Dataset Information

Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer.

ABSTRACT: Molecular dynamics simulations are used to calculate the time-dependent Stokes shift following photoexcitation of Trp-7 (W7) in myoglobin. In agreement with experiment, a long time (approximately 60 ps) component is observed. Since the long time Stokes shift component is absent when we repeat the calculation with protein frozen at the instant of photoexcitation, we firmly establish that protein flexibility is required to observe slow Stokes shift dynamics in this case. A transition between sub-states near the middle of a 30 ns ground-state trajectory gave us an opportunity to compare solvation dynamics in two different environments. While some of the superficial features are different, we find that the underlying dynamics are shared by the two isomers. It is necessary to look beyond a decomposition of the Stokes shift into protein and water contributions and probe the underlying dynamics of protein side groups, backbone, and water dynamics to obtain a full picture of the relaxation process. We analyze water residence times, diffusion, and reorientation dynamics in the hydration layer. We find slow components in each of these quantities and critically examine their origin and how they affect the observed Stokes shift.

SUBMITTER: Li T

PROVIDER: S-EPMC2818739 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer.

Li Tanping T Hassanali Ali A AA Singer Sherwin J SJ

The journal of physical chemistry. B 20081201 50

Molecular dynamics simulations are used to calculate the time-dependent Stokes shift following photoexcitation of Trp-7 (W7) in myoglobin. In agreement with experiment, a long time (approximately 60 ps) component is observed. Since the long time Stokes shift component is absent when we repeat the calculation with protein frozen at the instant of photoexcitation, we firmly establish that protein flexibility is required to observe slow Stokes shift dynamics in this case. A transition between sub-s ...[more]

PMID: 19368022

Similar Datasets

Project description:We present a comprehensive femtosecond (fs) transient absorption study of the [Ge9(Hyp)3]- (Hyp = Si(SiMe3)3) cluster solvated in tetrahydrofuran (THF) with special emphasis on intra- and intermolecular charge transfer mechanisms which can be tuned by exchange of the counterion and by dimerization of the cluster. The examination of the visible and the near infrared (NIR) spectral range reveals four different processes of cluster dynamics after UV (267/258 nm) photoexcitation related to charge transfer to solvent and localized excited states in the cluster. The resulting transient absorption is mainly observed in the NIR region. In the UV-Vis range transient absorption of the (neutral) cluster core with similar dynamics can be observed. By transferring concepts of: (i) charge transfer to the solvent known from solvated Na- in THF and (ii) charge transfer in bulk-like materials on metalloid cluster systems containing [Ge9(Hyp)3]- moieties, we can nicely interpret the experimental findings for the different compounds. The first process occurs on a fs timescale and is attributed to localization of the excited electron in the quasi-conduction band/excited state which competes with a charge transfer to the solvent. The latter leads to an excess electron initially located in the vicinity of the parent cluster within the same solvent shell. In a second step, it can recombine with the cluster core with time constants in the picosecond (ps) timescale. Some electrons can escape the influence of the cluster leading to a solvated electron or after interaction with a cation to a contact pair both with lifetimes exceeding our experimentally accessible time window of 1 nanosecond (ns). An additional time constant on a tens of ps timescale is pronounced in the UV-Vis range which can be attributed to the recombination rate of the excited state or quasi conduction band of Ge9-. In the dimer, the excess electron cannot escape the molecule due to strong trapping by the Zn cation that links the two cluster cores.

Project description:Formation of a transient [myoglobin (Mb), cytochrome b(5) (cyt b(5))] complex is required for the reductive repair of inactive ferri-Mb to its functional ferro-Mb state. The [Mb, cyt b(5)] complex exhibits dynamic docking (DD), with its cyt b(5) partner in rapid exchange at multiple sites on the Mb surface. A triple mutant (Mb(3M)) was designed as part of efforts to shift the electron-transfer process to the simple docking (SD) regime, in which reactive binding occurs at a restricted, reactive region on the Mb surface that dominates the docked ensemble. An electrostatically-guided brownian dynamics (BD) docking protocol was used to generate an initial ensemble of reactive configurations of the complex between unrelaxed partners. This ensemble samples a broad and diverse array of heme-heme distances and orientations. These configurations seeded all-atom constrained molecular dynamics simulations (MD) to generate relaxed complexes for the calculation of electron tunneling matrix elements (T(DA)) through tunneling-pathway analysis. This procedure for generating an ensemble of relaxed complexes combines the ability of BD calculations to sample the large variety of available conformations and interprotein distances, with the ability of MD to generate the atomic level information, especially regarding the structure of water molecules at the protein-protein interface, that defines electron-tunneling pathways. We used the calculated T(DA) values to compute ET rates for the [Mb(wt), cyt b(5)] complex and for the complex with a mutant that has a binding free energy strengthened by three D/E ? K charge-reversal mutations, [Mb(3M), cyt b(5)]. The calculated rate constants are in agreement with the measured values, and the mutant complex ensemble has many more geometries with higher T(DA) values than does the wild-type Mb complex. Interestingly, water plays a double role in this electron-transfer system, lowering the tunneling barrier as well as inducing protein interface remodeling that screens the repulsion between the negatively-charged propionates of the two hemes.

Dataset Information

Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer.

Publications

Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets