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Locating and Navigating Energy Transport Networks in Proteins

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2253))

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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.

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Acknowledgements

The authors are grateful to Prof. Takahisa Yamato for making available his program CURP and for a number of helpful discussions. Some of the work reviewed here is the result of a collaboration DML has enjoyed with Gerhard Stock and Sebastian Buchenberg on modeling energy dynamics in proteins. Support from NSF grants CHE-1361776 and CHE-1854271 is gratefully acknowledged.

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  1. Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, NV, USA

    Korey M. Reid & David M. Leitner

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  1. Korey M. Reid
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Correspondence to David M. Leitner .

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    Luisa Di Paola

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    Alessandro Giuliani

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Reid, K.M., Leitner, D.M. (2021). Locating and Navigating Energy Transport Networks in Proteins. In: Di Paola, L., Giuliani, A. (eds) Allostery. Methods in Molecular Biology, vol 2253. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1154-8_4

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