Tryptophan-containing peptide helices: interactions involving the indole side chain* (original) (raw)
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Carbohydrate Research, 1992
The conformational preference of the disaccharide a-L-Rhap-(1 -$2)-cY-L-Rhap-(l + OMe) (11 about the glycosidic torsion angles, I$ and ,wasstudiedbyNMRNOESYspectroscopyandmolecularmechanicscalculations.TheNOEdatawereconsistentwitheitheroftwodistinctconformationsclosetominimaonacalculated4/, was studied by NMR NOESY spectroscopy and molecular mechanics calculations. The NOE data were consistent with either of two distinct conformations close to minima on a calculated 4/,wasstudiedbyNMRNOESYspectroscopyandmolecularmechanicscalculations.TheNOEdatawereconsistentwitheitheroftwodistinctconformationsclosetominimaonacalculated4/ potential energy surface. Starting from the lowest energy conformation, a l-ns molecular dynamics (MD) trajectory was computed in vacua, from which the NOE curves were simulated and compared to the experimentally observed NOESY data. 0008-6215/92/$05.00 0 1992 -Elsevier Science Publishers B.V. All rights reserved 196 G. Widmalm et al. / Carbohydr. Res. 229 (1992) 195-211 disaccharide L-w-L-Rhap-(1 + 2)-a-L-Rhap-(1 + OMe) (1) based on NOESY and molecular mechanics studies. EXPERIMENTAL Disaccharide nomenclature conventions .-Atoms in the glycosyl group are assigned primed numbers; those in the methyl glycoside are unprimed. The glycosidic torsion angle 4 is defined by the atoms 0-5'-C-l'-O-2-C-2
NMR evidence for multiple conformations in a highly helical model peptide
Biochemistry, 1993
A monomeric model peptide, acetyl-WEAQAREALAKEAAARA-amide, has been structurally characterized using the complementary techniques of 'H 2D N M R and circular dichroism. Temperaturedependent CD measurements are consistent with a two-state helix/coil transition model and indicate a 65% contribution of helical conformers at 5 O C . Homonuclear 2D N M R experiments allowed the assignment of all proton resonances. The analysis of NOE-type cross-relaxation data established a large number of specific short-and medium-range N O E connectivities throughout the peptide, confirming the highly helical character of the peptide. However, the observation of long-range NOES between the methyl protons of leucine-9 and backbone and side-chain protons of amino acids located at the N-terminus, as well as other unusual NOES, unambiguously reflects the existence of significantly populated nonhelical structured conformers, indicating a multiconformational equilibrium. Implications of these observations with regard to secondary structure quantitation and current method limitations are discussed. Abstract published in Advance ACSAbstrucfs, November 15,1993.
Journal of the American Chemical Society, 1979
Proton magnetic resonance spectra were recorded in the temperature interval from +5 I to -64 "C at 360 MHz with alkaline CD30D solutions of the following compounds: H-Trp-OH. H-Trp-GIy-OH. H-Gly-Trp-OH and H-GI)-Trp-Cily-OH (which contain one tryptophyl residue); H-Gly-Trp-Gly-Trp-Cly-OH and H-Gly-Trp-(C,I~)2-Trp-Gly-Ot~ (which contain two tryptophyl residues spaced by glycyl residue(s)): H-Trp-Trp-OH. H-Trp-Trp-GI!-OH. H-GI)-Trp-Trp-OH. and H-Gly-Trp-Trp-Gly-OH (which contain two adjacent tryptophyl rcsidues). The following parametcrs have been derived from the cxperimental spectra and their dcpendcnce on temperature is discussed: ( I ) chemical shills of the nroiniitic protons; ( 2 ) chemical shifts and coupling constants of the C,,H-C,jH2 fragment of the tryptophyl residue: (3) anisochronistn of the glycine C,, protons (also in view of the possible presence of hydrogen-bonded structures of the pcptide backbone). On thc bahis of thcse parameters, the conforniational properties of the aromatic side chains (in tcrnis of rotanicr populations) and of the backbone (in terms of possible hydrogen-bonded conformers) are discussed. A thermod) niirnic analysis of the rotamer populations around the X I torsion angle of the tryptophyl side chain in the investigated compounds has been carried out. The enthalpy differences between the three classical rotamers G+, G-, and T are found to be linearly related to the respective entropy differences. For the favored conformer of H-Trp-Trp-0at low temperature, the detailed geometry is proposed, which is in agreement with the previously described spectroscopic properties of this molecule.
Journal of Physical Chemistry B, 1998
The photophysics of linear Aib-based hexapeptides (Aib) R-aminoisobutyric acid) of general formula Ac-Toac-(Aib) n-Trp-(Aib) r-OtBu (TnTrp), where n + r) 4, and Toac and Trp are a nitroxide spin labeled C R,R-disubstituted glycine and tryptophan, respectively, were investigated in methanol and dioxane solutions by steady-state and time-resolved fluorescence measurements. Another hexapeptide, i.e., Boc-(S)Bin-Ala-Aib-Toac-(Ala) 2-OtBu (T-Bin), carrying the same nitroxide derivative and a binaphthyl as the fluorophore was also studied by the same techniques. Quenching of the excited tryptophan or binaphthyl chromophore proceeds on a time scale from subnanoseconds to a few nanoseconds, depending on the conformers distribution in solution. CD and IR spectral patterns in methanol or CDCl 3 suggest that the backbone of the peptides examined is in the 3 10-helical conformation, thus preserving the structural features of the crystal state, as earlier determined by X-ray diffraction measurements. The fluorescence results were satisfactorily described by a dipole-dipole interaction mechanism, in which electronic energy transfer takes place from the excited tryptophan or binaphthyl to Toac, provided the mutual orientation between the fluorophore and Toac is taken into account. This implies that interconversion among conformational substates is slow on the time scale of the transfer process. Molecular mechanics calculations coupled with time decay data allowed us to build up the most probable structures of these peptides in methanol solution.
Biopolymers, 2000
The cis/trans conformational equilibrium intermolecular NOE, and molecular dynamics calculations. The temperature dependence of the cis/trans Ala(NH) protons are in the region expected for random-coil peptides in H 2 O (⌬␦/⌬T ϭ Ϫ9.0 and Ϫ8.9 ppb for the cis and trans isomers, respectively). The trans NH(CH 3 ) proton indicates smaller temperature dependence (⌬␦/⌬T ϳ Ϫ4.8 ppb) than that of the cis isomer (Ϫ7.5 ppb). 2D 1 H, 1 H NOESY experiments at 273 K demonstrate significant NOEs between ProH ␣ -AlaNH and AlaNH-NH(R) for the trans isomer. The experimental NOE data, coupled with computational analysis, can be interpreted by assuming that the trans isomer most likely adopts an ensemble of folded conformations. The C-CONH(CH 3 ) fragment exhibits significant conformational flexibility; however, a low-energy conformer resembles closely the II-turn folded conformations of the x-ray structure of the related model peptide trans-BuCO-L-Pro-Me-D-Ala-NHMe. On the contrary, the cis isomer adopts open conformations. Steady-state intermolecular solute-solvent Correspondence to: Ioannis P. Gerothanassis
Tryptophan rich peptides: Influence of indole rings on backbone conformation
Biopolymers, 2007
OMe (peptide 4)) helix-nucleating Aib residues give rise to the well-folded helical conformations in the chloroform solution. The results are indicative of a preference for helical folding in peptides containing a large number of Trp residues. Investigation of a tetrapeptide analog of peptide 2, Boc-W-U-G-W-OMe (peptide 5), in solution and in the crystal state (by X-ray diffraction), also indicates a preference for a helical fold. Additionally, peptide 5 is stabilized in crystals by both aromatic interactions and an array of weak interactions. Examination of Trp-rich sequences in protein structures, however, reveals no secondary structure preference, suggesting that other stabilizing interactions in a well-folded protein may offset the influence of indole rings on backbone conformations.
Tryptophan Interactions in Bacteriorhodopsin: A Heteronuclear Solid-State NMR Study †
Biochemistry, 2002
The bulky and amphiphilic nature of tryptophan residues makes them particularly interesting components of proteins. In bacteriorhodopsin, four of the eight tryptophan residues are in the active site, forming parts of the retinal binding pocket. In this work, we use solid-state NMR to study the interactions of the tryptophan residues in wild-type bacteriorhodopsin, in the resting state, and in critical intermediates of the proton-motive photocycle. The range of the chemical shifts of the indole nitrogens suggests that all eight of them are hydrogen bonded. Using difference spectroscopy, we isolate several changes in these hydrogen bonds in the early and late M states. As found earlier for the peptide backbone, some perturbations found in the early M state relax in the transition to the late M state while new perturbations arise. Interestingly, Rotational Echo DOuble Resonance (REDOR) difference spectroscopy of [20-13 C]retinal,-[indole-15 N]Trp-bR shows that indole of Trp182 is not involved in the significant hydrogen bond perturbations. We also use REDOR to measure dipolar interactions in [20-13 C]retinal,[indole-15 N]Trp-bR, and thereby determine the distance between the C 20 of retinal and the indole nitrogen of Trp182. The internuclear distance changes only slightly from the light-adapted state (3.36 ( 0.2 Å) to the early M state (3.16 ( 0.4 Å).
Biochemistry, 2010
Backbone amide dynamics studies were conducted on a temperature-sensitive mutant (L75F-TrpR) of the tryptophan repressor protein (TrpR) of Escherichia coli in its apo (i.e., no L-tryptophan corepressorbound) form. The 15 N NMR relaxation profiles of apo-L75F-TrpR were analyzed and compared to those of wild-type (WT) and super-repressor mutant (A77V) TrpR proteins, also in their apo forms. The 15 N NMR relaxation data ( 15 N-T 1 , 15 N-T 2 , and heteronuclear 15 N-{ 1 H}-nOe) recorded on all three aporepressors at a magnetic field strength of 600 MHz ( 1 H Larmor frequency) were analyzed to extract dynamics parameters, including diffusion tensor ratios (D ) /D^), correlation times (τ m ) for overall reorientations of the proteins in solution, reduced spectral density terms [J eff (0), J(0.87ω H ), J(ω N )], and generalized order parameters (S 2 ), which report on protein internal motions on the picosecond to nanosecond and slower microsecond to millisecond chemical exchange time scales. Our results indicate that all three aporepressors exhibit comparable D ) /D^ratios and characteristic time constants, τ m , for overall global reorientation, indicating that in solution, all three apoproteins display very similar overall shape, structure, and rotational diffusion properties. Comparison of 15 † multipulse sequence; CSA, chemical shift anisotropy; DIPSI, decoupling in the presence of scalar interactions; HSQC, heteronuclear single-quantum coherence spectroscopy; HTH, helix-turn-helix motif; IPTG, isopropyl β-thiogalactoside; 5-MT, 5-methyltryptophan; L-Trp, L-tryptophan; NMR, nuclear magnetic resonance; nOe, nuclear Overhauser effect; TrpR, tryptophan repressor; apo-WT-TrpR, wild-type apo-TrpR repressor; apo-L75F-TrpR, L75F mutant apo-TrpR repressor; A77V-TrpR, A77V mutant apo-TrpR repressor; ts, temperature-sensitive; WALTZ, wideband alternative-phase low-power technique for zero residual splitting.