Local Structure of β-Hairpin Isotopomers by FTIR, 2D IR, and Ab Initio Theory

Wang, Jianping; Chen, Jianxin; Hochstrasser, Robin M.

doi:10.1021/jp057564f

Cited by 124 publications

(219 citation statements)

References 71 publications

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“…The 2DIR technique distinguishes β-sheet structures by producing Z shape like spectra [18,19] when this particular structural motif is present. In the past decades a number of 2DIR studies have been reported of peptides and proteins in solution [16,[20][21][22][23][24][25][26][27][28][29][30][31][32][33] or confined in membranes [34][35][36][37][38], revealing structural details and conformational changes from femtosecond (fs) to nanosecond (ns) time scales, and the nature of dynamic environments. For the structure determination of peptides that are in gas phase or micro-solvated (surrounded by few solvent molecules) the mid-infrared spectroscopic technique has become a promising tool [39][40][41][42].…”

Section: Introductionmentioning

confidence: 99%

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

Roy

Lessing

Meisl

et al. 2011

The Journal of Chemical Physics

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We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D 2 O and compare with experimental observations.

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Section: Introductionmentioning

confidence: 99%

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

Roy

Lessing

Meisl

et al. 2011

The Journal of Chemical Physics

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“…1 Both static and dynamic fluorescence spectra can also monitor change of the tryptophan environment, 29,32 while IR absorption for the amide I band can be used to follow correlated secondary structural changes and dynamics during the unfolding process. 23,24,26,29,31,34,36,37 Among the original trpzip sequences, trpzip2 has been more widely studied, partly due to simplicity and increased solubility.…”

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confidence: 99%

Cross-Strand Coupling and Site-Specific Unfolding Thermodynamics of a Trpzip β-Hairpin Peptide Using ¹³C Isotopic Labeling and IR Spectroscopy

et al. 2009

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Conformational properties of a 12-residue tryptophan zipper (trpzip) -hairpin peptide (AWAWENGKWAWK-NH 2 , a modification of the original trpzip2 sequence) are analyzed under equilibrium conditions using ECD and IR spectra of a series of variants, singly and doubly C 1 -labeled with 13 C on the amide CdO. The characteristic features of the 13 CdO component of the amide I′ IR band and their sensitivity to the local structure of the peptide are used to differentiate stabilities for parts of the hairpin structure. Doubly labeled peptide spectra indicate that the ends of the -strands are frayed and that the center part is more stable as would be expected from formation of a stable hydrophobic core consisting of four tryptophan residues, and supported by MD simulations. NMR analyses were used to determine a best fit solution structure that is in close agreement with that of trpzip2, except for a small variation in the turn geometry. The distinct vibrational coupling patterns of the labeled sites based on this structure are also well matched by ab initio DFT-level calculations of their IR spectral patterns. Thermal unfolding of the peptides as studied with CD spectra could be fit with an apparent two-state transition model. ECD senses only the tryptophan interactions (tertiary-like) and their overall environment, as shown by TD-DFT modeling of the Trp-Trp π-π* ECD. However, variation of the amide I IR spectra of 13 C-isotopomers showed that the thermal unfolding process is not cooperative in terms of the peptide backbone (secondary structure), since the transition temperatures sensed for labeled modes differ from those for the whole peptide. The thermal data also evidence dependence on concentration and pH but these cause little spectral variation. This study illustrates the consequences of multistate conformational change at the residue-or sequence-specific level in a system whose structure is dominated by hydrophobic collapse.

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“…The amide-I vibrational mode of fibrils originates from the stretching motion of the CAO bond (coupled to in-phase NOH bending and COH stretching) (16) and can be used to monitor secondary structure variations (17). The simulated linear absorption of M42 ( Fig.…”

mentioning

confidence: 99%

“…However, isotope labeling and a judicious design of polarization configurations can be used to manipulate the 2DCS signals by enhancing desired spectral features. 13 C 18 O isotope labeling of a given peptide residue can induce a 65-cm Ϫ1 red shift of the amide-I vibrational frequency, creating peaks well separated from the unlabeled band and providing structural information on desired segments (17). Two-dimensional signals depend on interferences among many contributions (Liouville space pathways) (20).…”

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confidence: 99%

Simulation of two-dimensional infrared spectroscopy of amyloid fibrils

Zhuang

Abramavičius

Voronine

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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We propose to use infrared coherent two-dimensional correlation spectroscopy (2DCS) to characterize the fibril structure of Ab42, the dominant composition of Ab deposit, which is crucial for investigating its toxicity and aggregation mechanism. By optimizing the pulse polarization configurations with a genetic algorithm combined with sensitivity analysis, we obtained signals with well resolved cross-peak features attributed to the couplings within and between different structural motifs. These signals may provide new constraints for refining of the currently available NMR structure. Two-dimensional correlation spectroscopy also can differentiate the turn structure of Ab42 and other Ab derivatives.correlation spectroscopy ͉ four wave mixing T he accumulation of amyloid deposits (1, 2), misfolded peptide aggregates whose dominant component is a 39-to 43-residue A␤ peptide (3), has been identified as a major feature of the pathogenesis of Alzheimer's disease (AD) (4). Despite their identical residues 1-39 sequence, the various A␤ peptides have significantly different biochemical properties: The 42-residue derivative, A␤42, has a much stronger tendency to form fibrils in vitro (5) as compared with other derivatives. A␤42 also is slightly more hydrophobic compared with shorter analogs because of the additional more-hydrophobic residues at the end of the peptide strand. More importantly, the protease resistance of A␤42 is drastically higher from its analogs (6). The structural basis of these property differences is still unknown. Because of the fibril's noncrystalline, insoluble, and mesoscopically heterogeneous nature, NMR is the primary tool for fibril structure determination (7-10). It provides various structural constraints that, when combined with computational tools, such as geometry optimization and MD simulation, yield the current structural models.The most recent model of A␤42 structure was proposed by Riek (7) (denoted M42). M42 can be dissected into three motifs; residues 1-16 are randomly coiled, and residues 26-31 are the turn, and the rest form two ␤-strands. NMR structural information (7, 10) is primarily related to the ␤-strand. No information is available on the highly irregular coil segment. Because of the lack of structural constraints, the turn structure in this model is obtained by geometry optimization and depends heavily on the computational protocol and the empirical force field.The present simulation of two-dimensional correlation spectroscopy (2DCS) signals of A␤42 demonstrates that this technique can provide additional constraints for refining the structure and distinguishing the local structures among the models provided by various theoretical protocols consistent with the same NMR experimental constraints. We consider the photon echo technique whereby the fibril is subjected to three very short (Ϸ40 fs) infrared pulses propagating along the directions k 1 , k 2 , and k 3 , and the coherent signal is generated in the direction k x ϭ Ϫk 1 ϩ k 2 ϩ k 3 . Correlation plots are obtained by a dou...

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Local Structure of β-Hairpin Isotopomers by FTIR, 2D IR, and Ab Initio Theory

Cited by 124 publications

References 71 publications

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

Cross-Strand Coupling and Site-Specific Unfolding Thermodynamics of a Trpzip β-Hairpin Peptide Using ¹³C Isotopic Labeling and IR Spectroscopy

Simulation of two-dimensional infrared spectroscopy of amyloid fibrils

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Local Structure of β-Hairpin Isotopomers by FTIR, 2D IR, and Ab Initio Theory

Cited by 124 publications

References 71 publications

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

Cross-Strand Coupling and Site-Specific Unfolding Thermodynamics of a Trpzip β-Hairpin Peptide Using 13C Isotopic Labeling and IR Spectroscopy

Simulation of two-dimensional infrared spectroscopy of amyloid fibrils

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Cross-Strand Coupling and Site-Specific Unfolding Thermodynamics of a Trpzip β-Hairpin Peptide Using ¹³C Isotopic Labeling and IR Spectroscopy