72. LeVine MV, Weinstein H (2014) NbIT—a
new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT.
PLoS Comput Biol 10:e1003603. https://
doi.org/10.1371/journal.pcbi.1003603
73. Motlagh HN, Wrabl JO, Li J, Hilser VJ
(2014) The ensemble nature of allostery.
Nature 508:331–339
74. Liu T, Whitten ST, Hilser VJ (2006)
Ensemble-based signatures of energy propagation in proteins: a new view of an old phenomenon. Proteins 62:728–738
75. Zhuralev PI, Papoian GA (2010) Protein
functional landscapes, dynamics, allostery: a
tortuous path towards a universal theoretical
framework. Q Rev Biophys 43:295–332
76. Nagy AM, Raicu V, Miller RJD (2005) Nonlinear optical studies of heme protein dynamics: implications for proteins as hybrid states of
matter. Biochim Biophys Acta 1749:148–172
77. Miller RJD (1991) Vibrational energy relaxation and structural dynamics of heme proteins. Ann Rev Phys Chem 42:581–614
78. Royer WE, Knapp JE, Strand K, Heaslet HA
(2001) Cooperative hemoglobins: conserved
fold, diverse quaternary assemblies and allosteric mechanisms. Trends Biochem Sci
26:297–304
79. Royer WE, Zhu H, Gorr TA, Flores JF, Knapp
JE (2005) Allosteric hemoglobin assembly:
diversity and similarity. J Biol Chem
280:27477–27480
80. Laine JM, Amat M, Morgan BR, Royer WE,
Massi F (2014) Insight into the allosteric
mechanism of Scapharca dimeric hemoglobin.
Biochemist 53:7199–7210
81. Ikeda-Saito M, Yonetani T, Chiancone E,
Ascoli F, Verzili D, Antonini E (1983) Thermodynamic properties of oxygen equilibria of
dimeric and tetrameric hemoglobins from
Scapharca inaequivalvis. J Mol Biol
170:1009–1018
82. Gnanasekaran R, Xu Y, Leitner DM (2010)
Dynamics of water clusters confined in proteins: a molecular dynamics simulation study
of interfacial waters in a dimeric hemoglobin.
J Phys Chem B 114:16989–16996
83. Pardanani A, Gambacurta A, Ascoil F, Royer
WE (1998) Mutational destabilization of the
critical interface water cluster in Scapharca
dimeric hemoglobin: structural basis for
altered allosteric activity. J Mol Biol
284:729–739
84. Pardanani A, Gibson QH, Colotti G, Royer
WE (1997) Mutation of residue Phe 97 to
Leu disrupts the central allosteric pathway in
Scapharca dimeric hemoglobin. J Biol Chem
272:13171–13179
85. Royer WE, Pardanani A, Gibson QH, Peterson ES, Friedman JM (1996) Ordered water
molecules as key allosteric mediators in a
cooperative dimeric hemoglobin. Proc Natl
Acad Sci 93:14526–14531
86. Ceci P, Giangiacomo L, Boffi A, Chiancone E
(2002) The mutation K30D disrupts the only
salt bridge at the subunit interface of the
homodimeric hemoglobin from Scapharca
inaequivalvis and changes the mechanism of
cooperativity. J Biol Chem 277:6929–2933
87. Royer WE, Hendrickson WA, Chiancone E
(1990) Structural transitions upon ligand
binding in a cooperative dimeric hemoglobin.
Science 249:518–521
88. Elber R (2007) A milestoning study of the
kinetics of an allosteric transition: atomically
detailed simulations of deoxy Scapharca
hemoglobin. Biophys J 92:L85–L87
89. Sagnella DE, Straub JE (2001) Directed
energy “funneling” mechanism for heme
cooling following ligand photolysis or direct
excitation in solvated carbonmonoxy myoglobin. J Phys Chem B 105:7057–7063
90. Allen PB, Feldman JL (1993) Thermal conductivity of disordered harmonic solids. Phys
Rev B 48:12581–12588
91. Pandey HD, Leitner DM (2016) Thermalization and thermal transport in molecules. J
Phys Chem Lett 7:5062–5067
92. Pandey HD, Leitner DM (2017) Vibrational
energy transport in molecules and the statistical properties of vibrational modes. Chem
Phys 482:81–85
93. Leitner DM (2005) Heat transport in molecules and reaction kinetics: the role of quantum energy flow and localization. Adv Chem
Phys 130B:205–256
94. Leitner DM (2015) Quantum ergodicity and
energy flow in molecules. Adv Phys
64:445–517
95. Leitner DM, Wolynes PG (1996) Vibrational
relaxation and energy localization in polyatomics: effects of high-order resonances on
flow rates and the quantum ergodicity transition. J Chem Phys 105(24):11226–11236
96. Leitner DM, Wolynes PG (1996) Statistical
properties of localized vibrational eigenstates.
Chem Phys Lett 258:18–24
97. Yu X, Leitner DM (2003) Vibrational energy
transfer and heat conduction in a protein. J
Phys Chem B 107:1698–1707
98. Leitner DM, Gruebele M (2008) A quantum
model of restricted vibrational energy flow on
56
Korey M. Reid and David M. Leitner
new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT.
PLoS Comput Biol 10:e1003603. https://
doi.org/10.1371/journal.pcbi.1003603
73. Motlagh HN, Wrabl JO, Li J, Hilser VJ
(2014) The ensemble nature of allostery.
Nature 508:331–339
74. Liu T, Whitten ST, Hilser VJ (2006)
Ensemble-based signatures of energy propagation in proteins: a new view of an old phenomenon. Proteins 62:728–738
75. Zhuralev PI, Papoian GA (2010) Protein
functional landscapes, dynamics, allostery: a
tortuous path towards a universal theoretical
framework. Q Rev Biophys 43:295–332
76. Nagy AM, Raicu V, Miller RJD (2005) Nonlinear optical studies of heme protein dynamics: implications for proteins as hybrid states of
matter. Biochim Biophys Acta 1749:148–172
77. Miller RJD (1991) Vibrational energy relaxation and structural dynamics of heme proteins. Ann Rev Phys Chem 42:581–614
78. Royer WE, Knapp JE, Strand K, Heaslet HA
(2001) Cooperative hemoglobins: conserved
fold, diverse quaternary assemblies and allosteric mechanisms. Trends Biochem Sci
26:297–304
79. Royer WE, Zhu H, Gorr TA, Flores JF, Knapp
JE (2005) Allosteric hemoglobin assembly:
diversity and similarity. J Biol Chem
280:27477–27480
80. Laine JM, Amat M, Morgan BR, Royer WE,
Massi F (2014) Insight into the allosteric
mechanism of Scapharca dimeric hemoglobin.
Biochemist 53:7199–7210
81. Ikeda-Saito M, Yonetani T, Chiancone E,
Ascoli F, Verzili D, Antonini E (1983) Thermodynamic properties of oxygen equilibria of
dimeric and tetrameric hemoglobins from
Scapharca inaequivalvis. J Mol Biol
170:1009–1018
82. Gnanasekaran R, Xu Y, Leitner DM (2010)
Dynamics of water clusters confined in proteins: a molecular dynamics simulation study
of interfacial waters in a dimeric hemoglobin.
J Phys Chem B 114:16989–16996
83. Pardanani A, Gambacurta A, Ascoil F, Royer
WE (1998) Mutational destabilization of the
critical interface water cluster in Scapharca
dimeric hemoglobin: structural basis for
altered allosteric activity. J Mol Biol
284:729–739
84. Pardanani A, Gibson QH, Colotti G, Royer
WE (1997) Mutation of residue Phe 97 to
Leu disrupts the central allosteric pathway in
Scapharca dimeric hemoglobin. J Biol Chem
272:13171–13179
85. Royer WE, Pardanani A, Gibson QH, Peterson ES, Friedman JM (1996) Ordered water
molecules as key allosteric mediators in a
cooperative dimeric hemoglobin. Proc Natl
Acad Sci 93:14526–14531
86. Ceci P, Giangiacomo L, Boffi A, Chiancone E
(2002) The mutation K30D disrupts the only
salt bridge at the subunit interface of the
homodimeric hemoglobin from Scapharca
inaequivalvis and changes the mechanism of
cooperativity. J Biol Chem 277:6929–2933
87. Royer WE, Hendrickson WA, Chiancone E
(1990) Structural transitions upon ligand
binding in a cooperative dimeric hemoglobin.
Science 249:518–521
88. Elber R (2007) A milestoning study of the
kinetics of an allosteric transition: atomically
detailed simulations of deoxy Scapharca
hemoglobin. Biophys J 92:L85–L87
89. Sagnella DE, Straub JE (2001) Directed
energy “funneling” mechanism for heme
cooling following ligand photolysis or direct
excitation in solvated carbonmonoxy myoglobin. J Phys Chem B 105:7057–7063
90. Allen PB, Feldman JL (1993) Thermal conductivity of disordered harmonic solids. Phys
Rev B 48:12581–12588
91. Pandey HD, Leitner DM (2016) Thermalization and thermal transport in molecules. J
Phys Chem Lett 7:5062–5067
92. Pandey HD, Leitner DM (2017) Vibrational
energy transport in molecules and the statistical properties of vibrational modes. Chem
Phys 482:81–85
93. Leitner DM (2005) Heat transport in molecules and reaction kinetics: the role of quantum energy flow and localization. Adv Chem
Phys 130B:205–256
94. Leitner DM (2015) Quantum ergodicity and
energy flow in molecules. Adv Phys
64:445–517
95. Leitner DM, Wolynes PG (1996) Vibrational
relaxation and energy localization in polyatomics: effects of high-order resonances on
flow rates and the quantum ergodicity transition. J Chem Phys 105(24):11226–11236
96. Leitner DM, Wolynes PG (1996) Statistical
properties of localized vibrational eigenstates.
Chem Phys Lett 258:18–24
97. Yu X, Leitner DM (2003) Vibrational energy
transfer and heat conduction in a protein. J
Phys Chem B 107:1698–1707
98. Leitner DM, Gruebele M (2008) A quantum
model of restricted vibrational energy flow on
56
Korey M. Reid and David M. Leitner