features, future computational studies of energy transport in larger
proteins and protein complexes will be facilitated by any connections between protein dynamics and energy transfer that can be
identified. Work in these directions is in progress [172–175].
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.
References
1. Leitner DM, Straub JE (2009) Proteins:
energy, heat and signal flow. CRC Press,
Boca Raton, FL
2. Nguyen PH, Hamm P, Stock G (2009) Nonequilibrium molecular dynamics simulation of
photoinduced energy flow in peptides: theory
meets experiment. In: Leitner DM, Straub JE
(eds) Proteins: energy, heat and signal flow.
CRC Press, Boca Raton, FL, pp 149–168
3. Hassan S, Schade M, Shaw CP, Levy P, Hamm
P (2014) Response of villin headpiece-capped
gold nanoparticles to ultrafast laser heating. J
Phys Chem B 118:7954–7962
4. Botan V, Backus EHG, Pfister R, Moretto A,
Crisma M, Toniolo C, Nguyen PH, Stock G,
Hamm P (2007) Energy transport in peptide
helices. Proc Natl Acad Sci U S A
104:12749–12754
5. Backus EHG, Nguyen PH, Botan V, Pfister R,
Moretto A, Crisma M, Toniolo C, Stock G,
Hamm P (2008) Energy transport in peptide
helices: a comparison between high- and
low-energy excitations. J Phys Chem B
112:9091–9099
6. Backus EHG, Nguyen PH, Botan V,
Moretto A, Crisma M, Toniolo C, Zerbe O,
Stock G, Hamm P (2008) Structural flexibility of a helical peptide regulates vibrational
energy transport properties. J Phys Chem B
112:15487–15492
7. Backus EH, Bloem R, Pfister R, Moretto A,
Crisma M, Toniolo C, Hamm P (2009)
Dynamical transition in a small helical peptide
and its implication for vibrational energy
transport. J Phys Chem B 113:13405–13409
8. Kondoh M, Mizuno M, Mizutani Y (2016)
Importance of atomic contacts in vibrational
energy flow in proteins. J Phys Chem Lett
7:1950–1954
9. Fujii N, Mizuno M, Mizutani Y (2011) Direct
observation of vibrational energy flow in cytochrome c. J Phys Chem B 115:13057–13064
10. Fujii N, Mizuno M, Ishikawa H, Mizutani Y
(2014) Observing vibrational energy flow in a
protein with the spatial resolution of a single
amino acid residue. J Phys Chem Lett
5:3269–3273.
https://doi.org/10.1021/
jz501882h
11. Sagnella DE, Straub JE, Thirumalai D (2000)
Timescales and pathways for kinetic energy
relaxation in solvated proteins: application to
carbonmonoxy myoglobin. J Chem Phys
113:7702–7711
12. Bu L, Straub JE (2003) Simulating vibrational
energy flow in proteins: relaxation rate and
mechanism for heme cooling in cytochrome
c. J Phys Chem B 107:12339–12345
13. Ishikura T, Iwata Y, Hatano T, Yamato T
(2015) Energy exchange network of interresidue interactions within a thermally fluctuating protein: a computational study. J Comput Chem 36:1709–1718. https://doi.org/
10.1002/jcc.23989
14. Ishikura T, Yamato T (2006) Energy transfer
pathways relevant for long-range intramolecular signaling of photosensory protein
revealed by microscopic energy conductivity
analysis. Chem Phys Lett 432:533–537
15. Xu Y, Leitner DM (2014) Vibrational energy
flow through the green fluorescent proteinLocating and Navigating Energy Transport Networks in Proteins
53
proteins and protein complexes will be facilitated by any connections between protein dynamics and energy transfer that can be
identified. Work in these directions is in progress [172–175].
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.
References
1. Leitner DM, Straub JE (2009) Proteins:
energy, heat and signal flow. CRC Press,
Boca Raton, FL
2. Nguyen PH, Hamm P, Stock G (2009) Nonequilibrium molecular dynamics simulation of
photoinduced energy flow in peptides: theory
meets experiment. In: Leitner DM, Straub JE
(eds) Proteins: energy, heat and signal flow.
CRC Press, Boca Raton, FL, pp 149–168
3. Hassan S, Schade M, Shaw CP, Levy P, Hamm
P (2014) Response of villin headpiece-capped
gold nanoparticles to ultrafast laser heating. J
Phys Chem B 118:7954–7962
4. Botan V, Backus EHG, Pfister R, Moretto A,
Crisma M, Toniolo C, Nguyen PH, Stock G,
Hamm P (2007) Energy transport in peptide
helices. Proc Natl Acad Sci U S A
104:12749–12754
5. Backus EHG, Nguyen PH, Botan V, Pfister R,
Moretto A, Crisma M, Toniolo C, Stock G,
Hamm P (2008) Energy transport in peptide
helices: a comparison between high- and
low-energy excitations. J Phys Chem B
112:9091–9099
6. Backus EHG, Nguyen PH, Botan V,
Moretto A, Crisma M, Toniolo C, Zerbe O,
Stock G, Hamm P (2008) Structural flexibility of a helical peptide regulates vibrational
energy transport properties. J Phys Chem B
112:15487–15492
7. Backus EH, Bloem R, Pfister R, Moretto A,
Crisma M, Toniolo C, Hamm P (2009)
Dynamical transition in a small helical peptide
and its implication for vibrational energy
transport. J Phys Chem B 113:13405–13409
8. Kondoh M, Mizuno M, Mizutani Y (2016)
Importance of atomic contacts in vibrational
energy flow in proteins. J Phys Chem Lett
7:1950–1954
9. Fujii N, Mizuno M, Mizutani Y (2011) Direct
observation of vibrational energy flow in cytochrome c. J Phys Chem B 115:13057–13064
10. Fujii N, Mizuno M, Ishikawa H, Mizutani Y
(2014) Observing vibrational energy flow in a
protein with the spatial resolution of a single
amino acid residue. J Phys Chem Lett
5:3269–3273.
https://doi.org/10.1021/
jz501882h
11. Sagnella DE, Straub JE, Thirumalai D (2000)
Timescales and pathways for kinetic energy
relaxation in solvated proteins: application to
carbonmonoxy myoglobin. J Chem Phys
113:7702–7711
12. Bu L, Straub JE (2003) Simulating vibrational
energy flow in proteins: relaxation rate and
mechanism for heme cooling in cytochrome
c. J Phys Chem B 107:12339–12345
13. Ishikura T, Iwata Y, Hatano T, Yamato T
(2015) Energy exchange network of interresidue interactions within a thermally fluctuating protein: a computational study. J Comput Chem 36:1709–1718. https://doi.org/
10.1002/jcc.23989
14. Ishikura T, Yamato T (2006) Energy transfer
pathways relevant for long-range intramolecular signaling of photosensory protein
revealed by microscopic energy conductivity
analysis. Chem Phys Lett 432:533–537
15. Xu Y, Leitner DM (2014) Vibrational energy
flow through the green fluorescent proteinLocating and Navigating Energy Transport Networks in Proteins
53