Scaling of Rates of Vibrational Energy Transfer in Proteins with Equilibrium Dynamics and Entropy

Reid, Korey M.; Yamato, Takahisa; Leitner, David M.

doi:10.1021/acs.jpcb.8b07552

Cited by 30 publications

(87 citation statements)

References 73 publications

(139 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We have since examined computationally the relation between the local energy conductivity between non-bonded contacts interacting by hydrogen bonds and the variance in the distance of the hydrogen bond for myoglobin at 300 K (Reid et al 2018). We again found that, for non-bonded contacts interacting by short-range potentials, the energy transfer rate across the contact varies inversely with the variance in the contact length.…”

Section: Energy Exchange Network (Een) For Fixlmentioning

confidence: 92%

“…Energy flow in molecules influences chemical reaction kinetics, and the interpretation of a wide range of spectroscopic experiments on proteins requires information about energy relaxation and transport. We recently reviewed the status of computational studies of energy transport in proteins (Leitner and Yamato 2018). Here, we summarize recent developments in that area and new applications.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Recent developments in the computational study of protein structural and vibrational energy dynamics

Leitner

Yamato

2020

Biophys Rev

Self Cite

View full text Add to dashboard Cite

Recent developments in the computational study of energy transport in proteins are reviewed, including advances in both methodology and applications. The concept of energy exchange network (EEN) is discussed, and a recent calculation of EENs for the allosteric protein FixL is reviewed, which illustrates how residues and protein regions involved in the allosteric transition can be identified. Recent work has examined relations between EENs and protein dynamics as well as structure. We review some of the computational studies carried out on several proteins that explore connections between energy conductivity across polar contacts in proteins and between proteins and water and equilibrium dynamics of the contacts, and we discuss some of the recent experimental work that addresses this topic.

show abstract

Section: Energy Exchange Network (Een) For Fixlmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Recent developments in the computational study of protein structural and vibrational energy dynamics

Leitner

Yamato

2020

Biophys Rev

Self Cite

View full text Add to dashboard Cite

show abstract

“…They also found pathways for energy transport via hydrogen bonds between residues distantly positioned in the sequence of the 35-residue villin headpiece subdomain (Buchenberg et al 2016;Leitner et al 2015). Recently, Leitner and coworkers discussed the rates of vibrational energy transfer for short-range polar contacts, such as hydrogen bonds, as well as at interface in biomolecules in the thermal equilibrium (Leitner et al 2019;Reid et al 2018). They mentioned that analyzing energy transfer across the van der Waals contact using molecular dynamics simulation is challenging because of the small energy conductivity.…”

Section: Mechanism Of Energy Flow In Proteinmentioning

confidence: 99%

Role of atomic contacts in vibrational energy transfer in myoglobin

Mizuno

Mizutani

2020

Biophys Rev

View full text Add to dashboard Cite

Heme proteins are ideal systems to investigate vibrational energy flow at the atomic level. Upon photoexcitation, a large amount of excess vibrational energy is selectively deposited on heme due to extremely fast internal conversion. This excess energy is redistributed to the surrounding protein moiety and then to water. Vibrational energy flow in myoglobin (Mb) was examined using picosecond time-resolved anti-Stokes ultraviolet resonance Raman (UVRR) spectroscopy. We used the Trp residue directly contacting the heme group as a selective probe for vibrationally excited populations. Trp residues were placed at different position close to the heme by site-directed mutagenesis. This technique allows us to monitor the excess energy on residue-to-residue basis. Anti-Stokes UVRR measurements for Mb mutants suggest that the dominant channel for energy transfer in Mb is the pathway through atomic contacts between heme and nearby amino acid residues as well as that between the protein and solvent water. It is found that energy flow through proteins is analogous to collisional exchange processes in solutions.

show abstract

“…Since the structure and dynamics of protein molecules are highly anisotropic, the flow of energy and heat should also be anisotropic. By using biophysical computation methods, several groups have been engaged in the characterization of such energy transport processes in proteins [36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51]. We are particularly interested in how the energy relaxation process intervene in proteins control of their biological functions such as allostery.…”

Section: Heat and Energy Flowmentioning

confidence: 99%

Normal mode analysis and beyond

Yamato

Laprévôte

2019

BIOPHYSICS

Self Cite

View full text Add to dashboard Cite

Normal mode analysis provides a powerful tool in biophysical computations. Particularly, we shed light on its application to protein properties because they directly lead to biological functions. As a result of normal mode analysis, the protein motion is represented as a linear combination of mutually independent normal mode vectors. It has been widely accepted that the large amplitude motions throughout the entire protein molecule can be well described with a few low-frequency normal modes. Furthermore, it is possible to represent the effect of external perturbations, e.g., ligand binding, hydrostatic pressure, as the shifts of normal mode variables. Making use of this advantage, we are able to explore mechanical properties of proteins such as Young's modulus and compressibility. Within thermally fluctuating protein molecules under physiological conditions, tightly packed amino acid residues interact with each other through heat and energy exchanges. Since the structure and dynamics of protein molecules are highly anisotropic, the flow of energy and heat should also be anisotropic. Based on the harmonic approximation of the heat current operator, it is possible to analyze the communication map of a protein molecule. By using this method, the energy transfer pathways of photoactive yellow protein were calculated. It turned out that these pathways are similar to those obtained via the Green-Kubo formalism with equilibrium molecular dynamics simulations, indicating that normal mode analysis captures the intrinsic nature of the transport properties of proteins.

show abstract

Scaling of Rates of Vibrational Energy Transfer in Proteins with Equilibrium Dynamics and Entropy

Cited by 30 publications

References 73 publications

Recent developments in the computational study of protein structural and vibrational energy dynamics

Recent developments in the computational study of protein structural and vibrational energy dynamics

Role of atomic contacts in vibrational energy transfer in myoglobin

Normal mode analysis and beyond

Contact Info

Product

Resources

About