water interface: communication maps and
thermal boundary conductance. J Phys
Chem B 118:7818–7826
16. Xu Y, Leitner DM (2014) Communication
maps of vibrational energy transport in photoactive yellow protein. J Phys Chem A
118:7280–7287
17. Leitner DM, Buchenberg S, Brettel P, Stock
G (2015) Vibrational energy flow in the villin
headpiece subdomain: master equation simulations. J Chem Phys 142:075101
18. Agbo JK, Gnanasekaran R, Leitner DM
(2014) Communication maps: exploring
energy transport through proteins and water.
Isr J Chem 54:1065–1073
19. Leitner DM (2009) Frequency resolved communication maps for proteins and other nanoscale materials. J Chem Phys 130:195101
20. Gnanasekaran R, Agbo JK, Leitner DM
(2011) Communication maps computed for
homodimeric hemoglobin: computational
study of water-mediated energy transport in
proteins. J Chem Phys 135:065103
21. Agbo JK, Xu Y, Zhang P, Straub JE, Leitner
DM (2014) Vibrational energy flow across
heme-cytochrome c and cytochrome c-water
interfaces. Theor Chem Accounts 133:1504
22. Leitner DM (2016) Water-mediated energy
dynamics in a homodimeric hemoglobin. J
Phys Chem B 120:4019–4027
23. Buchenberg S, Leitner DM, Stock G (2016)
Scaling rules for vibrational energy transport
in proteins. J Phys Chem Lett 7:25–30
24. Martı ´nez L, Figueira ACM, Webb P,
Polikarpov I, Skaf MS (2011) Mapping the
intramolecular vibrational energy flow in proteins reveals functionally important residues. J
Phys Chem Lett 2:2073–2078
25. Leitner DM, Yamato T (2018) Mapping
energy transport networks in proteins. In:
Parrill AL, Lipkowitz KB (eds) Rev. Comp.
Chem, vol 31. Wiley, New York, pp 63–114
26. Leitner DM (2013) Thermal boundary conductance and rectification in molecules. J Phys
Chem B 117:12820–12828
27. Rubtsova NI, Rubtsov IV (2015) Vibrational
energy transport in molecules studied by
relaxation-assisted two-dimensional infrared
spectroscopy. Ann Rev Phys Chem
66:717–738
28. Sethi A, Eargle J, Black AA, Luthey-Schulten
Z (2009) Dynamical networks in tRNA: protein complexes. Proc Natl Acad Sci U S A
106:6620–6625
29. Ribeiro AAST, Ortiz V (2015) Energy propagation and network energetic coupling in proteins. J Phys Chem B 119:1835–1846
30. Ribeiro AAST, Ortiz V (2014) Determination
of signaling pathways in proteins through network theory: importance of the topology. J
Chem Theor Comput 10:1762–1769
31. DiPaola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
32. Feher VA, Durrant JD, Wart ATV, Amaro RE
(2014) Computational approaches to
mapping allosteric pathways. Curr Opin
Struct Biol 25:98–103
33. Gursoy A, Keskin O, Nussinov R (2008)
Topological properties of protein interaction
networks from a structural perspective. Biochem Soc Trans 36:1398–1403
34. Lee Y, Choi S, Hyeon C (2014) Mapping the
intramolecular
signal
transduction
of
G-protein coupled receptors. Proteins
82:727–743
35. Miao Y, Nichols SE, Gasper PM, Metzger VT,
McCammon JA (2013) Activation and
dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A
110:10982–10987
36. Del-Sol A, Fujihashi H, Amoros D, Nussinov
R (2006) Residues crucial for maintaining
short paths in network communication mediate signaling in proteins. Mol Sys Biol
2:2006.0019
37. Atilgan AR, Turgut D, Atilgan C (2007)
Screened nonbonded interactions in native
proteins manipulate optimal paths for robust
residue
communication.
Biophys
J
92:3052–3062
38. Woods KN (2014) Using THz time-scale
infrared spectroscopy to examine the role of
collective, thermal fluctuations in the formation of myoglobin allosteric communication
pathways and ligand specificity. Soft Matter
10:4387–4402
39. Woods KN, Pfeffer J (2015) Using THz spectroscopy, evolutionary network analysis methods, and MD simulation to map the evolution
of allosteric communication pathways in
c-type lysozymes. Mol Biol Evol 2:271–274
40. Achoch M, Dorantes-Gilardi R, Wymant C,
Feverati G, Salamatian K, Vuillon L, Lesieur C
(2016) Protein structural robustness to mutations: an in silico investigation. Phys Chem
Phys 16:13770–13780
41. Ribeiro AAST, Ortiz V (2016) A chemical
perspective on allostery. Chem Rev
116:6488–6502
42. Vuillon L, Lesieur C (2015) From local to
global changes in proteins: a network view.
Curr Opin Struct Biol 31:1–8
54
Korey M. Reid and David M. Leitner
thermal boundary conductance. J Phys
Chem B 118:7818–7826
16. Xu Y, Leitner DM (2014) Communication
maps of vibrational energy transport in photoactive yellow protein. J Phys Chem A
118:7280–7287
17. Leitner DM, Buchenberg S, Brettel P, Stock
G (2015) Vibrational energy flow in the villin
headpiece subdomain: master equation simulations. J Chem Phys 142:075101
18. Agbo JK, Gnanasekaran R, Leitner DM
(2014) Communication maps: exploring
energy transport through proteins and water.
Isr J Chem 54:1065–1073
19. Leitner DM (2009) Frequency resolved communication maps for proteins and other nanoscale materials. J Chem Phys 130:195101
20. Gnanasekaran R, Agbo JK, Leitner DM
(2011) Communication maps computed for
homodimeric hemoglobin: computational
study of water-mediated energy transport in
proteins. J Chem Phys 135:065103
21. Agbo JK, Xu Y, Zhang P, Straub JE, Leitner
DM (2014) Vibrational energy flow across
heme-cytochrome c and cytochrome c-water
interfaces. Theor Chem Accounts 133:1504
22. Leitner DM (2016) Water-mediated energy
dynamics in a homodimeric hemoglobin. J
Phys Chem B 120:4019–4027
23. Buchenberg S, Leitner DM, Stock G (2016)
Scaling rules for vibrational energy transport
in proteins. J Phys Chem Lett 7:25–30
24. Martı ´nez L, Figueira ACM, Webb P,
Polikarpov I, Skaf MS (2011) Mapping the
intramolecular vibrational energy flow in proteins reveals functionally important residues. J
Phys Chem Lett 2:2073–2078
25. Leitner DM, Yamato T (2018) Mapping
energy transport networks in proteins. In:
Parrill AL, Lipkowitz KB (eds) Rev. Comp.
Chem, vol 31. Wiley, New York, pp 63–114
26. Leitner DM (2013) Thermal boundary conductance and rectification in molecules. J Phys
Chem B 117:12820–12828
27. Rubtsova NI, Rubtsov IV (2015) Vibrational
energy transport in molecules studied by
relaxation-assisted two-dimensional infrared
spectroscopy. Ann Rev Phys Chem
66:717–738
28. Sethi A, Eargle J, Black AA, Luthey-Schulten
Z (2009) Dynamical networks in tRNA: protein complexes. Proc Natl Acad Sci U S A
106:6620–6625
29. Ribeiro AAST, Ortiz V (2015) Energy propagation and network energetic coupling in proteins. J Phys Chem B 119:1835–1846
30. Ribeiro AAST, Ortiz V (2014) Determination
of signaling pathways in proteins through network theory: importance of the topology. J
Chem Theor Comput 10:1762–1769
31. DiPaola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
32. Feher VA, Durrant JD, Wart ATV, Amaro RE
(2014) Computational approaches to
mapping allosteric pathways. Curr Opin
Struct Biol 25:98–103
33. Gursoy A, Keskin O, Nussinov R (2008)
Topological properties of protein interaction
networks from a structural perspective. Biochem Soc Trans 36:1398–1403
34. Lee Y, Choi S, Hyeon C (2014) Mapping the
intramolecular
signal
transduction
of
G-protein coupled receptors. Proteins
82:727–743
35. Miao Y, Nichols SE, Gasper PM, Metzger VT,
McCammon JA (2013) Activation and
dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A
110:10982–10987
36. Del-Sol A, Fujihashi H, Amoros D, Nussinov
R (2006) Residues crucial for maintaining
short paths in network communication mediate signaling in proteins. Mol Sys Biol
2:2006.0019
37. Atilgan AR, Turgut D, Atilgan C (2007)
Screened nonbonded interactions in native
proteins manipulate optimal paths for robust
residue
communication.
Biophys
J
92:3052–3062
38. Woods KN (2014) Using THz time-scale
infrared spectroscopy to examine the role of
collective, thermal fluctuations in the formation of myoglobin allosteric communication
pathways and ligand specificity. Soft Matter
10:4387–4402
39. Woods KN, Pfeffer J (2015) Using THz spectroscopy, evolutionary network analysis methods, and MD simulation to map the evolution
of allosteric communication pathways in
c-type lysozymes. Mol Biol Evol 2:271–274
40. Achoch M, Dorantes-Gilardi R, Wymant C,
Feverati G, Salamatian K, Vuillon L, Lesieur C
(2016) Protein structural robustness to mutations: an in silico investigation. Phys Chem
Phys 16:13770–13780
41. Ribeiro AAST, Ortiz V (2016) A chemical
perspective on allostery. Chem Rev
116:6488–6502
42. Vuillon L, Lesieur C (2015) From local to
global changes in proteins: a network view.
Curr Opin Struct Biol 31:1–8
54
Korey M. Reid and David M. Leitner