Lanthanoid tagging via an unnatural amino acid for protein structure characterization

		BioNMR > Educational resources > Journal club
Lanthanoid tagging via an unnatural amino acid for protein structure characterization

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

04-01-2017, 04:09 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

Lanthanoid tagging via an unnatural amino acid for protein structure characterization

Lanthanoid tagging via an unnatural amino acid for protein structure characterization

Abstract

Lanthanoid pseudo-contact shift (PCS) provides long-range structural information between a paramagnetic tag and protein nuclei. However, for proteins with native cysteines, site-specific attachment may only utilize functional groups orthogonal to sulfhydryl chemistry. Here we report two lanthanoid probes, DTTA-C3-yne and DTTA-C4-yne, which can be conjugated to an unnatural amino acid pAzF in the target protein via azide-alkyne cycloaddition. Demonstrated with ubiquitin and cysteine-containing enzyme EIIB, we show that large PCSs of distinct profiles can be generated for each tag/lanthanoid combination. The DTTA-based lanthanoid tags are associated with large magnetic susceptibility tensors owing to the rigidity of the tags. In particular, introduction of the DTTA-C3 tag affords intermolecular PCSs and enables structural characterization of a transient protein complex between ubiquitin and a UBA domain. Together, we have expanded the repertoire of paramagnetic tags and the applicability of paramagnetic NMR.

Source: Journal of Biomolecular NMR

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Characterization of Protein Tyrosine Phosphatase 1BInhibition by Chlorogenic Acid and Cichoric Acid Characterization of Protein Tyrosine Phosphatase 1BInhibition by Chlorogenic Acid and Cichoric Acid http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b01025/20161227/images/medium/bi-2016-01025j_0008.gif Biochemistry DOI: 10.1021/acs.biochem.6b01025 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/pzC-PLk80yY More...	nmrlearner	Journal club	0	12-27-2016 11:04 PM
Incorporation of an Unnatural Amino Acid as a Domain-SpecificFluorescence Probe in a Two-Domain Protein Incorporation of an Unnatural Amino Acid as a Domain-SpecificFluorescence Probe in a Two-Domain Protein http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b00898/20161129/images/medium/bi-2016-00898m_0004.gif Biochemistry DOI: 10.1021/acs.biochem.6b00898 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/W6SaDh6q3p0 More...	nmrlearner	Journal club	0	11-29-2016 09:02 PM
[NMR paper] The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids. The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7315-19-Wiley_FullText_120x30_orange.png Related Articles The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids. Biopolymers. 2013 Aug;99(8):548-61 Authors: Clark TD,...	nmrlearner	Journal club	0	04-23-2016 09:24 PM
[NMR paper] Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and (19)F-NMR. Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and (19)F-NMR. Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and (19)F-NMR. Nat Commun. 2015;6:8202 Authors: Yang F, Yu X, Liu C, Qu CX, Gong Z, Liu HD, Li FH, Wang HM, He DF, Yi F, Song C, Tian CL, Xiao KH, Wang JY, Sun JP Abstract Specific arrestin conformations are coupled to distinct downstream effectors, which underlie the functions of many...	nmrlearner	Journal club	0	09-09-2015 11:49 AM
Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA) Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA) Abstract The use of paramagnetic constraints in protein NMR is an active area of research because of the benefits of long-range distance measurements (>10Â*Ã?). One of the main issues in successful execution is the incorporation of a paramagnetic metal ion into diamagnetic proteins. The most common metal ion tags are relatively long aliphatic chains attached to the side chain of a...	nmrlearner	Journal club	0	11-28-2014 11:37 AM
[NMR paper] Three-dimensional structure and mimetic-membrane association of consensus 11-amino-acid motif from soybean lea3 protein. Three-dimensional structure and mimetic-membrane association of consensus 11-amino-acid motif from soybean lea3 protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary-Button_120x27px_FullText.gif Related Articles Three-dimensional structure and mimetic-membrane association of consensus 11-amino-acid motif from soybean lea3 protein. Biopolymers. 2012;98(1):59-66 Authors: Xue R, Liu Y, Zheng Y, Wu Y, Li X, Pei F, Ni J Abstract The occurrence of a highly conserved 11-mer repeating...	nmrlearner	Journal club	0	02-03-2013 10:19 AM
An efficient protocol for incorporation of an unnatural amino acid in perdeuterated recombinant proteins using glucose-based media An efficient protocol for incorporation of an unnatural amino acid in perdeuterated recombinant proteins using glucose-based media Abstract The in vivo incorporation of unnatural amino acids into proteins is a well-established technique requiring an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is incorporated at a position encoded by a TAG amber codon. Although this technology provides unique opportunities to engineer protein structures, poor protein yields are usually obtained in deuterated media, hampering its application in the protein NMR...	nmrlearner	Journal club	0	02-21-2012 03:40 AM
Site-specific labeling of proteins with NMR-active unnatural amino acids Site-specific labeling of proteins with NMR-active unnatural amino acids Abstract A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling...	nmrlearner	Journal club	0	01-09-2011 12:46 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