Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties

Backus, Ellen H. G.; Nguyen, Phuong H.; Botan, Virgiliu; Moretto, Alessandro; Crisma, Marco; Toniolo, Claudio; Zerbe, Oliver; Stock, Gerhard; Hamm, Peter

doi:10.1021/jp806403p

Cited by 56 publications

(116 citation statements)

References 46 publications

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“…The hindered rotational motion of the CO molecule, which is not covalently bound, results in a very sensitive response of its IR lineshape to temperature [16,17]. Compared to previous work [10][11][12][13][14], where we have used anharmonic frequency shifts of protein backbone C=O modes as a signature of local temperature, the mechanism of this thermometer is more direct and better understood.…”

Section: Discussionmentioning

confidence: 99%

Temperature Dependence of the Heat Diffusivity of Proteins

et al. 2011

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In a combined experimental-theoretical study, we investigated the transport of vibrational energy from the surrounding solvent into the interior of a heme protein, the sperm whale myoglobin double mutant L29W-S108L, and its dependence on temperature from 20 to 70 K. The hindered libration of a CO molecule that is not covalently bound to any part of the protein but is trapped in one of its binding pockets (the Xe4 pocket) was used as the local thermometer. Energy was deposited into the solvent by IR excitation. Experimentally, the energy transfer rate increased from (30 ps)−1 at 20 K to (8 ps)−1 at 70 K. This temperature trend is opposite to what is expected, assuming that the mechanism of heat transport is similar to that in glasses. In order to elucidate the mechanism and its temperature dependence, nonequilibrium molecular dynamics (MD) simulations were performed, which, however, predicted an essentially temperature-independent rate of vibrational energy flow. We tentatively conclude that the MD potentials overestimate the coupling between the protein and the CO molecule, which appears to be the rate-limiting step in the real system at low temperatures. Assuming that this coupling is anharmonic in nature, the observed temperature trend can readily be explained. In a combined experimental-theoretical study, we investigated the transport of vibrational energy from the surrounding solvent into the interior of a heme-protein, the sperm whale myoglobin double mutant L29W-S108L, in dependence of temperature from 20 K to 70 K. The hindered libration of a CO molecule that is not covalently bound to any part of the protein but is trapped in one of its binding pockets (the Xe4 pocket), was used as "local thermometer". Energy was deposited into the solvent by IR excitation. Experimentally, the energy transfer rate increased from (30 ps) −1 at 20 K to (8 ps) −1 at 70 K. This temperature trend is opposite to what is expected, assuming the mechanism of heat transport is similar to that in glasses. In order to elucidate the mechanism and its temperature dependence, non-equilibrium molecular dynamics (MD) simulations were performed, which, however, predicted an essentially temperature independent rate of vibrational energy flow. We tentatively conclude that the MD potentials overestimate the coupling between the protein and the CO molecule, which appears to be the rate limiting step in the real system at low temperatures. Assuming that this coupling is anharmonic in nature, the observed temperature trend can readily be explained.

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Section: Discussionmentioning

confidence: 99%

Temperature Dependence of the Heat Diffusivity of Proteins

et al. 2011

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“…In two follow-up papers, we have studied the dependence of the vibrational energy transport properties on the amount of energy we initially deposit (i.e. after excitation of the azobenzene chromophore with a 3 eV UV photon versus excitation of a peptide C=O oscillator with a 0.2 eV IR photon) [33], and the dependence on solvent temperature [34]. A couple of yet unexplained results emerged from these three pieces of work:…”

Section: Introductionmentioning

confidence: 99%

“…• Finally, one can switch the mechanism of transport after UV-pumping from diffusive at high solvent temperatures to ballistic at low solvent temperatures [34]. Counterintuitively, though, transport becomes less efficient as it becomes ballistic.…”

Section: Introductionmentioning

confidence: 99%

Vibrational energy transport in the presence of intrasite vibrational energy redistribution

Schade

Hamm

2009

The Journal of Chemical Physics

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Vibrational energy transport in the presence of intrasite vibrational energy redistribution AbstractThe mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e., on length scales of a few chemical bonds and time scales of a few picoseconds. This situation occurs, for example, during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time propagate the system fully quantum mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modeling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and time scales, the latter is governed by intrasite vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments.Vibrational energy transport in the presence of intra-site vibrational energy redistribution Marco Schade and Peter HammPhysikalisch-Chemisches Institut, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland (Dated: September 16, 2009) The mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e. on length scales of a few chemical bonds and timescales of a few picoseconds. This situation occurs for example during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time-propagate the system fully quantum-mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modelling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways how classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and timescales, the latter is governed by intra-site vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments.

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“…As in our previous studies [15][16][17][18] the isotope labels are placed by incorporating 13 C-l-Ala, since this amino acid is readily available commercially and does not destabilize the 3 10 -helix significantly. An urethane moiety was inserted between the linking group and the actual peptide to have an intrinsically spectrally resolved C=O group at the beginning of the helical chain.…”

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confidence: 99%

“…Single peptides can be considered the limit of infinitely small nanoparticle diameter. In this case energy is dissipated into the solvent in all directions and, if the peptide concentration is sufficiently low, does not affect other molecules [17]. In contrast, energy dissipated from a peptide in the capping layer can appear in the nearby neighbor ligand so that the heat signal does not decay.…”

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confidence: 99%

Vibrational Energy Transport through a Capping Layer of Appropriately Designed Peptide Helices over Gold Nanoparticles

et al. 2010

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Vibrational energy transport through a capping layer of appropriately designed peptide helices over gold nanoparticles Schade, M; Moretto, A; Donaldson, P M; Toniolo , C; Hamm, P Schade, M; Moretto, A; Donaldson, P M; Toniolo , C; Hamm, P (2010). Vibrational energy transport through a capping layer of appropriately designed peptide helices over gold nanoparticles. Nano Letters, 10(8) We design and characterize spherical gold nanoparticles, which are covalently linked to and completely covered by 310-helical peptides. These helices provide a scaffold to place 13 C=O isotope labels at defined distances from the gold surface, which we employ as local thermometers. Probing these reporter groups with transient infrared spectroscopy, we monitor the vibrational energy flow across the peptide capping layer following excitation of the nanoparticle plasmon resonance.

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Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties

Cited by 56 publications

References 46 publications

Temperature Dependence of the Heat Diffusivity of Proteins

Temperature Dependence of the Heat Diffusivity of Proteins

Vibrational energy transport in the presence of intrasite vibrational energy redistribution

Vibrational Energy Transport through a Capping Layer of Appropriately Designed Peptide Helices over Gold Nanoparticles

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