Electrostatic field around cytochrome c: theory and energy transfer experiment.

Abstract

Energy transfer in the "rapid diffusion" limit from electronically excited terbium(llI) chelates in three different charge states to horse heart ferricytochrome c was measured as a function of ionic strength. Theoretical rate constants calculated by numerical integration of the Forster integral (containing the Poisson-Boltzmann-generated protein electrostatic potential) were compared with the experimental data to evaluate the accuracy of protein electrostatic field calculations at the protein/solvent interface. Two dielectric formalisms were used: a simple coulombic/Debye-Huckel procedure and a finite difference method [Warwicker, J. & Watson, H. C. (1982)J. Mol. Biol. 157, 671-679] that accounts for the low-dielectric protein interior and the irregular protein/solvent boundary. Good agreement with experiment was obtained and the ionic-strength dependence of the reaction was successfully reproduced. The sensitivity of theoretical rate constants to the choices of effective donor sphere size and the energy transfer distance criterion was analyzed. Electrostatic potential and rate-constant calculations were carried out on sets of structures collected along two molecular dynamics trajectories of cytochrome c. Protein conformational fluctuations were shown to produce large variations in the calculated energy transfer-rate constant. We conclude that protein fluctuations and the resulting transient structures can play significant roles in biological or catalytic activities that are not apparent from examination of a static structure. For calculating protein electrostatics, large-scale low-frequency conformational fluctuations, such as charged side-chain reorientation, are established to be as important as the computational method for incorporating dielectric boundary effects.Electrostatic interactions are known to play a significant role in the biological activity of proteins, as indicated by the pH and ionic-strength dependence of virtually all protein reactions (1). Numerous studies have shown that reaction rates between proteins and charged substrates often depend strongly on the solution ionic strength. These observations have been taken to suggest that intermolecular electrostatic forces are important in facilitating the association of reaction complexes. To analyze specific interactions at the molecular level an accurate description of the electrostatic forces around the protein is essential. The electrostatic analysis of proteins by theoretical frameworks is usually couched in terms of the net charge and the dipole moment (2, 3), higher moments (4), or the full asymmetric charge distribution of a single structure derived by crystallography (5-10). One of the more rigorous approaches to the computation of the electrostatic field surrounding proteins in aqueous electrolyte solution involves the iteration of the Poisson-Boltzmann equation by the Warwicker-Watson (WW) algorithm (11). Starting with the protein crystal structure, this procedure accounts for (i) the irregular topography of the protein surfac...

Electrostatic effects in proteins: comparison of dielectric and charge models

“…From the spherical symmetry of e(r) it also appears that electrostatic interactions in proteins are not nearly as sensitive to shape as commonly thought. Moreover, the results obtained here are clearly in agreement with Northrup et al (1990), that the rigid molecule assumption seems to be reliable in most cases. The calculations presented here and previously, also show that in nearly all cases the SCP model yields results at least as reliable as those obtained from a numerical solution of the PB equation.…”

“…This assumption implies that there are no major conformational changes in solution, which appears to be the case for most (but not all) proteins. A recent analysis by Northrup et al (1990) seems to support this assumption, although the authors also concluded that details of the electrostatic effects require a consideration of protein flexibility. Due to its simplicity, the SCP could be implemented in calculating the electrostatic component of the potential functions used in molecular mechanics and molecular dynamics simulations.…”

Proton linkage of complex formation between cytochrome c and cytochrome b5: electrostatic consequences of protein-protein interactions

“…The involvement of charged residues in the specificity and stabilization of electrostatic complexes between a variety of electron transfer proteins is well documented (KostiS, 1991), though little is known about the pH dependence of these reactions. This deficiency is surprising because the electrostatic potential surface of a protein is defined by the protonation state of its constitutent titratable groups [for recent studies concerning this relationship, see Wendoloski and Matthew (1 989) and Northrup et al (1990)l. Although no detailed structural characterization of a complex formed by such proteins is available, much effort has gone into evaluating general features of model structures proposed on the basis of crystallographic information and electrostatic calculations concerning the individual components of the complex.…”

Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?

“…2.3 and the work of Swanson et al [54,83]). For each method of computing φ (SRF) (FFT of the explicit-solvent charge density or FDMG using implicit solvent with a pre-defined, low dielectric solute volume inside a high-dielectric solvent region), the electrostatic energy of an atom i in φ (SRF) was calculated using (7) for explicit solvent reaction fields, with variants and for the charged and uncharged solute simulations, respectively. Likewise, for implicit solvent reaction fields, the electrostatic energy is defined as (8) with variants and for the charged and uncharged solute simulations, respectively.…”

“…The electrostatic properties of solvated biomolecules are a subject of intense computational [1][2][3] as well as experimental interest [4][5][6][7]. The polar nature of water molecules influences the structure of proteins, nucleic acids, and lipid membranes.…”