Isotope-edited two-dimensional vibrational spectroscopy of trialanine in aqueous solution

Woutersen, Sander; Hamm, Peter

doi:10.1063/1.1336807

Cited by 198 publications

(275 citation statements)

References 35 publications

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“…Another structural study of alanine dipeptide using 13 C NMR 49 confirmed the presence of PP II conformation, but also suggests that a mixture of PP II and α R is more likely in water. The dominance of PP II in trialanine was reiterated by two-dimensional vibrational spectroscopy studies of Woutersen & Hamm 50,51 and later modified by the same authors to include around 20% of α R apart from PP II 52 . The experimental studies of Schweitzer-Stenner & Eker on trialanines 53,54 and tetraalanines 55 in water using polarized Raman, FT-IR and VCD spectroscopy confirm the dominance of PP II conformation in tetraalanines, while a 50:50 mixture of PP II and extended β-strand-like conformations was observed for trialanines.…”

Section: Force Field Validationmentioning

confidence: 99%

Comparison of multiple Amber force fields and development of improved protein backbone parameters

et al. 2006

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The ff94 force field that is commonly associated with the AMBER simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over stabilization of α-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of "AMBER" force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in AMBER of two sets of backbone φ/ψ dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the φ/ψ dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab-initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides, and better accord with experimental NMR relaxation data of test protein systems.

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Section: Force Field Validationmentioning

confidence: 99%

Comparison of multiple Amber force fields and development of improved protein backbone parameters

et al. 2006

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“…14 Extensive studies were performed on a small and flexible peptide, trialanine, and yielded the Ramachandran angles in good agreement with NMR studies. 8,9 For larger peptides the emphasis of 2D IR has been to relate certain patterns in the spectra to typical structural motifs as a-helix, 3 10 -helix, and -sheet. [14][15][16][17][18] However, the cross-peak pattern of other amide bands can provide additional structural information.…”

Section: Introductionmentioning

confidence: 99%

Electrostatic DFT Map for the Complete Vibrational Amide Band of NMA

2005

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An anharmonic vibrational Hamiltonian for the amide I, II, III, and A modes of N-methyl acetamide (NMA), recast in terms of the 19 components of an external electric field and its first and second derivative tensors (electrostatic DFT map), is calculated at the DFT(BPW91/6-31G(d,p)) level. Strong correlations are found between NMA geometry and the amide frequency fluctuations calculated using this Hamiltonian together with the fluctuating solvent electric field obtained from the MD simulations in TIP3 water. The amide I and A frequencies are strongly positively correlated with the CdO and N-H bond lengths. The CdO and C-N amide bond lengths are negatively correlated, suggesting the solvent-induced fluctuations of the contribution of zwitterionic resonance form. Sampling the global electric field in the entire region of the transition charge densities (TCDs) is required for accurate infrared line shape simulations. Collective electrostatic solvent coordinates which represent the fluctuations of the 10 lowest amide fundamental and overtone states are reported. Normal-mode analysis of an NMA-3H 2 O cluster shows that the 660 cm -1 to 1100 cm -1 oscillation found in the frequency autocorrelation functions of the amide modes may be ascribed to the two bending vibrations of intermolecular hydrogen bonds with the amide oxygen of NMA.

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“…Coupling parameters are central to interpretation of data used in recently proposed structural techniques that combine Raman polarization and IR data (even including VCD) [31][32][33] and are vital for the new 2D IR studies that both measure coupling and develop dynamic pictures of protein structure. [34][35][36][37][38][39][40] In a recent example, isotopic substitution of helical peptides was used to help determine site-specific coupling. 23 Helices and their interresidue interactions are now fairly well understood, but similar questions with -sheets are more difficult to resolve, due to their greater heterogeneity and multistranded nature, and they provide natural targets for applications of isotopic labels and their coupling.…”

Section: Introductionmentioning

confidence: 99%

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra

2005

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Isotopic substitution with 13 C on the amide CdO has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, -forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these -sheet systems the effect of the relative positions of the 13 C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local -structure formation, because coupling between close-lying CdO groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the CdO groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/ 6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results. IntroductionVibrational spectra, IR and Raman, have long been used to determine average secondary structure characteristics in peptides and proteins. 1-4 Like electronic circular dichroic (ECD) structural studies, the limited resolution of vibrational spectra normally provides sequence-averaged structural information in comparison to the localized details derivable from NMR and X-ray diffraction. Since optical spectra can provide inherently fast measures of structure and are generally applicable to all protein and peptide systems, increasing their information content is of wide interest. Vibrational spectra, in contrast to electronic spectra, have distinctive frequency shifts due to isotopic variation, which can be used to give site-specific characteristics to certain bands for selectively labeled peptides. In the past decade a number of studies have appeared where isotopic substitution was used to obtain better structural insight with IR spectra. [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] Isotopic labeling of the amide group has an important impact on vibrational spectra, be...

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Isotope-edited two-dimensional vibrational spectroscopy of trialanine in aqueous solution

Cited by 198 publications

References 35 publications

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Electrostatic DFT Map for the Complete Vibrational Amide Band of NMA

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra

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Isotope-edited two-dimensional vibrational spectroscopy of trialanine in aqueous solution

Cited by 198 publications

References 35 publications

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Electrostatic DFT Map for the Complete Vibrational Amide Band of NMA

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of 13C Isotopic Labeling on Infrared Spectra

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Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra