Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins

		BioNMR > Educational resources > Journal club
Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins

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

07-14-2012, 01:53 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins

Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins

Publication year: 2012
Source:Journal of Magnetic Resonance

Yi-Jan Lin, Donata K. Kirchner, Peter Güntert

Homodimeric proteins pose a difficulty for NMR structure determination because the degeneracy of the chemical shifts in the two identical monomers implies an ambiguity in all assignments of distance restraints. For homodimeric proteins, residues involved in the interface between two monomers provide essential intermolecular NOEs. The structure determination of homodimeric proteins hence relies strongly on chemical shift assignments of these interface residues. Our paper discusses the influence of the extent of 1H chemical shift assignments of interface residues on the structure determinations of homodimeric proteins using the CYANA program. The results reveal that successful structure determinations of homodimeric proteins with automated NOE assignment depend on the percentage of assigned interface residues and that a high completeness of around 80–90% of the 1H chemical shift assignment in the interface is needed for reliable NMR structure determinations of homodimeric proteins for which no experimental distinction between intra- and intermolecular NOEs, e.g. by filtered NOESY experiments, is available. Our results also show that RMSD and target function values are insufficient to judge the quality of homodimeric structures determined using automated NOE assignment. Structure determinations of homodimeric proteins by NMR using conventional NOESY experiments are thus possible but more challenging than for monomeric proteins.
Graphical abstract

Graphical abstract Highlights

? Impact of interface assignment completeness on homodimer structure determination. ? CYANA can calculate homodimer structures with automated NOE assignment. ? About 80–90% complete shift assignment in the interface needed for homodimers. ? Target function and RMSD values are not sufficient to judge homodimer structures.

Source: Journal of Magnetic Resonance

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Influence of chemical shift tolerances on NMR structure calculations using ARIA proto Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data. Related Articles Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data. J Biomol NMR. 2005 Jan;31(1):21-34 Authors: Fossi M, Linge J, Labudde D, Leitner D, Nilges M, Oschkinat H Large-scale protein structure determination by NMR via automatic assignment of NOESY spectra requires the adjustment of several parameters for optimal performance. Among those are the chemical shift...	nmrlearner	Journal club	0	11-24-2010 11:14 PM
[NMR paper] Influence of the completeness of chemical shift assignments on NMR structures obtaine Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. Related Articles Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. J Struct Funct Genomics. 2003;4(2-3):179-89 Authors: Jee J, Güntert P Reliable automated NOE assignment and structure calculation on the basis of a largely complete, assigned input chemical shift list and a list of unassigned NOESY cross peaks has recently become feasible for routine NMR protein...	nmrlearner	Journal club	0	11-24-2010 09:01 PM
NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived fr NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx. Related Articles NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx. Biomol NMR Assign. 2010 Oct 7; Authors: Naik MT, Chang CC, Naik NM, Kung CC, Shih HM, Huang TH Small Ubiquitin-like MOdifiers (SUMOs) are ubiquitin-like proteins known to covalently modify large number of cellular proteins. The mammalian SUMO family includes four paralogues, SUMO-1 through SUMO-4....	nmrlearner	Journal club	0	10-12-2010 02:52 PM
[NMR paper] 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary struct 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli. Related Articles 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli. J Biomol NMR. 1997 Feb;9(2):167-80 Authors: Yu J, Simplaceanu V, Tjandra NL, Cottam PF, Lukin JA, Ho C 1H, 13C, and 15N NMR assignments of the backbone atoms and beta-carbons have been made for liganded glutamine-binding protein (GlnBP) of Escherichia...	nmrlearner	Journal club	0	08-22-2010 03:31 PM
[NMR paper] Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronu Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy. Related Articles Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy. J Biomol NMR. 1996 Mar;7(2):89-98 Authors: Wang YS, Frederick AF, Senior MM, Lyons BA, Black S, Kirschmeier P, Perkins LM, Wilson O The growth factor receptor-bound protein-2 (Grb-2) is an adaptor protein that mediates signal transduction pathways. Chemical shift assignments were obtained for the SH2 domain of...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[NMR paper] 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnes 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnesium-binding characteristics of the Bacillus subtilis response regulator, Spo0F, determined by heteronuclear high-resolution NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and...	nmrlearner	Journal club	0	08-22-2010 03:50 AM
Analysis of and chemical shifts of cysteine and cystine residues in proteins: a quant Abstract Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the 13\textC\upalpha and 13\textC\upbeta chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed...	nmrlearner	Journal club	0	08-14-2010 04:19 AM
Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm John J. Kuszewski, Robin Augustine Thottungal, G. Marius Clore and Charles D. Schwieters Journal of Biomolecular NMR; 2008; 41(4); pp 221-239 Abstract: We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258–6273). The improved protocol includes...	Abe	Journal club	0	09-21-2008 11:43 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