Coordinate ion pair formation between EcoRI endonuclease and DNA

The free energy of the binding reaction between EcoRI restriction endonuclease and a specific cognate dodecadeoxynucleotide (d(CGCGAATTCGCG)) has contributions from both electrostatic and nonelectrostatic components. These contributions were dissected by measuring the effects of varying salt concentration on the equilibrium binding constant and applying the thermodynamic analyses of Record et al. (Record, M. T., Jr., Lohman, T. M., and deHaseth, P. L. (1976) J. Mol. Biol. 107, 145-158). Endonuclease mutation S187 (Arg 187 to Ser) (Greene, P. J., Gupta, M., Boyer, H. W., Brown, W. E., and Rosenberg, J. M. (1981) J. Biol. Chem. 256, 2143-2153) did not significantly affect the nonelectrostatic component but did perturb the electrostatic contribution to the binding energy (we are numbering the amino acid residues according to the DNA sequence). The former was determined by extrapolating the linear portion of the salt dependence curve (0.125 to 0.25 M KCl) to 1 M ionic strength, with the same result for both wild type and S187 endonucleases at both pH 6.0 and 7.4 (-8.5 +/- 1.5 kcal/mol or greater than 50% of the total binding free energy). The slopes of these same curves yield estimates of eight ionic interactions between wild type endonuclease and the DNA at both pH values. By contrast, binding of EcoRI-S187 to dodecanucleotide involves six charge-charge interactions at pH 6.0. Only two ionic interactions are observed at pH 7.4. This was unexpected since gel permeation chromatography demonstrated that the recognition complex for both wild type and S187 proteins contains an enzyme dimer and a DNA duplex. EcoRI-S187 endonuclease retains wild type DNA sequence specificity, and the rate of the phosphodiester hydrolysis step is also unchanged. Thus, electrostatic interactions are functionally separable from sequence recognition and strand cleavage. Our results also establish that arginine 187 plays a key role in the electrostatic function and suggest that it might be located at the DNA-protein interface. The disproportionate loss of ion pairs at pH 7.4 can be rationalized by a model which suggests that six conformationally mobile ionic groups on the protein act in a coordinated manner during the interaction with DNA.     

Interplay between the electrostatic membrane potential and conformational changes in membrane proteins

Transmembrane electrostatic membrane potential is a major energy source of the cell. Importantly, it determines the structure as well as function of charge‐carrying membrane proteins. Here, we discuss the relationship between membrane potential and membrane proteins, in particular whether the conformation of these proteins is integrally connected to the membrane potential. Together, these concepts provide a framework for rationalizing the types of conformational changes that have been observed in membrane proteins and for better understanding the electrostatic effects of the membrane potential on both reversible as well as unidirectional dynamic processes of membrane proteins.     

The geometries of interacting arginine-carboxyls in proteins

The geometries are reported for interacting arginine-carboxyl pairs obtained from 37 high resolution protein structures solved to a resolution of 2.0 A or better. The closest interatomic distance between the guanidinium and carboxyl is less than 4.2 A for 74 arginine and carboxyl groups, with the majority of these lying within hydrogen-bonding distance (2.6-3.0 A). Interacting pairs have been transformed into a common orientation, and arginine-carboxyl, and carboxyl-arginine geometries have been calculated. This has been defined in terms of the spherical polar angles T theta, T phi, and the angle P, between the guanidinium and carboxyl planes. Results show a clear preference for the guanidinium and carboxyl groups to be approximately coplanar, and for the carboxyl oxygens to hydrogen bond with the guanidinium nitrogens. Single nitrogen-single oxygen is the most common type of interaction, however twin nitrogen-twin oxygen interactions also occur frequently. The majority of these occur between the carboxyl oxygens and the NH1 and NE atoms of the arginine, and are only rarely observed for NH1 and NH2. The information presented may be of use in the modelling of arginine-carboxyl interactions within proteins.     

Spatial optimization of electrostatic interactions between the ionized groups in globular proteins

A model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge–charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge consetellations (generated by a Monte-Carlo technique). The statistical probability of occurrence of random structures with electrostatic energies lower than the energy of the native protein is suggested as a criterion for spatial optimization of the electrostatic interactions. The results support the hypothesis that the folding process optimizes the stabilizing effect of electrostatic interactions, but to very different degree for different proteins. A parallel analysis of ion pairs shows that the optimization of the electrostatic term in globular proteins has increasingly gone in the direction of rejecting the repulsive short contacts between charges of equal sign than of creating of more salt bridges (in comparison with the statistically expected number of shortrange ion pairs in the simulated random structures). It is observed that the decrease in the spatial optimization of the electrostatic interactions is usually compensated for by an appearance of disulfide bridges in the covalent structure of the examined proteins. © 1994 Wiley-Liss, Inc.     

Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility.

A new method for including local conformational flexibility in calculations of the hydrogen ion titration of proteins using macroscopic electrostatic models is presented. Intrinsic pKa values and electrostatic interactions between titrating sites are calculated from an ensemble of conformers in which the positions of titrating side chains are systematically varied. The method is applied to the Asp, Glu, and Tyr residues of hen lysozyme. The effects of different minimization and/or sampling protocols for both single-conformer and multi-conformer calculations are studied. For single-conformer calculations it is found that the results are sensitive to the choice of all-hydrogen versus polar-hydrogen-only atomic models and to the minimization protocol chosen. The best overall agreement of single-conformer calculations with experiment is obtained with an all-hydrogen model and either a two-step minimization process or minimization using a high dielectric constant. Multi-conformational calculations give significantly improved agreement with experiment, slightly smaller shifts between model compound pKa values and calculated intrinsic pKa values, and reduced sensitivity of the intrinsic pKa calculations to the initial details of the structure compared to single-conformer calculations. The extent of these improvements depends on the type of minimization used during the generation of conformers, with more extensive minimization giving greater improvements. The ordering of the titrations of the active-site residues, Glu-35 and Asp-52, is particularly sensitive to the minimization and sampling protocols used. The balance of strong site-site interactions in the active site suggests a need for including site-site conformational correlations.     

Determination of metformin in plasma using a new ion pair solid phase extraction technique and ion pair liquid chromatography

This article describes the development of the first ion pair solid phase extraction technique (IPSPE), which has been applied to the extraction of metformin from plasma samples. In addition an ion pair chromatographic method was developed for the specific HPLC determination of metformin. Several extraction and HPLC methods have been described previously for metformin, however, most of them did not solve the problems associated with the high polarity of this drug. Drug recovery in the developed method was found to be more than 98%. The limit of detection and limit of quantification was 3 and 5 ng/ml, respectively. The intraday and interday precision (measured by coefficient of variation, CV%) was always less than 9%. The accuracy (measured by relative error, R.E.%) was always less than 6.9%. Stability analysis showed that metformin is stable for at least 3 months when stored at -70 degrees C. The method has been applied to 150 patient samples as part of a medication adherence study.     

Local electrostatic optimization in proteins.

A simple electrostatic model has been used to investigate the extent to which the structure of protein molecules is organized to optimize the internal electrostatic interactions. We find that the model provides a favorable total intra-protein electrostatic energy for almost all polar and charged groups of atoms, suggesting a high degree of structural optimization. By contrast, a significant fraction of individual group-group interactions are found to be unfavorable. An analysis as a function of the range of interactions included shows the electrostatic organization is generally relatively short range (up to 6 or 7 A between group centers). Although the model is very simple, it is useful for assessing the overall quality of protein experimental structures, for pin-pointing some types of errors and as a guide to improving protein design.     

Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins.

The three-dimensional optimization of the electrostatic interactions between the charged amino acid residues and the peptide partial charges was studied by Monte-Carlo simulations on a set of 127 nonhomologous protein structures with known atomic coordinates. It was shown that this type of interaction is very well optimized for all proteins in the data set, which suggests that they are a valuable driving force, at least for the native side-chain conformations. Similar to the optimization of the charge-charge interactions (Spassov VZ, Karshikoff AD, Ladenstein R, 1995, Protein Sci 4:1516-1527), the optimization effect was found more pronounced for enzymes than for proteins without enzymatic function. The asymmetry in the interactions of acidic and basic groups with the peptide dipoles was analyzed and a hypothesis was proposed that the properties of peptide dipoles are a factor contributing to the natural selection of the basic amino acids in the chemical composition of proteins.     

Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper

In solution proteins often exhibit backbone and side-chain flexibility. Yet electrostatic interactions in proteins are sensitive to motions. Hence, here we study the contribution of ion pairs toward protein stability in a range of conformers which sample the conformational space in solution. Specifically, we focus on the electrostatic contributions of ion pairs to the stability of each of the conformers in the NMR ensemble of the c-Myc-Max leucine zipper and to their average energy minimized structure. We compute the electrostatic contributions of inter- and intra-helical ion pairs and of an ion pair network. We find that the electrostatic contributions vary considerably among the 40 NMR conformers. Each ion pair, and the network, fluctuates between being stabilizing and being destabilizing. This fluctation reflects the variability in the location of the ion pairing residues and in the geometric orientation of these residues, both with respect to each other and with respect to other charged groups in the rest of the protein. Ion pair interactions in the c-Myc-Max leucine zipper in solution depend on the protein conformer which is analyzed. Hence, the overall stabilizing (or destabilizing) contribution of an ion pair is conformer population-dependent. This study indicates that free energy calculations performed using the continuum electrostatics methodology are sensitive to protein conformational details.     

Enhanced ionic interaction in narrow pores and ion pair formation

The same physical phenomenon that gives rise to the increase in the electrostatic self-energy of an ion within a narrow water-filled pore is shown to result in interionic electrical interactions within the pore that are much stronger and of longer range than those between the same ions in the same solution in bulk. Because of the much enhanced attraction between ions of opposite charge within the pore the formation of ion pairs becomes likely, even for strong electrolytes that are fully dissociated in the same solution when not spatially confined. Some predicted consequences of ion pair formation in narrow pores that may be experimentally detected are discussed. It is shown that, in a simple passive pore, due to ion pair formation, an Ussing unidirectional flux ratio exponent of less than 1 is predicted. This is usually thought to characterize a carrier rather than a pore.     

Relationship between synthesis and cleavage of poliovirus-specific proteins.

Poliovirus proteinase was studied in vitro in lysates from poliovirus-infected HeLa cells. Preincubation of these lysates caused (i) a reduction in poliovirus proteinase activity and (ii) a partial dependence on exogenous mRNA for optimal translation. Proteins translated from endogenous poliovirus RNA in preincubated extracts from virus-infected HeLa cells are poorly cleaved. This cleavage deficiency is alleviated by adding fresh poliovirus RNA to the translation system, thus, allowing re-initiation to occur. This suggests that the poliovirus proteinase is highly unstable.     

Relationship between L-alanine and sodium ion transport in isolated renal tubules.

1. Rat renal tubules were isolated by incubation with collagenase. The Na+ concentration in the tubules at 37 degrees C was increased by additions of g-strophantin and L-alanine. The increase of Na+ in the presence of both g-strophantin and L-alanine was stronger than with either alone. 2. Radioactive sodium (22-Na), which was taken up by the tubules at 0 degrees C in K+-free medium, was more slowly washed out in the buffer with added g-strophantin than in the control buffer, but L-alanine had no effect. 3. At 0 degrees C incubation without K+, g-strophantin did not affect the 22-Na transport of the tubules. But under the same conditions, L-alanine increased Na+ uptake significantly, and in conjunction with it, L-alanine uptake was also increased. 4. The relationship between L-alanine uptake and intra- extracellular Na+ concentration gradients was linear. The ration of L-alanine to Na+ uptake at 0 degrees C was about 1:2. 5. In the incubation without K+ at 0 degrees C, L-alanine could be accumulated in tubules against the chemical concentration gradient (about 1.5-fold). 6. In the incubation without K+ at 37 degrees C, the L-alanine concentration in tubules after 5 min was already steady (Ci/Ce = 2.2), but with K+ it was not stabilized after 10 min. The ration Ci/Ce with K+ WAS HIGHER THAN WITHOUT K+. 7. G-Strophantin, p-hydroxymercuribenzoate, amiloride, and 2,4-dinitrophenol inhibited L-alanine uptake in the tubules and at the same time increased Na+ concentration. The relationship between the L-alanine uptakes inhibited by g-strophantin, amiloride and dinitrophenol, and the respective intra- extracellular Na+ concentration gradients was strikingly linear. But in the case of p-hydroxymercuribenzoate there was no correlation. 8. The results indicate that L-alanine transport into the renal tubules might be regulated mainly by the intra- extracellular Na+ concentration gradient and that inhibitors such as g-strophantin, amiloride, and dinitrophenol could have a secondary effect on the L-alanine transport which follows the change of Na+ concentration in cells. p-Hydroxymercuribenzoate might have an inhibiting effect on the binding of carrier with Na+ and/or L-alanine.     

Relationship between catalytic properties, fixed charge concentration and electrostatic potential of polyelectrolyte-bound enzymes

An equation for the calculation of the electrostatic potentials of polyelectrolyte-enzyme supports from electrostatic parameters has been derived by relating two different theories which describe the catalytic behaviour of polyelectrolyte-bound enzymes. The electrostatic potentials of polyionic supports have been determined by use of experimental results, on the one hand, from the fixed charge concentration and the ionic strength, on the other hand, from pH- and Km-shifts of immobilized enzymes. The accordance of potentials calculated from electrostatic and kinetic parameters confirms the macroscopic carrier-enzyme model.     

Extraction of membrane proteins in low ionic strengths]

Hemoglobin and the low molecular weight proteins 8 and 9 are extracted from ghosts during low ionic washing after the hypotonic hemolysis of erythrocytes. Furthermore, a loss of the proteins 4.5 and 7 was observed. The protein patterns of ghosts after isotonic hemolysis by freezing and thawing resemble the ghost protein patterns after hypotonic hemolysis and incomplete deprivation of Hb. Many if not all membrane proteins are eluted by repeated incubations of the ghosts in solutions of low ionic strength in the presence of EDTA. The spectrins, the proteins 5, 4.5, 7 and residual Hb are extracted preferentially. A selective extraction of the spectrins and the protein 5 is not detectable under these conditions. Often the spectrin bands are subdivided following low ionic incubation.