H-1H-15N multidimensional NMR spectroscopic studies of the 86 amino...	nmrlearner	Journal club	0	08-22-2010 03:29 AM
[NMR paper] Sequential proton NMR resonance assignments, circular dichroism, and structural prope Sequential proton NMR resonance assignments, circular dichroism, and structural properties of a 50-residue substrate-binding peptide from DNA polymerase I. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Sequential proton NMR resonance assignments, circular dichroism, and structural properties of a 50-residue substrate-binding peptide from DNA polymerase I. Arch Biochem Biophys. 1993 Feb 15;301(1):174-83 Authors: Mullen GP, Vaughn JB, Mildvan AS Peptide I, a 50-amino...	nmrlearner	Journal club	0	08-21-2010 11:53 PM
[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] Sequential 1H NMR assignments and secondary structure of an IgG-binding domain from p Sequential 1H NMR assignments and secondary structure of an IgG-binding domain from protein G. Related Articles Sequential 1H NMR assignments and secondary structure of an IgG-binding domain from protein G. Biochemistry. 1991 Jun 4;30(22):5335-40 Authors: Lian LY, Yang JC, Derrick JP, Sutcliffe MJ, Roberts GC, Murphy JP, Goward CR, Atkinson T Protein G is a member of a class of cell surface bacterial proteins from Streptococcus that bind IgG with high affinity. A fragment of molecular mass 6988, which retains IgG-binding activity, has been...	nmrlearner	Journal club	0	08-21-2010 11:16 PM
[NMR paper] Sequential 1H NMR assignments and secondary structure of the B domain of staphylococc Sequential 1H NMR assignments and secondary structure of the B domain of staphylococcal protein A: structural changes between the free B domain in solution and the Fc-bound B domain in crystal. Related Articles Sequential 1H NMR assignments and secondary structure of the B domain of staphylococcal protein A: structural changes between the free B domain in solution and the Fc-bound B domain in crystal. Biochemistry. 1990 Sep 18;29(37):8787-93 Authors: Torigoe H, Shimada I, Saito A, Sato M, Arata Y The recombinant B domain (FB) of staphylococcal...	nmrlearner	Journal club	0	08-21-2010 11:04 PM
[NMR paper] Determination of the secondary structural elements of chicken liver fatty acid bindin Determination of the secondary structural elements of chicken liver fatty acid binding protein by two-dimensional homonuclear NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles Determination of the secondary structural elements of chicken liver fatty acid binding protein by two-dimensional homonuclear NMR. Biopolymers. 1999 Jul;50(1):1-11 Authors: Schievano E, Mammi S, Peggion E A conformational study in solution of the fatty acid...	nmrlearner	Journal club	0	08-21-2010 04:03 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 On Trackbacks are Off Pingbacks are Off Refbacks are Off