Picosecond dynamics of a membrane protein revealed by 2D IR

Mukherjee, Prabuddha; Kass, Itamar; Arkin, Isaiah T.; Zanni, Martin T.

doi:10.1073/pnas.0508833103

Cited by 201 publications

(304 citation statements)

References 35 publications

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“…Clearly water has a greatly diminished averaging effect on the carbonyl groups in the hydrophobic core near Gly 79 in the micelle. Recent 2D IR experiments on another TM peptide have provided the residue dependence of this averaging (11). The water-soluble ␣-helices also showed significant spectral changes occurring within the first 200 fs that were attributed to these amide frequency fluctuations, but this ultrafast dynamics was much less prominent in the current GpA TM helix samples.…”

Section: Discussionmentioning

confidence: 99%

“…Recent applications of this method to biologically related molecules have yielded novel structural and dynamical results not readily obtainable by other methods for small peptides (7,8), soluble helices (9, 10), membrane-bound helices (11), lipids (12), ␤-sheets (13,14), and model secondary structures (15,16). The 2D IR approach is one that can be immediately applicable to a wide variety of sample types ranging from solutions to solids, including aqueous and lipid environments.…”

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confidence: 99%

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Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer

Fang

Senes

Cristian

et al. 2006

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

130

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The tertiary interactions between amide-I vibrators on the separate helices of transmembrane helix dimers were probed by ultrafast 2D vibrational photon echo spectroscopy. The 2D IR approach proves to be a useful structural method for the study of membrane-bound structures. The 27-residue human erythrocyte protein Glycophorin A transmembrane peptide sequence: KKITLIIFG79VMAGVIGTILLISWG94IKK was labeled at G79 and G94 with 13 tertiary interaction ͉ vibrational spectra ͉ multidimensional spectroscopy T wo-dimensional IR spectroscopy (1-6) is a promising new method with which to probe structures and their motions in complex systems. Recent applications of this method to biologically related molecules have yielded novel structural and dynamical results not readily obtainable by other methods for small peptides (7,8), soluble helices (9, 10), membrane-bound helices (11), lipids (12), ␤-sheets (13, 14), and model secondary structures (15, 16). The 2D IR approach is one that can be immediately applicable to a wide variety of sample types ranging from solutions to solids, including aqueous and lipid environments. The method exposes interactions between spatially nearby vibrational modes by converting three pulse photon echo signals into 2D spectral maps in the IR, analogous to 2D NMR spectra.The amide-I vibrational bands of polypeptides are highly degenerate because, for each residue, their frequencies are approximately the same and the interactions among them are not strong enough to separately display them as individual, assignable transitions. The combination of multiple isotope selection and 2D IR spectroscopy that spreads the transitions into two dimensions proves to be a useful strategy that can simplify and expose the underlying transitions of the diffuse amide bands and allow their features to be characterized at a residue level. For example the 2D IR spectrum of a water-soluble helix selectively substituted with 13 CA 16 O and 13 CA 18 O provided characteristics of pairs of coupled residues and the visualization of the sequence dependence of the structural dynamics (17). This paper introduces a comparable approach to investigate tertiary interactions between vibrational modes in Glycophorin A (GpA), a transmembrane (TM) dimer of interacting helices (Fig. 1). The GpA TM helix provides an excellent prototype for the study of TM helix association, a key event in the folding of membrane proteins (18). The dimer also is an appropriate model for these investigations, because it is stable in a variety of micelles, including SDS (19), and a solution NMR structure is available (20). There are two Gly residues at the dimer interface that allow an intimate contact of the main chain, a feature frequently observed in TM helical interfaces (21,22). Because vibrational coupling is sensitive to distance, the proximity of the backbones is advantageous. GpA also was selected because verification of the applicability of the 2D IR method to membrane protein aggregates is of great interest and because there is a chronic paucity o...

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer

Fang

Senes

Cristian

et al. 2006

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

130

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“…79 Proteins are rapidly interconverting within an ensemble of similar conformations. 64,[80][81][82] A subset of these rapidly interconverting states may be favorable for binding a given substrate. A different subset of conformations may accommodate a structurally heterologous ligand.…”

Section: B the Influence Of Substrate Binding Of Enzyme Dynamicsmentioning

confidence: 99%

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Finkelstein

Zheng

Ishikawa

et al. 2007

Phys. Chem. Chem. Phys.

148

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Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.

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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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Picosecond dynamics of a membrane protein revealed by 2D IR

Cited by 201 publications

References 35 publications

Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer

Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

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

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