DOI: 10.1073/pnas.0701762104. Energy transport in peptide helices

10.1073/pnas.0701762104

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

We investigate energy transport through an α-aminoisobutyric acid-based 3 10 -helix dissolved in chloroform in a combined experimental-theoretical approach. Vibrational energy is locally deposited at the N terminus of the helix by ultrafast internal conversion of a covalently attached, electronically excited, azobenzene moiety. Heat flow through the helix is detected with subpicosecond time resolution by employing vibrational probes as local thermo meters at various distances from the heat source. The experiment is supplemented by detailed nonequilibrium molecular dynamics (MD) simulations of the process, revealing good qualitative agreement with experiment: Both theory and experiment exhibit an almost instantaneous temperature jump of the reporter units next to the heater which is attributed to the direct impact of the isomerizing azobenzene moiety. After this impact event, helix and azobenzene moiety appear to be thermally decoupled. The energy deposited in the helix thermalizes on a subpicosecond timescale and propagates along the helix in a diffusive-like process, accompanied by a significant loss into the solvent. However, in terms of quantitative numbers, theory and experiment differ. In particular, the MD simulation seems to overestimate the heat diffusion constant (2 Å 2 ps −1 from the experiment) by a factor of five.

Bibliography

Botan, V., Backus, E. H. G., Pfister, R., Moretto, A., Crisma, M., Toniolo, C., Nguyen, P. H., Stock, G., & Hamm, P. (2007). Energy transport in peptide helices. Proceedings of the National Academy of Sciences, 104(31), 12749â12754.

Authors 9

Virgiliu Botan (first)
Ellen H. G. Backus (additional)
Rolf Pfister (additional)
Alessandro Moretto (additional)
Marco Crisma (additional)
Claudio Toniolo (additional)
Phuong H. Nguyen (additional)
Gerhard Stock (additional)
Peter Hamm (additional)

References 47 Referenced 184

10.1088/0031-8949/20/3-4/013
10.1021/jp026462b
X Yu, DM Leitner J Chem Phys 122, 054902. (2005). / J Chem Phys by Yu X (2005)
DM Leitner Adv Chem Phys 130, 205–256 (2005). / Adv Chem Phys by Leitner DM (2005)
10.1073/pnas.83.23.8982
10.1016/0009-2614(90)85172-9
10.1016/S0009-2614(01)00156-7
10.1021/jp0107917
10.1529/biophysj.106.084996
10.1073/pnas.0409083102
10.1116/1.576265
10.1021/j100096a005
10.1016/S0006-3495(94)80793-3
10.1021/jp980492q
10.1126/science.278.5337.443
10.1146/annurev.pc.42.100191.003053
10.1016/j.cplett.2006.07.085
10.1063/1.1765092
10.1126/science.1071293
10.1126/science.1102074
10.1002/bip.20357
10.1021/ja00373a018
10.1021/ma00147a013
10.1021/bi00481a001
10.1002/1097-0282(2001)60:6<396::AID-BIP10184>3.0.CO;2-7
10.1016/S0009-2614(97)00531-9
10.1002/hlca.660410222
10.1016/S1010-6030(96)04497-8
10.1063/1.473392
10.1016/0968-0004(91)90142-I
10.1021/ja00199a051
10.1021/ja9537383
T Dahinten, J Baier, A Seilmeier Chem Phys Lett 232, 239–245 (1998). / Chem Phys Lett by Dahinten T (1998)
10.1103/RevModPhys.50.607
10.1063/1.458741
GC Pimentel, A McClellan The Hydrogen Bond (Freeman, San Francisco, 1960). / The Hydrogen Bond by Pimentel GC (1960)
10.1073/pnas.92.16.7292
10.1002/prot.20696
10.1021/ja01202a082
10.1021/ja00383a031
CH Li Chem Abstr 59, 10239e–10240e (1963). / Chem Abstr by Li CH (1963)
10.1021/ja00063a082
10.1002/jcc.20291
WF van Gunsteren, SR Billeter, AA Eising, PH Hünenberger, P Krüger, AE Mark, WRP Scott, IG Tironi Biomolecular Simulation: The GROMOS96 Manual and User Guide (Vdf Hochschulverlag AG, Eidgenössische Technische Hochschule Zürich, Zürich, 1996). / Biomolecular Simulation: The GROMOS96 Manual and User Guide by van Gunsteren WF (1996)
10.1080/00268979400101331
10.1002/prot.20485
10.1016/j.chemphys.2005.08.047

Dates

Type	When
Created	18 years, 1 month ago (July 23, 2007, 9:18 p.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 4:27 p.m.)
Indexed	2 months ago (June 19, 2025, 1:24 p.m.)
Issued	18 years ago (July 31, 2007)
Published	18 years ago (July 31, 2007)
Published Online	18 years ago (July 31, 2007)
Published Print	18 years ago (July 31, 2007)

Funders 0

None

BibTeX

@article{Botan_2007, title={Energy transport in peptide helices}, volume={104}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0701762104}, DOI={10.1073/pnas.0701762104}, number={31}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Botan, Virgiliu and Backus, Ellen H. G. and Pfister, Rolf and Moretto, Alessandro and Crisma, Marco and Toniolo, Claudio and Nguyen, Phuong H. and Stock, Gerhard and Hamm, Peter}, year={2007}, month=jul, pages={12749–12754} }

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