Site-specific vibrational dynamics of the CD3ζ membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy

Mukherjee, Prabuddha; Krummel, Amber T.; Fulmer, Eric C.; Kass, Itamar; Arkin, Isaiah T.; Zanni, Martin T.

doi:10.1063/1.1718332

Cited by 112 publications

(178 citation statements)

References 47 publications

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“…The stretching frequency of a CAO group involved in a hydrogen bond depends on the length of this hydrogen bond (35,36), and the spectral inhomogeneity of the CAO bands therefore most likely arises from a distribution of CAO⅐⅐⅐H hydrogen-bond lengths. Such distributions of CAO⅐⅐⅐H hydrogen-bond lengths have been observed previously in other molecular systems (37)(38)(39)(40).…”

Section: Methodssupporting

confidence: 61%

Probing the structure of a rotaxane with two-dimensional infrared spectroscopy

Larsen

Bodis

Buma

et al. 2005

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

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Femtosecond 2D-IR spectroscopy has been used to study the structure of a [2]rotaxane composed of a benzylic amide macrocycle that is mechanically interlocked onto a succinamide-based thread. Both the macrocycle and the thread contain carbonyl groups, and by determining the coupling between the stretching modes of these groups from the cross-peaks in the 2D-IR spectrum, the structure of the macrocycle-thread system has been probed. Our results demonstrate that 2D-IR spectroscopy can be used to observe structural changes in molecular devices on a picosecond time scale.femtosecond IR spectroscopy ͉ molecular machines I t has recently become possible to synthesize molecules that function like mechanical devices (1-4), such as switches (5-7), motors (8-11), brakes (12), turnstiles (13), and elevators (14). These manmade molecular machines can be considered as nanoscale versions of their macroscopic analogues. However, many well known macroscopic concepts no longer apply at a molecular level. For instance, the concept of viscous friction becomes meaningless as the size of moving object approaches that of the molecules of the surrounding medium and as the time scale of the motion approaches that of the molecules of this medium (15). This regime of device operation is a new one, where the elementary component motions (rotations around covalent bonds and the making and breaking of hydrogen bonds) and the fluctuations of the surroundings both take place on the picosecond or subpicosecond time scale. Hence, for a detailed understanding of the physics and chemistry of molecular devices, experiments that probe their motion on an ultrafast time scale are essential, and the insights obtained from such experiments should be important for potential applications.A promising technique for such experiments is 2D-IR spectroscopy. With 2D-IR spectroscopy, molecular conformations are determined by measuring couplings between molecular vibrations. The method was inspired by multidimensional NMR spectroscopy, in which couplings between nuclear spins are used for structure resolution (16). Like nuclear spins, normal modes are often well localized in the molecule (especially when they involve stretching of specific chemical bonds), and the coupling between them is mainly dipolar. The 2D-IR spectrum can therefore give direct access to the conformation of a molecule or its parts (17-23). The important advantage of 2D-IR spectroscopy as compared with 2D-NMR spectroscopy is its time resolution: The conformation can be determined with a time resolution determined by the free-induction decay of the transition, which is generally Ͻ1 ps. As a consequence, 2D-IR spectroscopy can be used to study motion in molecular systems on a time scale comparable to that of the elementary molecular motions. To this purpose, one triggers the motion (typically with a short optical pulse) and monitors the subsequent structural changes by recording 2D-IR spectra at different time delays with respect to the external trigger. In this way, a ''movie'' of the molecular...

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Section: Methodssupporting

confidence: 61%

Probing the structure of a rotaxane with two-dimensional infrared spectroscopy

Larsen

Bodis

Buma

et al. 2005

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

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“…The 2DIR technique has been applied to proteins in solution. [5][6][7][8][9][10] However, most studies have focused on spectra with zero waiting time. Using the waiting time dependence gives a direct way to study system dynamics, including population relaxation.…”

Section: Introductionmentioning

confidence: 99%

Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

Dijkstra¹,

Jansen²,

Bloem³

et al. 2007

The Journal of Chemical Physics

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Two-dimensional infrared spectroscopy is capable of following the transfer of vibrational energy between modes in real time. We develop a method to include vibrational relaxation in simulations of two-dimensional infrared spectra at finite temperature. The method takes into account the correlated fluctuations that occur in the frequencies of the vibrational states and in the coupling between them as a result of interaction with the environment. The fluctuations influence the two-dimensional infrared line shape and cause vibrational relaxation during the waiting time, which is included using second-order perturbation theory. The method is demonstrated by applying it to the amide-I and amide-II modes in N-methylacetamide in heavy water. Stochastic information on the fluctuations is obtained from a molecular dynamics trajectory, which is converted to time dependent frequencies and couplings with a map from a density functional calculation. Solvent dynamics with the same frequency as the energy gap between the two amide modes lead to efficient relaxation between amide-I and amide-II on a 560fs time scale. We show that the cross peak intensity in the two-dimensional infrared spectrum provides a good measure for the vibrational relaxation.

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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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Site-specific vibrational dynamics of the CD3ζ membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy

Cited by 112 publications

References 47 publications

Probing the structure of a rotaxane with two-dimensional infrared spectroscopy

Probing the structure of a rotaxane with two-dimensional infrared spectroscopy

Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

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

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