A differential scanning calorimetric study of the effects of metal ions, substrate/product, substrate analogues and chaotropic anions on the thermal denaturation of yeast enolase 1.

The thermal denaturation of yeast enolase 1 was studied by differential scanning calorimetry (DSC) under conditions of subunit association/dissociation, enzymatic activity or substrate binding without turnover and substrate analogue binding. Subunit association stabilizes the enzyme, that is, the enzyme dissociates before denaturing. The conformational change produced by conformational metal ion binding increases thermal stability by reducing subunit dissociation. 'Substrate' or analogue binding additionally stabilizes the enzyme, irrespective of whether turnover is occurring, perhaps in part by the same mechanism. More strongly bound metal ions also stabilize the enzyme more, which we interpret as consistent with metal ion loss before denaturation, though possibly the denaturation pathway is different in the absence of metal ion. We suggest that some of the stabilization by 'substrate' and analogue binding is owing to the closure of moveable polypeptide loops about the active site, producing a more 'closed' and hence thermostable conformation.

BiGGER: a new (soft) docking algorithm for predicting protein interactions.

A new computationally efficient and automated "soft docking" algorithm is described to assist the prediction of the mode of binding between two proteins, using the three-dimensional structures of the unbound molecules. The method is implemented in a software package called BiGGER (Bimolecular Complex Generation with Global Evaluation and Ranking) and works in two sequential steps: first, the complete 6-dimensional binding spaces of both molecules is systematically searched. A population of candidate protein-protein docked geometries is thus generated and selected on the basis of the geometric complementarity and amino acid pairwise affinities between the two molecular surfaces. Most of the conformational changes observed during protein association are treated in an implicit way and test results are equally satisfactory, regardless of starting from the bound or the unbound forms of known structures of the interacting proteins. In contrast to other methods, the entire molecular surfaces are searched during the simulation, using absolutely no additional information regarding the binding sites. In a second step, an interaction scoring function is used to rank the putative docked structures. The function incorporates interaction terms that are thought to be relevant to the stabilization of protein complexes. These include: geometric complementarity of the surfaces, explicit electrostatic interactions, desolvation energy, and pairwise propensities of the amino acid side chains to contact across the molecular interface. The relative functional contribution of each of these interaction terms to the global scoring function has been empirically adjusted through a neural network optimizer using a learning set of 25 protein-protein complexes of known crystallographic structures. In 22 out of 25 protein-protein complexes tested, near-native docked geometries were found with C(alpha) RMS deviations < or =4.0 A from the experimental structures, of which 14 were found within the 20 top ranking solutions. The program works on widely available personal computers and takes 2 to 8 hours of CPU time to run any of the docking tests herein presented. Finally, the value and limitations of the method for the study of macromolecular interactions, not yet revealed by experimental techniques, are discussed.

Distribution analysis of the variation of B-factors of X-ray crystal structures; temperature and structural variations in lysozyme.

The B-factor (isotropic temperature factor) data for X-ray structures of hen egg-white lysozyme from the study of Young et al. (Young, Dewan, Nave, and Tilton J. Appl. Cryst. 1993, 26, 309-319) potentially contain information about the relative contributions of static and dynamic variation to these factors. The six structures of the protein were obtained at two widely different temperatures (100 and 298 K), with two crystal forms (monoclinic and tetragonal) and other experimental differences. In addition, the monoclinic lysozyme crystals with two molecules per asymmetric unit allow direct examination of variation between structures determined under identical conditions at both temperatures. The B-factors from these structures all have complex distribution functions as might be expected considering all of the influences that these values must reflect. The empirical cumulative distribution functions (eCDF's) of these data show that they are representative of complex, multicomponent distributions. Distribution analysis using the DANFIP procedure (Wampler, Anal. Biochemistry 1990, 186, 209-218) of the data sets reveals that they can be modeled as four to six Gaussian subpopulations, that these subpopulations do not correlate with specific atom types, specific amino acid residues or fixed locations in the structure. While they do seem to correlate with localized groupings of atoms, these grouping vary from structure to structure even within the same crystal under the same conditions. Temperature seems to have a global effect in this case, but it is clear that other factors including experimental error influence the distribution of B-factors within a given structure. This analysis also helps explain the oft observed lack of atomic level correlation between experimental B-factors and calculated mean square displacements from molecular dynamics simulations.

A model for the unusual kinetics of thermal denaturation of rubredoxin.

The thermal denaturation of the simple, redox-active iron protein rubredoxin is characterized by a slow, irreversible decay of the characteristic red color of the iron center at elevated temperatures in the presence of oxygen at pH 7.8. The denaturation rate is essentially constant and the time period for complete bleaching is nearly independent of protein concentration. These two characteristics of the kinetics can be fit by a simple self-catalyzed kinetics model consisting of the combination of a first-order decay and catalysis by some product of that decay, i.e., dP/dt = k1[A] + (k2[P][A])/(K(m) + [A]), where A is native rubredoxin, P, is unspecified product, k1 is a first-order rate constant, and k2 and K(m) are the catalytic constants. In order for the second term to be of this simple form over the full course of a decay, the model must include the condition that the reaction is effectively irreversible. This model has properties which suggest other biological roles in regulation (changes in k1 or k2 can dramatically modulate the kinetics), in timing (titer-independent fixed reaction time), and in self-activation reactions. At one extreme (k1 >> k2) the kinetics becomes exponential, but at the other extreme (k2 >> k1) they show a dramatic and rapid terminal increase after a lag period. Some obvious possible roles in the kinetics of programmed cell death, prion disease, and protease autoactivation are discussed.

Electrostatic potential derived charges for enzyme cofactors: methods, correlations, and scaling for organic cofactors.

The correlations between electrostatic potential (ESP) derived atomic charges for a wide range of different quantum mechanical approaches and basis sets have been investigated for both small and large organic structures including several enzyme cofactors. The previously observed linear correlation between ESP charges calculated by different approaches has been verified to extend to many different basis sets and procedures including effective core potential (ECP) basis sets, density functional theory (DFT) approaches, a hybrid Hartree-Fock (HF)/DFT approach, and inclusion of electron correlation corrections. Above a threshold level of complexity, most procedures and basis sets give results that correlate very well (linear correlation coefficients > 0.99), including several procedures that have reasonable computational costs for large molecules. These procedures have been used to calculate ESP charges for five different types and forms of enzyme cofactors: biotin, pyridoxal-5'-phosphate, pyridoxamine-5'-phosphate, and the flavin mononucleotide in two different oxidation states.

Evidence for a ternary complex formed between flavodoxin and cytochrome c3: 1H-NMR and molecular modeling studies.

Small electron-transfer proteins such as flavodoxin (16 kDa) and the tetraheme cytochrome c3 (13 kDa) have been used to mimic, in vitro, part of the complex electron-transfer chain operating between substrate electron donors and respiratory electron acceptors, in sulfate-reducing bacteria (Desulfovibrio species). The nature and properties of the complex formed between these proteins are revealed by 1H-NMR and molecular modeling approaches. Our previous study with the Desulfovibrio vulgaris proteins [Moura, I., Moura, J.J. G., Santos, M.H., & Xavier, A. V. (1980) Cienc. Biol. (Portugal) 5, 195-197; Stewart, D.E. LeGall, J., Moura, I., Moura, J. J. G., Peck, H.D. Jr., Xavier, A. V., Weiner, P. K., & Wampler, J.E. (1988) Biochemistry 27, 2444-2450] indicated that the complex between cytochrome c3 and flavodoxin could be monitored by changes in the NMR signals of the heme methyl groups of the cytochrome and that the electrostatic surface charge (Coulomb's law) on the two proteins favored interaction between one unique heme of the cytochrome with flavodoxin. If the interaction is indeed driven by the electrostatic complementarity between the acidic flavodoxin and a unique positive region of the cytochrome c3, other homologous proteins from these two families of proteins might be expected to interact similarly. In this study, three homologous Desulfovibrio cytochromes c3 were used, which show a remarkable variation in their individual isoelectric points (ranging from 5.5 to 9.5). On the basis of data obtained from protein-protein titrations followed at specific proton NMR signals (i.e., heme methyl resonances), a binding model for this complex has been developed with evaluation of stoichiometry and binding constants. This binding model involves one site on the cytochromes c3 and two sites on the flavodoxin, with formation of a ternary complex at saturation. In order to understand the potential chemical form of the binding model, a structural model for the hypothetical ternary complex, formed between one molecule of Desulfovibrio salexigens flavodoxin and two molecules of cytochrome c3, is proposed. These molecular models of the complexes were constructed on the basis of complementarity of Coulombic electrostatic surface potentials, using the available X-ray structures of the isolated proteins and, when required, model structures (D. salexigens flavodoxin and Desulfovibrio desulfuricans ATCC 27774 cytochrome c3) predicted by homology modeling.

Computational chemistry and molecular modeling of electron-transfer proteins.

The methods of computational chemistry and molecular modeling are becoming more and more accessible to biochemists with the advent of fast, inexpensive graphics workstations and well-tested computer programs. The state of the art in small molecules allows chemists to use these programs as "black boxes" and be confident of the results at an amazingly high level of precision. This is not the case, however, for biological macro-molecules at this time. Therefore, it is necessary before using the programs listed in Section I that we familiarize ourselves with their theoretical basis and limitations. It is also important that they be used in the context of the accumulated literature on their use. The survey given in this chapter is intended as an introduction to these tools and as a source for initiating the discovery process with the literature cited.

Modeling the structure of Pyrococcus furiosus rubredoxin by homology to other X-ray structures.

The three-dimensional structure of rubredoxin from the hyperthermophilic archaebacterium, Pyrococcus furiosus, has been modeled from the X-ray crystal structures of three homologous proteins from Clostridium pasteurianum, Desulfovibrio gigas, and Desulfovibrio vulgaris. All three homology models are similar. When comparing the positions of all heavy atoms and essential hydrogen atoms to the recently solved crystal structure (Day, M. W., et al., 1992, Protein Sci. 1, 1494-1507) of the same protein, the homology model differ from the X-ray structure by 2.09 A root mean square (RMS). The X-ray and the zinc-substituted NMR structures (Blake, P. R., et al., 1992b, Protein Sci. 1, 1508-1521) show a similar level of difference (2.05 A RMS). On average, the homology models are closer to the X-ray structure than to the NMR structures (2.09 vs. 2.42 A RMS).

Investigations of the thermostability of rubredoxin models using molecular dynamics simulations.

The affects of differences in amino acid sequence on the temperature stability of the three-dimensional structure of the small beta-sheet protein, rubredoxin (Rd), was revealed when a set of homology models was subjected to molecular dynamics simulations at relatively high temperatures. Models of Rd from the hyperthermophile, Pyrococcus furiosus (Pf), an organism that grows optimally at 100 degrees C, were compared to three mesophilic Rds of known X-ray crystal structure. Simulations covering the limits of known Rd thermostabilities were carried out at temperatures of 300 K, 343 K, 373 K, and 413 K. They suggest that Rd stability is correlated with structural dynamics. Because the dynamic behavior of three Pf Rd models was consistently different from the dynamic behavior of the three mesophilic Rd structures, detailed analysis of the temperature-dependent dynamic behavior was carried out. The major differences between the models of the protein from the hyperthermophile and the others were: (1) an obvious temperature-dependent transition in the mesophilic structures not seen with the Pf Rd models, (2) consistent AMBER energy for the Pf Rd due to differences in nonbonded interaction terms, (3) less variation in the average conformations for the Pf Rd models with temperature, and (4) the presence of more extensive secondary structure for the Pf Rd models. These unsolvated dynamics simulations support a simple, general hypothesis to explain the hyperthermostability of Pf Rd. Its structure simplifies the conformational space to give a single minimum accessible over an extreme range of temperatures, whereas the mesophilic proteins sample a more complex conformational space with two or more minima over the same temperature range.

Molecular dynamics simulations of the cytochrome c3-rubredoxin complex from Desulfovibrio vulgaris.

Molecular dynamics simulations have been carried out on the complex formed between the tetraheme cytochrome c3 and the iron protein rubredoxin from the sulfate-reducing bacterium Desulfovibrio vulgaris. These simulations were performed both with explicit solvent water molecules included, and without solvent molecules using a distance-dependent dielectric constant to approximate the screening effects of solvent. The results of both simulations are strikingly different, indicating that the representation of environmental effects is important in such simulations. For example, a striking adaptation of the two proteins seen in the nonsolvated simulation is not seen when explicit solvent water is included; in fact, the complex appears to become weaker in the solvated simulation. Nonetheless, the iron-iron distance decreases more significantly in the solvated simulation than in the nonsolvated simulation. It was found that in both cases molecular dynamics optimized the structures further than energy minimization alone.

Occurrence and role of cis peptide bonds in protein structures.

It has been widely assumed that the occurrence of cis peptide bonds in proteins is quite rare due to unfavorable contacts between adjacent amino acid residues in this isomeric form. To investigate this assumption, the Brookhaven Protein Data Bank was examined for the occurrences of cis peptide bonds. Out of 31,005 amide bonds, only 17, or 0.05%, are cis, while 99 of the 1534 imide bonds (X-Pro), or 6.5%, are cis. These figures are considerably less than the distribution predicted on the basis of the potential energy difference between the cis and trans isomeric forms and experimental data on small peptides. It is not known whether the lower than expected occurrence of cis peptide bonds arises from constraints imposed by the protein environment, or from assumptions made in the solution of the X-ray crystal structures. However, when the occurrence of cis bonds in the data base is examined relative to the resolution of the structures, the number of cis bonds increases with increasing resolution. The distributions seen for these peptide omega bonds in the data base are not the same shape as the distributions predicted from simple potential energy barriers. They are sharper in the main, but they are also broader at the base with significant numbers of nonplanar peptide bonds. Cis peptide bonds are found primarily in bends and turns and, in the case of cis imide bonds (X-PRO), this correlation is so high that it suggests a specific role for cis imide groups in such structures.

Cytoplasmic pH of Dictyostelium discoideum amebae during early development: identification of two cell subpopulations before the aggregation stage.

Development of the cellular slime mold Dictyostelium discoideum is initiated by the removal of nutrients, and results in formation of a mature fruiting body composed of two cell types, the stalk and spore cells. A considerable body of evidence supports the hypothesis that cytoplasmic pH may be an essential regulator of the choice to differentiate in either the prestalk or prespore pathway. We have devised methods for measurement and analysis of intracellular pH in developing Dictyostelium amebae in order to assess directly the potential role of cytoplasmic pH in regulating the pathway of differentiation. The intracellular pH of single D. discoideum amebae during development and in intact slugs has been measured using the pH-sensitive indicator pyranine in a low light level microspectrofluorometer. We have used the ATP-mediated loading method to introduce pyranine into these cells. Cells loaded by the ATP method appear healthy, have no detectable defects in development, and exhibit a similar population distribution of intracellular pH to those loaded by sonication. The intracellular pH of populations comprised of single amebae was found to undergo a transient acidification during development resulting in a bimodal distribution of intracellular pH. The subpopulations were characterized by fitting two gaussian distributions to the data. The number of cells in the acidic intracellular pH subpopulation reached a maximum 4 h after initiation of development, and had returned to a low level by 7 h of development. In addition, a random sample of single amebae within a slug had a median intracellular pH of 7.2, nearly identical to the median pH (7.19) of similarly treated vegetative cells. No gradient of intracellular pH along the anterior to posterior axis of the slug was detected. Our data demonstrate the existence of two distinct subpopulations of cells before the aggregation stage of development in Dictyostelium, and offers support for the hypothesis that changes in intracellular pH contribute to development in D. discoideum.

Analysis of the probability distribution of small random samples by nonlinear fitting of integrated probabilities.

Small random samples of biochemical and biological data are often representative of complex distribution functions and are difficult to analyze in detail by conventional means. The common approaches reduce the data to a few representative parameters (such as their moments) or combine the data into a histogram plot. Both approaches reduce the information content of the data. By fitting the empirical cumulative distribution function itself with models of integrated probability distributions, the information content of the raw data can be fully utilized. This approach, distribution analysis by nonlinear fitting of integrated probabilities, allows analysis of normally distributed samples, truncated data sets, and multimodal distributions with a single, powerful data processing procedure.

Electron transport in sulfate-reducing bacteria. Molecular modeling and NMR studies of the rubredoxin--tetraheme-cytochrome-c3 complex.

A hypothetical model of the complex formed between the iron-sulfur protein rubredoxin and the tetraheme cytochrome c3 from the sulfate-reducing bacteria Desulfovibrio vulgaris (Hildenborough) has been proposed utilizing computer graphic modeling, computational methods and NMR spectroscopy. The proposed complex appears feasible on the basis of complementary electrostatic interaction and steric factors and is consistent with the data from NMR experiments. In this model, the non-heme iron atom of rubredoxin is in close proximity to heme 1 of cytochrome c3. The complex is stabilized by charge-pair interactions and hydrogen bonds. This complex is compared to the flavodoxin-cytochrome c3 complex previously proposed [Stewart, D. E., LeGall, J., Moura, I., Moura, J. J. G., Peck, H. D. Jr, Xavier, A. V., Weiner, P. K. & Wampler, J. E. (1988) Biochemistry 27, 2444-2450] and new NMR data shows that both proteins interact with the same heme group of the cytochrome as postulated.

Measurement of the cytoplasmic pH of Dictyostelium discoideum using a low light level microspectrofluorometer.

Pyranine was employed as a sensitive pH indicator in a low light level microspectrofluorometer. The in vivo and in vitro standard curves of the 460/410-nm fluorescence excitation ratio of pyranine as a function of pH are identical. Therefore, pyranine is specifically sensitive to cytoplasmic pH in Dictyostelium. The cytoplasmic pH of single cells in a population of Dictyostelium discoideum amoebae was obtained for the first time. The median cytoplasmic pH of vegetative amoebae was 7.19. Carbonyl cyanide m-chlorophenylhydrazone, a mitochondrial uncoupler and a protonophore, lowered the median cytoplasmic pH to 6.12 when the extracellular pH was 6.1. This result is in accord with the protonophore activity of carbonyl cyanide m-chlorophenylhydrazone. Interest in the cytoplasmic pH of Dictyostelium has been greatly stimulated by the theory that cytoplasmic acidification promotes development of pre-stalk cells, while cytoplasmic alkalinization favors the pre-spore pathway (Gross, J. D., J. Bradbury, R. R. Kay, M. J. Peacey. 1983. Nature (Lond.). 303:244-245). The theory postulates that diethylstilbestrol (DES), an inducer of stalk cell differentiation and a plasma membrane proton translocating ATPase inhibitor, should cause acidification of the cytosol. Previous measurements of the effects of stalk cell inducers including DES on intracellular pH using 31P nuclear magnetic resonance measurements have failed to confirm the predictions of the theory, and have suggested that significant modification of the model may be required. Using pyranine as the pH indicator, we find that the median cytoplasmic pH in cells treated with 10 microM DES dropped from 7.19 to pH 6.02. This effect is consistent with the pharmacological action of DES and with the proposal that DES, a stalk cell inducer, should acidify the cytosol. These results provide direct support for the theory that cytoplasmic pH is an essential regulator of the developmental pathway in Dictyostelium.

A hypothetical model of the flavodoxin-tetraheme cytochrome c3 complex of sulfate-reducing bacteria.

A hypothetical model of the flavodoxin-tetraheme cytochrome c3 electron-transfer complex from the sulfate-reducing bacterium Desulfovibrio vulgaris has been constructed by using interactive computer graphics based on electrostatic potential field calculations and previous NMR experiments. Features of the proposed complex are (1) van der Waals contact between the flavin mononucleotide prosthetic group of flavodoxin and one heme of the cytochrome, (2) unique complementarity of electrostatic fields between the region surrounding this heme and the region surrounding the exposed portion of the flavin mononucleotide group of flavodoxin, and (3) no steric interferences between the two polypeptide chains in the complex. This complex is consistent with all structural and spectroscopic data available.

Visualization of bioluminescence as a marker of gene expression in rhizobium-infected soybean root nodules.

The linked structural genes lux A and lux B, encoding bacterial luciferase of a marine bacterium Vibrio harveyi, were fused with the nitrogenase nifD promoter from Bradyrhizobium japonicum and with the P1 promoter of pBR322. Both fusions were integrated into the B. japonicum chromosome by site-specific recombination. Soybean roots infected with the two types of rhizobium transconjugants formed nitrogen-fixing nodules that produced bright blue-green light. Cells containing the P1 promoter/lux AB fusion resulted in continuously expressed bioluminescence in both free-living rhizobium and in nodule bacteriods. However, when under control of the nifD promoter, luciferase activity was found only in introgen-fixing nodules. Light emission from bacteroids allowed us to visualize and to photograph nodules expressing this marker gene fusion in vivo at various levels of resolution, including within single, living plant cells. Localization of host cells containing nitrogen-fixing bacteroids within nodule tissue was accomplished using low-light video microscopy aided by realtime image processing techniques developed specifically to enhance extreme low-level luminescent images.

A flexible, computer-controlled video microscope capable of quantitative spatial, temporal, and spectral measurements.

A video microscope system has been constructed and tested that incorporates computer-controlled video cameras for high-resolution and low-light microscopy. The low-light camera system involves a dual microchannel plate-image intensifier capable of photon gain as high as 500 000 and a gated silicone-intensified target vidicon to achieve usable photon sensitivity with a noise equivalent signal of only 2 photons (500 nm) per pixel per second. We have compared the limitations and capabilities of this camera system with those of a high-resolution video camera and conventional photomicroscopy. Uses of the low-light camera coupled to a computer system include image acquisition of weak-light images from self-luminous specimens, fluorescence microscopy with weak exciting light, kinetic resolution of calcium-mediated events as monitored by the calcium-sensitive bioluminescence of aequorin, and spatially resolved spectroscopic measurements. Flexible use of this system in these various applications is possible because it allows operation with illumination intensities over a dynamic range of 100 000:1.

Earthworm bioluminescence: characterization of high specific activity Diplocardia longa luciferase and the reaction it catalyzes.

Diplocardia longa luciferase purified by an improved procedure differs from that first described by Bellisario et al. [Bellisario, R., Spencer, T. E., & Cormier, M. J. (1972) Biochemistry 11, 2256-2266] in having much higher specific activity (40X) and firmly bound, EPR-silent copper. Improved assay conditions suggest that this protein acts as a catalyst in a bioluminescent reaction involving the degradation of 3-(isovalerylamino)-1-hydroxypropane hydroperoxide. This substrate is formed spontaneously on the addition of hydrogen peroxide to D. longa luciferin (3-(isovalerylamino)propanal). The quantum yield of the bioluminescence for this substrate is 3%. Detailed physical and chemical analyses of high specific activity D. longa luciferase indicate that it is a large (300000 daltons), asymmetric (f/fo=1.63, with 0.4 g/g hydration), multisubunit enzyme. It contains carbohydrate (6%), lipid (2%), and copper (up to 4 mol/30000 daltons). The amino acid composition is unusual with 11% by weight of the residues being either proline or hydroxyproline.