A chromatographic approach to the determination of relative free energies of interaction between hydrophobic and amphiphilic amino acid side chains

Computational completion of the Aurora interaction region of N-Myc in the Aurora a kinase complex

Inhibiting protein-protein interactions of the Myc family is a viable pharmacological strategy for modulation of the levels of Myc oncoproteins in cancer. Aurora A kinase (AurA) and N-Myc interaction is one of the most attractive targets of this strategy because formation of this complex blocks proteasomal degradation of N-Myc in neuroblastoma. Two crystallization studies have captured this complex (PDB IDs: 5g1x, 7ztl), partially resolving the AurA interaction region (AIR) of N-Myc. Prompted by the missing N-Myc fragment in these crystal structures, we modeled the complete structure between AurA and N-Myc, and comprehensively analyzed how the incomplete and complete N-Myc behave in complex by molecular dynamics simulations. Molecular dynamics simulations of the incomplete PDB complex (5g1x) repeatedly showed partial dissociation of the short N-Myc fragment (61-89) from the kinase. The missing N-Myc (19-60) fragment was modeled utilizing the N-terminal lobe of AurA as the protein-protein interaction surface, wherein TPX2, a well-known partner of AurA, also binds. Binding free energy calculations along with flexibility analysis confirmed that the complete AIR of N-Myc stabilizes the complex, accentuating the N-terminal lobe of AurA as a binding site for the missing N-Myc fragment (19-60). We further generated additional models consisting of only the missing N-Myc (19-60), and the fused form of TPX2 (7-43) and N-Myc (61-89). These partners also formed more stable interactions with the N-terminal lobe of AurA than did the incomplete N-Myc fragment (61-89) in the 5g1x complex. Altogether, this study provides structural insights into the involvement of the N-terminus of the AIR of N-Myc and the N-terminal lobe of AurA in formation of a stable complex, reflecting its potential for effective targeting of N-Myc.

Inactivation and Site-specific Oxidation of Aquatic Extracellular Bacterial Leucine Aminopeptidase by Singlet Oxygen

Extracellular enzymes are master recyclers of organic matter, and to predict their functional lifetime, we need to understand their environmental transformation processes. In surface waters, direct and indirect photochemical transformation is a known driver of inactivation. We investigated molecular changes that occur along with inactivation in aminopeptidase, an abundant class of extracellular enzymes. We studied the inactivation kinetics and localized oxidation caused by singlet oxygen, ¹O₂, a major photochemically derived oxidant toward amino acids. Aminopeptidase showed second-order inactivation rate constants with ¹O₂ comparable to those of free amino acids. We then visualized site-specific oxidation kinetics within the three-dimensional protein and demonstrated that fastest oxidation occurred around the active site and at other reactive amino acids. However, second-order oxidation rate constants did not correlate strictly with the ¹O₂-accessible surface areas of those amino acids. We inspected site-specific processes by a comprehensive suspect screening for 723,288 possible transformation products. We concluded that histidine involved in zinc coordination at the active site reacted slower than what was expected by its accessibility, and we differentiated between two competing reaction pathways of ¹O₂ with tryptophan residues. This systematic analysis can be directly applied to other proteins and transformation reactions.

Free energies of amino acid adsorption on silica in neutral aqueous medium as estimated from high-performance liquid-chromatographic retention data

Equilibrium constants (K) and free energies (-ΔG) of amino acid adsorption on silica in a neutral aqueous medium were calculated from the retention values measured by means of high-performance liquid chromatography on a silica gel column. For most amino acids (with the exception of proline) -ΔG values were negative andK < 1, thus showing very low adsorption. Influence of the structure of theα-substituent on adsorbability is analyzed. A linear dependence of -ΔG on the number of aliphatic carbon atoms was shown for the series: glycine-alanine-valine-leucine-isoleucine.

Self-interaction chromatography: a tool for the study of protein-protein interactions in bioprocessing environments

We describe a new protein characterization technique called self-interaction chromatography (SIC), which exploits the specificity of protein-protein interactions that is common to protein aggregates and enables the rapid screening of protein formulation additives as physical stabilizers against aggregation. This technique also enables the identification of specific interaction sites and the determination of their relative importance for self-association. Mannitol, glycine, and dextran 40 were tested for their stabilizing effect toward the model protein lysozyme. Dextran 40 exhibited a poor stabilizing effect. While mannitol stabilized both the native and acid-denatured forms of lysozyme, glycine stabilized the native form with respect to the denatured species. These results are in good agreement with findings in the formulation literature. The SIC shows tremendous potential as a rapid formulation development tool. We also screened two putative interaction sites for involvement in the self-association of lysozyme and estimated the associated binding energies using a binding isotherm model that we developed. The sites screened consisted of residues 41-48 and 125-128 and were selected based on their apparent importance in forming crystal contacts in several different crystal forms of lysozyme. Of the two sites, only residues 125-128 were found to influence self-association under the conditions we employed. Because the success of this technique depends on the exploitation of self-interactions between native species, several important applications are also suggested such as separating native from misfolded or variant species and probing site utilization in aggregation versus crystallization phenomena.

Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions

We perform a statistical analysis of atomic distributions as a function of the distance R from the molecular geometrical center in a nonredundant set of compact globular proteins. The number of atoms increases quadratically for small R, indicating a constant average density inside the core, reaches a maximum at a size-dependent distance R(max), and falls rapidly for larger R. The empirical curves turn out to be consistent with the volume increase of spherical concentric solid shells and a Fermi-Dirac distribution in which the distance R plays the role of an effective atomic energy epsilon(R) = R. The effective chemical potential mu governing the distribution increases with the number of residues, reflecting the size of the protein globule, while the temperature parameter beta decreases. Interestingly, betamu is not as strongly dependent on protein size and appears to be tuned to maintain approximately half of the atoms in the high density interior and the other half in the exterior region of rapidly decreasing density. A normalized size-independent distribution was obtained for the atomic probability as a function of the reduced distance, r = R/R(g), where R(g) is the radius of gyration. The global normalized Fermi distribution, F(r), can be reasonably decomposed in Fermi-like subdistributions for different atomic types tau, F(tau)(r), with Sigma(tau)F(tau)(r) = F(r), which depend on two additional parameters mu(tau) and h(tau). The chemical potential mu(tau) affects a scaling prefactor and depends on the overall frequency of the corresponding atomic type, while the maximum position of the subdistribution is determined by h(tau), which appears in a type-dependent atomic effective energy, epsilon(tau)(r) = h(tau)r, and is strongly correlated to available hydrophobicity scales. Better adjustments are obtained when the effective energy is not assumed to be necessarily linear, or epsilon(tau)*(r) = h(tau)*r(alpha,), in which case a correlation with hydrophobicity scales is found for the product alpha(tau)h(tau)*. These results indicate that compact globular proteins are consistent with a thermodynamic system governed by hydrophobic-like energy functions, with reduced distances from the geometrical center, reflecting atomic burials, and provide a conceptual framework for the eventual prediction from sequence of a few parameters from which whole atomic probability distributions and potentials of mean force can be reconstructed.

Evaluation of methods for measuring amino acid hydrophobicities and interactions

The concept of hydrophobicity has been addressed by researchers in all aspects of science, particularly in the fields of biology and chemistry. Over the past several decades, the study of the hydrophobicity of biomolecules, particularly amino acids has resulted in the development of a variety of hydrophobicity scales. In this review, we discuss the various methods of measuring amino acid hydrophobicity and provide explanations for the wide range of rankings that exist among these published scales. A discussion of the literature on amino acid interactions is also presented. Only a surprisingly small number of papers exist in this rather important area of research; measuring pairwise amino acid interactions will aid in understanding structural aspects of proteins.

Chromatographic approach for determining the relative membrane permeability of drugs

With the aid of the experimental dependence of the theoretical plate height (H) on the flow-rate (U), values of diffusion coefficients as the permeation rate, of the compounds in a polymeric stationary phase were calculated from solute mass transfer. This approach is proposed for modeling the relative diffusion rate of a drug within the membrane. After the successful separation of opioid compounds using a C(18) derivatized polystyrene-divinylbenzene polymer HPLC column, the slopes of H-U plots increase quantitatively in the order of meperidine<alfentanil<fentanyl<sufentanil, indicating that the large mass transfer resistance slows down the penetration of molecules. A constant intercept for the experimental plate height supports the proposal interpretation. A good correlation between the diffusion coefficients and hydrophobicity (log P(oct)) from the traditional shake-flask method was obtained for the opioid compounds, demonstrating that the more lipophilic molecules penetrate deeper into the stationary phase leading to a lower migration rate under the specified conditions. Plot of the diffusion coefficients versus potency ratio for different opioids after intravenous administration reflect the values of the dynamic process in drug studies. The work herein differs from existing studies by measuring the permeability of drugs into the stationary phase rather than providing membrane partition coefficients for a series of analogues. Thus, the study of drug permeability combined with other physico-chemical properties, such as hydrophobicity, may provide additional information on drug-membrane interactions.

Folding protein models with a simple hydrophobic energy function: the fundamental importance of monomer inside/outside segregation

The present study explores a "hydrophobic" energy function for folding simulations of the protein lattice model. The contribution of each monomer to conformational energy is the product of its "hydrophobicity" and the number of contacts it makes, i.e., E(h,c) = -Sigma N/i=1 c(i)h(i) = -(h.c) is the negative scalar product between two vectors in N-dimensional cartesian space: h = (h1,., hN), which represents monomer hydrophobicities and is sequence-dependent; and c = (c(1),., c(N)), which represents the number of contacts made by each monomer and is conformation-dependent. A simple theoretical analysis shows that restrictions are imposed concomitantly on both sequences and native structures if the stability criterion for protein-like behavior is to be satisfied. Given a conformation with vector c, the best sequence is a vector h on the direction upon which the projection of c - c is maximal, where c is the diagonal vector with components equal to c, the average number of contacts per monomer in the unfolded state. Best native conformations are suggested to be not maximally compact, as assumed in many studies, but the ones with largest variance of contacts among its monomers, i.e., with monomers tending to occupy completely buried or completely exposed positions. This inside/outside segregation is reflected on an apolar/polar distribution on the corresponding sequence. Monte Carlo simulations in two dimensions corroborate this general scheme. Sequences targeted to conformations with large contact variances folded cooperatively with thermodynamics of a two-state transition. Sequences targeted to maximally compact conformations, which have lower contact variance, were either found to have degenerate ground state or to fold with much lower cooperativity.

Thermodynamics of interactions between amino acid side chains: experimental differentiation of aromatic-aromatic, aromatic-aliphatic, and aliphatic-aliphatic side-chain interactions in water

A stationary phase for high-pressure liquid chromatography has been prepared by derivatizing microparticulate silica gel with functionality mimicking the side chain of isoleucine. The chromatographic retentions of a series of hydrophobic and amphiphilic amino acid analytes on this stationary phase (Ile MSP) using an aqueous mobile phase were measured as a function of temperature from 273 K to 323 K. Observed temperature dependencies are consistent with a constant change in heat capacity, DeltaC degrees P, upon binding of the analyte to the stationary phase. The curvatures of plots of retention data versus temperature (related to the magnitude of DeltaC degrees P) are distinctly different for retention of aromatic and aliphatic analytes, with retention of aliphatic analytes Val, Ile, and Leu exhibiting the characteristic signature of the hydrophobic effect, i.e., a large negative DeltaC degrees P upon desolvation from water and a maximum of retention around room temperature. Retention of aromatic analytes (Trp, Phe, and Tyr) involves smaller heat capacity changes and pronounced negative enthalpies of interaction with the stationary phase. Estimates of DeltaC degrees P for the interactions of analyte side chains with the Ile side chain were obtained by fitting the temperature dependence of retention to an expression derived from thermodynamic considerations and chromatographic theory. Similar estimates were made for interactions with the Phe side chain, using previously published data for a phenylalanine mimic stationary phase (Phe MSP) (. Protein Sci. 1:786-795). As with the Ile MSP, the retentions of aliphatic analytes show temperature dependencies markedly different from those of aromatic analytes. Data from both phases indicate that a realistic differentiation can be made between the interactions of various types of amino acid side chains tested (i.e., aliphatic/aliphatic, aliphatic/aromatic, and aromatic/aromatic) by comparison of the corresponding thermodynamic functions for pairwise interactions. The retention of leucine on the Phe MSP and that of phenylalanine on the Ile MSP showed similar DeltaC degrees P values, suggesting that the aromatic-aliphatic interaction is reasonably independent of the residue attached to the stationary phase. This result is consistent with a one-to-one interaction and suggests a simple way to estimate the column-dependent phase factor, making it possible to compare entropies and free energies of interaction obtained using different MSPs. The possibilities for using MSP-derived interaction potentials in folding simulations are discussed.

Monte Carlo simulations of protein folding using inexact potentials: how accurate must parameters be in order to preserve the essential features of the energy landscape?

BACKGROUND

Monte Carlo simulations of the cubic lattice protein model with engineered sequences were performed in order to address the issue of potential accuracy required for folding. The potential used for sequence selection played the role of the 'real' potential and different levels of inaccuracy were introduced by addition of noise.

RESULTS

The dependence of successful folding probability on potential noise was found to be sigmoidal and sequence-specific and can be described by an expression analytically derived from a simple theoretical model in which the density of states of the system contains a continuous region approximated by a Gaussian distribution separated from the unique native conformation by a large energy gap.

CONCLUSIONS

The decrease in folding probability with potential inaccuracy results from an average decrease in the energy gap. Sequences with large energy gaps support larger inaccuracies while retaining the ability to fold properly. As the energy gap is known to correlate with thermal stability, we suggest a simple criterion for specific real sequence selection in order to maximize success probability in realistic folding simulations.

A structure-based model for cytochrome P450cam-putidaredoxin interactions

Putidaredoxin (Pdx) is a Fe2S2 ferredoxin which acts as the physiological reductant of cytochrome P-450cam (CYP101). A model for the solution structure of oxidized Pdx has been determined using NMR methods (Pochapsky et al (1994) Biochemistry 33, 6424-6432). 1H-15N correlations and redox-dependent amide exchange rates have also been described (Lyons et al (1996) Protein Sci 5, 627-639). Data obtained from mutagenesis and kinetic measurements concerning the interactions of Pdx and CYP101 are summarized. A model for the structure of the homologous ferredoxin adrenodoxin (Adx) is also described, and data concerning Adx activity are discussed in relation to this structure. The structures of Pdx and CYP101 were used as starting points for molecular modeling and molecular dynamics simulations. Close approach between the metal centers of the two proteins and interaction between aromatic residues on the surfaces of the proteins are premised. The resulting complex exhibits three intermolecular salt bridges, five intermolecular hydrogen bonds and a 12 A distance between the metal centers. The first direct observations of interaction between Pdx and CYP101 (by two-dimensional NMR of 15N-labeled Pdx in solution with CYP101) are described. The results of the NMR experiments indicate that conformational gating of the electron transfer complex between CYP101 and Pdx may be important.