Does Arginine Remain Protonated in the Lipid Membrane? Insights from Microscopic pKa Calculations

Free energy perturbation calculations are carried out to estimate the effective pK_a of an arginine (Arg) sidechain as a function of its location in the dipalmitoylphosphatidylcholine bilayer. Similar to previous all-atom simulations of the voltage sensor domain of a potassium channel in the membrane with charged Arg residues, the membrane and water structures deform to stabilize the charge of the Arg analog. As a result, the computed pK_a is >7 throughout the membrane although the value is very close to 7 near the center of the bilayer. With additional stabilizations from negatively charged amino acids or lipid molecules, it is reasonable to expect that Arg in membrane proteins (once in the membrane) can adopt the protonated state despite the low dielectric nature of the bulk lipid membrane.     

A New PAMPA Model Proposed on the Basis of a Synthetic Phospholipid Membrane

The purpose of this work was to investigate the synthetic phospholipid dependence of permeability measured by parallel artificial membrane permeability assay (PAMPA) method. Three phospholipids with hydrophobic groups of different lengths and phosphorylcholine as the hydrophilic group were concisely synthesized. Ten model drug molecules were selected because of their distinct human fraction absorbed (%FA) values and various pK_a characteristics. In vitro drug permeation experiments were designed to determine the effect of the incubation time (4–20 h), pH gradient (4.6–9.32) and carbon chain length (8, 10, 12) on the drug permeability through the synthetic phospholipid membrane in the PAMPA system. The results showed that intensive and significant synthetic phospholipids dependence of permeability influenced by the length of lipid’s hydrophobic carbon chain. The effective permeability constant (P_e) of each drug increased rapidly with time, then decreased slightly after reaching the maximum; the pH gradient changed the drug permeability according to the pH-partition hypothesis for drugs with diverse pK_a values; and longer hydrophobic chains in the synthetic phospholipid membrane improved the drug permeability, as observed for all test drugs at almost all incubation time points. This newly proposed PAMPA model considered the synthetic phospholipid membrane and showed good P_e-%FA correlation for the passive transport of drugs, making it a helpful supplementary method for PAMPA systems.     

Chemical versus Mechanical Perturbations on the Protonation State of Arginine in Complex Lipid Membranes: Insights from Microscopic pKa Calculations

Charged amino acids such as Arginine play important roles in many membrane-mediated biological processes such as voltage gating of ion channels and membrane translocation of cell penetration peptides. It is well established that local membrane deformation and formation of water defects are crucial to the stabilization of charged species in contact with the membrane, which suggests that mechanical properties of the membrane are relevant although a clear connection has not been established. As a quantitative measure, we study how changes in the composition and therefore mechanical properties of a lipid bilayer influence the pK_a of Arg in the membrane center using free energy simulations. Compared to previous studies in a single-component lipid bilayer containing saturated lipids or lipids with a modest degree of unsaturation, substantially larger pK_a shifts are observed in the presence of highly unsaturated lipid tails and cholesterol. Moreover, the underlying molecular mechanisms for the pK_a perturbation are distinct in different systems, with the unsaturated lipid tails mainly destabilizing the charged state of Arg and the cholesterol stabilizing the neutral state of Arg. The observed behaviors in both cases are at odds with predictions based on mechanical considerations at a mesoscopic level—highlighting that, while mechanical considerations are useful for stimulating hypothesis, their applicability to dissecting phenomena at the molecular-length scale is rather limited.     

Accurate Aqueous Proton Dissociation Constants Calculations for Selected Angiotensin-Converting Enzyme Inhibitors

Abstract

Studies that allow computing values of aqueous proton dissociation constants (pK_a), gas phase proton affinities, and the free energy of solvation have been performed for six members of angiotensin-I-converting enzyme (ACE) inhibitor family (captopril, enalaprilat, imidaprilat, ramiprilat, perindoprilat, and spiraprilat). Density functional theory (DFT) calculations using PBE1PBE functional on optimized molecular geometries have been carried out to investigate the thermodynamics of gas-phase protonation. The conductor-like polarizable continuum model (CPCM) solvation method at various levels of theory was applied to calculate the free energy of solvation for the ACE inhibitors and their respective anions. The CPCM solvation calculations were performed on both gas-phase and solvent-phase optimized structures. The combination of gas-phase and solvation energies according to the thermodynamic cycle enabled us to compute accurate pK_a values for the all studied molecules.     

pK(a) values for the unfolded state under native conditions explain the pH-dependent stability of PGB1

Understanding the role of electrostatics in protein stability requires knowledge of these interactions in both the folded and unfolded states. Electrostatic interactions can be probed experimentally by characterizing ionization equilibria of titrating groups, parameterized as pK_a values. However, pK_a values of the unfolded state are rarely accessible under native conditions, where the unfolded state has a very low population. Here, we report pK_a values under nondenaturing conditions for two unfolded fragments of the protein G B1 domain that mimic the unfolded state of the intact protein. pK_a values were determined for carboxyl groups by monitoring their pH-dependent ¹³C chemical shifts. Monte Carlo simulations using a Gaussian chain model provide corrections for changes in electrostatic interactions that arise from fragmentation of the protein. Most pK_a values for the unfolded state agree well with model values, but some residues show significant perturbations that can be rationalized by local electrostatic interactions. The pH-dependent stability was calculated from the experimental pK_a values of the folded and unfolded states and compared to experimental stability data. The use of experimental pK_a values for the unfolded state results in significantly improved agreement with experimental data, as compared to calculations based on model data alone.     

Properties of Hexadecaprenyl Monophosphate/Dioleoylphosphatidylcholine Vesicular Lipid Bilayers

In our study we investigated hemispherical phospholipid bilayer membranes and phospholipid vesicles made from hexadecaprenyl monophosphate (C₈₀-P), dioleoylphosphatidylocholine (DOPC) and their mixtures by voltammetric and transmission electron microscopy (TEM) techniques. The current-voltage characteristics, the membrane conductance-temperature relationships and the membrane breakdown voltage have been measured for different mixtures of C₈₀-P/DOPC. The membrane hydrophobic thickness and the activation energy of ion migration across the membrane have been determined. Hexadecaprenyl monophosphate decreased in comparison with DOPC bilayers, the membrane conductance, increased the activation energy and the membrane breakdown voltage for the various value of C₈₀-P/DOPC mole ratio, respectively. The TEM micrographs of C₈₀-P, DOPC and C₈₀-P/DOPC lipid vesicles showed several characteristic structures, which have been described. The data indicate that hexadecaprenyl monophosphate modulates the surface curvature of the membranes by the formation of aggregates in liquid-crystalline phospholipid membranes. We suggest that the dynamics and conformation of hexadecaprenyl monophosphate in membranes depend on the transmembrane electrical potential. The electron micrographs indicate that polyprenyl monophosphates with single isoprenyl chains form lipid vesicular bilayers. The thickness of the bilayer, evaluated from the micrographs, was 11 ± 1 nm. This property creates possibility of forming primitive bilayer lipid membranes by long single-chain polyprenyl phosphates in abiotic conditions. It can be the next step in understanding the origin of protocells. Received: 10 January 2000/Revised: 7 June 2000     

Molecular Dynamics Simulations of Phospholipid Bilayers

Abstract

Molecular dynamics (MD) simulations at 37°C have been performed on three phospholipid bilayer systems composed of the lipids DLPE, DOPE, and DOPC. The model used included 24 explicit lipid molecules and explicit waters of solvation in the polar head group regions, together with constant-pressure periodic boundary conditions in three dimensions. Using this model, a MD simulation samples part of an infinite planar lipid bilayer. The lipid dynamics and packing behavior were characterized. Furthermore, using the results of the simulations, a number of diverse properties including bilayer structural parameters, hydrocarbon chain order parameters, dihedral conformations, electron density profile, hydration per lipid, and water distribution along the bilayer normal were calculated. Many of these properties are available for the three lipid systems chosen, making them well suited for evaluating the model and protocols used in these simulations by direct comparisons with experimental data. The calculated MD behavior, chain disorder, and lipid packing parameter, i.e. the ratio of the effective areas of hydrocarbon tails and head group per lipid (a_t/a_h), correctly predict the aggregation preferences of the three lipids observed experimentally at 37°C, namely: a gel bilayer for DLPE, a hexagonal tube for DOPE, and a liquid crystalline bilayer for DOPC. In addition, the model and conditions used in the MD simulations led to good agreement of the calculated properties of the bilayers with available experimental results, demonstrating the reliability of the simulations. The effects of the cis unsaturation in the hydrocarbon chains of DOPE and DOPC, compared to the fully saturated one in DLPE, as well as the effects of the different polar head groups of PC and PE with the same unsaturated chains on the lipid packing and bilayer structure have been investigated. The results of these studies indicate the ability of MD methods to provide molecular-level insights into the structure and dynamics of lipid assemblies.     

Fatty acid interdigitation in stratum corneum model membranes: a neutron diffraction study

The influence of the chain length of the free fatty acid (FFA) in a stratum corneum (SC) lipid model membrane composed of N-(alpha-hydroxyoctadecanoyl)-phytosphingosine (CER [AP]), cholesterol (Ch), FFA and cholesterol sulphate (ChS) was investigated by neutron diffraction. The internal nanostructure of the SC lipid membrane in addition to the water distribution function was determined via calculation of the neutron scattering length density profile (Fourier profile). The Fourier profiles of the studied SC model membranes revealed that such membranes have a repeat distance approximately equal to the membrane thickness. Increasing the chain length of the FFA in the CER[AP] based model membrane did not cause an alteration of the internal nanostructure but led to a decrease in the membrane repeat distance from 45.6 A (palmitic acid, C16:0) to 43.7 A (cerotic acid, C26:0) due to a partial interdigitation of the FFA chains. Ceramide [AP] forces the long chain fatty acids to incorporate into the unchanged spacing of the bilayer, thereby obligating the FFA protrude partly through opposing leaflet. Furthermore, the longer chained free fatty acids tend to form a new separate so-called "fatty acid rich phase". Therefore, the elongation of the chain length of the FFA decreases the solubility of the FFA in the SC model membrane based on CER[AP].     

Decrease of elastic moduli of DOPC bilayers induced by a macrolide antibiotic, azithromycin

The elastic properties of membrane bilayers are key parameters that control its deformation and can be affected by pharmacological agents. Our previous atomic force microscopy studies revealed that the macrolide antibiotic, azithromycin, leads to erosion of DPPC domains in a fluid DOPC matrix [A. Berquand, M. P. Mingeot-Leclercq, Y. F. Dufrene, Real-time imaging of drug-membrane interactions by atomic force microscopy, Biochim. Biophys. Acta 1664 (2004) 198-205.]. Since this observation could be due to an effect on DOPC cohesion, we investigated the effect of azithromycin on elastic properties of DOPC giant unilamellar vesicles (GUVs). Microcinematographic and morphometric analyses revealed that azithromycin addition enhanced lipid membranes fluctuations, leading to eventual disruption of the largest GUVs. These effects were related to change of elastic moduli of DOPC, quantified by the micropipette aspiration technique. Azithromycin decreased both the bending modulus (k_c, from 23.1 ± 3.5 to 10.6 ± 4.5 k_BT) and the apparent area compressibility modulus (K_app, from 176 ± 35 to 113 ± 25 mN/m). These data suggested that insertion of azithromycin into the DOPC bilayer reduced the requirement level of both the energy for thermal fluctuations and the stress to stretch the bilayer. Computer modeling of azithromycin interaction with DOPC bilayer, based on minimal energy, independently predicted that azithromycin (i) inserts at the interface of phospholipid bilayers, (ii) decreases the energy of interaction between DOPC molecules, and (iii) increases the mean surface occupied by each phospholipid molecule. We conclude that azithromycin inserts into the DOPC lipid bilayer, so as to decrease its cohesion and to facilitate the merging of DPPC into the DOPC fluid matrix, as observed by atomic force microscopy. These investigations, based on three complementary approaches, provide the first biophysical evidence for the ability of an amphiphilic antibiotic to alter lipid elastic moduli. This may be an important determinant for drug: lipid interactions and cellular pharmacology.     

Thermodynamics and kinetics of phospholipid monomer-vesicle interaction

Resonance energy transfer between acyl chain labeled (7-nitro-2,1,3-benzoxadiazol-4-yl)phosphatidylcholine (NBD-PC) and head group labeled (lissamine rhodamine B sulfonyl)phosphatidylethanolamine (N-Rh-PE) was used to monitor the rate of NBD-PC transfer between two populations of dioleoylphosphatidylcholine (DOPC) vesicles. Equilibration of NBD-PC between DOPC vesicles occurs by the diffusion of soluble monomers through the water phase, which is a first-order process. Conditions were used such that the apparent transfer rate constant is equal to the rate constant for monomer-vesicle dissociation into solution. The partition distribution of NBD-PC between DOPC vesicles and water was determined by measuring the loss of NBD-PC from vesicles into solution following the dilution of small amounts of vesicles in buffer. The acyl chain length and temperature dependence of both the rate and partition measurements were determined, and a free energy diagram for NBD-PC-soluble monomer-vesicle interactions was constructed. The conclusions of this analysis are the following: NBD-PC dissociation from and association with the bilayer require passage through a high-energy transition state resulting predominantly from enthalpic energy. The activation energy for NBD-PC-vesicle dissociation becomes more positive and the standard free energy of NBD-PC transfer from water to vesicles becomes more negative with increasing acyl chain length. The standard free energy of transfer for NBD-PC from water to vesicles results predominantly from differences in enthalpy between the membrane and water phases. The enthalpy of activation for association increases with acyl chain length and is larger than expected for an aqueous diffusion-limited process in bulk water.     

The effect of the chain length distribution of free fatty acids on the mixing properties of stratum corneum model membranes

The stratum corneum (SC) plays a fundamental role in the barrier function of the skin. The SC consists of corneocytes embedded in a lipid matrix. The main lipid classes in the lipid matrix are ceramides (CERs), cholesterol (CHOL) and free fatty acids (FFAs). The aim of this study was to examine the effect of the chain length of FFAs on the thermotropic phase behavior and mixing properties of SC lipids. Fourier transform infrared spectroscopy and Raman imaging spectroscopy were used to study the mixing properties using either protonated or deuterated FFAs. We selected SC model lipid mixtures containing only a single CER, CHOL and either a single FFA or a mixture of FFAs mimicking the FFA SC composition. The single CER consists of a sphingoid base with 18 carbon atoms and an acyl chain with a chain length of 24 carbon atoms. When using lignoceric acid (24 carbon atoms) or a mixture of FFAs, the CER and FFAs participated in mixed crystals, but hydration of the mixtures induced a slight phase separation between CER and FFA. The mixed crystalline structures did not phase separate during storage even up to a time period of 3 months. When using palmitic acid (16 carbon atoms), a slight phase separation was observed between FFA and CER. This phase separation was clearly enhanced during hydration and storage. In conclusion, the thermotropic phase behavior and the mixing properties of the SC lipid mixtures were shown to strongly depend on the chain length and chain length distribution of FFAs, while hydration enhanced the phase separation.     

Highly perturbed pKa values in the unfolded state of hen egg white lysozyme

The majority of pK_a values in protein unfolded states are close to the amino acid model pK_a values, thus reflecting the weak intramolecular interactions present in the unfolded ensemble of most proteins. We have carried out thermal denaturation measurements on the WT and eight mutants of HEWL from pH 1.5 to pH 11.0 to examine the unfolded state pK_a values and the pH dependence of protein stability for this enzyme. The availability of accurate pK_a values for the folded state of HEWL and separate measurements of mutant-induced effects on the folded state pK_a values, allows us to estimate the pK_a values of seven acidic residues in the unfolded state of HEWL. Asp-48 and Asp-66 display pK_a values of 2.9 and 3.1 in our analysis, thus representing the most depressed unfolded state pK_a values observed to date. We observe a strong correlation between the folded state pK_a values and the unfolded state pK_a values of HEWL, thus suggesting that the unfolded state of HEWL possesses a large degree of native state characteristics.     

Steady-state characteristics of the proton receptor in the somatic membrane of rat sensory neurons

Steady-state characteristics of proton-activated permeability of the somatic membrane of rat sensory neurons were studied. Transmembrane ionic currents arising in response to application of solutions with low pH were measured during intracellular perfusion and simultaneous voltage clamping. A rapid change in proton concentration in the external medium was produced by a modified rapid application method. Steady-state desensitization of proton-induced permeability was found to develop in the region of weakly alkaline values (pK_a 7.15). The mechanism of desensitization is highly cooperative: Hill's parameter for dose-effect dependences was close to 7. Activation also is cooperative, but its Hill's parameters is about 2. Calcium and magnesium cations compete with protons, changing pK_a of dose-effect relationships for desensitization and activation, but they have only a weak effect on the value of Hill's parameter.     

A Permeability Study of O2 and the Trace Amine p-Tyramine through Model Phosphatidylcholine Bilayers

We study here the permeability of the hydrophobic O₂ molecule through a model DPPC bilayer at 323K and 350K, and of the trace amine p-tyramine through PC bilayers at 310K. The tyramine results are compared to previous experimental work at 298K. Nonequilibrium work methods were used in conjunction to simultaneously obtain both the potential of mean force (PMF) and the position dependent transmembrane diffusion coefficient, D(z), from the simulations. These in turn were used to calculate the permeability coefficient, P, through the inhomogeneous solubility-diffusion model. The results for O₂ are consistent with previous simulations, and agree with experimentally measured P values for PC bilayers. A temperature dependence in the permeability of O₂ through DPPC was obtained, with P decreasing at higher temperatures. Two relevant species of p-tyramine were simulated, from which the PMF and D(z) were calculated. The charged species had a large energetic barrier to crossing the bilayer of ~ 21 kcal/mol, while the uncharged, deprotonated species had a much lower barrier of ~ 7 kcal/mol. The effective in silico permeability for p-tyramine was calculated by applying three approximations, all of which gave nearly identical results (presented here as a function of the pK_a). As the permeability value calculated from simulation was highly dependent on the pK_a of the amine group, a further pK_a study was performed that also varied the fraction of the uncharged and zwitterionic p-tyramine species. Using the experimental P value together with the simulated results, we were able to label the phenolic group as responsible for the pK_a1 and the amine for the pK_a2, that together represent all of the experimentally measured pK_a values for p-tyramine. This agrees with older experimental results, in contrast to more recent work that has suggested there is a strong ambiguity in the pK_a values.     

Proton translocation in hydrogen bonds with large proton polarizability formed between a Schiff base and phenols

OH…N ? O^?…H⁺N hydrogen bonds formed between N-all-transretinylidene butylamine (Schiff base) and phenols (1:1) are studied by IR spectroscopy. It is shown that both proton limiting structures of these hydrogen bonds have the same weight with Δ pK_a (50%) = (pK_a protonated Schiff base minus pK_a phenol) = 5.5. With the largely symmetrical systems, continua demonstrate that these hydrogen bonds show great proton polarizability. In the Schiff base + tyrosine system in a non-polar solvent the residence time of the proton at the tyrosine residue is much larger than that at the Schiff base. In CH₂CCl₂ these hydrogen bonds show, however, still proton polarizability, i.e., the position of the proton transfer equilibrium OH…N ? O^?…H⁺N is shifted to and fro as function of the nature of the environment of this hydrogen bond. Consequences regarding bacteriorhodopsin are discussed.     

The role of membrane thickness in charged protein–lipid interactions

Charged amino acids are known to be important in controlling the actions of integral and peripheral membrane proteins and cell disrupting peptides. Atomistic molecular dynamics studies have shed much light on the mechanisms of membrane binding and translocation of charged protein groups, yet the impact of the full diversity of membrane physico-chemical properties and topologies has yet to be explored. Here we have performed a systematic study of an arginine (Arg) side chain analog moving across saturated phosphatidylcholine (PC) bilayers of variable hydrocarbon tail length from 10 to 18 carbons. For all bilayers we observe similar ion-induced defects, where Arg draws water molecules and lipid head groups into the bilayers to avoid large dehydration energy costs. The free energy profiles all exhibit sharp climbs with increasing penetration into the hydrocarbon core, with predictable shifts between bilayers of different thickness, leading to barrier reduction from 26 kcal/mol for 18 carbons to 6 kcal/mol for 10 carbons. For lipids of 10 and 12 carbons we observe narrow transmembrane pores and corresponding plateaus in the free energy profiles. Allowing for movements of the protein and side chain snorkeling, we argue that the energetic cost for burying Arg inside a thin bilayer will be small, consistent with recent experiments, also leading to a dramatic reduction in pK_a shifts for Arg. We provide evidence that Arg translocation occurs via an ion-induced defect mechanism, except in thick bilayers (of at least 18 carbons) where solubility-diffusion becomes energetically favored. Our findings shed light on the mechanisms of ion movement through membranes of varying composition, with implications for a range of charged protein–lipid interactions and the actions of cell-perturbing peptides. This article is part of a Special Issue entitled: Membrane protein structure and function.     

Relationship Between Body Fat Mass and Free Fatty Acid Kinetics in Men and Women

An increased release of free fatty acids (FFAs) into plasma likely contributes to the metabolic complications associated with obesity. However, the relationship between body fat and FFA metabolism is unclear because of conflicting results from different studies. The goal of our study was to determine the inter‐relationships between body fat, sex, and plasma FFA kinetics. We determined FFA rate of appearance (R_a) in plasma, by using stable isotopically labeled tracer techniques, during basal conditions in 106 lean, overweight, and obese, nondiabetic subjects (43 men and 63 women who had 7.0–56.0% body fat). Correlation analyses demonstrated: (i) no differences between men and women in the relationship between fat mass (FM) and total FFA R_a (µmol/min); (ii) total FFA R_a increased linearly with increasing FM (r = 0.652, P < 0.001); (iii) FFA R_a per kg FM decreased in a curvilinear fashion with increasing FM (r = ?0.806; P < 0.001); (iv) FFA R_a in relationship to fat‐free mass (FFM) was greater in obese than lean subjects and greater in women than in men; and (v) abdominal fat itself was not an important determinant of total FFA R_a. We conclude that total body fat, not regional fat distribution or sex, is an important modulator of the rate of FFA release into plasma. Although increased adiposity is associated with a decrease in fatty acid release in relationship to FM, this downregulation is unable to completely compensate for the increase in FM, so total FFA R_a and FFA R_a with respect to FFM are greater in women than in men and in obese than in lean subjects.     

Effect of phosphatidylcholine bilayer thickness and molecular order on the binding of the antimicrobial peptide maculatin 1.1

Antimicrobial peptides (AMPs) interact directly with bacterial membrane lipids. Thus, changes in the lipid composition of bacterial membranes can have profound effects on the activity of AMPs. In order to understand the effect of bilayer thickness and molecular order on the activity of AMPs, the interaction of maculatin 1.1 (Mac1.1) with phosphatidylcholine (PC) model membranes composed of different monounsaturated acyl chain lengths between 14 and 22 carbons was characterised by dual polarisation interferometry (DPI) and 31P and 1H solid-state NMR techniques. The thickness and bilayer order of each PC bilayer showed a linear dependence on the acyl chain length. The binding of Mac1.1 exhibited a biphasic dependency between the amount of bound Mac1.1 and bilayer thickness, whereby the mass of bound peptide increased from C14 to C16 and then decreased from C16 to C22. Significant perturbation of 31P chemical shift anisotropy (CSA) values was only observed for DOPC (C18) and DEPC (C22), respectively. In the case of DEPC, the greater range in CSA indicated different headgroup conformations or environments in the presence of Mac1.1. Overall, the results indicated that there is a significant change in the bilayer order upon binding of Mac1.1 and this change occurred in a co-operative manner at higher concentrations of Mac1.1 with increasing bilayer thickness and order. Overall, an optimum bilayer thickness and lipid order may be required for effective membrane perturbation by Mac1.1 and increasing the bilayer thickness and order may counteract the activity of Mac1.1 and play a role in antimicrobial resistance to AMPs.     

The effects of pK(a) tuning on the thermodynamics and kinetics of folding: design of a solvent-shielded carboxylate pair at the a-position of a coiled-coil

The tuning of the pK_a of ionizable residues plays a critical role in various protein functions, such as ligand-binding, catalysis, and allostery. Proteins harness the free energy of folding to position ionizable groups in highly specific environments that strongly affect their pK_a values. To investigate the interplay among protein folding kinetics, thermodynamics, and pK_a modulation, we introduced a pair of Asp residues at neighboring interior positions of a coiled-coil. A single Asp residue was replaced for an Asn side chain at the a-position of the coiled-coil from GCN4, which was also crosslinked at the C-terminus via a flexible disulfide bond. The thermodynamic and kinetic stability of the system was measured by circular dichroism and stopped-flow fluorescence as a function of pH and concentration of guanidine HCl. Both sets of data are consistent with a two-state equilibrium between fully folded and unfolded forms. Distinct pK_a values of 6.3 and 5.35 are assigned to the first and second protonation of the Asp pair; together they represent an energetic difference of 5 kcal/mol relative to the protonation of two Asp residues with unperturbed pK_a values. Analysis of the rate data as a function of pH and denaturant concentration allowed calculation of the kinetic constants for the conformational transitions of the peptide with the Asp residues in the doubly protonated, singly protonated, and unprotonated forms. The doubly and singly protonated forms fold rapidly, and a ϕ-value analysis shows that their contribution to folding occurs subsequent to the transition state ensemble for folding. By contrast, the doubly charged state shows a reduced rate of folding and a ϕ-value near 0.5 indicative of a repulsive interaction, and possibly also heterogeneity in the transition state ensemble.     

Catalytic subunit of cAMP-dependent protein kinase: Electrostatic features and peptide recognition

The electrostatic field was calculated for the mammalian cAMP-dependent protein kinase (PKA) catalytic subunit (C-subunit) complexed with a 20-residue peptide from a heat stable protein kinase inhibitor (PKI: 5–24). The electrostatic field was also calculated for the C-subunit complexed with a modeled heptapeptide substrate that has been used extensively in structure/function studies for the C-subunit. Perturbations in the electrostatic free energy were calculated when single ionizable active site residues were mutated to alanine. These perturbations in electrostatic free energy were correlated to changes in the binding energy measured in a charge-to-alanine scan of the homologous yeast C-subunit by M. J. Zoller and C. S. Gibbs [(1991) Journal of Biological Chemistry, Vol. 266, pp. 8923–8931; C. S. Gibbs and M. J. Zoller (1991) Biochemistry, Vol. 30, p. 22]. This analysis indicated that the substrate binding parameters primarily depend on electrostatic interactions between a substrate or inhibitor and the C-subunit. Amino acid replacements that led to large perturbations in the electrostatic field are listed in the text. pK_a shifts were also calculated for the substrate's phosphate accepting atom, the serine hydroxyl oxygen, when the active site ionizable residues were changed to structurally similar uncharged amino acids. The theoretical mutation of three active site residues caused large shifts in this parameter: E91Q, D166N, and D184N. The calculated pK_a shifts for these mutants indicate that the rate of phosphotransfer should be markedly reduced in these cases. This prediction has been experimentally confirmed for the D166N mutant. The correlation between calculated electrostatic free energy changes and measured binding energy, and pK_a shifts with phosphotransfer for C-subunit mutants were within experimental error of the measurements. The calculations of electrostatic energy and ΔpK_a have identified previously unconsidered active site residues in the mammalian C-subunit that contribute to binding energy and phosphotransfer. © 1996 John Wiley & Sons, Inc.