Polyunsaturated fatty acids inhibit Kv1.4 by interacting with positively charged extracellular pore residues

Polyunsaturated fatty acids (PUFAs) modulate voltage-gated K(+) channel inactivation by an unknown site and mechanism. The effects of ω-6 and ω-3 PUFAs were investigated on the heterologously expressed Kv1.4 channel. PUFAs inhibited wild-type Kv1.4 during repetitive pulsing as a result of slowing of recovery from inactivation. In a mutant Kv1.4 channel lacking N-type inactivation, PUFAs reversibly enhanced C-type inactivation (Kd, 15-43 μM). C-type inactivation was affected by extracellular H(+) and K(+) as well as PUFAs and there was an interaction among the three: the effect of PUFAs was reversed during acidosis and abolished on raising K(+) Replacement of two positively charged residues in the extracellular pore (H508 and K532) abolished the effects of the PUFAs (and extracellular H(+) and K(+)) on C-type inactivation but had no effect on the lipoelectric modulation of voltage sensor activation, suggesting two separable interaction sites/mechanisms of action of PUFAs. Charge calculations suggest that the acidic head group of the PUFAs raises the pKa of H508 and this reduces the K(+) occupancy of the selectivity filter, stabilizing the C-type inactivated state.

The role of electrostatics in protein-protein interactions of a monoclonal antibody

Understanding how protein-protein interactions depend on the choice of buffer, salt, ionic strength, and pH is needed to have better control over protein solution behavior. Here, we have characterized the pH and ionic strength dependence of protein-protein interactions in terms of an interaction parameter kD obtained from dynamic light scattering and the osmotic second virial coefficient B22 measured by static light scattering. A simplified protein-protein interaction model based on a Baxter adhesive potential and an electric double layer force is used to separate out the contributions of longer-ranged electrostatic interactions from short-ranged attractive forces. The ionic strength dependence of protein-protein interactions for solutions at pH 6.5 and below can be accurately captured using a Deryaguin-Landau-Verwey-Overbeek (DLVO) potential to describe the double layer forces. In solutions at pH 9, attractive electrostatics occur over the ionic strength range of 5-275 mM. At intermediate pH values (7.25 to 8.5), there is a crossover effect characterized by a nonmonotonic ionic strength dependence of protein-protein interactions, which can be rationalized by the competing effects of long-ranged repulsive double layer forces at low ionic strength and a shorter ranged electrostatic attraction, which dominates above a critical ionic strength. The change of interactions from repulsive to attractive indicates a concomitant change in the angular dependence of protein-protein interaction from isotropic to anisotropic. In the second part of the paper, we show how the Baxter adhesive potential can be used to predict values of kD from fitting to B22 measurements, thus providing a molecular basis for the linear correlation between the two protein-protein interaction parameters.

Freezing and folding behavior in simple off-lattice heteropolymers

We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All 10 heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered states dominated by single chain conformations. These results are in contrast with the theoretical predictions of the random energy model for heteropolymers, from which we would expect continuous transitions to glassy behavior at low temperatures.

Biochemical and genetic evidence for a family of heterotrimeric G-proteins in Trichomonas vaginalis

We have cloned a single copy gene from the human parasite Trichomonas vaginalis that encodes a putative protein of 402 amino acids with approximately 35% sequence identity to known alpha subunits of heterotrimeric G-proteins. It contains the characteristic GTP binding domains G-1 to G-5 with the key residues conserved. The new sequence has an unusual N-terminal extension of approximately 70 residues that cannot be aligned to reference G-proteins and which is characterised by proline-rich repeats. To investigate the expression and cellular localisation of the protein we produced specific antisera against a recombinant fusion protein. The antisera recognised a protein of an apparent molecular mass of 51 kDa in protein extracts from T. vaginalis and immunofluorescent microscopy established that the protein is localised to discrete endomembranes. Using a protocol designed to purify mammalian heterotrimeric G-proteins incorporating a GTPgammaS binding assay, we isolated two proteins from Trichomonas that are recognised by an heterologous GA/1 antisera raised to a peptide of the conserved G-1 domain of G-protein alpha subunits. These two proteins have an apparent molecular mass of 61 and 48 kDa, respectively, larger and smaller than the translation product of the cloned gene. Consistent with these results, the GA/1 antisera did not cross-react with the fusion protein produced from the gene we have cloned. These data suggest T. vaginalis possesses more than one heterotrimeric G-protein alpha subunit. Based on the sequence features of the cloned gene and the biochemical properties of the purified proteins, we suggest that these alpha subunits are likely to be part of classic heterotrimeric G-protein complexes.

A second eIF4E protein in Schizosaccharomyces pombe has distinct eIF4G-binding properties

The eukaryotic cap-binding proteins belonging to the eIF4E family are generally involved in mediating the recruitment of ribosomes to capped mRNA. We described previously a cap-binding protein (now called eIF4E1) in Schizosaccharomyces pombe that appears to have all of the usual structural and functional attributes of an eIF4E. We have now characterised a new type of cap-binding protein (eIF4E2) from this organism, which at the amino acid sequence level, is 52% identical and 59% similar to eIF4E1. eIF4E2 is not essential in S.pombe but has some novel properties that may be related to a special function in the cell. The ratio of eIF4E2:eIF4E1 in the cell shifts in favour of eIF4E2 at higher temperatures. Despite having all of the dorsal face amino acids that have so far been associated with eIF4G binding to eIF4E1, eIF4E2 binds the eIF4E-binding domain of S.pombe eIF4G >10(2)-times weaker than eIF4E1 in vitro. The eIF4E2 cap-binding affinity is in the typical micromolar range. The results suggest that eIF4E2 is not active on the main pathway of translation initiation in fission yeast but might play a role in the adaptation strategy of this organism under specific growth conditions. Moreover, they provide insight into the molecular characteristics required for tight binding to eIF4G.

A quantitative molecular model for modulation of mammalian translation by the eIF4E-binding protein 1

Translation initiation is a key point of regulation in eukaryotic gene expression. 4E-binding proteins (4E-BPs) inhibit initiation by blocking the association of eIF4E with eIF4G, two integral components of the mRNA cap-binding complex. Phosphorylation of 4E-BP1 reduces its ability to bind to eIF4E and thereby to compete with eIF4G. A novel combination of biophysical and biochemical tools was used to measure the impact of phosphorylation and acidic side chain substitution at each potentially modulatory site in 4E-BP1. For each individual site, we have analyzed the effects of modification on eIF4E binding using affinity chromatography and surface plasmon resonance analysis, and on the regulatory function of the 4E-BP1 protein using a yeast in vivo model system and a mammalian in vitro translation assay. We find that modifications at the two sites immediately flanking the eIF4E-binding domain, Thr(46) and Ser(65), consistently have the most significant effects, and that phosphorylation of Ser(65) causes the greatest reduction in binding affinity. These results establish a quantitative framework that should contribute to understanding of the molecular interactions underlying 4E-BP1-mediated translational regulation.

Modelling of auxin-binding protein 1 suggests that its C-terminus and auxin could compete for a binding site that incorporates a metal ion and tryptophan residue 44

Sequence comparison indicates that auxin-binding protein 1 (ABP1) belongs to a family of proteins with the core beta-barrel structure of the vicilins. Previous modelling within this family correctly predicted metal-ion binding and oligomeric properties of oxalate oxidase. ABP1 also contains a putative metal-ion-binding cluster of amino acids, adjacent to a tryptophan side chain, leading to a proposed auxin-binding site that incorporates metal-ion interaction with the auxin carboxylate. Modelling implicates W44 (Zea mays ABP1) in auxin binding, rather than W136 or W151. Reduced sequence similarity for the C-terminal region prevents model building. It is proposed that one of these C-terminal tryptophans, along with a neighbouring negatively charged side chain, occupies the binding pocket in the absence of auxin, thereby linking auxin binding to conformational change and C-terminal involvement in signalling.

Modeling a prion protein dimer: predictions for fibril formation

Models of structural transition in prion protein (PrP) focus on the domain visualised by solution NMR. Accumulating evidence suggests that the adjacent and highly conserved nonpolar segment, as well as PrP-membrane interactions, should also be considered. Calculations predict that membrane-induced structural destabilisation is mediated by stabilisation of the unfolded form. Comparative analysis of PrP structures leads to a model for PrP dimerisation that incorporates the nonpolar segment. A prediction that PrP will interact with the PrP-like protein (Dpl) to form a heterodimer, but that Dpl will not form a homodimer, can be tested. Modelling is discussed in the context of ataxias associated with the expression of Dpl or truncated PrP in transgenic animals lacking wild-type PrP. A PrP(C) dimer model forms the basis for considering the geometry of PrP(Sc) fibril formation.

Buried charged surface in proteins

BACKGROUND

The traditional picture of charged amino acids in globular proteins is that they are almost exclusively on the outside exposed to the solvent. Buried charges, when they do occur, are assumed to play an essential role in catalysis and ligand binding, or in stabilizing structure as, for instance, helix caps.

RESULTS

By analyzing the amount and distribution of buried charged surface and charges in proteins over a broad range of protein sizes, we show that buried charge is much more common than is generally believed. We also show that the amount of buried charge rises with protein size in a manner which differs from other types of surfaces, especially aromatic and polar uncharged surfaces. In large proteins such as hemocyanin, 35% of all charges are greater than 75% buried. Furthermore, at all sizes few charged groups are fully exposed. As an experimental test, we show that replacement of the buried D178 of muconate lactonizing enzyme by N stabilizes the enzyme by 4.2 degrees C without any change in crystallographic structure. In addition, free energy calculations of stability support the experimental results.

CONCLUSIONS

Nature may use charge burial to reduce protein stability; not all buried charges are fully stabilized by a prearranged protein environment. Consistent with this view, thermophilic proteins often have less buried charge. Modifying the amount of buried charge at carefully chosen sites may thus provide a general route for changing the thermophilicity or psychrophilicity of proteins.

Modelling charge interactions in the prion protein: predictions for pathogenesis

Calculations are presented for the pH-dependence of stability and membrane charge complementarity of prion protein fragments. The theoretical results are compared with reported characterisations of prion protein folding in vitro. Discussion of models for conformational change and pathogenesis in vivo leads to the prediction of amino acids that could mediate sensitivity to the endosomal pH and to a design strategy for recombinant prion proteins with an increased susceptibility to prion proteinSc-like properties in vitro. In this model, the protective effect of certain basic polymorphisms can be interpreted in terms of oligomerisation on a negatively-charged surface.

Simplified methods for pKa and acid pH-dependent stability estimation in proteins: removing dielectric and counterion boundaries

Much computational research aimed at understanding ionizable group interactions in proteins has focused on numerical solutions of the Poisson-Boltzmann (PB) equation, incorporating protein exclusion zones for solvent and counterions in a continuum model. Poor agreement with measured pKas and pH-dependent stabilities for a (protein, solvent) relative dielectric boundary of (4,80) has lead to the adoption of an intermediate (20,80) boundary. It is now shown that a simple Debye-Huckel (DH) calculation, removing both the low dielectric and counterion exclusion regions associated with protein, is equally effective in general pKa calculations. However, a broad-based discrepancy to measured pH-dependent stabilities is maintained in the absence of ionizable group interactions in the unfolded state. A simple model is introduced for these interactions, with a significantly improved match to experiment that suggests a potential utility in predicting and analyzing the acid pH-dependence of protein stability. The methods are applied to the relative pH-dependent stabilities of the pore-forming domains of colicins A and N. The results relate generally to the well-known preponderance of surface ionizable groups with solvent-mediated interactions. Although numerical PB solutions do not currently have a significant advantage for overall pKa estimations, development based on consideration of microscopic solvation energetics in tandem with the continuum model could combine the large deltapKas of a subset of ionizable groups with the overall robustness of the DH model.

Modeling based on the structure of vicilins predicts a histidine cluster in the active site of oxalate oxidase

It is known that germin, which is a marker of the onset of growth in germinating wheat, is an oxalate oxidase, and also that germins possess sequence similarity with legumin and vicilin seed storage proteins. These two pieces of information have been combined in order to generate a 3D model of germin based on the structure of vicilin and to examine the model with regard to a potential oxalate oxidase active site. A cluster of three histidine residues has been located within the conserved beta-barrel structure. While there is a relatively low level of overall sequence similarity between the model and the vicilin structures, the conservation of amino acids important in maintaining the scaffold of the beta-barrel lends confidence to the juxtaposition of the histidine residues. The cluster is similar structurally to those found in copper amine oxidase and other proteins, leading to the suggestion that it defines a metal-binding location within the oxalate oxidase active site. It is also proposed that the structural elements involved in intermolecular interactions in vicilins may play a role in oligomer formation in germin/oxalate oxidase.

Modeling charge interactions and redox properties in DsbA

Accurate prediction of charge interactions in macromolecules presents a significant challenge for computational biology. A model for the low Cys30 pKa and oxidizing power of DsbA (Gane, P. J., Freedman, R. B., and Warwicker, J. (1995) J. Mol. Biol. 249, 376-387) has been investigated experimentally (Hennecke, J., Spleiss, C., and Glockshuber, R. (1997) J. Biol. Chem. 272, 189-195), with substitutions for Glu37 and Glu38 and with residues 38-40 removed. Measured changes in Cys30 pKa and redox potential were relatively small and reported to be in contrast to model predictions. It is now shown, particularly with calculations of wild-type:mutant differences for a range of salt concentrations, that the data are consistent with the model and support the key finding that a number of different factors contribute to the oxidizing power of DsbA, so that any particular one need not necessarily be large. A feature of the model is a low protein dielectric, and higher values (which are becoming popular in predictions of pH dependence) are inconsistent with both the difference data and the wild-type Cys30 pKa.

A hypothesis describing a potential link between molecular structure and TSE strains

In considering a protein-only model for prion pathogenesis in TSEs, one key challenge is to explain the existence of strains. These have traditionally been characterised by neuropathology and incubation times and more recently through biochemical analysis of prion protein (PrP), which shows differences in protease-resistant fragment size and glycoform ratios. It is now suggested that PrP possesses two faces which on the basis of conservation and non-polar nature could each (physiologically) interact either with membrane or with neighbouring protein. This model leads to the construction of two clearly different membrane-attached PrP orientations, with consequences for protease resistance and glycoform incorporation that qualitatively match to experiment.

Improving pKa calculations with consideration of hydration entropy

Continuum dielectric modelling of electrostatics interactions in macromolecules provides a valuable tool in the study of structure-function relationships, but falls short of providing consistently accurate calculated pKas. It is suggested that the model can be significantly improved with the inclusion of a term that estimates the entropy associated with first hydration shell solvent ordering, with reference to computed results for cysteines in DsbA and thioredoxin, and aspartic and glutamic acids in a number of proteins. The modification is based on the geometry of charge burial and an hydration number, which is adjustable (by fit to experiment), and is uniform within each class of ionizable group studied. The potential for further development is clear within this framework, since experiment and simulation can furnish non-adjustable, ionizable group-specific, hydration numbers.

Species barriers in a model for specific prion protein dimerisation

It has been proposed that the most highly conserved sequence segment within the prion protein (PrP) may be involved in dimer formation within both the normal (PrPC) and misfolded (PrPSc) forms. This hypothesis is now examined in the context of amino acids known to be involved in species barriers or in disease modifying polymorphisms, and the structure of a mouse PrP fragment. These locations can be plausibly explained on the basis of the specific dimer model, so that a potential role for a conserved dimerisation element in prion disease progression cannot be excluded.

A molecular model for interfacial activation in phospholipase A2

Electrostatic calculations predict that amino-terminal conformation and ionisation contribute significantly to transition state stability in phospholipase A2, so that control of these factors by binding to aggregated substrate provides a plausible mechanism for interfacial activation. In particular, it is suggested that a part of the pH dependence of interfacial activity may arise from transient deprotonation of an ordered amino-terminus. Interface charge and the detailed structure of the interfacial complex are also predicted to influence catalytic activity. The model is compared with available biochemical data.

A model for prion protein dimerisation based on alpha-helical packing

Residues 109-122 of the human prion protein (PrP) are highly conserved across species, and are predicted to be alpha-helical in PrPc, the cellular form. A computational search of the potential for alpha-helical dimerisation has been made for residues 109-122. The conformation which consistently scores highest in terms of burying non-polar surface area is a tight association involving alanine, glycine and valine residues. A model of heterodimerisation for PrPc and PrPSc (the misfolded form) is presented in which species barrier mutations would arise from interaction specificities that would follow, at least in part, the same framework as formation of a putative homodimer.

Calculation of Cys 30 delta pKa's and oxidising power for DsbA mutants

DsbA possesses a redox active disulphide, with the equilibrium strongly shifted towards the reduced form as compared to its structural homologue, thioredoxin. It is widely believed that the two amino acids that separate the active site cysteines play a crucial role in determining oxidising power within the thioredoxin family. Data concerning redox and pKa properties for DsbA mutants in this region are available. Electrostatics calculations show reasonable agreement with the experimental data, and support the suggestion that amino acids outside of the CXXC active site sequence are as important in determining oxidising power within the thioredoxin family as are those within it.

A model for vicilin solubility at mild acidic pH, based on homology modelling and electrostatics calculations

The crystallographic structures of jack bean canavalin and French bean phaseolin have been used to construct a homology model of the storage vicilin of cocoa. Reported molecular weights for cocoa storage protein subunits correlate with proteolysis at the site of a large hydrophilic insert in the mature protein. Burial of the hydrophobic amino acids on trimer formation is a strongly conserved feature in the vicilin family. Histidine residues also sit at the monomer-monomer interfaces of the trimer and are likely to contribute to the decreased solubility of cocoa vicilin at mild acidic pH, which is generally considered to be caused solely by aggregation near to the isoelectric point. Electrostatic calculations suggest that such an arrangement of histidine residues in the absence of specific counterion binding will not favour the particular geometry of trimer formation below neutral pH. Higher order aggregates that do not exclude histidine charge from the solvent may be favoured, aiding the precipitation of cocoa vicilin at mild acidic pH. This suggestion is considered for the vicilin family. The hypothesis could contribute to an understanding of the pH and ionic strength dependence of vicilin solubility in vitro, and possibly of the behaviour of vicilins in the seed storage environment.

Increased activity of porcine pancreatic phospholipase A2 by designed long-range electrostatic stabilisation of the transition state

Stabilisation of the catalytic transition state by long-range charge interactions has been tested with mutagenesis for porcine pancreatic phospholipase A2. Electrostatics calculations were used to determine locations which would interact preferentially with one part of the dipolar charge separation that is believed to develop in the transition state. Experiment shows increased enzyme activity relative to wild-type recombinant enzyme for mutants N97D and N101D, consistent with the design.

A molecular model for the redox potential difference between thioredoxin and DsbA, based on electrostatics calculations

The disulphide active sites of thioredoxin and DsbA are known to possess a high degree of structural homology. However, DsbA is a much stronger oxidant than thioredoxin. The redox potential difference between DsbA and thioredoxin has been measured to be 160 mV, equivalent to a shift of 15.4 kJ/mol in the reduced/oxidised equilibrium. Electrostatics calculations have been used to study the relative stabilities of the reduced forms of the two proteins. Model calculations suggest that much of the redox potential difference between DsbA and thioredoxin arises form altered stabilisation of the exposed and ionised thiolates of the reduced forms, supporting suggestions previously made on the basis of experimental studies. The calculations have been used to construct a molecular model for the difference in thiolate stabilisation. Although specific interactions, such as thiolate-NH 35 (thioredoxin)/33 (DsbA), provide substantial stabilisation in each reduced protein, the difference between thioredoxin and DsbA is predicted to reside in several side-chain and main-chain groups acting in concert. Residues H32 and Q97 in DsbA are predicted to contribute, along with substantial regions of the polypeptide backbone in the protein domain which is common to DsbA and thioredoxin. Increased thiolate stabilisation by the peptide dipoles is suggested to arise from altered main-chain disposition, and the effect of the additional protein domain of DsbA on the electric field. Peptide dipoles in a region of about 20 residues close to the active site disulphide are predicted to contribute significantly to the redox potential difference.

An unequivocal example of cysteine proteinase activity affected by multiple electrostatic interactions

The role of electrostatic interactions between the ionizable Asp158 and the active site thiolate-imidazolium ion pair of some cysteine proteinases has been the subject of controversy for some time. This study reports the expression of wild type procaricain and Asp158Glu, Asp158Asn and Asp158Ala mutants from Escherichia coli. Purification of autocatalytically matured enzymes yielded sufficient fully active material for pH (kcat/Km) profiles to be obtained. Use of both uncharged and charged substrates allowed the effects of different reactive enzyme species to be separated from the complications of electrostatic effects between enzyme and substrate. At least three ionizations are detectable in the acid limb of wild type caricain and the Glu and Asn mutants. Only two pKa values, however, are detectable in the acid limb using the Ala mutant. Comparison of pH activity profiles shows that whilst an ionizable residue at position 158 is not essential for the formation of the thiolate-imidazolium ion pair, it does form a substantial part of the electrostatic field responsible for increased catalytic competence. Changing the position of this ionizable group in any way reduces activity. Complete removal of the charged group reduces catalytic competence even further. This work indicates that hydronations distant to the active site are contributing to the electrostatic effects leading to multiple active ionization states of the enzyme.

The activity of porcine pancreatic phospholipase A2 in 20% alcohol/aqueous solvent, by experiment and electrostatics calculations

The activity of porcine pancreatic phospholipase A2 (pla2), measured at pH 8, is reduced when methanol or ethanol is added to the aqueous solution. Finite difference electrostatics calculations were used to study the effect of modelling mixed solvents on the pKas of histidine 48 and the amino-terminal group, both of which influence the pH-dependence of catalysis. Calculations and experiment indicate that these pKa values cannot account for the activity reduction. Charge separation in the transition state is destabilized in 20% alcohol solvent relative to 100% aqueous solvent. The calculated values, which are combinations of stabilizing and destabilizing contributions, are in qualitative agreement with experiment. Saturating dielectric theory is used to model solvent water ordering in a high electric field, and water dielectric structure is assumed to dominate at the 20% alcohol level. The observed agreement demonstrates the utility of transition state stabilization theory and continuum solvent modelling. It is further suggested that electrostatic effects on kcat contribute to the pH-dependence of activity around pH 7, and to previously reported activity changes for charge mutants.

Improved continuum electrostatic modelling in proteins, with comparison to experiment

Electrostatic interactions in macromolecules can be calculated with the method of finite differences applied to a continuum model. The accuracy of dielectric and counterion continuum modelling has been tested for long-range interactions by comparison with available experimental data over a range of ionic strengths. Various model parameters have been adjusted. Some have little effect, such as protein dielectric and the selection of Van der Waals radii. It is shown that the reduction in interaction due to dielectric effects is overestimated when a dielectric constant of 80 is assigned to all solvent accessible regions. Improved agreement is seen when the effects of the Kirkwood correlation sphere and dielectric saturation are included. Further support for the use of dielectric saturation arises from a correlation of solvent polarization saturation with crystallographic ordered water structure. Calculations over the medium ionic strength range indicate that requiring counterions to maintain a solvent layer places too great a restriction on their approach to the protein-solvent interface. However, counterion accessibility that coincides with the solvent accessible region gives too much interaction damping. Modelling of observed ion binding sites suggests that a counterion response which includes an ion desolvation term, obtained by difference calculation, will improve the computation of ionic strength effects. This study demonstrates that there is scope for improvement in continuum electrostatics calculations, and shows that progress is possible with the inclusion of physically realistic solvent and counterion properties at the protein surface.

Model for the differential stabilities of rhinovirus and poliovirus to mild acidic pH, based on electrostatics calculations

Previous calculations of electrostatic interactions in the rhinovirus capsid have identified a subset of histidine residues, paired with lysine or arginine, that may be involved in pH-induced conformational changes related to viral uncoating. Further calculations with the finite difference method, accounting for the dielectric environment of the ionizable groups, suggest that charge burial in the crystal conformation will prevent protonation of these histidine residues in the pentamer-pentamer interface. Calculations with a modelled pentamer-pentamer interface in which three beta-strands are removed recover mildly acidic pKa values for the histidines. These results are discussed in the context of the structural interactions of these three beta-strands, which form a beta-sheet extension from the rest of the capsid, and with regard to the conformation of the homologous beta-sheet extension in poliovirus, which also possesses homologous histidine-lysine/arginine pairs. A model is developed in which the structural stability of the beta-sheet extension is related to the difference in acid stability of rhinovirus and poliovirus. It is suggested that, for poliovirus prior to cell receptor binding, the beta-sheet extension is stable at pH 3, the pentamer-pentamer interface histidines remain buried, and the virus is acid-stable. Cell receptor binding of poliovirus destabilizes the beta-sheet extension and the acid lability that is proposed to result could be involved in viral uncoating. For rhinovirus it is suggested that the observed conformational change in the absence of cell receptor binding involves a further acidic pH-activated process or conformational fluctuations that rearrange the beta-sheet extension and expose the pentamer-pentamer interface histidine residues to the acidic medium. Sequence analysis and electrostatics calculations reveal an aspartic acid in the beta-sheet extension that may have different pKa values in rhinovirus and poliovirus.

Changes in activity of porcine phospholipase A2 brought about by charge engineering of a major structural element to alter stability

We have modified the stability of porcine phospholipase A2 by charge engineering. The mutations are situated at the N-terminal of a major helix and are N89D and N89D/E92Q. This engineering has significantly altered the activity of the enzyme to aggregated and monomeric substrates. A N89D/E92K mutant is more stable but considerably less active than wild type. An N89D mutant is more stable and of similar activity to wild type. The substantial change in activity may be due to direct interaction of residue 92 with aggregated substrate or may be via second calcium binding. Second calcium binding may be more probable as activity against monomers is also affected. Additional calcium binding may therefore be an important way of manipulating the activity of phospholipase A2.

Modification of the stability of phospholipase A2 by charge engineering

Electrostatic interactions play an important role in stabilizing the folded conformation of globular proteins. Here we predict the change in stability of charge engineered mutants, construct these mutants and compare the predicted change in stability with that observed. The change in stability was correctly predicted for two of the three mutants and the factors responsible for the discrepancy between observation and prediction for the third mutant are discussed.

A theoretical study of the acidification of the rhinovirus capsid

Electrostatic calculations for human rhinovirus 14 indicate that histidine-base residue pairs in the region of a beta-strand interaction between pentamers may be involved in a pH-induced process that leads to the release of viral RNA. Other picornavirus sequences are examined for these residue pairs, a subset of which is present in enteroviruses. Foot and mouth disease virus possesses one of the residue pairs, and cardioviruses, which undergo a separate pH and halide ion-induced capsid dissociation, possess none.

Investigating protein-protein interaction surfaces using a reduced stereochemical and electrostatic model

A method of calculating the electrostatic potential energy between two molecules, using finite difference potential, is presented. A reduced charge set is used so that the interaction energy can be calculated as the two static molecules explore their full six-dimensional configurational space. The energies are contoured over surfaces fixed to each molecule with an interactive computer graphics program. For two crystal structures (trypsin-trypsin inhibitor and anti-lysozyme Fab-lysozyme), it is found that the complex corresponds to highly favourable interacting regions in the contour plots. These matches arise from a small number of protruding basic residues interacting with enhanced negative potential in each case. The redox pair cytochrome c peroxidase-cytochrome c exhibits an extensive favourably interacting surface within which a possible electron transfer complex may be defined by an increased electrostatic complementarity, but a decreased electrostatic energy. A possible substrate transfer configuration for the glycolytic enzyme pair glyceraldehyde phosphate dehydrogenase-phosphoglycerate kinase is presented.

Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent

Two observations suggest that DNA, upon binding to E. coli catabolite gene activator protein (CAP), is sharply bent by a total angle of at least 100-150 degrees: (1) The electrostatic potential field of CAP shows regions of positive potential that form a ramp on 3 sides of the protein. (2) The DNA binding site size as determined by DNA ethylation interference with binding, (Majors: "Control of the E. coli Lac Operon at the Molecular Level." Ph.D. Thesis, Harvard University, Cambridge, 1977) and by relative affinities of DNA fragments of various lengths (Liu-Johnson et al.: Cell 47:995-1005, 1986) requires severe bending of the DNA to maintain its favorable electrostatic contact with the protein.

Continuum dielectric modelling of the protein-solvent system, and calculation of the long-range electrostatic field of the enzyme phosphoglycerate mutase

The numerical continuum electrostatic method presented previously (Warwicker, J. & Watson, H. C. (1982) J. Mol. Biol., 157, 671-679), is developed with an improved analysis of the protein-solvent system. Inclusion in the model of saturable solvent dielectric, and counterions is discussed and presented. A number of long-range electrostatic field calculations are made on bovine pancreatic trypsin inhibitor to demonstrate the differences between various solvent and counterion models. The long-range potential field, due to polar side-chain and alpha-helix dipole charge, is calculated for the glycolytic enzyme phosphoglycerate mutase. The positive potential in and around the catalytic cleft region is sufficiently large to suggest that it may play a role in long-range attraction of the enzyme's negatively charged substrates. Analogous systems with charge-charge interactions in solvent water are considered. It is suggested that a long-range enzyme-substrate attractive force-field may, in part, offset the repulsive energy arising from overlap of hydration shells between enzyme and substrate.

Electrostatic field of the large fragment of Escherichia coli DNA polymerase I

The electrostatic field of the large fragment of Escherichia coli DNA polymerase I (Klenow fragment) has been calculated by the finite difference procedure on a 2 A grid. The potential field is substantially negative at physiological pH (reflecting the net negative charge at this pH). The largest regions of positive potential are in the deep crevice of the C-terminal domain, which is the proposed binding site for the DNA substrate. Within the crevice, the electrostatic potential has a partly helical form. If the DNA is positioned to fulfil stereochemical requirements, then the positive potential generally follows the major groove and (to a lesser extent) the negative potential is in the minor groove. Such an arrangement could stabilize DNA configurations related by screw symmetry. The histidine residues of the Klenow fragment give the positive field of the groove a sensitivity to relatively small pH changes around neutrality. We suggest that the histidine residues could change their ionization states in response to DNA binding, and that this effect could contribute to the protein-DNA binding energy.