Two-Dimensional NMR Experiments for the Assignment of Aromatic Side Chains in13C-labeled Proteins

Prompers, Jeanine J.; Groenewegen, A.; Hilbers, Cornelis W.; Pepermans, Henri

doi:10.1006/jmre.1997.1277

Cited by 31 publications

(33 citation statements)

References 19 publications

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“…For aromatic side chains, CB(CGCD)HD, CB(CGCDCE)HE (Yamazaki et al 1993a), 1 H– 13 C HSQC CParo (Zuiderweg et al 1996), 2D 13 C- 1 H CT HSQC, and 2D 13 C– 1 H CT HSQCaro were recorded. Aromatic C γ –H β correlations were detected using CG(CB)HB experiments (Prompers et al 1998). Carbonyl 13 C side chain resonances of Asx and Glx residues were assigned using H2(C)CO (Kay et al 1990; Powers et al 1991; Yamazaki et al 1993b) and (HBGCBG)CO(CBGCABCON)H (Tollinger et al 2002) experiments.…”

Section: Methods and Experimentsmentioning

confidence: 99%

1H, 13C, and 15N resonance assignment of photoactive yellow protein

et al. 2012

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Section: Methods and Experimentsmentioning

confidence: 99%

1H, 13C, and 15N resonance assignment of photoactive yellow protein

et al. 2012

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“… a Cavanagh et al 1991; b Palmer et al 1991; c Palmer et al 1992; d Kay et al 1990b; e Powers et al 1991; f Panchal et al 2001; g Muhandiram and Kay 1994; h Ottiger and Bax 1997; i Andre et al 2007; j Fesik and Zuiderweg 1990; k Marion et al 1989a; l Marion et al 1989b; m Zhang et al 1994; n Ikura et al 1991; o Kay et al 1990a; p Ikura et al 1991; q Logan et al 1993; r Vuister and Bax 1992; s Konrat et al 1997; t Tollinger et al 2002; u Oda et al 1994; v Majumdar and Zuiderweg 1993; w Prompers et al 1998; x Yamazaki et al 1993a; Y Zuiderweg et al 1996; z Bax et al 1990…”

Section: Methods and Experimentsmentioning

confidence: 99%

100% complete assignment of non-labile 1H, 13C, and 15N signals for calcium-loaded calbindin D9k P43G

et al. 2010

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Here we present the 100% complete assignment chemical shift of non-labile 1H, 15N and 13C nuclei of Calbindin D9k P43G. The assignment includes all non-exchangeable side chain nuclei, including ones that are rarely reported, such as LysNζ as well as the termini. NMR experiments required to achieve truly complete assignments are discussed. To the best of our knowledge our assignments for Calbindin D9k extend beyond previous studies reaching near-completeness (Vis et al. in Biochem 33:14858–14870, 1994; Yamazaki et al. in J Am Chem Soc 116:6464–6465, 1994; Yamazaki et al. in Biochem 32:5656–5669, 1993b).

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“…To obtain the amide 1 H and 15 N assignment of the homotypic human I-BABP : GCA and human I-BABP : GCDA complexes, the assignment of the heterotypic complex was transferred to the corresponding spectra and confirmed by 3D gradient enhanced CBCACONNH [41] experiments performed on uniformly [U- [42], 3D HCC-TOCSY-NNH [42] and 3D g-HCCH-TOCSY [43] experiments. Aromatic assignments were established by a series of 2D experiments that exploit scalar couplings between the aliphatic H b and the aromatic C c , and then subsequently between the aromatic C c and the aromatic ring protons (2D CG(CB)HB, 2D CG(CD)HD, 2D CG(CDCE)HE) [44]. Interproton distance restraints were obtained from aliphatic and aromatic 3D 13 C NOESY-HSQC [45] NH NOESY [47] and 3D MetMet-NOESY [48] experiments.…”

Section: Nmr Data Collection and Structure Calculationmentioning

confidence: 99%

Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR

et al. 2016

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Besides aiding digestion, bile salts are important signal molecules exhibiting a regulatory role in metabolic processes. Human ileal bile acid binding protein (I‐BABP) is an intracellular carrier of bile salts in the epithelial cells of the distal small intestine and has a key role in the enterohepatic circulation of bile salts. Positive binding cooperativity combined with site selectivity of glycocholate and glycochenodeoxycholate, the two most abundant bile salts in the human body, make human I‐BABP a unique member of the family of intracellular lipid binding proteins. Solution NMR structure of the ternary complex of human I‐BABP with glycocholate and glycochenodeoxycholate reveals an extensive network of hydrogen bonds and hydrophobic interactions stabilizing the bound bile salts. Conformational changes accompanying bile salt binding affects four major regions in the protein including the C/D, E/F and G/H loops as well as the helical segment. Most of these protein regions coincide with a previously described network of millisecond time scale fluctuations in the apo protein, a motion absent in the bound state. Comparison of the heterotypic doubly ligated complex with the unligated form provides further evidence of a conformation selection mechanism of ligand entry. Structural and dynamic aspects of human I‐BABP–bile salt interaction are discussed and compared with characteristics of ligand binding in other members of the intracellular lipid binding protein family. Protein Data Bank Accession Numbers The coordinates of the 10 lowest energy structures of the human I‐BABP : GCDA : GCA complex as well as the distance restraints used to calculate the final ensemble have been deposited in the Brookhaven Protein Data Bank with accession number http://www.rcsb.org/pdb/search/structidSearch.do?structureId=2MM3.

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Two-Dimensional NMR Experiments for the Assignment of Aromatic Side Chains in13C-labeled Proteins

Cited by 31 publications

References 19 publications

1H, 13C, and 15N resonance assignment of photoactive yellow protein

1H, 13C, and 15N resonance assignment of photoactive yellow protein

100% complete assignment of non-labile 1H, 13C, and 15N signals for calcium-loaded calbindin D9k P43G

Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR

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