Quantitative evaluation of interproton distances in peptides by two-dimensional overhauser effect spectroscopy

Saulitis, Juris; Liepiņš, Edvards

doi:10.1016/0022-2364(90)90087-p

Cited by 17 publications

(13 citation statements)

References 21 publications

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“…Conditions used were 22"C, pH 2.5, H,O/D,O (9: 1 by vol. (Bradley et al, 1990;Saulitis and Liepins, 1990). The temperature coefficients are all within the range measured for model peptides (Jimtnez et al, 1986).…”

Section: Thermolysin 245-260supporting

confidence: 55%

“…The averaged I m J Z c N n e q and IaN,nJZaN8q ratios are 2.3 and 1.0, respectively. These values differ from those expected for an extended chain (0.02,0.24) and are closer to those expected for a completely helical chain (3.81, 4.76) (Bradley et al, 1990;Saulitis and Liepins, 1990). More clear-cut evidence is the stretch of aa (i,i+ 3) NOE cross-correlations found within the region 301 -3 11.…”

Section: Thermolysin 299-316 Fragmentsupporting

confidence: 49%

“…However, the only presence of sequential NN NOE connectivities is not by itself enough evidence for helix formation, because weak sequential NN NOE cross-peaks can be found even in random or extended chains (Dyson and Wright, 1991). However, relative intensities of sequential and intraresidue NOE connectivities is an efficient empirical index for it (Bradley et al, 1990;Saulitis and Liepins, 1990). Thus, residues in helical structures show intensity ratios between sequential NN and aN NOE cross-peaks (ZmJaN8,) and between intraresidue aN and sequential aN NOE connectivities (ZaNmJZaNq) larger than one.…”

Section: Thermolysin 233-248mentioning

confidence: 99%

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CD and ¹H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

Jiménez

Bruix

González

et al. 1993

European Journal of Biochemistry

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The propensity of the peptide fragments 233-248, 245-260, 258-276, 279-298 and 299-316 from the thermolysin C-terminal domain to form non-random structures has been examined by CD and two-dimensional NMR spectroscopy. The conformational properties of these fragments have been studied in aqueous solution and in the mixed solvent trifluoroethanol/H,O (3 : 7 by vol.). Small but detectable populations of helical structures (up to 10-20%) in aqueous solution have been found for the fragments 233-248,279-298 and 299-316. These populations are remarkably enhanced (50-70%) in the more hydrophobic mixed solvent, where the fragment 258-276 also forms a comparable helical population. These four fragments are helical in the native crystal structure and the spanning of the corresponding helices in the isolated peptides in solution matches very closely the ones in the native structure. In contrast, the fragment 245-260, an D-loop in the crystal, remains unstructured in both solvents. Medium-range NOE between protons in sidechains indicate the adoption of preferred sidechain conformations accompanying helix formation. Results are in agreement with the framework model of folding, in which native elements of secondary structure are formed first and folding follows from the collapse of these structural elements.

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Section: Thermolysin 245-260supporting

confidence: 55%

Section: Thermolysin 299-316 Fragmentsupporting

confidence: 49%

Section: Thermolysin 233-248mentioning

confidence: 99%

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CD and ¹H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

Jiménez

Bruix

González

et al. 1993

European Journal of Biochemistry

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“…Both reduced (red) and oxidized (ox) forms of Cys were separately analyzed. These observed random coil chemical shifts were compared to those obtained for model tetrapeptides CF,CO-GGXA-OCH, by Bundi and Wiithrich in aqueous solution [44], AS,,, (observed- [44] [60]. With this reference, identical d,, and dNN distances to those obtained with NHSer4 -NHThrS reference were found (data not shown).…”

Section: Residuementioning

confidence: 64%

Three‐Dimensional Structure of the Highly Conserved Seventh Transmembrane Domain of G‐Protein‐Coupled Receptors

Berlose

Convert

Brunissen

et al. 1994

European Journal of Biochemistry

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The S/T-XI-X,-N-P-X,-X,-Y highly conserved sequence of the seventh transmembrane (TM VII) segment of G-protein-coupled receptors is not present in the photon receptor bacteriorhodopsin TM VII domain. Despite this noticeable discrepancy in sequence, the X-ray structure of bacteriorhodopsin is generally used as the key structure for modelling all G-protein-coupled receptors. Thus, a kinked truns-Pro helix is usually accepted for the TM VII three-dimensional structure of G-proteincoupled receptors, although Asn-Pro dipeptide mainly induces a type UIII /3-turn conformation in both model peptides and proteins. NMR studies in various solvents and molecular calculations were undertaken in order to gain insight into the conformational behaviour of a 15-residue peptide from the tachykinin NK-1 TM VII domain incorporating this common sequence. The low solubility of this membrane-embedded peptide precludes methanol or micellar systems mimicking membrane environment; thus only dimethylsulfoxide (Me,SO) or chlorofonn/Me,SO mixture could be used. We also found that perfluoro-tert-butanol, which has not been previously used for NMR studies, constitutes an excellent alternative solvent for the analysis of hydrophobic peptides. The postulated kinked truns-Pro helix was only present as a minor conformer in Me,SO and an equilibrium between helical and extended structures existed. From NOE data a type I/III ,&structure, centered around Pro9-Ile10, probably stabilized by an Asx turn, may be postulated. Addition of chloroform in Me,SO increased the percentage of folded structures but no preferential conformation could be proposed. In perfluoro-tert-butanoI/CD,OD (9 : 1) the N-and C-terminal regions presented an a-helical structure, and these two domains were linked by a hinge around Asn-Pro with a y-turn for the preceding residue Tyr7 and either a type I/III p-turn around Pro9-IlelO or cxR orientations for these residues, which are both stabilized by an Asx turn. As determined by energy calculations, these structures were equally as stable as the kinked truns-Pro helix and could constitute key structures for analysing the conformational changes and/or the dynamics of TM VII segment induced by the ligand when interacting with the receptor.The apparent similarity in the hydropathicity profiles of G-protein-coupled receptors [ 1 -41 with that of bacteriorhodopsin [5] has led to the use of this integral membrane protein as a starting point for predicting their three-dimensional structures [6-121, even though bacteriorhodopsin is not coupled to G-proteins. The currently accepted proposal for the topography of G-protein-coupled receptors includes seven transmembrane-spanning domains (TM I-VII) joined together by extracellular and cytoplasmic loops, with the Nterminal side in the extracellular cleft and the C-terminal residues in the cytoplasm. This model, which was first deduced Correspondence to S .

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“…For comparison, the Q NOE values of residues in native ubiquitin, calculated from the NMR structure, are also shown. The value of Q NOE depends predominantly on the value of c for residue i, because the distances between H a (i + 1) and H N (i + 1) atoms of residues in the most important backbone conformations are similar (Saulitis and Liepins 1990). Thus, the Q NOE values can be used to determine the ratio between the population of the a R conformation and the populations within the broad b basin that contains both b and P II conformations.…”

Section: Ratios Of Noe Connectivities In Urea-denatured Ubiquitinmentioning

confidence: 99%

Electrostatic screening and backbone preferences of amino acid residues in urea‐denatured ubiquitin

Avbelj¹,

Grdadolnik²

2007

Protein Science

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Local structures in denatured proteins may be important in guiding a polypeptide chain during the folding and misfolding processes. Existence of local structures in chemically denatured proteins is a highly controversial issue. NMR parameters [coupling constants 3 J(H a ,H N ) and chemical shifts] of chemically denatured proteins in general deviate little from their values in small peptides. These peptides were presumed to be completely unstructured; therefore, it was considered that chemically denatured proteins are random coils. But recent experimental studies show that small peptides adopt relatively stable structures in aqueous solutions. Small deviations of the NMR parameters from their values in small peptides may thus actually indicate the existence of local structures in chemically denatured proteins. Using NMR data and theoretical predictions we show here that fluctuating b-strands exist in urea-denatured ubiquitin (8 M urea at pH 2). Residues in such b-strands populate more frequently the left side of the broad b region of u-c space. Urea-denatured ubiquitin contains no detectable b-sheet secondary structures; nevertheless, the fluctuating b-strands in urea-denatured ubiquitin coincide to the b-strands in the native state. Formation of b-strands is in accord with the electrostatic screening model of unfolded proteins. The free energy of a residue in an unfolded protein is in this model determined by the local backbone electrostatics and its screening by backbone solvation. These energy terms introduce strong electrostatic coupling between neighboring residues, which causes cooperative formation of b-strands in denatured proteins. We propose that fluctuating b-strands in denatured proteins may serve as initiation sites to form fibrils.Keywords: forces and stability; protein structure/folding; computational analysis of protein structure; protein structure prediction; chemically denatured proteins; NMR spectroscopy; prions Supplemental material: see www.proteinscience.org Characterizing local structures of denatured proteins is crucial for understanding the protein folding (Baldwin 1986) and misfolding processes. Chemically denatured proteins unfolded in 8 M urea or GdmCl are generally highly opened and solvent-exposed polypeptides with no detectable a R -helix or b-sheet secondary structures. Proteins under such strong denaturing conditions are considered to be completely unfolded (Dill and Shortle 1991). It was commonly assumed that these proteins are true random coils that can be described by Flory's random coil model (Flory 1969). The random coil model predicts that residues in unfolded proteins populate mainly the broad b region of u-c space, which contains about equally probable b (u % À120°and c % 120°) and P II (u % À65°, c % 145°) conformations.A growing number of experimental studies show that chemically denatured proteins display a certain degree of Reprint requests to: Franc Avbelj, National Institute of Chemistry, Hajdrihova 19, SI 1115 Ljubljana, Slovenia; e-mail: Franc.Avbelj@ki.si;...

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Quantitative evaluation of interproton distances in peptides by two-dimensional overhauser effect spectroscopy

Cited by 17 publications

References 21 publications

CD and ¹H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

CD and ¹H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

Three‐Dimensional Structure of the Highly Conserved Seventh Transmembrane Domain of G‐Protein‐Coupled Receptors

Electrostatic screening and backbone preferences of amino acid residues in urea‐denatured ubiquitin

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Quantitative evaluation of interproton distances in peptides by two-dimensional overhauser effect spectroscopy

Cited by 17 publications

References 21 publications

CD and 1H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

CD and 1H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

Three‐Dimensional Structure of the Highly Conserved Seventh Transmembrane Domain of G‐Protein‐Coupled Receptors

Electrostatic screening and backbone preferences of amino acid residues in urea‐denatured ubiquitin

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Product

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CD and ¹H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

CD and ¹H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin