Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids

Erhan Deniz, Luis Valiño-Borau, Jan G. Löffler, Katharina B. Eberl, Adnan Gulzar, Steffen Wolf, Patrick M. Durkin, Robert Kaml, Nediljko Budisa, Gerhard Stock () and Jens Bredenbeck ()
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Erhan Deniz: Goethe University Frankfurt
Luis Valiño-Borau: Albert Ludwigs University
Jan G. Löffler: Goethe University Frankfurt
Katharina B. Eberl: Goethe University Frankfurt
Adnan Gulzar: Albert Ludwigs University
Steffen Wolf: Albert Ludwigs University
Patrick M. Durkin: Technical University Berlin
Robert Kaml: Technical University Berlin
Nediljko Budisa: Technical University Berlin
Gerhard Stock: Albert Ludwigs University
Jens Bredenbeck: Goethe University Frankfurt

Nature Communications, 2021, vol. 12, issue 1, 1-8

Abstract: Abstract Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.

Date: 2021
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DOI: 10.1038/s41467-021-23591-1

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