Chapter 4
Locating and Navigating Energy Transport Networks
in Proteins
Korey M. Reid and David M. Leitner
Abstract
We review computational methods to locate energy transport networks in proteins that are based on the
calculation of local energy diffusion in nanoscale systems. As an illustrative example, we discuss energy
transport networks computed for the homodimeric hemoglobin from Scapharca inaequivalvis, where
channels for facile energy transport, which include the cluster of water molecules at the interface of the
globules, have been found to lie along pathways that experiments reveal are important in allosteric
processes. We also review recent work on master equation simulations to model energy transport dynamics,
including efforts to relate rate constants in the master equation to protein structural dynamics. Results for
apomyoglobin involving relations between fluctuations in the length of hydrogen bonds and the energy flux
between them are presented.
Key words Energy transport networks, Allostery, Water cluster, Nonbonded networks
1 Introduction
Progress in locating energy transport pathways in proteins both
computationally and experimentally has been proceeding at a rapid
pace [1]. Time-resolved IR and Raman techniques, e.g., have
provided detailed pictures of the nature and rate of energy transport
in peptides and proteins [2–7], including recent advances in identifying transport through individual amino acids of several heme
proteins [8–10]. Energy transport pathways have since some time
been identified by molecular simulations [11, 12], with recent
focus on the development of coarse-graining approaches [13–25],
some of which have exploited analogies to thermal transport in
other molecular materials [26, 27]. Network analysis has been
applied to facilitate identification of pathways and residues that
control protein dynamics [28–51], where a variety of definitions
of a network have been adopted, including those that incorporate
distance, conformational fluctuations, and energy criteria. The
energy transport channels of a protein form a network, and analysis
Luisa Di Paola and Alessandro Giuliani (eds.), Allostery: Methods and Protocols, Methods in Molecular Biology, vol. 2253,
https://doi.org/10.1007/978-1-0716-1154-8_4, © Springer Science+Business Media, LLC, part of Springer Nature 2021
37
Locating and Navigating Energy Transport Networks
in Proteins
Korey M. Reid and David M. Leitner
Abstract
We review computational methods to locate energy transport networks in proteins that are based on the
calculation of local energy diffusion in nanoscale systems. As an illustrative example, we discuss energy
transport networks computed for the homodimeric hemoglobin from Scapharca inaequivalvis, where
channels for facile energy transport, which include the cluster of water molecules at the interface of the
globules, have been found to lie along pathways that experiments reveal are important in allosteric
processes. We also review recent work on master equation simulations to model energy transport dynamics,
including efforts to relate rate constants in the master equation to protein structural dynamics. Results for
apomyoglobin involving relations between fluctuations in the length of hydrogen bonds and the energy flux
between them are presented.
Key words Energy transport networks, Allostery, Water cluster, Nonbonded networks
1 Introduction
Progress in locating energy transport pathways in proteins both
computationally and experimentally has been proceeding at a rapid
pace [1]. Time-resolved IR and Raman techniques, e.g., have
provided detailed pictures of the nature and rate of energy transport
in peptides and proteins [2–7], including recent advances in identifying transport through individual amino acids of several heme
proteins [8–10]. Energy transport pathways have since some time
been identified by molecular simulations [11, 12], with recent
focus on the development of coarse-graining approaches [13–25],
some of which have exploited analogies to thermal transport in
other molecular materials [26, 27]. Network analysis has been
applied to facilitate identification of pathways and residues that
control protein dynamics [28–51], where a variety of definitions
of a network have been adopted, including those that incorporate
distance, conformational fluctuations, and energy criteria. The
energy transport channels of a protein form a network, and analysis
Luisa Di Paola and Alessandro Giuliani (eds.), Allostery: Methods and Protocols, Methods in Molecular Biology, vol. 2253,
https://doi.org/10.1007/978-1-0716-1154-8_4, © Springer Science+Business Media, LLC, part of Springer Nature 2021
37