Libraries of atomic multipole moments for precise modeling of electrostatic properties of amino acids

Summary Contemporary theoretical models used in describing electrostatic properties of amino acids in polypeptides rely usually on atomic point charges. Recently noted defects of such models in reproducing protein folding originate from the inadequate representation of the electrostatic term, in particular inability of atomic charges to account for local anisotropy of molecular charge distribution. Such defects could be corrected by multicenter multipole moments derived directly from any high quality quantum chemical wavefunctions. This is illustrated by comparison of monopole and multipole electrostatic interactions between some amino acids within glutathione S-transferase.High quality Point Charge Models (PCM) can be derived analytically from multipole moment databases. Preliminary results suggest that torsional potentials are controlled by electrostatic interactions of atomic multipoles.Examples illustrating various uses of multicenter multipole moment databases of protein building blocks in modeling various properties of amino acids and polypeptides have been described, including calculation of molecular electrostatic potentials, electric fields, interactions between amino acid residues, estimates of pK_a shifts and changes in catalytic activity induced by amino acid substitutions in mutated enzymes.     

Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases

Triose phosphate isomerase (TIM) is a diffusion-controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate glyceraldehyde 3-phosphate (GAP) with the homodimeric enzyme's active sites. Translational and orientational steering of GAP toward the active sites by the electrostatic field of chicken muscle TIM has been observed in previous Brownian dynamics (BD) simulations. Here we report simulations of the association of GAP with TIMs from four species with net charges at pH 7 varying from -12e to +12e. Computed second-order rate constants are in good agreement with experimental data. The BD simulations and computation of average Boltzmann factors of substrate–protein interaction energies show that the protein electrostatic potential enhances the rates for all the enzymes. There is much less variation in the computed rates than might be expected on the basis of the net charges. Comparison of the electrostatic potentials by means of similarity indices shows that this is due to conservation of the local electrostatic potentials around the active sites which are the primary determinants of electrostatic steering of the substrate. Proteins 31:406–416, 1998. © 1998 Wiley-Liss, Inc.     

Intermolecular potentials for alpha-glycine from Raman and infrared scattering measurements

The frequencies of intermolecular modes in alpha-glycine-d0 and -d5 have been measured at 300 and 85 K by Raman and infrared scattering techniques. These frequencies were analyzed in terms of simple analytic interatomic potentials. Buckingham potentials were assumed for the nonbonded and hydrogen-bond interactions, and Coulomb and screened Coulomb potentials were assumed for the electrostatic interactions. The observed frequencies are well described by the simple model and the parameters of the hydrogen-bond potentials and the molecular charge distribution were determined from the analysis.     

The electrostatic basis for the interfacial binding of secretory phospholipases A2.

Biochemical and structural data suggest that electrostatic forces play a critical role in the binding of secretory phospholipases A2 to substrate aggregates (micelles, vesicles, monolayers, and membranes). This initial binding (adsorption) of the enzyme to the interface is kinetically distinct from the subsequent binding of substrate to the buried active site. Thus, in the absence of specific active-site interactions, electrostatic forces operating at the molecular surface may orient and hold the enzyme at the interface. We have calculated the electrostatic potentials for 10 species of secretory phospholipases A2 whose atomic coordinates have been determined by x-ray crystallography. Most of these enzymes show a marked electrostatic sidedness that is accentuated to a variable degree by the presence of the essential cofactor calcium ion. This asymmetry suggests a discrete interfacial binding region on the protein's surface, the location of which is in general agreement with proposals derived from the results of chemical modification, mutational, and crystallographic experiments.     

Receptor binding properties of four-helix-bundle growth factors deduced from electrostatic analysis

Hormones of the hematopoietin class mediate signal transduction by binding to specific transmembrane receptors. Structural data show that the human growth hormone (hGH) forms a complex with a homodimeric receptor and that hGH is a member of a class of hematopoietins possessing an antiparallel 4-α-helix bundle fold. Mutagenesis experiments suggest that electrostatic interactions may have an important influence on hormone-receptor recognition. In order to examine the specificity of hormone-receptor complexation, an analysis was made of the electrostatic potentials of hGH, interleukin-2 (IL-2), interleukin-4 (IL-4), granulocyte colony-stimulating factor (G-CSF), granulocyte-macrophage colony-stimulating factor (GM-CSF), and the hGH and IL-4 receptors. The binding surfaces of hGH and its receptor, and of IL-4 and its receptor, show complementary electrostatic potentials. The potentials of the hGH and its receptor display approximately 2-fold rotational symmetry because the receptor subunits are identical. In contrast, the potentials of GM-CSF and IL-2 lack such symmetry, consistent with their known high affinity for hetero-oligomeric receptors. Analysis of the electrostatic potentials supports a recently proposed hetero-oligomeric model for a high-affinity IL-4 receptor and suggests a possible new receptor binding mode for G-CSF; it also provides valuable information for guiding structural and mutagenesis studies of signal-transducing proteins and their receptors.     

Atomistic simulations of competition between substrates binding to an enzyme

Although the idea that electrostatic potentials generated by enzymes can guide substrates to active sites is well established, it is not always appreciated that the same potentials can also promote the binding of molecules other than the intended substrate, with the result that such enzymes might be sensitive to the presence of competing molecules. To provide a novel means of studying such "electrostatic competition" effects, computer simulation methodology has been developed to allow the diffusion and association of many solute molecules around a single enzyme to be simulated. To demonstrate the power of the methodology, simulations have been conducted on an artificial fusion protein of citrate synthase (CS) and malate dehydrogenase (MDH) to assess the chances of oxaloacetate being channeled between the MDH and CS active sites. The simulations demonstrate that the probability of channeling is strongly dependent on the concentration of the initial substrate (malate) in the solution. In fact, the high concentrations of malate used in experiments appear high enough to abolish any channeling of oxaloacetate. The simulations provide a resolution of a serious discrepancy between previous simulations and experiments and raise important questions relating to the observability of electrostatically mediated substrate channeling in vitro and in vivo.     

Sampling field heterogeneity at the heme of c-type cytochromes by spectral hole burning spectroscopy and electrostatic calculations

We report on a comparative investigation of the heme pocket fields of two Zn-substituted c-type cytochromes-namely yeast and horse heart cytochromes c-using a combination of hole burning Stark spectroscopy and electrostatic calculations. The spectral hole burning experiments are consistent with different pocket fields experienced at the hemes of the respective cytochromes. In the case of horse heart Zn-cytochrome c, two distinguishable electronic origins with different electrostatic properties are observed. The yeast species, on the other hand, displays a single electronic origin. Electrostatic calculations and graphics modeling using the linearized finite-difference Poisson-Boltzmann equation performed at selected time intervals on nanosecond-molecular dynamics trajectories show that the hemes of the respective cytochromes sample different potentials as they explore conformational space. The electrostatic potentials generated by the protein matrix at the heme show different patterns in both cytochromes, and we suggest that the cytochromes differ by the number of "electrostatic substates" that they can sample, thus accounting for the different spectral populations observed in the two cytochromes.     

The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions

A statistical analysis of ion pairs in protein crystal structures shows that their abundance with respect to uncharged controls is accurately predicted by a Boltzmann-like function of electrostatic potential. It appears that the mechanisms of protein folding and/or evolution combine to produce a "thermal" distribution of local nonbonded interactions, as has been suggested by statistical-mechanical theories. Using this relationship, we develop a maximum likelihood methodology for estimation of apparent energetic parameters from the data base of known structures, and we derive electrostatic potential functions that lead to optimal agreement of observed and predicted ion-pair frequencies. These are similar to potentials of mean force derived from electrostatic theory, but departure from Coulombic behavior is less than has been suggested.     

Molecular Parameterisation and the Theoretical Calculation of Electrode Potentials

The difference in reduction potentials between ortho and para-benzoquinones has been calculated. The employs gas phase ab initio and semi-empirical computations in combination with free energy perturbation theory applied to gas and solution phase Monte Carlo simulations. The effects on calculated results of altering solute electrostatic parameterisation in solution phase simulations is examined. Atom centred charges derived from the molecular electrostatic potentials, MEPs, from optimised ab initio wavefunctions and charges generated by consideration of hydrogen bonded complexes are considered. Parameterisation of hydroxyl torsions in hydroquinone molecules is treated in a physically realistic manner. The coupled torsional system of the ortho-hydrobenzoquinone molecule is described by a potential energy surface calculated using gas phase AM1 semi-empirical computations rather than the simple torsional energy functions frequently employed in such calculations. Calculated differences in electrode potentials show that the electrostatic interactions of quinone and hydroquinone molecules in aqueous solution are not well described by atom centred charges derived from ab initio calculated MEPs. Moreover, results in good agreement with the experimental reduction potential difference can be obtained by employing high level ab initio calculations and solution phase electrostatic parameters developed by consideration of hydrogen bonded complexes.     

Determinants of functionality in the ubiquitin conjugating enzyme family

The E2 enzymes are key enzymes in the ubiquitin and ubiquitin-like protein ligation pathways. To understand the functionality of the different E2 enzymes, we analyzed 190 protein sequences and 211 structures and electrostatic potentials. Key findings include: The ScUbc1 orthologs are defined by a C-terminal UBA domain. An N-terminal sequence motif that is highly conserved in all E2s except for Cdc34 orthologs is important for the stabilization of the L7 loop and is likely to be involved in E1 binding. ScUbc11p has a different electrostatic potential from E2-Cp and other proteins with which it has high sequence similarity but different functionality. All the E2s known to ubiquitinate histones have a negative potential. The members of the NCUBE family have a positive electrostatic potential, although its form is different from that of the SUMO conjugating E2s. The specificities of only the ScUbc4/Ubc5 and ScUbc1p orthologs are reflected in their L4 and L7 loops.     

Comparison of protein electrostatic potential along the catalytic triad of serine proteinases

Intraproteic electrostatic potentials along the catalytic triad in serine proteinases are compared for eight enzymes for which three-dimensional co-ordinates are available. We used our bond-increment method to calculate the potential and we considered all protein atoms, including hydrogens. It was found that counter ions which may be located in the vicinity of charged surface side chains play a decisive role in determining enzymatic action. If ionizable side chains are neutralized the electrostatic potential curve across the catalytic triad is of minimum character in all investigated enzymes. It stabilizes the (-+-) charge distribution which models the Ser- -His+ -Asp- transition state structure which is formed during the catalytic process. Based on the close similarity of the electrostatic pattern in various enzymes we call attention to the possibility that convergent evolution produced not only the effective catalytic triad but also a minimum-type potential which accelerates the enzymatic reaction.     

江浙蝮蛇毒酸性与碱性磷脂酶A_2溶液构象变化的差示扫描量热法研究

运用差示扫描量热法,在不同ｐＨ值的缓冲溶液内和各种浓度的碱土族氯化物溶液内,研究了来自江浙蝮蛇（ＡｇｋｉｓｔｒｏｄｏｎｈａｌｙｓＰａｌｌａｓ）毒的酸性与碱性磷脂酶外Ａ２（ＰＬＡ２）的热变性过程。得到表征这两种酶溶液构象变化的热力学参数。依据这些参数研究了两者的溶液构象及其变化。在ｐＨ４．５以下,分子净荷正电的这两种酶在溶液中不形成可热致伸展的有序构象;ｐＨ高于４．５时,Ａｓｐ和Ｇｌｕ的侧链羧基以负离子形式存在有利于有序构象的稳定。Ｈｉｓ是决定ＰＬＡ２活力和热稳定性的重要残基。磷酸根离子和这两种酶有结合作用而降低有序构象的热稳定性。碱土族阳离子除和这两种酶结合外,还以依赖于离子强度的方式复杂地影响酶的溶液构象,但其作用不完全是静电性的,是或多或少地随离子的不同而不同的。计算给出酸性ＰＬＡ２的△Ｈｃｄ．     

Electrostatic potentials of tumour promoters

Molecular-modelling studies and quantum-chemical calculations have been undertaken on a variety of structurally unrelated tumour promoters. The modelling studies reveal some broad areas of agreement in the associated electrostatic potentials for the molecules TPA, teleocidin, aplysiatoxin and ingenol. Azulene-type derivatives were used as models for inactive and active tumour promoters in the quantum chemical studies. The results obtained from these calculations of the electrostatic potentials show very little difference between active and inactive compounds, thus suggesting that other factors are of importance in these systems.     

Enzyme stabilization by glutaraldehyde crosslinking of adsorbed proteins on aminated supports

The stabilization achieved by different immobilization protocols have been compared using three different enzymes (glutaryl acylase (GAC), D-aminoacid oxidase (DAAO), and glucose oxidase (GOX)): adsorption on aminated supports, treatment of this adsorbed enzymes with glutaraldehyde, and immobilization on glutaraldehyde pre-activated supports. In all cases, the treatment of adsorbed enzymes on amino-supports with glutaraldehyde yielded the higher stabilizations: in the case of GOX, a stabilization over 400-fold was achieved. After this treatment, the enzymes could no longer be desorbed from the supports using high ionic strength (suggesting the support-protein reaction). Modification of the enzymes immobilized on supports that did not offer the possibility of react with glutaraldehyde showed the same stability that the non modified preparations demonstrating that the mere chemical modification did not have effect on the enzyme stability. This simple strategy seems to permit very good results in terms of immobilization rate and stability, offering some advantages when compared to the immobilization on glutaraldehyde pre-activated supports.     

Binding of substituted phenol and aniline derivatives to the corn protein zein studied by high-performance liquid chromatography

The interaction of 12 substituted phenol, three aminophenol and four substituted aniline derivatives with the corn protein zein was studied on zein-coated silica and alumina stationary phases by high-performance liquid chromatography using bidistilled water as mobile phase. Solutes were eluted from the zein-coated supports with different retention times indicating that they bind to the protein with different forces. They were more strongly retained on silica-based than on alumina-based support proving that the original adsorptive character of the support remains even after impregnation. The retention of solutes on both zein-coated stationary phases significantly depended on the steric and electronic parameters of solutes and was independent of the calculated and measured lipophilicity parameters, indicating that hydrophobic forces are not included in the interaction of zein with these class of solutes. It has been concluded that the interaction is governed by steric and electrostatic forces.     

Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices

The importance of the promoter sequences in the function regulation of several important mycobacterial pathogens creates the necessity to design simple and fast theoretical models that can predict them. This work proposes two DNA promoter QSAR models based on pseudo-folding lattice network (LN) and star-graphs (SG) topological indices. In addition, a comparative study with the previous RNA electrostatic parameters of thermodynamically-driven secondary structure folding representations has been carried out. The best model of this work was obtained with only two LN stochastic electrostatic potentials and it is characterized by accuracy, selectivity and specificity of 90.87%, 82.96% and 92.95%, respectively. In addition, we pointed out the SG result dependence on the DNA sequence codification and we proposed a QSAR model based on codons and only three SG spectral moments.     

Ionic Strength-Dependent Physicochemical Factors in Cytochrome c3 Regulating the Electron Transfer Rate

The effect of ionic strength on the macroscopic and microscopic redox potentials and the heme environment of cytochrome c₃ from Desulfovibrio vulgaris Miyazaki F have been investigated by NMR and electrochemical methods. The redox potentials of this tetraheme protein are found to be ionic strength-dependent. Especially, the microscopic redox potentials of hemes 2 and 3 at the fourth reduction step increase significantly with increasing ionic strength, which is in contradiction to the theoretical expectation. The coordinated imidazole proton signals are unaffected by ionic strength. However, the methyl and propionate proton signals of hemes 1 and 4 showed significant ionic strength dependencies that are distinct from those for hemes 2 and 3. This heme classification is the same as that found in the ionic strength dependencies of the microscopic redox potentials at the fourth reduction step. Furthermore, the effect of ionic strength on the electrostatic potentials at the heme irons has been examined on the theoretical basis. The electrostatic potential at heme 4 changes up to 1 M ionic strength, which was not expected from the observations reported on cytochromes so far. These results are discussed in connection with the reported anomalous ionic strength dependency of the reduction rate of cytochrome c₃.     

The electrostatic molecular potential of tRNAPhe. IV. The potentials and steric accessibilities of sites associated with the bases.

The sites of the 76 nucleic acid bases of tRNAPhe potentially reactive towards electrophiles are studied by calculations on the associated molecular electrostatic potentials and the static steric accessibilities. Each of these sites is treated in its environment within the macromolecule. The influence of various schemes of screening by countercations of the backbone phosphates on the electrostatic potentials is investigated. The possible significance of the potentials and accessibilities in connection with observed chemical reactivities is discussed.     

Key roles of enzyme positions and membrane surface potentials in the properties of biomimetic membranes

The coupling of diffusion, reaction, and electrostatic interactions existing in the microenvironment of permeable and charged bi-enzymatic membranes has led to the concept of biomimetic membranes. These membranes permit the active and specific transport of small hydrophilic molecules against their concentration gradients, at constant temperature and pressure. This study shows that such membranes behave in totally different ways, depending both on the relative position of the two enzymes, either within or outside the ionic double layer, and on the membrane surface potentials.