Related ArticlesNMR strategy for determining Xaa-Pro peptide bond configurations in proteins: mutants of staphylococcal nuclease with altered configuration at proline-117.
Biochemistry. 1993 Nov 9;32(44):11810-8
Authors: Hinck AP, Eberhardt ES, Markley JL
A general approach has been developed for configurational analysis (cis or trans) of Xaa-Pro peptide bonds in proteins. This approach, which entails selective 13C labeling of Xaa and Pro residues in the protein and isotope-edited NMR, has been applied to mutants of staphylococcal nuclease with suspected altered configurations of the Lys116-Pro117 peptide bond. The technique for monitoring proline configurations is based on differences in interproton distances between the H alpha of residue Xaa and the proline H delta or H alpha protons. Short (< 2.5 A) Xaa H alpha-Pro H delta interproton distances are diagnostic for the trans configuration, whereas short (< 2.5 A) Xaa H alpha-Pro H alpha interproton distances are diagnostic for the cis configuration. Biosynthetic incorporation of [alpha-13C]Xaa and [delta-13C]proline facilitates detection of trans Xaa-Pro peptide bonds, whereas incorporation of [alpha-13C]Xaa and [alpha-13C]proline facilitates detection of cis Xaa-Pro peptide bonds. Provided that the Xaa-Pro peptide bond is unique within the protein sequence, symmetric off-diagonal NOE cross peaks in the isotope-edited NOE spectrum allow for simultaneous chemical shift assignment and determination of the prolyl peptide bond geometry. We have used this technique to determine the predominant configuration of the Lys116-Pro117 peptide bond in recombinant V8 staphylococcal nuclease A (H124L) and two of its single amino acid mutants (D77A+H124L and G79S+H124L). The results are consistent with conclusions reached on the basis of indirect arguments concerning changes in the chemical shifts of histidine 1H epsilon 1 NMR signals.(ABSTRACT TRUNCATED AT 250 WORDS)
Improved accuracy in measuring one-bond and two-bond 15N,13Cα coupling constants in proteins by double-inphase/antiphase (DIPAP) spectroscopy
Improved accuracy in measuring one-bond and two-bond 15N,13Cα coupling constants in proteins by double-inphase/antiphase (DIPAP) spectroscopy
Abstract An extension to HN(CO-α/β-N,Cα-J)-TROSY (Permi and Annila in J Biomol NMR 16:221â??227, 2000) is proposed that permits the simultaneous determination of the four coupling constants 1 J Nâ?²(i)Cα(i), 2 J HN(i)Cα(i), 2 J Cα(iâ??1)Nâ?²(i), and 3 J Cα(iâ??1)HN(i) in 15N,13C-labeled proteins. Contrasting the original scheme, in which two separate subspectra exhibit the 2 J CαNâ?² coupling as inphase and antiphase splitting (IPAP), we...
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[NMR paper] A strategy for the NMR characterization of type II copper(II) proteins: the case of t
A strategy for the NMR characterization of type II copper(II) proteins: the case of the copper trafficking protein CopC from Pseudomonas Syringae.
Related Articles A strategy for the NMR characterization of type II copper(II) proteins: the case of the copper trafficking protein CopC from Pseudomonas Syringae.
J Am Chem Soc. 2003 Jun 18;125(24):7200-8
Authors: Arnesano F, Banci L, Bertini I, Felli IC, Luchinat C, Thompsett AR
CopC from Pseudomonas syringae was found to be a protein capable of binding both Cu(I) and Cu(II) at two different...
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[NMR paper] Differential isotype labeling strategy for determining the structure of myristoylated
Differential isotype labeling strategy for determining the structure of myristoylated recoverin by NMR spectroscopy.
Related Articles Differential isotype labeling strategy for determining the structure of myristoylated recoverin by NMR spectroscopy.
J Biomol NMR. 1998 Feb;11(2):135-52
Authors: Tanaka T, Ames JB, Kainosho M, Stryer L, Ikura M
The three-dimensional solution structure of recombinant bovine myristoylated recoverin in the Ca(2+)-free state has been refined using an array of isotope-assisted multidimensional heteronuclear NMR...
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[NMR paper] Determining the structures of large proteins and protein complexes by NMR.
Determining the structures of large proteins and protein complexes by NMR.
Related Articles Determining the structures of large proteins and protein complexes by NMR.
Trends Biotechnol. 1998 Jan;16(1):22-34
Authors: Clore GM, Gronenborn AM
Recent advances in multidimensional NMR methodology to obtain 1H, 15N and 13C resonance assignments, interproton-distance and torsion-angle restraints, and restraints that characterize long-range order have, coupled with new methods of structure refinement, permitted solution structure of proteins in excess...
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Strategy for complete NMR assignment of disordered proteins with highly repetitive se
Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments
Abstract A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high...
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Strategy for complete NMR assignment of disordered proteins with highly repetitive se
Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments.
Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments.
J Biomol NMR. 2010 Oct 2;
Authors: MotáÄ?ková V, NováÄ?ek J, Zawadzka-Kazimierczuk A, Kazimierczuk K, ZÃ*dek L, Sanderová H, Krásný L, KoźmiÅ?ski W, SklenáÅ? V
A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly...
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Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts
Abstract We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and 13Cβ chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-13Cγ, Promega calculates the statistical probability that a Xaa-Pro peptide bond...
NMR strategy for determining Xaa-Pro peptide bond configurations in proteins: mutants
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