The prototropic behavior of alpha-chymotrypsin and chymotrypsinogen in water and formaldehyde. An examination of the reactivity of the amino groups in formaldehyde

Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems

An ability to accurately simulate the dynamic behavior of concentrated macromolecular solutions would be of considerable utility in studies of a wide range of biological systems. With this goal in mind, a Brownian dynamics (BD) simulation method is reported here that allows systems to be modeled that comprise in excess of 1000 protein molecules, all of which are treated in atomic detail. Intermolecular forces are described in the method using an energy function that incorporates electrostatic and hydrophobic interactions and that is calibrated to reproduce experimental thermodynamic information with a single adjustable parameter. Using the method, BD simulations have been performed over a wide range of pH and ionic strengths for three proteins: hen egg white lysozyme (HEWL), chymotrypsinogen, and T4 lysozyme. The simulations reproduce experimental trends in second virial coefficients (B(22)) and translational diffusion coefficients, correctly capture changes in B(22) values due to single amino acid substitutions, and reveal a new explanation for the difficulties reported previously in the literature in reproducing B(22) values for protein solutions of very low ionic strength. In addition, a strong correlation is found between a residue's probability of being involved in a protein-protein contact in the simulations and its probability of being involved in an experimental crystal contact. Finally, exploratory simulations of HEWL indicate that the simulation model also gives a promising description of behavior at very high protein concentrations (approximately 250 g/L), suggesting that it may provide a suitable computational framework for modeling the complex behavior exhibited by macromolecules in cellular conditions.

The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment

The large dipole moment of globular proteins has been well known because of the detailed studies using dielectric relaxation and electro-optical methods. The search for the origin of these dipolemoments, however, must be based on the detailed knowledge on protein structure with atomic resolutions. At present, we have two sources of information on the structure of protein molecules: (1) x-ray databases obtained in crystalline state; (2) NMR databases obtained in solution state. While x-ray databases consist of only one model, NMR databases, because of the fluctuation of the protein folding in solution, consist of a number of models, thus enabling the computation of dipole moment repeated for all these models. The aim of this work, using these databases, is the detailed investigation on the interdependence between the structure and dipole moment of protein molecules. The dipole moment of protein molecules has roughly two components: one dipole moment is due to surface charges and the other, core dipole moment, is due to polar groups such as N--H and C==O bonds. The computation of surface charge dipole moment consists of two steps: (A) calculation of the pK shifts of charged groups for electrostatic interactions and (B) calculation of the dipole moment using the pK corrected for electrostatic shifts. The dipole moments of several proteins were computed using both NMR and x-ray databases. The dipole moments of these two sets of calculations are, with a few exceptions, in good agreement with one another and also with measured dipole moments.

Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient

Interactions between proteins are often sufficiently weak that their study through the use of conventional structural techniques becomes problematic. Of the few techniques capable of providing experimental measures of weak protein-protein interactions, perhaps the most useful is the second virial coefficient, B(22), which quantifies a protein solution's deviations from ideal behavior. It has long been known that B(22) can in principle be computed, but only very recently has it been demonstrated that such calculations can be performed using protein models of true atomic detail (Biophys. J. 1998, 75:2469-2477). The work reported here extends these previous efforts in an attempt to develop a transferable energetic model capable of reproducing the experimental trends obtained for two different proteins over a range of pH and ionic strengths. We describe protein-protein interaction energies by a combination of three separate terms: (i) an electrostatic interaction term based on the use of effective charges, (ii) a term describing the electrostatic desolvation that occurs when charged groups are buried by an approaching protein partner, and (iii) a solvent-accessible surface area term that is used to describe contributions from van der Waals and hydrophobic interactions. The magnitude of the third term is governed by an adjustable, empirical parameter, gamma, that is altered to optimize agreement between calculated and experimental values of B(22). The model is applied separately to the proteins lysozyme and chymotrypsinogen, yielding optimal values of gamma that are almost identical. There are, however, clear difficulties in reproducing B(22) values at the extremes of pH. Explicit calculation of the protonation states of ionizable amino acids in the 200 most energetically favorable protein-protein structures suggest that these difficulties are due to a neglect of the protonation state changes that can accompany complexation. Proper reproduction of the pH dependence of B(22) will, therefore, almost certainly require that account be taken of these protonation state changes. Despite this problem, the fact that almost identical gamma values are obtained from two different proteins suggests that the basic energetic formulation used here, which can be evaluated very rapidly, might find use in dynamical simulations of weak protein-protein interactions at intermediate pH values.

Effect of solution pH on protein transport through ultrafiltration membranes

Although a number of previous studies have demonstrated that solution pH can have a dramatic effect on protein transport through ultrafiltration membranes, the exact origin of this behavior has been unclear. Experimental data were obtained for the transport of a broad range of proteins with different surface charge and molecular weight. The effective hydrodynamic size of the proteins was evaluated using size-exclusion chromatography. The membrane charge, both before and after exposure to a given protein, was evaluated using streaming potential measurements. In most cases, the electrostatic interactions were dominated by the distortion of the electrical double layer surrounding the protein, leading to a distinct maximum in protein transmission at the protein isoelectric point. Attractive electrostatic interactions did occur when the protein and membrane had a large opposite charge, causing a second maximum in transmission at a pH between the isoelectric points of the protein and membrane. The sieving data were in good agreement with theoretical calculations based on available models for the partitioning of charged solutes in cylindrical pores. Copyright 1999 John Wiley & Sons, Inc.

Molecular origins of osmotic second virial coefficients of proteins

The thermodynamic properties of protein solutions are determined by the molecular interactions involving both solvent and solute molecules. A quantitative understanding of the relationship would facilitate more systematic procedures for manipulating the properties in a process environment. In this work the molecular basis for the osmotic second virial coefficient, B22, is studied; osmotic effects are critical in membrane transport, and the value of B22 has also been shown to correlate with protein crystallization behavior. The calculations here account for steric, electrostatic, and short-range interactions, with the structural and functional anisotropy of the protein molecules explicitly accounted for. The orientational dependence of the protein interactions is seen to have a pronounced effect on the calculations; in particular, the relatively few protein-protein configurations in which the apposing surfaces display geometric complementarity contribute disproportionately strongly to B22. The importance of electrostatic interactions is also amplified in these high-complementarity configurations. The significance of molecular recognition in determining B22 can explain the correlation with crystallization behavior, and it suggests that alteration of local molecular geometry can help in manipulating protein solution behavior. The results also have implications for the role of protein interactions in biological self-organization.

Measurement and computation of the dipole moment of globular proteins III: Chymotrypsin

The dipole moments of alpha- and gamma-chymotrypsin are determined experimentally using the dielectric constant measuring method. The values thus obtained are compared with the results of the electric dichroism measurements for alpha-chymotrypsins by other investigators. The agreement is reasonably good, if not satisfactory. The cause of difference appears to be due to the difficulty of finding the correct internal field. The interaction between two neighboring dipoles is found to be a minor component of the local fields. Secondly, the dipole moment of alpha-chymotrypsin was computed using Protein Data Bases. The dipole moment of proteins consists of two major components, the moment due to fixed surface charges and the core moment due to polar chemical bonds. The method of calculation was described in detail in previous papers. The pK shifts of polar side chains were calculated using the methods of Tanford et al. and its modification by Warshel et al. The agreement between measured and calculated dipole moments is satisfactory.

The nature of protein dipole moments: experimental and calculated permanent dipole of alpha-chymotrypsin

The electric dichroism of alpha-chymotrypsin has been measured in buffers of various pH values and ion compositions. The stationary dichroism obtained as a function of the electric field strength is not compatible with an induced dipole mechanism and clearly shows that alpha-chymotrypsin is associated with a substantial permanent dipole moment. After correction for the internal directing electric field according to a sphere model, the dipole moment is 1.6 X 10(-27) C m at pH 8.3 (corresponding to 480 D). This value decreases with decreasing pH (to 1.2 X 10(-27) C m at pH 4.2), but is almost independent of the monovalent salt concentration in the range from 2 to 12 mM and of Mg2+ addition up to 1 mM. The assignment of the permanent dipole moment is confirmed by analysis of the dichroism rise curves. The dichroism decay time constants of (31 +/- 1) ns at 2 degrees C can be represented by a spherical model with a radius of 25-26 A, which is consistent with the known X-ray structure. The limiting linear dichroism is slightly dependent on the buffer composition and demonstrates subtle variations of the protein structure. As a complement to the experimental results, electric and hydrodynamic parameters of alpha-chymotrypsin have been calculated according to the known X-ray structure. Bead model simulations provide the center of diffusion, which is used to calculate dipole moments according to the equilibrium charge distribution evaluated from standard pK values.(ABSTRACT TRUNCATED AT 250 WORDS)

The role of amino-terminal alanine in the control of conformation and activity of alpha-chymotrypsin

Novel acetylated derivatives of three different three-chained chymotrypsins were prepared from bovine chymotrypsinogen A and their catalytic properties and kinetics of denaturation in urea were compared with those of the corresponding non-acetylated enzymes. Measurements of the Km (apparent) as a function of pH confirmed earlier findings of Valenzuela and Bender [J. Biol. Chem. 248, 4909-4914 (1973)] that the alpha-species of chymotrypsin is much more sensitive to reversible inactivation at high pH compared to its sister three-chained chymotrypsins, alpha 1 and kappa-chymotrypsin. Similarly, the denaturation rate constants in 8 M urea of alpha-chymotrypsin were much more sensitive to high pH than alpha 1 and kappa-chymotrypsin. The urea denaturation study showed a transition at about pH 8 to a more urea-sensitive form of alpha-chymotrypsin, whereas alpha 1 and kappa-chymotrypsin were relatively insensitive to a change in pH from 6.5 to 10. When the N-terminal Ala149 of alpha-chymotrypsin was acetylated, thus preventing protonation of the N terminus, the active enzyme derivative displayed the same Km (app) vs pH profile as alpha 1 and kappa-chymotrypsin. Urea denaturation studies with this masked derivative also showed that the pH-dependent transition of native alpha-chymotrypsin at pH 8 was eliminated. These results demonstrate that it is the presence of the protonated Ala149 residue in alpha-chymotrypsin that accounts for much of the hypersensitivity of this enzyme species to inactivation and urea denaturation in the pH region 7.5-10.

Acylation of the alanine149 N-terminal of alpha-chymotrypsin and its effect on catalytic function

A novel, active derivative of alpha-chymotrypsin was prepared from alanine-neochymotrypsinogen in which the epsilon-amino groups and the alpha-amino group of N-terminal Ala149 were acetylated. The catalytic properties at neutral and alkaline pH of this enzyme derivative were compared with those of a control alpha-chymotrypsin derivative in which only the epsilon-amino groups were acetylated. While the Km (app) of the two derivatives were the same at pH 7 to 8, at more alkaline pH the derivative having the masked Ala149 had much lower Km (app) values than the control. It is concluded that the inactivation of alpha-chymotrypsin at high pH is linked, at least in part, to the ionization state of its N-terminal Ala149 group.