Investigating the dielectric effects of channel pore water on the electrostatic barriers of the permeation ion by the finite difference Poisson-Boltzmann method

In this paper, the finite difference Poisson-Boltzmann (FDPB) method with four dielectric constants is developed to study the effect of dielectric saturation on the electrostatic barriers of the permeation ion. In this method, the inner shape of the channel pore is explicitly represented, and the fact that the dielectric constant inside the channel pore is different from that of bulk water is taken into account. A model channel system which is a right-handed twist bundle with four α-helical segments is provided for this study. From the FDPB calculations, it is found that the difference of the ionic electrostatic solvation energy for wider domains depends strongly on the pore radius in the vicinity of the ion when the pore dielectric constant is changed from 78 to 5. However, the electrostatic solvation energy of the permeation ion can not be significantly affected by the dielectric constant in regions with small pore radii. Our results indicate that the local electrostatic interactions inside the ion channel are of major importance for ion electrostatic solvation energies, and the effect of dielectric saturation on the electrostatic barriers is coupled to the interior channel dimensions. Received: 28 January 1997 / Accepted: 24 September 1997     

Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

We have compared the predictions of ligand‐binding affinities from several methods based on end‐point molecular dynamics simulations and continuum solvation, that is, methods related to MM/PBSA (molecular mechanics combined with Poisson–Boltzmann and surface area solvation). Two continuum‐solvation models were considered, viz., the Poisson–Boltzmann (PB) and generalised Born (GB) approaches. The nonelectrostatic energies were also obtained in two different ways, viz., either from the sum of the bonded, van der Waals, nonpolar solvation energies, and entropy terms (as in MM/PBSA), or from the scaled protein–ligand van der Waals interaction energy (as in the linear interaction energy approach, LIE). Three different approaches to calculate electrostatic energies were tested, viz., the sum of electrostatic interaction energies and polar solvation energies, obtained either from a single simulation of the complex or from three independent simulations of the complex, the free protein, and the free ligand, or the linear‐response approximation (LRA). Moreover, we investigated the effect of scaling the electrostatic interactions by an effective internal dielectric constant of the protein (?_int). All these methods were tested on the binding of seven biotin analogues to avidin and nine 3‐amidinobenzyl‐1H‐indole‐2‐carboxamide inhibitors to factor Xa. For avidin, the best results were obtained with a combination of the LIE nonelectrostatic energies with the MM+GB electrostatic energies from a single simulation, using ?_int = 4. For fXa, standard MM/GBSA, based on one simulation and using ?_int = 4–10 gave the best result. The optimum internal dielectric constant seems to be slightly higher with PB than with GB solvation. © Proteins 2012; © 2012 Wiley Periodicals, Inc.     

Effective water model for Monte Carlo simulations of proteins

We present an effective theory for water. Our goal is to formulate on accurate model for the effects of solvation on protein dynamics, without incurring the huge computational cost and the slow temporal evolution typical of molecular dynamics simulations of liquids. We replace the individual water molecules in an all-atom potential with a local dielectric density field, with self interactions given by the Landau-Ginzburg free energy and external interactions by Lennard-Jones forces at the surface of the protein atoms. We explore conformational space with finite temperature Monte Carlo dynamics, using parallel Langevin and Fourier acceleration algorithms well suited to data-parallel computer architectures such as the Connection Machine. To establish the validity of our approximations, we compare our electrostatic contribution to the solvalion energy with the results of Lim, Bashford, and Karplus using a conventional static continuum dielectric cavity model, and the non electrostatic contributions with estimates of hydrophohic surface free energy. Our model can also accommodate ionic charges and temperature fluctuations, We propose future investigations extending our effective theory of solvation to include explicit orientational entropy and hydroxen-bonding terms. © 1995 John Wiley & Sons, Inc.     

DAPI binding to the DNA minor groove: a continuum solvent analysis

A continuum solvent model based on the generalized Born (GB) or finite-difference Poisson-Boltzmann (FDPB) approaches has been employed to compare the binding of 4'-6-diamidine-2-phenyl indole (DAPI) to the minor groove of various DNA sequences. Qualitative agreement between the results of GB and FDPB approaches as well as between calculated and experimentally observed trends regarding the sequence specificity of DAPI binding to B-DNA was obtained. Calculated binding energies were decomposed into various contributions to solvation and DNA-ligand interaction. DNA conformational adaptation was found to make a favorable contribution to the calculated total interaction energy but did not change the DAPI binding affinity ranking of different DNA sequences. The calculations indicate that closed complex formation is mainly driven by nonpolar contributions and was found to be disfavored electrostatically due to a desolvation penalty that outbalances the attractive Coulomb interaction. The calculated penalty was larger for DAPI binding to GC-rich sequences compared with AT-rich target sequences and generally larger for the FDPB vs the GB continuum model. A radial interaction profile for DAPI at different distances from the DNA minor groove revealed an electrostatic energy minimum a few Angstroms farther away from the closed binding geometry. The calculated electrostatic interaction up to this distance is attractive and it may stabilize a nonspecific binding arrangement.     

Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide.

Solvation effects play a profound role in the energetics of protein folding. While a continuum dielectric model of solvation may provide a sufficiently accurate estimate of the solvation effects, until now this model was too computationally expensive and unstable for folding simulations. Here we proposed a fast yet accurate and robust implementation of the boundary element solution of the Poisson equation, the REBEL algorithm. Using our earlier double-energy scheme, we included for the first time the mathematically rigorous continuous REBEL solvation term in our Biased Probability Monte Carlo (BPMC) simulations of the peptide folding. The free energy of a 23-residue beta beta alpha-peptide was then globally optimized with and without the solvation electrostatics contribution. An ensemble of beta beta alpha conformations was found at and near the global minimum of the energy function with the REBEL electrostatic solvation term. Much poorer correspondence to the native solution structure was found in the "control" simulations with a traditional method to account for solvation via a distance-dependent dielectric constant. Each simulation took less than 40 h (21 h without electrostatic solvation calculation) on a single Alpha 677 MHz CPU and involved more than 40,000 solvation energy evaluations. This work demonstrates for the first time that such a simulation can be performed in a realistic time frame. The proposed procedure may eliminate the energy evaluation accuracy bottleneck in folding simulations.     

Continuum electrostatic model for the binding of cytochrome c2 to the photosynthetic reaction center from Rhodobacter sphaeroides

Electrostatic interactions are important for protein-protein association. In this study, we examined the electrostatic interactions between two proteins, cytochrome c(2) (cyt c(2)) and the reaction center (RC) from the photosynthetic bacterium Rhodobacter sphaeroides, that function in intermolecular electron transfer in photosynthesis. Electrostatic contributions to the binding energy for the cyt c(2)-RC complex were calculated using continuum electrostatic methods based on the recent cocrystal structure [Axelrod, H. L., et al. (2002) J. Mol. Biol. 319, 501-515]. Calculated changes in binding energy due to mutations of charged interface residues agreed with experimental results for a protein dielectric constant epsilon(in) of 10. However, the electrostatic contribution to the binding energy for the complex was close to zero due to unfavorable desolvation energies that compensate for the favorable Coulomb attraction. The electrostatic energy calculated as a function of displacement of the cyt c(2) from the bound position showed a shallow minimum at a position near but displaced from the cocrystal configuration. These results show that although electrostatic steering is present, other short-range interactions must be present to contribute to the binding energy and to determine the structure of the complex. Calculations made to model the experimental data on association rates indicate a solvent-separated transition state for binding in which the cyt c(2) is displaced approximately 8 A above its position in the bound complex. These results are consistent with a two-step model for protein association: electrostatic docking of the cyt c(2) followed by desolvation to form short-range van der Waals contacts for rapid electron transfer.     

An evaluation of Poisson-Boltzmann electrostatic free energy calculations through comparison with experimental mutagenesis data

For systems involving highly and oppositely charged proteins, electrostatic forces dominate association and contribute to biomolecular complex stability. Using experimental or theoretical alanine-scanning mutagenesis, it is possible to elucidate the contribution of individual ionizable amino acids to protein association. We evaluated our electrostatic free energy calculations by comparing calculated and experimental data for alanine mutants of five protein complexes. We calculated Poisson-Boltzmann electrostatic free energies based on a thermodynamic cycle, which incorporates association in a reference (Coulombic) and solvated (solution) state, as well as solvation effects. We observe that Coulombic and solvation free energy values correlate with experimental data in highly and oppositely charged systems, but not in systems comprised of similarly charged proteins. We also observe that correlation between solution and experimental free energies is dependent on dielectric coefficient selection for the protein interior. Free energy correlations improve as protein dielectric coefficient increases, suggesting that the protein interior experiences moderate dielectric screening, despite being shielded from solvent. We propose that higher dielectric coefficients may be necessary to more accurately predict protein-protein association. Additionally, our data suggest that Coulombic potential calculations alone may be sufficient to predict relative binding of protein mutants.     

Evaluation of the conformational free energies of loops in proteins

In this paper we discuss the problem of including solvation free energies in evaluating the relative stabilities of loops in proteins. A conformational search based on a gas-phase potential function is used to generate a large number of trial conformations. As has been found previously, the energy minimization step in this process tends to pack charged and polar side chains against the protein surface, resulting in conformations which are unstable in the aqueous phase. Various solvation models can easily identify such structures. In order to provide a more severe test of solvation models, gas phase conformations were generated in which side chains were kept extended so as to maximize their interaction with the solvent. The free energies of these conformations were compared to that calculated for the crystal structure in three loops of the protein E. coli RNase H, with lengths of 7, 8, and 9 residues. Free energies were evaluated with a finite difference Poisson-Boltzmann (FDPB) calculation for electrostatics and a surface area-based term for nonpolar contributions. These were added to a gas-phase potential function. A free energy function based on atomic solvation parameters was also tested. Both functions were quite successful in selecting, based on a free energy criterion, conformations quite close to the crystal structure for two of the three loops. For one loop, which is involved in crystal contacts, conformations that are quite different from the crystal structure were also selected. A method to avoid precision problems associated with using the FDPB method to evaluate conformational free energies in proteins is described. © 1994 John Wiley & Sons, Inc.     

Electrostatic effects in proteins: comparison of dielectric and charge models.

Two approaches for calculating electrostatic effects in proteins are compared and ana analysis is presented of the dependence of calculated properties on the model used to define the charge distribution. Changes in electrostatic free energy have been calculated using a screened Coulomb potential (SCP) with a distance-dependent effective dielectric permittivity to model bulk solvent effects and a finite difference approach to solve the Poisson-Boltzmann (FDPB) equation. The properties calculated include shifts in dissociation constants of ionizable groups, the effect of annihilating surface charges on the binding of metals, and shifts in redox potentials due to changes in the charge of ionizable groups. In the proteins considered the charged sites are separated by 3.5-12 A. It is shown that for the systems studied in this distance range the SCP yields calculated values which are at least as accurate as those obtained from solution of the FDPB equation. In addition, in the distance range 3-5 A the SCP gives substantially better results than the FDPB equation. Possible sources of this difference between the two methods are discussed. Shifts in binding constants and redox potentials were calculated with several standard charge sets, and the resulting values show a variation of 20-40% between the 'best' and 'worst' cases. From this study it is concluded that in most applications, changes in electrostatic free energies can be calculated economically and reliably using an SCP approach with a single functional form of the screening function.     

On the calculation of electrostatic interactions in proteins

In this paper we present a classical treatment of electrostatic interactions in proteins. The protein is treated as a region of low dielectric constant with spherical charges embedded within it, surrounded by an aqueous solvent of high dielectric constant, which may contain a simple electrolyte. The complete analysis includes the effects of solvent screening, polarization forces, and self energies, which are related to solvation energies. Formulae, and sample calculations of forces and energies, are given for the special case of a spherical protein. Our analysis and model calculations point out that any consistent treatment of electrostatic interactions in proteins should account for the following. Solvent polarization is an important factor in the calculation of pairwise electrostatic interactions. Solvent polarization substantially affects both electrostatic energies and forces acting upon charges. No simple expression for the effective dielectric constant, Deff, can generally be valid, since Deff is a sensitive function of position. Solvent screening of pairwise interactions involving dipolar groups is less effective than the screening of charges. In fact for many interactions involving dipoles, solvent screening can be essentially ignored. The self energy of charges makes a large contribution to the total electrostatic energy of a protein. This must be compensated by specific interactions with other groups in the protein. Strategies for applying our analysis to proteins whose structures are known are discussed.     

A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins

An analysis of the screened Coulomb potential--implicit solvent model (SCP--ISM) is presented showing that general equations for both the electrostatic and solvation free energy can be derived in a continuum approach, using statistical averaging of the polarization field created by the solvent around the molecule. The derivation clearly shows how the concept of boundary, usually found in macroscopic approaches, is eliminated when the continuum model is obtained from a microscopic treatment using appropriate averaging techniques. The model is used to study the alanine dipeptide in aqueous solution, as well as the discrimination of native protein structures from misfolded conformations. For the alanine dipeptide the free energy surface in the phi--psi space is calculated and compared with recently reported results of a detailed molecular dynamics simulation using an explicit representation of the solvent, and with other available data. The study showed that the results obtained using the SCP--ISM are comparable to those of the explicit water calculation and compares favorably to the FDPB approach. Both transition states and energy minima show a high correlation (r > 0.98) with the results obtained in the explicit water analysis. The study of the misfolded structures of proteins comprised the analysis of three standard decoy sets, namely, the EMBL, Park and Levitt, and Baker's CASP3 sets. In all cases the SCP--ISM discriminated well the native structures of the proteins, and the best-predicted structures were always near-native (cRMSD approximately 2 A).     

Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides

We have extended and applied a multicoordinate free energy method, chemical Monte Carlo/Molecular Dynamics (CMC/MD), to calculate the relative free energies of different amino acid side-chains. CMC/MD allows the calculation of the relative free energies for many chemical species from a single free energy calculation. We have previously shown its utility in host:guest chemistry (Pitera and Kollman, J Am Chem Soc 1998;120:7557-7567)1 and ligand design (Eriksson et al., J Med Chem 1999;42:868-881)2, and here demonstrate its utility in calculations of amino acid properties and protein stability. We first study the relative solvation free energies of N-methylated and acetylated alanine, valine, and serine amino acids. With careful inclusion of rotameric states, internal energies, and both the solution and vacuum states of the calculation, we calculate relative solvation free energies in good agreement with thermodynamic integration (TI) calculations. Interestingly, we find that a significant amount of the unfavorable solvation of valine seen in prior work (Sun et al., J Am Chem Soc 1992;114:6798-6801)3 is caused by restraining the backbone in an extended conformation. In contrast, the solvation free energy of serine is calculated to be less favorable than expected from experiment, due to the formation of a favorable intramolecular hydrogen bond in the vacuum state. These monomer calculations emphasize the need to accurately consider all significant conformations of flexible molecules in free energy calculations. This development of the CMC/MD method paves the way for computations of protein stability analogous to the biochemical technique of "exhaustive mutagenesis." We have carried out just such a calculation at position 133 of T4 lysozyme, where we use CMC/MD to calculate the relative stability of eight different side-chain mutants in a single free energy calculation. Our T4 calculations show good agreement with the prior free energy calculations of Veenstra et al. (Prot Eng 1997;10:789-807)4 and excellent agreement with the experiments of Mendel et al. (Science 1992;256:1798-1802).     

Partitioning of amino-acid analogues in a five-slab membrane model

The positional preferences of the twenty amino-acid residues in a phospholipid bilayer are investigated by calculating the solvation free energy of the corresponding side chain analogues using a five-slab continuum electrostatic model. The side-chain analogues of the aromatic residues tryptophan and tyrosine are found to partition in the head-group region, due to compensation between the increase of the non-polar component of the solvation free energy at the boundary with the aqueous region and the decrease in the electrostatic component. The side chain analogue of phenylalanine differs from the other aromatic molecules by being able to partition in both the head-group region and the membrane core. This finding is consistent with experimental findings of the position of phenylalanine in membrane helices. Interestingly, the charged side-chain analogues of arginine and lysine are shown to prefer the head-group region in an orientation that allows the charged moiety to interact with the aqueous layer. The orientation adopted is similar to the “snorkelling” effect seen in lysine and arginine residues in membrane helices. In contrast, the preference of the charged side-chain analogues of histidine (protonated) and aspartate (deprotonated) for the aqueous layer is shown to be due to a steep decrease in the electrostatic component of the solvation free energy at the boundary to the aqueous region. The calculations allow an understanding of the origins of side chain positioning in membranes and are thus useful in understanding membrane-protein:lipid thermodynamics.     

Ions in water: characterizing the forces that control chemical processes and biological structure

The continuum electrostatics model of Debye and Hückel [P. Debye and E. Hückel, On the theory of electrolytes. I. Freezing point depression and related phenomena., Phys. Z. 24 (1923) 185-206.] and its successors utilize a macroscopic dielectric constant and assume that all interactions involving ions are strictly electrostatic, implying that simple ions in water generate electric fields strong enough to orient water dipoles over long distances. However, solution neutron and X-ray diffraction indicate that even di- and tri-valent ions do not significantly alter the density or orientation of water more than two water molecules (5 A) away. Therefore the long range electric fields (generated by simple ions) which can be detected by various resonance techniques such as fluorescence resonance energy transfer over distances of 30 A (about 11 water diameters) or more must be weak relative to the strength of water-water interactions. Two different techniques indicate that the interaction of water with anions is by an approximately linear hydrogen bond, suggesting that the dominant forces on ions in water are short range forces of a chemical nature.     

Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state

The physical nature underlying intermolecular interactions between two rod-like winter flounder antifreeze protein (AFP) molecules and their implication for the mechanism of antifreeze function are examined in this work using molecular dynamics simulations, augmented with free energy calculations employing a continuum solvation model. The energetics for different modes of interactions of two AFP molecules is examined in both vacuum and aqueous phases along with the water distribution in the region encapsulated by two antiparallel AFP backbones. The results show that in a vacuum two AFP molecules intrinsically attract each other in the antiparallel fashion, where their complementary charge side chains face each other directly. In the aqueous environment, this attraction is counteracted by both screening and entropic effects. Therefore, two nearly energetically degenerate states, an aggregated state and a dissociated state, result as a new aspect of intermolecular interaction in the paradigm for the mechanism of action of AFP. The relevance of these findings to the mechanism of function of freezing inhibition in the context of our work on Antarctic cod antifreeze glycoprotein (Nguyen et al., Biophysical Journal, 2002, Vol. 82, pp. 2892-2905) is discussed.     

Numerical study of the force network ensemble

The force network ensemble of Snoeijer et al. (Force network ensemble: a new approach to static granular matter, Phys. Rev. Lett. 92 (2004), 054302) is a convenient model to study networks of contact forces that are typically present in granular matter. Recently, we have shown that it is possible to extremely accurately determine the probability distribution of contact forces in the framework of this ensemble (van Eerd et al., Tail of the contact force distribution in static granular materials, Phys. Rev. E 75 (2007), 060302(R); Tighe et al., Entropy maximisation in the force network ensemble for granular solids, Phys. Rev. Lett. 100 (2008), 238001). In this work, we review several important details of these computations. In particular, we study in detail the angle-resolved contact force distribution, finite-size effects, the maximum allowed shear stress and the effect of walls. In addition, we investigate how well the force network ensemble resembles systems with ‘real’ interactions.     

Free energy determinants of tertiary structure and the evaluation of protein models

We develop a protocol for estimating the free energy difference between different conformations of the same polypeptide chain. The conformational free energy evaluation combines the CHARMM force field with a continuum treatment of the solvent. In almost all cases studied, experimentally determined structures are predicted to be more stable than misfolded "decoys." This is due in part to the fact that the Coulomb energy of the native protein is consistently lower than that of the decoys. The solvation free energy generally favors the decoys, although the total electrostatic free energy (sum of Coulomb and solvation terms) favors the native structure. The behavior of the solvation free energy is somewhat counterintuitive and, surprisingly, is not correlated with differences in the burial of polar area between native structures and decoys. Rather. the effect is due to a more favorable charge distribution in the native protein, which, as is discussed, will tend to decrease its interaction with the solvent. Our results thus suggest, in keeping with a number of recent studies, that electrostatic interactions may play an important role in determining the native topology of a folded protein. On this basis, a simplified scoring function is derived that combines a Coulomb term with a hydrophobic contact term. This function performs as well as the more complete free energy evaluation in distinguishing the native structure from misfolded decoys. Its computational efficiency suggests that it can be used in protein structure prediction applications, and that it provides a physically well-defined alternative to statistically derived scoring functions.