Proton, carbon, and nitrogen chemical shifts accurately delineate differences and similarities in secondary structure between the homologous proteins IRAP and IL-1β

Stockman, Brian J.; Scahill, Terrence A.; Strakalaitis, Nancy A.; Brunner, David P.; Yem, Anthony W.; Deibel, Martin R.

doi:10.1007/bf02192848

Cited by 9 publications

(2 citation statements)

References 15 publications

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“…lB, which shows an overlay of the backbone atoms of the two proteins. The alignment is based on homologous B-strands as defined previously [16,17]. For this subset of 100 residues, the RMS deviation between the two proteins for the backbone N, C" and C' atoms is 2.27 A.…”

Section: Resultsmentioning

confidence: 99%

Solution structure of human interleukin‐1 receptor antagonist protein

Stockman¹,

Scahill²,

Strakalaitis³

et al. 1994

FEBS Letters

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Interleukin-1 receptor antagonist protein (IRAP) is a naturally occurring inhibitor of the interleukin-1 receptor. In contrast to IL-lb, IRAP binds to the IL-l receptor but does not elicit a physiological response. We have determined the solution structure of IRAP using NMR spectroscopy. While the overall topology of the two 153-residue proteins is quite similar, functionally critical differences exist concerning the residues of the linear amino acid sequence that constitute structurally homologous regions in the two proteins. Structurally homologous residues important for IL-l receptor binding are conserved between IRAP and IL-l/!?. By contrast, structurally homologous residues critical for receptor activation are not conserved between the two proteins.

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Section: Resultsmentioning

confidence: 99%

Solution structure of human interleukin‐1 receptor antagonist protein

Stockman¹,

Scahill²,

Strakalaitis³

et al. 1994

FEBS Letters

Self Cite

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“…Among many examples that might be cited would be analyses of shift changes upon formation of a ternary complex in staphylococcal nuclease (Wang et al, 1992), the binding of calcium to calbindin D9k (Skelton et al, 1992), an analysis of secondary structure in mutant zinc-fingers (Lee et al, 1992), a comparison of shifts in interleukin analogues (Stockman et al, 1992), and an analysis of the interaction between proteins in a bacterial phosphotransferase system (Chen et al, 1993). In real situations, there may be additional shift contributions (e.g.…”

Section: Discussionmentioning

confidence: 99%

Analysis of proton chemical shifts in regular secondary structure of proteins

1994

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The contribution of peptide groups to H alpha and H beta proton chemical shifts can be modeled with empirical equations that represent magnetic anisotropy and electrostatic interactions [Osapay, K. and Case, D.A. (1991) J. Am. Chem. Soc., 113, 9436-9444]. Using these, a model for the 'random coil' reference state can be generated by averaging a dipeptide over energetically allowed regions of torsion-angle space. Such calculations support the notion that the empirical constant used in earlier studies arises from neighboring peptide contributions in the reference state, and suggest that special values be used for glycine and proline residues, which differ significantly from other residues in their allowed phi, psi-ranges. New constants for these residues are reported that provide significant improvements in predicted backbone shifts. To illustrate how secondary structure affects backbone chemical shifts we report calculations on oligopeptide models for helices, sheets and turns. In addition to suggesting a physical mechanism for the widely recognized average difference between alpha and beta secondary structures, these models suggest several additional regularities that should be expected: (a) H alpha protons at the edges of beta-sheets will have a two-residue periodicity; (b) the H alpha 2 and H alpha 3 protons of glycine residues will exhibit different shifts, particularly in sheets; (c) H beta protons will also be sensitive to local secondary structure, but in different directions and to a smaller extent than H alpha protons; (d) H alpha protons in turns will generally be shifted upfield, except those in position 3 of type I turns. Examples of observed shift patterns in several proteins illustrate the application of these ideas.

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Amino Acids, Peptides and Proteins: Chemical Shifts

Case

2007

Encyclopedia of Magnetic Resonance

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Proton, carbon, and nitrogen chemical shifts accurately delineate differences and similarities in secondary structure between the homologous proteins IRAP and IL-1β

Cited by 9 publications

References 15 publications

Solution structure of human interleukin‐1 receptor antagonist protein

Solution structure of human interleukin‐1 receptor antagonist protein

Analysis of proton chemical shifts in regular secondary structure of proteins

Amino Acids, Peptides and Proteins: Chemical Shifts

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