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

  • 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.
Author:Erhan DenizORCiD, Luis Valiño BorauORCiDGND, Jan Gerrit LöfflerORCiDGND, Katharina Barbara EberlGND, Adnan GulzarORCiDGND, Steffen WolfORCiDGND, Patrick M. Durkin, Robert KamlORCiD, Nediljko BudisaORCiDGND, Gerhard StockORCiDGND, Jens BredenbeckORCiD
Parent Title (English):Nature Communications
Publisher:Nature Publishing Group
Place of publication:[London]
Document Type:Article
Date of Publication (online):2021/06/02
Date of first Publication:2021/06/02
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2023/10/13
Tag:Computational biophysics; Energy transfer; Infrared spectroscopy; Proteins
Issue:art. 3284
Article Number:3284
Page Number:8
First Page:1
Last Page:8
We acknowledge DFG funding (BR 3746/4-1; BU1404/9-1; INST 161/722-1; STO 247/10-2, INST 39/963-1 FUGG) as well as funding by the Canada Research Chairs Program (grant no. 950-231971).

This work has been supported by the DFG via the Research Unit FOR5099 “Reducing complexity of nonequilibrium systems”, the High Performance and Cloud Computing Group at the Rechenzentrum of the University of Freiburg, the state of Baden-Württemberg through bwHPC and the DFG (bwForCluster NEMO RV bw18A004), and the Black Forest Grid Initiative.

Open Access funding enabled and organized by Projekt DEAL.
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 54 Chemie / 540 Chemie und zugeordnete Wissenschaften
5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Licence (German):License LogoCreative Commons - CC BY - Namensnennung 4.0 International