Statistics of protein electrostatics.

Molecular dynamics simulations of a small redox-active protein plastocyanin address two questions. (i) Do protein electrostatics equilibrate to the Gibbsian ensemble? (ii) Do the electrostatic potential and electric field inside proteins follow the Gaussian distribution? The statistics of electrostatic potential and electric field are probed by applying small charge and dipole perturbations to different sites within the protein. Nonergodic (non-Gibbsian) sampling is detectable through violations of exact statistical rules constraining the first and second statistical moments (fluctuation-dissipation relations) and the linear relation between free-energy surfaces of the collective coordinate representing the Hamiltonian electrostatic perturbation.

Protein Medium Facilitates Electron Transfer in Photosynthetic Heliobacterial Reaction Center.

This computational study addresses the question of how large membrane-bound proteins of electron transport chains facilitate fast vector-based charge transport. We study electron transfer reactions following ultrafast initial charge separation induced by absorption of light by P primary pair and leading to the electron localization at the A cofactor. Two subsequent, much slower reactions, electron transfer to the iron-sulfur cluster F and reduction of the menaquinone (MQ) cofactor, are studied by combining molecular dynamics simulations, electronic structure calculations, and theoretical modeling.

Remarkable Insensitivity of Protein Diffusion to Protein Charge.

Friction to translational diffusion of ionic particles in polar liquids should scale linearly with the squared ion charge, according to standard theories. Substantial slowing of translational diffusion is expected for proteins in water. In contrast, our simulations of charge mutants of green fluorescent proteins in water show remarkable insensitivity of the translational diffusion constant to protein's charge in the range of charges between -29 and +35.

Comment on "Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin" by O. Kontkanen, D. Biriukov and Z. Futera, , 2023, , 12479.

Polarizability is a fundamental property of all molecular systems describing the deformation of the molecular electronic density in response to an applied electric field. The question of whether polarizability of the active site needs to be included in theories of enzymatic activity remains open. Hybrid quantum mechanical/molecular mechanical calculations are hampered by difficulties faced by many quantum-chemistry algorithms to provide sufficiently accurate estimates of the anisotropic second-rank tensor of molecular polarizability.

Electron Tunneling in Biology: When Does it Matter?

Electrons can tunnel between cofactor molecules positioned along biological electron transport chains up to a distance of ≃ 20 Å on the millisecond time scale of enzymatic turnover. This tunneling range determines the design of biological energy chains facilitating the cross-membrane transport of electrons. Tunneling distance and cofactors' redox potentials become the main physical parameters affecting the rate of electron transport.

Effect of Water Deuteration on Protein Electron Transfer.

Traditional theories of long-range protein electron transfer describe the reaction rate in terms of the tunneling distance and the reaction free energy. They do not recognize two physical effects: (i) local wetting of the active site by hydration water and (ii) protein identity affecting the rate through dynamics and flexibility. We find, by molecular dynamics simulations, a significant, ∼25 times, slowing down of the rate of protein electron transfer upon deuteration.

Theory of Protein Charge Transfer: Electron Transfer between Tryptophan Residue and Active Site of Azurin.

One reaction step in the conductivity relay of azurin, electron transfer between the Cu-based active site and the tryptophan residue, is studied theoretically and by classical molecular dynamics simulations. Oxidation of tryptophan results in electrowetting of this residue. This structural change makes the free energy surfaces of electron transfer nonparabolic as described by the Q-model of electron transfer.

Enhanced Molecular Diffusivity through Destructive Interference between Electrostatic and Osmotic Forces.

Molecular charge asymmetrically distributed in a diffusing tagged particle causes a nonzero electrostatic force balanced by an opposing van der Waals (vdW) force. Fluctuations of electrostatic and vdW forces are highly correlated, and they destructively interfere in the force variance. This phenomenology is caused by the formation of a structurally frozen hydration layer for a particle diffusing in water and is responsible for a substantial speedup of translational diffusion compared to traditional theories of dielectric friction.

Driving Forces of Protein Diffusion.

Diffusivity of a protein (a Brownian particle) is caused by random molecular collisions in the Stokes-Einstein picture. Alternatively, it can be viewed as driven by unbalanced stochastic forces acting from water on the protein. Molecular dynamics simulations of protein mutants carrying different charges are analyzed here in terms of the van der Waals (vdW) and electrostatic forces acting on the protein.

Effective Dielectric Constant of Water at the Interface with Charged C Fullerenes.

The dipolar susceptibility of interfacial water and the corresponding interface dielectric constant were calculated from numerical molecular dynamics simulations for neutral and charged states of buckminsterfullerene C. Dielectric constants in the range 10-22, depending on temperature and solute charge, were found. These values are consistent with recent reports for biological and nanometer-scale interfaces.

Interfacial structural crossover and hydration thermodynamics of charged C in water.

Classical molecular dynamics simulations of the hydration thermodynamics, structure, and dynamics of water in hydration shells of charged buckminsterfullerenes are presented in this study. Charging of fullerenes leads to a structural transition in the hydration shell, accompanied by creation of a significant population of dangling O-H bonds pointing toward the solute. In contrast to the well accepted structure-function paradigm, this interfacial structural transition causes nearly no effect on either the dynamics of hydration water or on the solvation thermodynamics.