Protein-water electrostatics and principles of bioenergetics.
نویسندگان
چکیده
Despite its diversity, life universally relies on a simple basic mechanism of energy transfer in its energy chains-hopping electron transport between centers of electron localization on hydrated proteins and redox cofactors. Since many such hops connect the point of energy input with a catalytic site where energy is stored in chemical bonds, the question of energy losses in (nearly activationless) electron hops, i.e., energetic efficiency, becomes central for the understanding of the energetics of life. We show here that standard considerations based on rules of Gibbs thermodynamics are not sufficient, and the dynamics of the protein and the protein-water interface need to be involved. The rate of electronic transitions is primarily sensitive to the electrostatic potential at the center of electron localization. Numerical simulations show that the statistics of the electrostatic potential produced by hydration water are strongly non-Gaussian, with the breadth of the electrostatic noise far exceeding the expectations of the linear response. This phenomenon, which dramatically alters the energetic balance of a charge-transfer chain, is attributed to the formation of ferroelectric domains in the protein's hydration shell. These dynamically emerging and dissipating domains make the shell enveloping the protein highly polar, as gauged by the variance of the shell dipole which correlates with the variance of the protein dipole. The Stokes-shift dynamics of redox-active proteins are dominated by a slow component with the relaxation time of 100-500 ps. This slow relaxation mode is frozen on the time-scale of fast reactions, such as bacterial charge separation, resulting in a dramatically reduced reorganization free energy of fast electronic transitions. The electron transfer activation barrier becomes a function of the corresponding rate, self-consistently calculated from a non-ergodic version of the transition-state theory. The peculiar structure of the protein-water interface thus provides natural systems with two "non's"-non-Gaussian statistics and non-ergodic kinetics-to tune the efficiency of the redox energy transfer. Both act to reduce the amount of free energy released as heat in electronic transitions. These mechanisms are shown to increase the energetic efficiency of protein electron transfer by up to an order of magnitude compared to the "standard picture" based on canonical free energies and the linear response approximation. In other words, the protein-water tandem allows both the formation of a ferroelectric mesophase in the hydration shell and an efficient control of the energetics by manipulating the relaxation times.
منابع مشابه
Proton-Electrostatic Localization: Explaining the Bioenergetic Conundrum in Alkalophilic Bacteria
The decades-longstanding energetic conundrum of alkalophilic bacteria as to how they are able to synthesize ATP has now, for the first time, been clearly solved using the proton-electrostatics localization hypothesis [Bioenergetics 1:104; doi:10.4172/2167-7662.1000104]. This is a major breakthrough advance in understanding proton-coupling bioenergetics over the Nobel-prize work of Peter Mitchel...
متن کاملOn the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes
Interfacial waters are increasingly appreciated as playing a key role in protein-protein interactions. We report on a study of the prediction of interfacial water positions by both Molecular Dynamics and explicit solvent-continuum electrostatics based on the Dipolar Poisson-Boltzmann Langevin (DPBL) model, for three test cases: (i) the barnase/barstar complex (ii) the complex between the DNase ...
متن کاملAPPLICATION OF CHARGED SYSTEM SEARCH ALGORITHM TO WATER DISTRUBITION NETWORKS OPTIMIZATION
A charged system search algorithm (CSS) is applied to the optimal cost design of water distribution networks. This algorithm is inspired by the Coulomb and Gauss’s laws of electrostatics in physics. The CSS utilizes a number of charged particles which influence each other based on their fitness values and their separation distances considering the governing law of Coulomb. The well-known benchm...
متن کاملUnderstanding the Results of Electrostatics Calculations: Visualizing Molecular 'Isopotential' Surfaces
• To learn more about actually performing the electrostatics calculation and loading the raw results (e.g., an OpenDX-formatted volumetric map) into, say, a PyMOL session (using PyMOL’s APBS plugin), one can visit http://dx.doi.org/10.1371/journal.pcbi.1000918 and click on “Video S2” – Electrostatics screencast (near the bottom; see ref [4] for more on this). Also, it would be a good idea to vi...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Physical chemistry chemical physics : PCCP
دوره 12 47 شماره
صفحات -
تاریخ انتشار 2010