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The wall and multivalent counterion effects on the electrostatic force between like-charged spherical particles confined in a charged pore.

The effect of wall confinement (wall charge and wall-sphere separation distance) on the electrostatic force between two charged spheres confined in a long charged pore in symmetric and asymmetric electrolytes have been quantified by solving the nonlinear Poisson-Boltzmann equation (PBE), using adaptive finite elements combined with error minimization techniques. The computed force indicated the strong effect of the wall potential on the reduction of the repulsive force for all type of electrolytes. The influence of the wall effect was reduced when the valence of the electrolyte was increased. A significant reduction in the repulsive force between the two spheres was also observed when the distance between the pore wall and the sphere surface was reduced. A smaller long-range repulsive interaction was observed between spheres when the solutions contained multivalent counterions as compared with a monovalent solution. However, at short ranges of separation distances multivalent counterions increase the electrostatic repulsive force between the spheres. The effect of the dimensionless radius of the spheres on the electrostatic force between them has been determined and a significant reduction observed as the dimensionless radius was reduced.

Journal Article↗

Determination of electrostatic potential around specific locations on the surface of actin by diffusion-enhanced fluorescence resonance energy transfer.

In this study we have established systematic procedures for the measurement of electrostatic potentials around specific and localized portions of protein surfaces. Diffusion-enhanced fluorescence energy transfer was used for these determinations. Energy transfer from donor molecules to freely diffusing acceptors is sensitive to the electrostatic potential around the donor when the acceptors possess electric charges. To quantify this sensitivity phenomenon in a controllable environment, we observed energy transfer from excited terbium chelate donors of known electric charge to a series of acceptors of different charges but bearing the same chromophore group. The rate of energy transfer was calculated theoretically (considering the structural arrangement of charged groups around the chromophore center), as well as determined experimentally (by time-resolved detection of terbium luminescence), with the two values obtained by the different means in close agreement. Having established the validity of this procedure using a relatively simple system, we studied the electrostatic conditions around two specific sites on the surface of actin molecules. A negative potential was found at both sites; the potential at one location (around the myosin binding site) was nearly neutralized by the addition of myosin subfragment-1, while the potential at the other site (around the phalloidin binding site) was not significantly affected.

Actins↗

Destabilization of a protein helix by electrostatic interactions.

Electrostatic interactions between charged residues and the helix dipole in a protein were investigated by protein engineering methods. In ribonuclease T1, two surface-exposed acidic residues (Glu28 and Asp29) are located near the carboxyl terminus of the alpha-helix between residues 13 and 29. They were replaced, individually and in concert, by the uncharged amides Gln28 and Asn29, and the stabilities of the wild-type protein and its variants were determined as a function of pH. The effects of the two mutations are additive. Either one leads to a marginal destabilization by 0.7 kJ/mol at pH 2 but to a strong stabilization by about 3.2 kJ/mol at pH 7. This suggests that the deprotonations of Glu28 and Asp29 reduce the free energy of stabilization of folded ribonuclease T1 by about 4 kJ/mol each. This destabilization is probably caused by unfavorable electrostatic interactions of Glu28 and Asp29 with the negative end of the helix dipole. The activation energies for the unfolding of the different variants of ribonuclease T1 change in parallel with the differences in the thermodynamic stability when the pH is varied. This indicates that the unfavorable electrostatic interactions of Glu28 and Asp29 are lost very early in unfolding, and are not present in the activated state of unfolding.

Asparagine↗

Characterization of the electrostatic perturbation of a catalytic site (Cys)-S-/(His)-Im+H ion-pair in one type of serine proteinase architecture by kinetic and computational studies on chemically mutated subtilisin variants.

We have used two structurally well-characterized serine proteinase variants, subtilisins Carlsberg and BPN', to produce (Cys)-S-/(His)-Im+H ion-pairs by chemical mutation in well defined, different, electrostatic microenvironments. These ion-pairs have been characterized by pH-dependent rapid reaction kinetics using, as reactivity probes, thiol-specific time dependent inhibitors, 2,2'-dipyridyl disulfide and 4,4'-dipyrimidyl disulfide, that differ in the protonation states of their leaving groups in acidic media, computer modelling and electrostatic potential calculations. Both ion-pairs possess nucleophilic character, identified by the striking rate maxima in their reactions with 2,2'-dipyridyl disulfide in acid media. In the Carlsberg enzyme, the (Cys220)-S-/(His63)-Im+H ion-pair is produced by protonic dissociation with pKa 4.1 and its reactivity is not perturbed by any detectable electrostatic influence other than the deprotonation of His63 (pKa 10.2). In the BPN' enzyme, the analogous, (Cys221)-S-/(His64)-Im+H ion-pair is produced by protonic dissociation with pKa 5.1 and its reactivity is affected by an ionization with pKa 3.5 in addition to the deprotonation of His64 (pKa > or = 10.35). It is a striking result that calculations using finite difference solutions of the Poisson-Boltzmann equation provide a value of the pKa difference between the two enzyme catalytic sites (0.97) in close agreement with the value (1.0) determined by reactivity probe kinetics when a protein dielectric constant of 2 is assumed and water molecules within 5 A of the catalytic site His residue are included. The pKa difference is calculated to be 0.84 when the water molecules are not included and a protein dielectric constant of 20 is assumed. The calculations also identify Glu156 in the BPN' enzyme (which is Ser in the Carlsberg enzyme) as the main individual source of the pKa shift. The additional kinetically influential pKa of 3.5 is assigned to Glu156 by examining the non-covalent interactions between the 2-pyridyl disulfide reactivity probe and the enzyme active centre region.

2,2'-Dipyridyl↗

Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar.

The electrostatic enhancement of the association rate of barnase and barstar is calculated using a transition-state theory like expression and atomic-detail modeling of the protein molecules. This expression predicts that the rate enhancement is simply the average Boltzmann factor in the region of configurational space where association occurs instantaneously in the diffusion-controlled limit. Based on experimental evidence, this "transition state" is defined by configurations in which, relative to the stereospecifically bound complex, the two proteins are shifted apart by approximately 8 A (so a layer of water can be accommodated in the interface) and the two binding surfaces are rotated away by 0 degrees to 3 degrees. The values of the average Boltzmann factor, calculated by solving the Poisson-Boltzmann equation, for the wild-type complex and 16 complexes with single mutations are found to correlate well with experimental results for the electrostatic rate enhancement. The predicted rate enhancement is found to be somewhat insensitive to the precise definition of the transition state, due to the long-range nature of electrostatic interactions. The experimental ionic strength dependence of the rate enhancement is also reasonably reproduced.

Bacterial Proteins↗

Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters.

The information about the conformational behavior of monomeric helical peptides in solution, as well as the alpha-helix stability in proteins, has been previously utilized to derive a database with the energy contributions for various interactions taking place in an alpha-helix: intrinsic helical propensities, side-chain-side-chain interactions, main-chain-main-chain hydrogen bonds, and capping effects. This database was implemented in an algorithm based on the helix/coil transition theory (AGADIR). Here, we have modified this algorithm to include previously described local motifs: hydrophobic staple, Schellman motif and Pro-capping motif, new variants of these, and newly described side-chain-side-chain interactions. Based on recent experimental data we have introduced a position dependence of the helical propensities for some of the 20 amino acid residues. A new electrostatic model that takes into consideration all electrostatic interactions up to 12 residues in distance in the helix and random-coil conformations, as well as the effect of ionic strength, has been implemented. We have synthesized and analyzed several peptides, and used data from peptides already analysed by other groups, to test the validity of our electrostatic model. The modified algorithm predicts, with an overall standard deviation value of 6.6 (maximum helix is 100%), the helical, content of 778 peptides of which 223 correspond to wild-type and modified protein fragments. To improve the prediction potential of the algorithm and to have a direct comparison with nuclear magnetic resonance data, the algorithm now predicts the conformational shift of the CalphaH protons, 13Calpha and 3JalphaN values. We have found that for those peptides correctly predicted from the point of view of circular dichroism, the prediction of the NMR parameters is very good.

Algorithms↗

Protein chemistry at membrane interfaces: non-additivity of electrostatic and hydrophobic interactions.

Non-specific binding of proteins and peptides to charged membrane interfaces depends upon the combined contributions of hydrophobic (DeltaG(HPhi)) and electrostatic (DeltaG(ES)) free energies. If these are simply additive, then the observed free energy of binding (DeltaG(obs)) will be given by DeltaG(obs)=DeltaG(HPhi)+DeltaG(ES), where DeltaG(HPhi)=-sigma(NP)A(NP) and DeltaG(ES)=zFphi. In these expressions, A(NP) is the non-polar accessible area, sigma(NP) the non-polar solvation parameter, z the formal peptide valence, F the Faraday constant, and phi the membrane surface potential. But several lines of evidence suggest that hydrophobic and electrostatic binding free energies of proteins at membrane interfaces, such as those associated with cell signaling, are not simply additive. In order to explore this issue systematically, we have determined the interfacial partitioning free energies of variants of indolicidin, a cationic proline-rich antimicrobial peptide. The synthesized variants of the 13 residue peptide covered a wide range of hydrophobic free energies, which allowed us to examine the effect of hydrophobicity on electrostatic binding to membranes formed from mixtures of neutral and anionic lipids. Although DeltaG(obs) was always a linear function of DeltaG(HPhi), the slope depended upon anionic lipid content: the slope was 1.0 for pure, zwitterionic phosphocholine bilayers and 0.3 for pure phosphoglycerol membranes. DeltaG(obs) also varied linearly with surface potential, but the slope was smaller than the expected value, zF. As observed by others, this suggests an effective peptide valence z(eff) that is smaller than the formal valence z. Because of our systematic approach, we were able to establish a useful rule-of-thumb: z(eff) is reduced relative to z by about 20 % for each 3 kcal mol(-1) (1 kcal=4.184 kJ) favorable increase in DeltaG(HPhi). For neutral phosphocholine interfaces, we found that DeltaG(obs) could be predicted with remarkable accuracy using the Wimley-White experiment-based interfacial hydrophobicity scale.

Amino Acid Sequence↗

Electrostatic stabilization of a thermophilic cold shock protein.

The cold shock protein Bc-Csp from the thermophile Bacillus caldolyticus differs from its mesophilic homolog Bs-CspB from Bacillus subtilis by 15.8 kJ mol(-1) in the Gibbs free energy of denaturation (DeltaG(D)). The two proteins vary in sequence at 12 positions but only two of them, Arg3 and Leu66 of Bc-Csp, which replace Glu3 and Glu66 of Bs-CspB, are responsible for the additional stability of Bc-Csp. These two positions are near the ends of the protein chain, but close to each other in the three-dimensional structure. The Glu3Arg exchange alone changed the stability by more than 11 kJ mol(-1). Here, we elucidated the molecular origins of the stability difference between the two proteins by a mutational analysis. Electrostatic contributions to stability were characterized by measuring the thermodynamic stabilities of many variants as a function of salt concentration. Double and triple mutant analyses indicate that the stabilization by the Glu3Arg exchange originates from three sources. Improved hydrophobic interactions of the aliphatic moiety of Arg3 contribute about 4 kJ mol(-1). Another 4 kJ mol(-1) is gained from the relief of a pairwise electrostatic repulsion between Glu3 and Glu66, as in the mesophilic protein, and 3 kJ mol(-1) originate from a general electrostatic stabilization by the positive charge of Arg3, which is not caused by a pairwise interaction. Mutations of all potential partners for an ion pair within a radius of 10 A around Arg3 had only marginal effects on stability. The Glu3-->Arg3 charge reversal thus optimizes ionic interactions at the protein surface by both local and global effects. However, it cannot convert the coulombic repulsion with another Glu residue into a corresponding attraction. Avoidance of unfavorable coulombic repulsions is probably a much simpler route to thermostability than the creation of stabilizing surface ion pairs, which can form only at the expense of conformational entropy.

Amino Acid Sequence↗

Electrostatic potential around actin.

We presume that tension of contracting muscle originates from electrostatic force experienced by actin and myosin. We suppose that a high-energy state of myosin-ADP-Pi interacts with actin, transferring the stored energy to actin, and that the actin excited in this way develops around itself electric field which exerts sliding force against charged myosin heads. To explore the idea, first we conjectured how electric charges on actin produce electric field in the axial direction, and second we experimentally examined electrostatic circumstances around actin in solution and in muscle fibers by optimizing diffusion-enhanced fluorescence energy transfer. In the experiments, Tb ion, which has a long excited-state lifetime, was used as donor. To introduce Tb to actin, Tb-DTPA-phalloin and Tb-DTPA-maleimide were synthesized. As acceptors with electric charges (Za = -3 to +2), rhodamine B that was conjugated with various amino acids or their derivatives was used. The fluorescence energy transfer efficiency (ET) was estimated from the shortening in the lifetime of Tb. The electrostatic circumstances around actin were inferred from the ET-Za relation. When Tb was introduced at Cys-374 of actin, the Tb-site was found in negative electric potential. S-1 binding to the labeled actin neutralized the electric potential almost completely. Tb-DTPA-phalloin bound to actin seemed to reside in the vicinity of tryptophan residue(s). Electric potential around the phalloin site was negative. S-1 binding to the actin slightly reduced the negativity. In glycerinated fibers in the rigor state, the phalloin site was again found in negative potential. When fibers were transferred from an ADP-rigor solution to an active solution, the negative electric potential was neutralized to some extent. The direction of this change could not be explained by detachment of crossbridges from actin, since the detachment should have given an opposite direction of changes in the electric potential. Thus, this observation may indicate that electric potential characteristic of the active state occurs at actin surfaces.

Actins↗

Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects.

Electrostatic interactions have always been considered an important factor governing ligand-receptor interactions. Previous work in this field has established the existence of electrostatic complementarity between the ligand and its receptor site. However, this property has not been treated rigorously, and the description remains largely qualitative. In this work, 34 data sets of high quality were chosen from the Brookhaven Protein Databank. The electrostatic complementary has been calculated between the surface potentials; complementarity is absent between adjacent or neighbouring atoms of the ligand and the receptor. There is little difference between complementarities on the total ligand surface and the interfacial region. Altering the homogeneous dielectric to distance-dependent dielectrics reduces the complementarity slightly, but does not affect the pattern of complementarity.

Amino Acid Sequence↗

Quantum chemical study on the interaction of some bisphosphonates and Ca2+: the role of molecular electrostatic potentials in the prediction of binding geometry.

Molecular electrostatic potentials have been used to model the calcium binding properties of some bisphosphonate drugs, which are used to treat various bone diseases. The mechanism of action involves the binding of bisphosphonates to the bone surface, where calcium plays an important role. Electrostatic potential maps derived from ab initio partial charges have been compared with both the crystal structure and the fully optimized ab initio structure of (dichloro)methylene-bisphosphonate-calcium ion complex. Molecular electrostatic potentials can correctly predict the calcium binding geometry of bisphosphonate-type compounds and this type of information can be used in the practical drug design work.

Calcium↗

The association of human coagulation factors VIII, IXa and X with phospholipid vesicles involves both electrostatic and hydrophobic interactions.

Blood coagulation factor X (FX) is converted to its active form (FXa) by a membrane bound multi-protein enzyme complex, comprised of factor VIII (FVIII), factor IXa (FIXa) and FX. Characterization of the molecular forces involved in the association of these proteins with phospholipids is crucial to understanding how these proteins bind to the lipid milieux of physiological membranes. In this report, the molecular forces involved in the association of FVIII, FIXa or FX with phospholipid vesicles (PLV) were characterized by ligand affinity chromatographic analyses. Treating FVIII-affinity columns with agents that disrupt electrostatic interactions caused elution of 15.2% of the total bound PLV, while agents that disrupt hydrophobic interactions caused elution of 84.8% of the total bound PLV. These results demonstrate that the association of PLV with FVIII is primarily hydrophobic. In contrast, the association of PLV with FIXa or FX is largely the result of electrostatic forces. This was established by observing that 71.3% and 78.9% of the total bound PLV was eluted from FIXa- and FX-affinity columns, respectively, by agents that disrupt electrostatic interactions. Of the total bound PLV, 28.7% and 21.2% were eluted from FIXa- and FX-affinity columns, respectively, by agents that disrupt hydrophobic interactions. These data demonstrate that hydrophobic forces play a heretofore unrecognized role in the association of PLV with FIXa or FX.

Blood Coagulation Factors↗

A quantitative analysis of elastic, entropic, electrostatic, and osmotic forces within relaxed skinned muscle fibers.

The elastic behavior of mechanically skinned skeletal muscle fibers in relaxing solution is modelled using equations developed by Flory (1953) for the elasticity of non-biological polymers. Mechanically, the relaxed skinned fiber is considered to be a semi-crystalline network of inextensible polymer chains, which are periodically cross-linked and which are bathed in an aqueous medium. We consider (1) configurational elastic forces in the network, (2) entropic forces due to mixing of polymer and water, (3) electrostatic forces due to fixed charges on the muscle proteins and mobile charges in the bathing solution, and (4) compressive forces due to large colloids in the bathing solution. Van der Waals forces are not considered since calculations show that they are probably negligible under our conditions. We derive an expression which relates known quantities (ionic strength, osmotic compressive pressure, and fiber width), experimentally estimated quantities (fixed charge density and volume fraction of muscle proteins), and derived quantities (concentration of cross-links and a parameter reflecting the interaction energy between protein and water). The model was tested by comparison with observed changes in skinned fiber width under a variety of experimental conditions which included changes in osmotic compressive pressure, pH, sarcomere length, and ionic strength. Over a wide range of compressive pressure (0-36 atm) the theory predicted the nonlinear relation between fiber width and logarithm of pressure. The direction and magnitude of the decrease in width when pH was decreased to 4 could be modelled assuming the fixed charge density on the protein network was 0.34 moles of electrons per liter protein, a value in accordance with the estimates of others. The relation between width and sarcomere length over the complete range of compressive pressures could be modelled with the assumption that the number of cross-links increases somewhat with sarcomere length. Changes of width with ionic strength were modelled assuming that increasing salt concentration both increased the electrostatic shielding of fixed charges and decreased the number of cross-links. The decrease of fiber width in 1% glutaraldehyde was modelled by assuming that the concentration of crosslinks increased by some 10%. The theory predicted the order of magnitude but not the detailed shape of the passive tension-length relation which may indicate that, as with non-biological polymers, the theory does not adequately describe the behavior of semi-crystalline networks at high degrees of deformation. In summary, the theory provides a semiquantitative approach to an understanding of the nature and relative magnitudes of the forces underlying the mechanical behavior of relaxed skinned fibers. It indicates, for instance, that when fibers are returned to near their in vivo size with 3% PVP, the forces in order of their importance are: (elastic forces) approximately (entropic forces) greater than (electrostatic forces) approximately (osmotic compressive forces).

Animals↗

Dimethonium, a divalent cation that exerts only a screening effect on the electrostatic potential adjacent to negatively charged phospholipid bilayer membranes.

Calcium and other alkaline earth cations change the electrostatic potential adjacent to negatively charged bilayer membranes both by accumulating in the aqueous diffuse double layer adjacent to the membrane and by adsorbing to the phospholipids. The effects of these cations on the electrostatic potential are described adequately by the Gouy-Chapman-Stern theory. We report the results of experiments with ethane-bis-trimethylammonium, a cation that has been termed "dimethonium" or "ethamethonium" in analogy with hexamethonium (hexane-1,6-bis-trimethylammonium) and decamethonium (decane-1,10-bis-trimethylammonium). We examined the effect of dimethonium on the zeta potential of multilamellar vesicles formed from the negative lipid phosphatidylserine (PS) and from 5:1 phosphatidylcholine/phosphatidylserine mixtures in solutions containing 0.1, 0.01 and 0.001 M sodium, cesium, or tetramethylammonium chloride. We also examined the effect of dimethonium on the conductance of planar PS bilayer membranes and the 31P NMR signal from sonicated PS vesicles formed in 0.1 M NaCl. We found no evidence that dimethonium adsorbs specifically to bilayer membranes. All the results, except for those obtained with vesicles of low charge density formed in a solution with a high salt concentration, are consistent with the predictions of the Gouy-Chapman theory. We conclude that dimethonium, which does not have the pharmacological effects of hexamethonium and decamethonium, is a useful divalent cation for physiologists interested in investigating electrostatic potentials adjacent to biological membranes.

Bis-Trimethylammonium Compounds↗

Protein electrostatic surface distribution can determine whether calcium oxalate crystal growth is promoted or inhibited.

Acidic proteins found in mineralized tissues act as nature's crystal engineers, where they play a key role in promoting or inhibiting the growth of minerals such as hydroxyapatite and calcium oxalate. Despite their importance in such fundamental physiological processes as bone and tooth formation, however, there is remarkably little known of the protein structure-function relationships that govern crystal recognition. We have taken a model system approach to elucidate some of the relationships between protein surface chemistry and secondary crystal growth of biological minerals. We show here that the distribution of electrostatic surface charge on our model protein, Protein G, determined whether the secondary growth of calcium oxalate, the principal mineral phase of kidney stones, was promoted or inhibited when the proteins were preadsorbed at low and equivalent surface coverages of <10%. The native Protein G, which contains 10 surface carboxylates, increased the rate of calcium oxalate growth from aqueous solution under constant composition conditions up to 97%, whereas a site-directed mutant with six of the surface charges removed inhibited the growth rate by 60%. The adsorption isotherms of both proteins were determined and suggested that the differences in electrostatic surface properties also lead to differences in protein orientation on the crystal surface. These results demonstrate that differences in electrostatic surface potential of proteins can directly determine whether secondary calcium oxalate growth is promoted or inhibited, and a model is proposed that suggests the distribution of carboxylate residues determines the interrelated binding orientation and exposed surface chemistry of the adsorbed Protein G.

Amino Acid Sequence↗

Binding and electrostatic attraction of lanthanum (La3+) and aluminum (Al3+) to wheat root plasma membranes.

A general model for the sorption of trivalent cations to wheat-root (Triticum aestivum L cv. Scout 66) plasma membranes (PM) has been developed and includes the first published coefficients for La3+ and Al3+ binding to a biological membrane. Both ions are rhizotoxic, and the latter ion is the principal contributor to the toxicity of acidic soils around the world. The model takes into account both the electrostatic attraction and the binding of cations to the negatively charged PM surface. Ion binding is modeled as the reaction P- + IZ <==> 'PIZ-1 in which P- represents a negatively charged PM ligand, located in an estimated area of 540 A2, and IZ represents an ion of charge Z. Binding constants for the reaction were assigned for K+ (1 M-1) and Ca2+ (30 M-1) and evaluated experimentally for La3+ (2200 M-1) and H+ (21,500 M-1). Al sorption is complicated by Al3+ hydrolysis that yields hydroxoaluminum species that are also sorbed. Binding constants of 30 and 1 M-1 were assigned for AlOH2+ and Al(OH)+2, respectively, then a constant for Al3+ (20,000 m-1) was evaluated experimentally using the previously obtained values for K+, Ca2+ and H+ binding. Electrostatic attraction was modeled according to Gouy-Chapman theory. Evaluation of parameters was based upon the sorption of ions to PM vesicles suspended in solutions containing variable concentrations of H+, Ca2+ and La3+ or Al3+. Use of small volumes, and improved assay techniques, allowed the measurement of concentration depletions caused by sorption to vesicles. Some independent confirmation of our model is provided by substantial agreement between our computations and two published reports of La3+ effects upon zeta potentials of plant protoplasts. The single published report concerning the electrostatic effects of Al on cell membranes is in essential agreement with the model.

Absorption↗

Influence of protein flexibility on the electrostatic energy landscape in gramicidin A.

We describe an electrostatic model of the gramicidin A channel that allows protein atoms to move in response to the presence of a permeating ion. To do this, molecular dynamics simulations are carried out with a permeating ion at various positions within the channel. Then an ensemble of atomic coordinates taken from the simulations are used to construct energy profiles using macroscopic electrostatic calculations. The energy profiles constructed are compared to experimentally-determined conductance data by inserting them into Brownian dynamics simulations. We find that the energy landscape seen by a permeating ion changes significantly when we allow the protein atoms to move rather than using a rigid protein structure. However, the model developed cannot satisfactorily reproduce all of the experimental data. Thus, even when protein atoms are allowed to move, the dielectric model used in our electrostatic calculations breaks down when modeling the gramicidin channel.

Computer Simulation↗

Density functional and electrostatics study of oxidized and reduced ribonucleotide reductase; comparisons with methane monooxygenase.

A combined broken symmetry density functional and electrostatics approach has been used to examine the active sites of the resting (RNR(ox)) and reduced (RNR(red)) forms of class I type ribonucleotide reductase in the protein and solvent environment. Active site cluster geometries and Heisenberg J values are discussed in the context of the available protein data. The total electrostatic interaction energy in the protein comprises a large reaction field component and a much smaller protein field term, the former suggesting strong dielectric polarization between the cluster and protein-solvent dielectrics; the latter is indicative of a very weak link to the protein environment. Decomposition of the protein field term elucidates the major electrostatic interactions between amino acid residues in the RNR R2 local environment and the active site cluster, enabling an energetic comparison of structurally equivalent residues with a related diiron protein, methane monooxygenase.

Binding Sites↗