Integrated and dispersed photon echo studies of nitrile stretching vibration of 4-cyanophenol in methanol

117

Abstract2D IR spectroscopy was used to probe the hydrophobic core structure of the 35-residue Villin headpiece subdomain, HP35, by monitoring the C≡N vibrational stretching band of a cyano substituted phenylalanine (Phe). The presence of two humps in the vibrational frequency distribution in the folded equilibrium state is revealed. They represent two states that exchange more slowly than ca. 10 ps. The two CN stretch mode peak frequencies (and their equilibrium populations) are 2228.7 (44%) and 2234.5 cm −1 (56%). The two CN modes have different frequency-frequency correlation times of 7.4 ps and 1.6 ps respectively. These results suggest that the population with the higher frequency CN group is partly exposed whereas the other CN mode experiences a hydrophobic like environment. KeywordsNitrile probe; Two dimensional infrared spectroscopy; Villin headpiece; protein structural heterogeneity; cyanophenylalanineThe increasing availability of molecular dynamics simulations of protein structural fluctuations and of folding pathways 1-4 raises interesting questions about how the implied, detailed, microscopic predictions, which often involve ultrafast structural fluctuations, can be tested by real time experiments that monitor events that occur faster than the rate determining steps of conventional kinetics experiments. 5 Different peptide conformations necessarily have different dispositions of backbone and side chains so that they have different vibrational spectra. Two dimensional infrared spectroscopy (2D IR) 6-9 is a method of choice for examining protein structural constraints and their fluctuations over a broad time range. The peptide backbone amide groups have coupling parameters that are in principle deducible from these multidimensional infrared methods. The parameters of 2D IR in turn relate to the "instantaneous" backbone structure. The inverse bandwidth of commonly occurring vibrational transitions sets a time scale of a few picoseconds, such that conformational exchanges would have to occur faster than this to be motionally averaged. 10 Thus all the major structures anticipated in peptide conformational dynamics are expected to be spectrally distinct in 2D IR and with better resolution than FTIR.The dynamics within the vibrational frequency distribution of a mode, often referred to as spectral diffusion, signifies the time dependent structure of the immediate environment of the mode. This information is contained in the frequency-frequency correlation functions obtained from 2D IR. 9 Measurements of these correlations over a wide range of times reveal the dynamics local to an amide as well as those associated with the coupling between modes on different sections of the secondary structure. 9,11 These concepts apply equally well to the vibrational modes of probes that are engineered into the backbone or side chains of the peptides. The probes could be non-perturbative isotopologues or chemically modified residues as in the present paper.Nitrile groups have been very useful as vibrational probes of biolog...

supporting

confidence: 87%

supporting

confidence: 80%

The Two-Dimensional Vibrational Echo of a Nitrile Probe of the Villin HP35 Protein

Urbanek

Vorobyev

Serrano

et al. 2010

117

“…As shown (Figure 5), the (normalized) autocorrelation function decays rapidly in a bimodal fashion, similar to that observed for other nitrile compounds 15,16,17,30. The vibrational pure dephasing constant,

T_{2}^{*} = 1 / \int_{0}^{\infty} d t M false(t false)

, was estimated to be 0.25 ps.…”

supporting

confidence: 81%

Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water

Waegele

Gai

2010

The bandwidth of the nitrile (C≡N) stretching vibration of 5-cyanotryptophan shows a significant broadening upon hydration. Thus, it has been proposed to be a useful infrared probe of the local hydration environment of proteins. However, the molecular mechanism underlying this hydrationinduced spectral broadening is not known, making interpretation of the experimental results difficult. Herein, we investigate how interactions of water with various sites of 5-cyanoindole, the sidechain of 5-cyanotryptophan, affect its C≡N stretching vibration via a combined electronic structure/ molecular dynamics approach. It is found that, besides those interactions with the nitrile group, interactions of water with the indole ring also play a significant role in mediating the C≡N stretching frequency. Thus, this study provides a molecular basis for understanding how hydration affects the C≡N stretching band of 5-cyanotryptophan. In addition, an empirical model, which includes interactions of water with both the nitrile and indole groups, is developed for predicting the C≡N stretching vibrational band via molecular dynamics simulations.Keywords 5-cyanoindole; 5-cyanotryptophan; nitrile stretching vibration; infrared probe; electrostatic map; spectral modeling It is well known that the C≡N stretching vibration of a nitrile group is sensitive to its environment. [1][2][3][4] Thus, several nitrile-derivatized, non-natural amino acids, including pcyanophenylalanine, cyanoalanine, and cyanylated cyteine, have been used as infrared (IR) reporters of local conformation and/or electrostatics of peptides 5-9 and proteins.10 -12 These applications are primarily based on the premise that the C≡N stretching frequency shifts upon a change in the immediate environment of the corresponding non-natural amino acid. However, recently we have shown that in the case of 5-cyanotryptophan it is the bandwidth of the C≡N stretching vibrational band, instead of its peak frequency, that is more sensitive to the hydration status of the IR reporter. 13 In fact, the bandwidth of the C≡N stretching vibrational band of 5-cyanoindole (Figure 1), which is the sidechain of 5-cyanotryptophan, is increased from ∼8.7 cm −1 to ∼15.6 cm −1 when the solvent is changed from tetrahydrofuran (THF) to water, whereas the band frequency shows only a slight blue shift (∼4 cm −1 ). In addition, the C≡N stretching band of 5-cyanoindole in water is also significantly broader than those of other model nitrile compounds (i.e., acetonitrile 1, 2 , 5, p-tolunitrile5, and methyl cyanate14 , 15).Given the range of lifetimes (∼1-5 ps) measured for the C≡N stretching vibration of several related nitrile compounds, 16, 17 it seems unlikely that lifetime broadening plays a dominant *To whom correspondence should be addressed. mwaegele@sas.upenn.edu. Supporting Information Available: Details of the molecular dynamics simulation, the vibrational frequency analysis, and band shape calculation. This material is available free of charge via the Internet at http://pubs.acs.org. role i...

“…The vibrational lifetimes of a few nitriles have been measured and they typically range from ~1 to 5 ps in water. 62,63,70,71 …”

Section: Site-specific Vibrational Probesmentioning

confidence: 99%

Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules

Waegele

Culik

Gai

2011

153

181

Elucidating the underlying molecular mechanisms of protein folding and function is a very exciting and active research area, but poses significant challenges. This is due in part to the fact that existing experimental techniques are incapable of capturing snapshots along the ‘reaction coordinate’ in question with both sufficient spatial and temporal resolutions. In this regard, recent years have seen increased interests and efforts in development and employment of site-specific probes to enhance the structural sensitivity of spectroscopic techniques in conformational and dynamical studies of biological molecules. In particular, the spectroscopic and chemical properties of nitriles, thiocyanates, and azides render these groups attractive for the interrogation of complex biochemical constructs and processes. Here, we review their signatures in vibrational, fluorescence and NMR spectra and their utility in the context of elucidating chemical structure and dynamics of protein and DNA molecules.