Interior and surface of monomeric proteins

A study of the molecular sources of nonideal osmotic pressure of bovine serum albumin solutions as a function of pH

The nonideal osmotic pressure of bovine serum albumin (BSA) solutions was studied extensively by Scatchard and colleagues. The extent of pH- and salt-dependent nonideality changes are large and unexplained. In 1992, Fullerton et al. derived new empirical expressions to describe solution nonideal colligative properties including osmotic pressure (Fullerton et al. 1992. Biochem. Cell Biol. 70:1325-1331). These expressions are based on the concepts of volume occupancy and hydration force. Nonideality is accurately described by a solute/solvent interaction parameter I and an "effective" osmotic molecular weight Ae. This paper uses the interaction-corrected nonideal expressions for osmotic pressure to calculate the hydration I values and "effective" osmotic molecular weight of BSA, Ae, as a function of pH. Both factors vary in a predictable manner due to denaturing of the BSA molecule. Both contribute to an increase in osmotic pressure for the same protein concentration as the solution pH moves away from the isoelectric point. Increased nonideality is caused by larger hydration resulting from larger solvent-accessible surface areas and by the decrease in "effective" osmotic molecular weight, Ae, due to segmental motion of denatured (filamentous) molecules.

Probing weakly polar interactions in cytochrome c

Theoretical, statistical, and model studies suggest that proteins are stabilized by weakly polar attractions between sulfur atoms and properly oriented aromatic rings. The two sulfur-containing amino acids, methionine and cysteine, occur frequently among functional alleles in random mutant libraries of Saccharomyces cerevisiae iso-1-cytochrome c genes at positions that form a weakly polar aromatic-aromatic interaction, the wild-type protein. To determine if a weakly polar sulfur-aromatic interaction replaced the aromatic-aromatic interaction, the structure and stability of two variants were examined. Phenylalanine 10, which interacts with tyrosine 97, was replaced by methionine and cysteine. The cysteine was modified to form the methionine and cysteine analog, S-methyl cysteine (CysSMe). Proton NMR studies indicate that changing Phe 10 to Met or CysSMe affects only local structure and that the structures of sulfur-containing variants are nearly identical. Analysis of chemical shifts and nuclear Overhauser effect data indicates that both sulfur-containing side chains are in position to form a weakly polar interaction with Tyr 97. The F10M and F10CSMe variants are 2-3 kcal mol-1 less stable than iso-1-cytochrome c at 300 K. Comparison of the stabilities of the F10M and F10CSMe variants allows evaluation of the potential weakly polar interaction between the additional sulfur atom of F10CSMe and the aromatic moiety of Tyr 97. The F10CSMe;C102T variant is 0.7 +/- 0.3 kcal mol-1 more stable than the F10M;C102T protein. The increased stability is explained by the difference in hydrophobicity of the sulfur-containing side chains. We conclude that any weakly polar interaction between the additional sulfur and the aromatic ring is too weak to detect or is masked by destabilizing contributions to the free energy of denaturation.

HYDRO: a program for protein hydropathy predictions

VAX/VMS programs for predicting protein hydropathy from amino acid sequence with several parameters are described. The hydropathy propensities of amino acids were normalised to make the different scales and predictions comparable. Another program package can be used to study similarity on the secondary structural level by comparing, for example, hydropathy predictions. These methods can provide valuable information also when there is only low sequence similarity. Amino acid residue accessibilities can be shown for known three-dimensional structures in addition to predictions. The programs can further be used for searching for a suitable prediction method and window size for a group of related proteins when the structure of at least one representative is known.

Environmental characteristics of residues in proteins: three-dimensional molecular hydrophobicity potential approach

A new method for quantitative estimation of surrounding hydrophobicity for residues in proteins is proposed. It is based on the formalism of three-dimensional molecular hydrophobicity potential (3D MHP) and includes calculation of 3D MHP created by all atoms in a system "molecule+surrounding water". We calculated 3D MHP in the geometrical centers of residues for 23 proteins (from Protein Data Bank) surrounded by water layers 12-15 A thick. These data, plotted along the protein sequence (1D MHP profiles) contain comprehensive information on protein, water, prosthetic groups and neighbouring domains contributions to residue environment. 1D MHP profiles generated by water molecules strongly correlate with standard accessibility profiles based on calculations of exposed surface areas. The results confirm recently observed interrelation between the resonance Raman cross sections of tryptophan residues and polarity of their microenvironment. 3D MHP contributions (and related 1D MHP profiles) to residue environment from protein atoms, heme in myoglobin, flavin in flavodoxin as well as neighbouring domains in pyruvate kinase were characterized. 3D MHP data for rubredoxin in native and totally extended conformations reveal striking deviations reflecting the influence of long-range interactions between residues far removed in the sequence. Statistical analysis of 3D MHP data yields a new hydrophobicity scale (MHPS) that correlates with several commonly used scales obtained by a variety of complementary techniques.

Refined three-dimensional solution structure of a snake cardiotoxin: analysis of the side-chain organization suggests the existence of a possible phospholipid binding site

The solution structure of toxin gamma (60 residues, 4 disulfides) from Naja nigricollis was determined by proton nmr and molecular modeling with DIANA and X-PLOR. The structures were calculated using 489 distance and 81 dihedral angle constraints. The average atomic rms deviation between the nine refined structures and the average structure is 0.118 nm for the backbone atoms. Toxin gamma has an overall folding consisting of three loops stabilized by the four disulfides and forming a two- and a three-stranded beta-sheet (loop I and loops II, III, respectively). The same type of folding has been observed for two homologous cardiotoxins. The very close similarity of the solution structure of toxin gamma and the crystal structure of toxin VII4 includes details of the topological arrangement of numerous side chains. Among these are the conserved residues K12, K18, K35, and Y22, known to be critical for the cytolytic activity of toxin gamma. A cluster of hydrophobic side chains organized around Y22 is found on one side of the three-stranded beta-sheet and is spatially close to a group of three lysines (K12, K18, K35). The side chains of these lysines form a cationic site that can accommodate the binding of a phosphate ion as found in the crystal structure of toxin VII4. The hydrophobic cluster constitutes a possible binding site for the hydrophobic moiety of phospholipids. Together with the complementary cationic site, this hydrophobic surface can form a conserved site by which cardiotoxins bind to membrane phospholipids.

Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar

BACKGROUND

Protein-protein recognition is fundamental to most biological processes. The information we have so far on the interfaces between proteins comes largely from several protease-inhibitor and antigen-antibody complexes. Barnase, a bacterial ribonuclease, and barstar, its natural inhibitor, form a tight complex which provides a good model for the study and design of protein-protein non-covalent interactions.

RESULTS

Here we report the structure of a complex between barnase and a fully functional mutant of barstar determined by X-ray analysis. Barstar is composed of three parallel alpha-helices stacked against a three-stranded parallel, beta-sheet, and sterically blocks the active site of the enzyme with an alpha-helix and adjacent loop. The buried surface in the interface between the two molecules totals 1630 A2. The barnase-barstar complex is predominantly stabilized by charge interactions involving positive charges in the active site of the enzyme. Asp39 of barstar binds to the phosphate-binding site of barnase, mimicking enzyme-substrate interactions.

CONCLUSION

The phosphate-binding site of the enzyme is the anchor point for inhibitor binding. We propose that this is also likely to be the case for other ribonuclease inhibitors.

Crystal structure of TGF-beta 2 refined at 1.8 A resolution

The crystal structure of TGF-beta 2 has been refined using data collected with synchrotron radiation (CHESS) to 1.8 A resolution with a residual R (= sigma magnitude of Fo-magnitude of Fc/sigma magnitude of Fo) factor of 17.3%. The model consists of 890 protein atoms from all 112 residues and 59 water molecules. The monomer of TGF-beta 2 assumes a rather extended conformation and lacks a well-defined hydrophobic core. Surface accessibility calculations show only 44% of the nonpolar surface is buried in the monomer. In contrast, 55.8% of the nonpolar surface area is buried when the two monomers form a dimer, a typical value for globular proteins. This includes a 1300 A2 buried interface area that is largely hydrophobic. Sequence comparisons using a profile derived from the refined TGF-beta 2 structure suggest that the cluster of four disulfides (three intramonomeric disulfide bonds 15-78, 44-109, 48-111 forming a disulfide knot, and one intermonomeric disulfide 77-77) together with the extended beta strand region constitutes the conserved structural motif for the TGF-beta superfamily. This structural motif, without the 77-77 disulfide bond, defines also the common fold for a general family of growth factors, including the nerve growth factor and platelet-derived growth factor families. The fold is conserved only at the monomer level, while the active forms are dimers, suggesting that dimerization plays an important role in regulating the binding of these cytokines to their receptors and in modulating the biological responses.

Why are the same protein folds used to perform different functions?

A small number of folding patterns describe in outline most of the known protein globules, the same folds being found in non-homologous proteins with different functions. We show that the 'popular' folding patterns are those which, due to some thermodynamic advantages of their structure, can be stabilized by a lot of random sequences. In contrast, the folds which are rarely or never observed in natural globular proteins can be stabilized only by a tiny number of random sequences. The advantageous folds are few, they tolerate various primary structures, and therefore they can and ought to perform different functions. A connection between the inherent 'weak points' of protein folding patterns and positions of active sites are discussed.

The nonhelical structure of antifreeze protein type III

Antifreeze proteins (AFPs) are present in the blood of some marine fishes and inhibit the growth of ice crystals at subzero temperatures by adsorption to the ice lattice. The solution structure of a Type III AFP was determined by two-dimensional nuclear magnetic resonance spectroscopy. These measurements indicate that this 66-residue protein has an unusual fold in which eight beta strands form two sheets of three antiparallel strands and one sheet of two antiparallel strands, and the triple-stranded sheets are packed orthogonally into a beta sandwich. This structure is completely different from the amphipathic, helical structure observed for Type I AFPs.

Kinetic analysis of the hydrodynamic transition accompanying protein folding using size exclusion chromatography. 1. Denaturant dependent baseline changes

Size exclusion profiles of proteins with persistent conformations exhibit broad asymmetric peaks whose shape and elution times are dependent on denaturant concentration. The collective elution profiles were precisely simulated by an apparent binding model that treats the denaturant dependence in terms of an apparent matrix binding. The model requires three experimentally measurable parameters: the elution time for the unbound protein, an apparent association equilibrium constant for binding, and an apparent exchange time for binding. The denaturant dependence for each of these parameters is related to the accessible surface area of the protein.

Residue solvent accessibilities in the unfolded polypeptide chain

The difference of solvent accessibilities in the native and unfolded states of the protein is used as a measure of the hydrophobic contribution to the free energy of folding. We present a new approximation of amino acids solvent accessibilities in the unfolded state based on the 1-ns molecular dynamics simulation of Ala-X-Ala tripeptides at a temperature of 368 K. The standard accessibility values averaged from the molecular dynamics study are significantly lower from those previously obtained by considering only selected conformations of Ala-X-Ala tripeptides.

Crystal packing in six crystal forms of pancreatic ribonuclease

We compare the molecular packing of bovine pancreatic ribonuclease A (RNase A) in six crystal forms, two grown with alcohol, three with high salt and one with polyethylene glycol as a precipitant. The six packings differ in the number of molecules in contact and in the extent of the contacts, which bury 1570 A2 to 2790 A2 of the RNase surface. Regions of the protein surface involved in the six packings cover almost the whole RNase molecule. The abundance of polar interactions, about one per 200 A2, is the same in all types of precipitants. All molecule-to-molecule contacts are different in the six crystal forms, except for the one that forms a RNase dimer. The dimer has a large interface covering 1800 A2 and eight to ten polar interactions. Its presence in the three salt-grown crystal forms suggests that it is an intermediate in salt induced crystallization. In contrast, the two alcohol-grown forms contain only small interfaces, implying a different mechanism of nucleation.

X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus

The structures of the oxidized and reduced forms of the rubredoxin from the archaebacterium, Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, have been determined by X-ray crystallography to a resolution of 1.8 A. Crystals of this rubredoxin grow in space group P2(1)2(1)2(1) with room temperature cell dimensions a = 34.6 A, b = 35.5 A, and c = 44.4 A. Initial phases were determined by the method of molecular replacement using the oxidized form of the rubredoxin from the mesophilic eubacterium, Clostridium pasteurianum, as a starting model. The oxidized and reduced models of P. furiosus rubredoxin each contain 414 nonhydrogen protein atoms comprising 53 residues. The model of the oxidized form contains 61 solvent H2O oxygen atoms and has been refined with X-PLOR and TNT to a final R = 0.178 with root mean square (rms) deviations from ideality in bond distances and bond angles of 0.014 A and 2.06 degrees, respectively. The model of the reduced form contains 37 solvent H2O oxygen atoms and has been refined to R = 0.193 with rms deviations from ideality in bond lengths of 0.012 A and in bond angles of 1.95 degrees. The overall structure of P. furiosus rubredoxin is similar to the structures of mesophilic rubredoxins, with the exception of a more extensive hydrogen-bonding network in the beta-sheet region and multiple electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other residues (the amino-terminal nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen group of Phe 29). The influence of these and other features upon the thermostability of the P. furiosus protein is discussed.

Correlation functions as a tool for protein modeling and structure analysis

Proteins present unique folding structures whose conformations are determined primarily by their amino acid sequences. At present, there is no algorithm that would correlate the sequences with the structures determined by X-ray analysis or NMR. Comparative modeling of a new protein sequence based on the known structure of a functionally related protein promises to yield model structures that may provide relevant properties of the protein. To analyze the quality of a model structure, a set of correlation functions was derived from calculations on a subset of proteins from the structure database. Twenty-three highly resolved protein structures with resolutions of at least 1.7 A from various protein families were used as the primary database. The purpose of this initial work was to find highly sensitive functions (including statistical error limits for the parameters) that describe properties of "real" proteins. Each correlation described is characterized by the correlation coefficient, the parameters for linear or nonlinear regression (coefficients of the equation), standard deviation and variance, and the confidence limits describing the statistical probability for values to occur within these limits, e.g., the natural variability of the property under examination. In addition, a method was developed for creating reasonably misfolded proteins. The ability of a correlation function to discriminate between the native structure and the misfolded conformations is expressed by the reliability index, which indicates the sensitivity of a correlation function. The term correlation functions thus summarizes a variety of efforts to find a mathematical description for the properties of protein structures, for their correlation, and for their significance.

Alpha-helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at solvent-exposed surfaces

The importance of amino acid side-chains in helix stability has been investigated by making a series of mutations at the N-caps, C-caps and internal positions of the solvent-exposed faces of the two alpha-helices of barnase. There is a strong positional and context dependence of the effect of a particular amino acid on stability. Correlations have been found that provide insight into the physical basis of helix stabilization. The relative effects of Ala and Gly (or Ser) may be rationalized on the basis of solvent-accessible surface areas: burial of hydrophobic surface stabilizes the protein as does exposure to solvent of unpaired hydrogen bond donors or acceptors in the protein. There is a good correlation between the relative stabilizing effects of Ala and Gly at internal positions with the total change in solvent-accessible hydrophobic surface area of the folded protein on mutation of Ala----Gly. The relationship may be extended to the N and C-caps by including an extra term in hydrophilic surface area for the solvent exposure of the non-intramolecularly hydrogen-bonded main-chain CO, NH or protein side-chain hydrogen bonding groups. The requirement for solvent exposure of the C-cap main-chain CO groups may account for the strong preference for residues having positive phi and psi angles at this position, since this alpha L-conformation results in the largest solvent exposure of the C-terminal CO groups. Glycine in an alpha L-conformation results in the greatest exposure of these CO groups. Further, the side-chains of His, Asn, Arg and Lys may, with positive phi and psi-angles, form a hydrogen bond with the backbone CO of residue in position C -3 (residues are numbered relative to the C-cap). The preferences at the C-cap are Gly much greater than His greater than Asn greater than Arg greater than Lys greater than Ala approximately Ser approximately greater than Asp. The preferences at the N-cap are determined by hydrogen bonding of side-chains or solvent to the exposed backbone NH groups and are: Thr approximately Asp approximately Ser greater than Gly approximately Asn greater than Gln approximately Glu approximately His greater than Ala greater than Val much greater than Pro. These general trends may be obscured when mutation allows another side-chain to become a surrogate cap.(ABSTRACT TRUNCATED AT 400 WORDS)

Analysis of side-chain organization on a refined model of charybdotoxin: structural and functional implications

The spatial organization of side chains on a refined model of charybdotoxin is presented. First, the structural role of two groups of well-defined, low-accessible side chains (Thr3, Val5, Val16, Leu20, Cys33 and Leu20, His21, Thr23, Cys17, Cys35) is discussed. These side chains are conserved in three out of the five known scorpion toxins acting on K+ channels. Interestingly, they are not conserved in scyllatoxin which presents a slightly different secondary structure organization. Second, the spatial organization of all positively charged residues is analyzed. Comparison with the results presented by Park and Miller [(1992) Biochemistry (preceding paper in this issue)] shows that all functionally important positive residues are located on the beta-sheet side of the toxin. These results are different from those obtained by Auguste et al. [(1992) Biochemistry 31, 648-654] on scyllatoxin, which blocks a different type of K+ channel. This study shows, in fact, that functionally important positive residues are located on the helix side of the toxin. Thus, charybdotoxin and scyllatoxin, which present the same global fold, interact with two different classes of K+ channels by two different parts of the motif.

Modeling microdomains: the surface area of globin helices

The accessible surface areas of 53 high-resolution globin helices are correlated with molecular weight. The linear fit is assessed for statistical accuracy using a boot-strap analysis, and by comparison to the areas of 13 ideal polyalanine alpha-helices. The accessible area of the unfolded helices is compared with the folded values before helix-helix packing. An analytical physical model is presented to explain the correlation, and to provide an analytical value for the surface area parameter in the diffusion-collision model of protein folding.

Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution

The factor for inversion stimulation (FIS) binds as a homodimeric molecule to a loose 15 nucleotide consensus sequence in DNA. It stimulates DNA-related processes, such as DNA inversion and excision, it activates transcription of tRNA and rRNA genes and it regulates its own synthesis. FIS crystallizes as a homodimer, with 2 x 98 amino acid residues in the asymmetric unit. The crystal structure was determined with multiple isomorphous replacement and refined to an R-factor of 19.2% against all the 12,719 X-ray data (no sigma-cutoff) extending to 2.0 A resolution. The two monomers are related by a non-crystallographic dyad axis. The structure of the dimer is modular, with the first 23 amino acid residues in molecule M1 and the first 24 in molecule M2 disordered and not "seen" in the electron density. The polypeptide folds into four alpha-helices, with alpha A, alpha A' (amino acid residues 26 to 40) and alpha B, alpha B' (49 to 69) forming the core of the FIS dimer, which is stabilized by hydrophobic forces. To the core are attached "classical" helix-turn-helix motifs, alpha C, alpha D (73 to 81 and 84 to 94) and alpha C', alpha D'. The connections linking the helices are structured by two beta-turns for alpha A/alpha B, and alpha C1 type extensions are observed at the C termini of helices alpha B, alpha C and alpha D. Helices alpha D and alpha D' contain 2 x 6 positive charges; they are separated by 24 A and can bind adjacent major grooves in B-type DNA if it is bent 90 degrees. The modular structure of FIS is also reflected by mutation experiments; mutations in the N-terminal part and alpha A interfere with FIS binding to invertases, and mutations in the helix-turn-helix motif interfere with DNA binding.

The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability

Barnase is described anatomically in terms of its substructures and their mode of packing. The surface area of hydrophobic residues buried on formation and packing of the structural elements has been calculated. Changes in stability have been measured for 64 mutations, 41 constructed in this study, strategically located over the protein. The purpose is to provide: (1) information on the magnitudes of changes in stabilization energy for mutations of residues that are important in maintaining the structure; and (2) probes for the folding pathway to be used in subsequent studies. The majority of mutations delete functional moieties of side-chains or make isosteric changes. The energetics of the interactions are variable and context-dependent. The following general conclusions may be drawn, however, from this study about the classes of interactions that stabilize the protein. (1) Truncation of buried hydrophobic side-chains has, in general, the greatest effect on stability. For fully buried residues, this averages at 1.5 kcal mol-1 per methylene group with a standard deviation of +/- 0.6 kcal mol-1. Truncation of partly exposed leucine, isoleucine or valine residues that are in the range of 50 to 80 A2 of solvent-accessible area (30 to 50% of the total solvent-accessible area on a Gly-X-Gly tripeptide, i.e. those packed against the surface) has a smaller, but relatively constant effect on stability, at 0.81 kcal mol-1 per methylene group with a statistical standard deviation of +/- 0.18 kcal mol-1. (2) There is a very poor correlation between hydrophobic surface area buried and the free energy change for an extensive data set of hydrophobic mutants. The best correlation is found to be between the free energy change and the number of methylene groups within a 6 A radius of the hydrophobic groups deleted. (3) Burial of the hydroxyl group of threonine in a pocket that is intended for a gamma-methyl group of valine costs 2.5 kcal mol-1, in the range expected for the loss of two hydrogen bonds.(ABSTRACT TRUNCATED AT 400 WORDS)

Effect of alanine versus glycine in alpha-helices on protein stability

The rational design of proteins requires knowledge of the helix-forming propensities (s-values) of the different amino acids. There is, however, considerable controversy about the relative values for alanine and glycine. We find from experiments on mutants of barnase that the relative effect of Ala versus Gly on helix stability depends crucially on the position in the helix (whether they are at the ends (caps) or are internal) and the context (the influence of their neighbours). Glycine is greatly preferred at the N and C caps. At internal positions, Ala stabilizes the helix relative to Gly by 0.4 to 2 kcal mol-1. The variation results from a combination of burial of hydrophobic surface on folding and interference with hydrogen bonding of the protein with solvent. There is a good empirical correlation between the relative stabilizing effects of Ala and Gly with the total change in solvent-accessible hydrophobic surface area of the folded protein on mutation of Gly to Ala. It is not valid to assign to each amino acid a unique s-value that is generally applicable to all positions in all helices in all proteins.

Thermodynamics of unfolding of the alpha-amylase inhibitor tendamistat. Correlations between accessible surface area and heat capacity

Unfolding of the small alpha-amylase inhibitor tendamistat (74 residues, 2 disulfide bridges) has been characterized thermodynamically by high sensitivity scanning microcalorimetry. To link the stability parameters with structural information we use heat capacity group parameters and water accessible surface areas to calculate the change in heat capacity on unfolding of tendamistat. Our results show that both the group parameter and surface area approaches provide a reasonable, though not perfect, basis for delta Cp calculations. When using the experimentally determined temperature-independent heat capacity increase of 2.89 kJ mol-1 K-1 tendamistat exhibits convergence of thermodynamic parameters at about 140 degrees C, in agreement with recent predictions of the temperature at which the hydrophobic hydration is supposed to disappear. Despite the apparent support of this new view of the hydrophobic effect, there are inconsistencies in the interpretation of the thermodynamic parameters and these are addressed in the Discussion. The specific stability of tendamistat is similar to that of modified bovine pancreatic trypsin inhibitor, with only two of the native three disulfide bridges intact. This observation confirms our previous conclusion that disulfide bridges affect significantly the enthalpy and entropy of unfolding. The recent study by Doig & Williams provides additional convincing support for this conclusion. The predictive scheme proposed by these authors permits a fair estimate of the Gibbs free energy and enthalpy changes of these two proteins.

Malate dehydrogenase from Chlorobium vibrioforme, Chlorobium tepidum, and Heliobacterium gestii: purification, characterization, and investigation of dinucleotide binding by dehydrogenases by use of empirical methods of protein sequence analysis

Malate dehydrogenase (MDH; EC 1.1.1.37) from strain NCIB 8327 of the green sulfur bacterium Chlorobium vibrioforme was purified to homogeneity by triazine dye affinity chromatography followed by gel filtration. Purification of MDH gave an approximately 1,000-fold increase in specific activity and recoveries of typically 15 to 20%. The criteria of purity were single bands on sodium dodecyl sulfate (SDS) and nondenaturing polyacrylamide electrophoresis (PAGE) and the detection of a single N terminus in an Edman degradation analysis. MDH activity was detected in purified preparations by activity staining of gels in the direction of malate oxidation. PAGE and gel filtration (Sephadex G-100) analyses showed the native enzyme to be a dimer composed of identical subunits both at room temperature and at 4 degrees C. The molecular weight of the native enzyme as estimated by gel filtration was 77,000 and by gradient PAGE was 74,000. The subunit molecular weight as estimated by SDS-gradient PAGE was 37,500. N-terminal sequences of MDHs from C. vibrioforme, Chlorobium tepidum, and Heliobacterium gestii are presented. There are obvious key sequence similarities in MDHs from the phototrophic green bacteria. The sequences presented probably possess a stretch of amino acids involved in dinucleotide binding which is similar to that of Chloroflexus aurantiacus MDH and other classes of dehydrogenase enzymes but unique among MDHs.

Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 A resolution

The three-dimensional structure of the monomeric bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from Escherichia coli has been refined at 2.0 A resolution, using oscillation film data obtained from synchrotron radiation. The model includes the complete protein (452 residues), two phosphate ions and 628 water molecules. The final R-factor is 17.3% for all observed data between 15 and 2 A resolution. The root-mean-square deviations from ideal bond lengths and bond angles are 0.010 A and 3.2 degrees, respectively. The structure of N-(5'-phosphoribosyl)anthranilate isomerase: indole-3-glycerol-phosphate synthase from E. coli comprises two beta/alpha-barrel domains that superimpose with a root-mean-square deviation of 2.03 A for 138 C alpha-pairs. The C-terminal domain (residues 256 to 452) catalyses the PRAI reaction and the N-terminal domain (residues 1 to 255) catalyses the IGPS reaction, two sequential steps in tryptophan biosynthesis. The enzyme has the overall shape of a dumb-bell, resulting in a surface area that is considerably larger than normally observed for monomeric proteins of this size. The active sites of the PRAI and the IGPS domains, both located at the C-terminal side of the central beta-barrel, contain equivalent binding sites for the phosphate moieties of the substrates N-(5'-phosphoribosyl) anthranilate and 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate. These two phosphate binding sites are identical with respect to their positions within the tertiary structure of the beta/alpha-barrel, the conformation of the residues involved in phosphate binding and the hydrogen-bonding network between the phosphate ions and the protein. The active site cavities of both domains contain similar hydrophobic pockets that presumably bind the anthranilic acid moieties of the substrates. These similarities of the tertiary structures and the active sites of the two domains provide evidence that N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from E. coli results from a gene duplication event of a monomeric beta/alpha-barrel ancestor.

Peptide-binding specificity of the molecular chaperone BiP

Members of the heat-shock protein family (hsp70s) can distinguish folded from unfolded proteins. This property is crucial to the role of hsp70s as molecular chaperones and is attributable to the amino-acid specificity of the peptide-binding site. The specificity for peptide ligands is investigated using a set of peptides of random sequence but defined chain length. The peptide-binding site selects for aliphatic residues and accommodates them in an environment energetically equivalent to the interior of a folded protein.

Side-chain clusters in protein structures and their role in protein folding

A method has been developed to detect dense clusters of residue side-chains in proteins, where contact is based upon the percentage of the maximum possible for a given residue type. The clusters represent protein sites with the highest degree of interaction amongst their member residues, while contacts with the environment surrounding the cluster are lower in number. The method has been applied to three distinct structural sets of proteins to check for consistency: mixed alpha-helical/beta-sheet proteins, all beta-strand proteins, and all alpha-helical proteins. A number of cluster features generated from these sets are of general interest for protein folding. (1) A majority of the clusters, comprising three to four residues on average, are localized near the protein surfaces and not within the protein cores. (2) The clusters have preferences for the N- and C-terminal ends of alpha-helices and beta-strands in alpha/beta and alpha-proteins, while beta-proteins utilize the middle strand regions more often. A number of clusters connect three or more beta-strands and/or alpha-helices. (3) More than half of the clusters display residue pairs with oppositely charged atoms within 4.5 A of each other. (4) The residue composition of the clusters does not show correlation with hydrophobicity measures but rather with side-chain volume and surface. The highly preferred cluster residues are (in order of decreasing preference) Trp, His, Arg, Tyr, Glu, Gln and Phe. Clusters with extensive internal contacts in related haemoglobin and immunoglobulin tertiary structures show respective conservation. Several examples illustrate "strategic" folding positions in proteins that often bring together a number of sheets and/or helices, suggesting a folding model in which largely preformed secondary structures are joined together in a cluster induced collapse. Alternatively, the clusters may form at some stage in the folding process to reduce considerably the searchable conformational space and help maintain the proper folding pathway. The clusters also provide hints for site-directed mutagenesis and protein engineering experiments as they are also suggested to be important for structural stability.

Isoenthalpic and isoentropic temperatures and the thermodynamics of protein denaturation

The standard enthalpy or entropy change upon transfer of a small nonpolar molecule from a nonaqueous phase into water at a given temperature is generally different for different solute species. However, if the heat capacity change is independent of temperature, there exists a temperature at which the enthalpy or the entropy change becomes the same for all solute species within a given class. Similarly, the enthalpy or the entropy change of protein denaturation, when extrapolated to high temperature assuming a temperature-independent heat capacity change, shows a temperature at which its value becomes the same for many different globular proteins on a per weight basis. It is shown that the existence of these temperatures can be explained from a common formalism based on a linear relationship between the thermodynamic quantity and a temperature-independent molecular property that characterizes the solute or the protein. For the small nonpolar molecule transfer processes, this property is the surface area or the number of groups that are brought in contact with water. For protein denaturation, it is suggested that this property measures the polar/nonpolar mix of the internal interaction within the protein interior. Under a certain set of assumptions, this model leads to the conclusion that the nonpolar and the polar groups of the protein contribute roughly equally to the stability of the folded state of the molecule and that the solvent-accessible surface area of the denatured form of a protein is no more than about two-thirds that of the fully extended form.

"Soft docking": matching of molecular surface cubes

Molecular recognition is achieved through the complementarity of molecular surface structures and energetics with, most commonly, associated minor conformational changes. This complementarity can take many forms: charge-charge interaction, hydrogen bonding, van der Waals' interaction, and the size and shape of surfaces. We describe a method that exploits these features to predict the sites of interactions between two cognate molecules given their three-dimensional structures. We have developed a "cube representation" of molecular surface and volume which enables us not only to design a simple algorithm for a six-dimensional search but also to allow implicitly the effects of the conformational changes caused by complex formation. The present molecular docking procedure may be divided into two stages. The first is the selection of a population of complexes by geometric "soft docking", in which surface structures of two interacting molecules are matched with each other, allowing minor conformational changes implicitly, on the basis of complementarity in size and shape, close packing, and the absence of steric hindrance. The second is a screening process to identify a subpopulation with many favorable energetic interactions between the buried surface areas. Once the size of the subpopulation is small, one may further screen to find the correct complex based on other criteria or constraints obtained from biochemical, genetic, and theoretical studies, including visual inspection. We have tested the present method in two ways. First is a control test in which we docked the components of a molecular complex of known crystal structure available in the Protein Data Bank (PDB). Two molecular complexes were used: (1) a ternary complex of dihydrofolate reductase, NADPH and methotrexate (3DFR in PDB) and (2) a binary complex of trypsin and trypsin inhibitor (2PTC in PDB). The components of each complex were taken apart at an arbitrary relative orientation and then docked together again. The results show that the geometric docking alone is sufficient to determine the correct docking solutions in these ideal cases, and that the cube representation of the molecules does not degrade the docking process in the search for the correct solution. The second is the more realistic experiment in which we docked the crystal structures of uncomplexed molecules and then compared the structures of docked complexes with the crystal structures of the corresponding complexes. This is to test the capability of our method in accommodating the effects of the conformational changes in the binding sites of the molecules in docking.(ABSTRACT TRUNCATED AT 400 WORDS)

Protein interactions with surface-immobilized metal ions: structure-dependent variations in affinity and binding capacity with temperature and urea concentration

We have used equilibrium binding analyses to evaluate the influence of temperature and urea on the affinity of hen egg white lysozyme and bovine pancreatic ribonuclease A for surface-immobilized Cu(II) ions. Linear Scatchard plots suggested that these model proteins were interacting with immobilized metal ions via a single class of intermediate-affinity (Kd = 10-40 microM) binding sites. Alterations in temperature had little or no effect on the immobilized Cu(II) binding capacity of either protein. Temperature effects on the interaction affinity, however, were protein-dependent and varied considerably. The affinity of lysozyme for immobilized Cu(II) ions was significantly decreased with increased temperature (0 degree C-37 degrees C), yet the affinity of ribonuclease did not vary measurably over the same temperature range. The van 't Hoff plot (1n K vs 1/T) for lysozyme suggests a straight line relationship (single mechanism) with a delta H of approximately -5.5 kcal/mol. Urea effects also varied in a protein-dependent manner. A 10-fold reduction in the affinity of lysozyme for the immobilized Cu(II) was observed with the urea concentrations up to 3 M; yet urea had no effect on the affinity of ribonuclease for the immobilized metal ions. Although the interaction capacity of lysozyme with the immobilized Cu(II) ions was decreased by 50% in 3 M urea, ribonuclease interaction capacity was not diminished in urea. Thus, temperature- and urea-dependent alterations in protein-metal ion interactions were observed for lysozyme but not ribonuclease A. The complete, yet reversible, inhibition of lysozyme- and ribonuclease-metal ion interactions by carboxyethylation with low concentrations of diethylpyrocarbonate provided direct evidence of histidyl involvement. The differential response of these proteins to the effects of temperature and urea was, therefore, interpreted based on calculated solvent-accessibilities and surface distributions of His residues, individual His residue pKa values, and specific features of the protein surface structure in the immediate environment of the surface-exposed histidyl residues. Possible interaction mechanisms involved in protein recognition of macromolecular surface-immobilized metal ions are presented.

Immunological mapping of fine molecular surface structures of citrate synthase enzymes from different cell types

Citrate synthase (EC 4.1.3.7), which is present in all living organisms as a key enzyme in aerobic energy metabolism, is one of the most highly phylogenetically conserved enzymes known in terms of its primary and active site structure. However, in terms of other parameters such as in vitro stability, tolerance to changes in pH, degree of self-polymerization, etc., citrate synthases from different sources are markedly different. These divergences can be observed even between isoforms of the enzyme within the same species. Data documenting these diversities suggest that a high degree of difference in tertiary structures may occur. Therefore, the surface profiles of citrate synthase enzymes from yeast, pig, rat, tomato and Escherichia coli were investigated with immunological methods using monoclonal antibody families generated against either pig citrate synthase (alpha-PCS) or yeast citrate synthase-2 (alpha-YCS-2). A high degree of homology of enzyme epitopes was detected on the mitochondrial citrate synthases originating from yeast, tomato, pig and rat cells. Major differences were found between the hexameric citrate synthase originating from E. coli compared with those dimeric forms prepared from eukaryotic cells. Only modest similarities were detected between the highly homologous peroxisomal and mitochondrial yeast citrate synthases. Furthermore, a point mutation of one of the catalytic residues (H274R on recombinant pig and H313R on yeast enzyme) of mitochondrial citrate synthase (CS-1) resulted in a significant increase in immunological similarity with the peroxisomal isoenzyme (CS-2). These findings are discussed in terms of the possible mechanism of evolution of CS-2 in yeast.

Energetics of repacking a protein interior

To test whether interactions in the hydrophobic core of a protein can be adequately modeled based on the properties of a liquid hydrocarbon, we measured the unfolding free energies of the wild-type bacteriophage f1 gene V protein and 29 mutants with apolar substitutions at positions 35 and 47. Stability changes arising from identical mutations at these two buried sites are quite different, suggesting that one site is more rigid than the other. Reversals of residues at positions 35 and 47 confirm that their environments are distinct. Mutants containing weakly polar residues at these two sites suggest that the protein interior is more polar than a liquid hydrocarbon. Interactions between residues at the two sites appear to be minimal. These observations are compatible with a view of protein interiors that incorporates properties of liquid hydrocarbons but also includes polar interactions and a site-dependent "packing energy" associated with changes in internal structure.

Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications

We have determined hydrophobicity parameters for the side chains of 22 common post- or cotranslationally modified amino acyl residues and for the standard unmodified amino acids as well. This "comprehensive" parameter set is the first such reported. Parameters determined for the side chains of the standard 20 amino acids correlate well with those of widely accepted sets. Our parameters have also been evaluated by hydrophobicity profiles and by transverse hydrophobic moment calculations on cytosolic, secreted, and membranous model proteins, with favorable results. Many of the hydrophobicity parameters for the post- or cotranslationally modified derivatives are of remarkable magnitude, especially those for oligosaccharide-bound Asn and fatty-acylated Cys or amino terminus. Thus, the comprehensive parameter set determined here greatly extends our ability to analyze homology, membrane directedness, and folding potential of proteins.

Secondary structure perturbations in salt-induced protein precipitates

The secondary structure implications of precipitation induced by a chaotropic salt, KSCN, and a structure stabilizing salt, Na2SO4, were studied for twelve different proteins. alpha-helix and beta-sheet content of precipitate and native structures were estimated from the analysis of amide I band Raman spectra. A statistical analysis of the estimated perturbations in the secondary structure contents indicated that the most significant event is the formation of beta-sheet structures with a concomitant loss of alpha-helix on precipitation with KSCN. The conformational changes for each protein were also analyzed with respect to elements of primary, secondary and tertiary structure existing in the native protein; primary structure was quantified by the fractions of hydrophobic and charged amino acids, secondary structure by x-ray estimates of alpha-helix and beta-sheet contents of native proteins and tertiary structure by the dipole moment and solvent-accessible surface area. For the KSCN precipitates, factors affecting beta-sheet content included the fraction of charged amino acids in the primary sequence and the surface area. Changes in alpha-helix content were influenced by the initial helical content and the dipole moment. The enhanced beta-sheet contents of precipitates observed in this work parallel protein structural changes occurring in other aggregative phenomena.

Statistical descriptors for the size and shape of globular proteins

The atomic structures of proteins epitomize the ideas of complexity and irregularity in three-dimensional objects. For such objects, size and shape are difficult to quantify, and therefore the development of unbiased parameters for these properties could facilitate their description. Statistical analysis of the frequency distribution of interatomic distances in protein structures of different classes has revealed two numerical descriptors that correlate with physicochemical properties of these macromolecules. The median (mu) of the distribution correlates (r greater than .98, n = 45) with variables indicative of size (e.g., molecular weight and radius of gyration). The exponent of the Box-Cox transformation lambda, used for converting this distribution into a symmetrical one, correlated (r = .75, n = 43) with a general dimensionless shape parameter defined as the combination of the shape-related accessible surface (A0s), molecular volume (V), and radius of gyration (Rg) in the form s = (A0sRg/V). It is suggested that for globular proteins lambda is a function of both the shape parameter s and the fractal dimension D of the protein surface. These objective descriptors of size and shape could be useful to describe other complex objects.

Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 A resolution. Subunit interactions and active site

The X-ray structure of the quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase from spinach with CO2, Mg2+ and a reaction-intermediate analogue (CABP) has been determined and refined at 2.4 A resolution. Cyclic non-crystallographic symmetry averaging around the molecular 4-fold axis and phase combination were used to improve the initial multiple isomorphous replacement phases. A model composed of one large subunit and one small subunit was built in the resulting electron density map, which was of excellent quality. Application of the local symmetry gave an initial model of the L8S8 molecule with a crystallographic R-value of 0.43. Refinement of this initial model was performed by a combination of conventional least-squares energy refinement and molecular dynamics simulation using the XPLOR program. Three rounds of refinement, interspersed with manual rebuilding at the graphics display, resulted in a model containing all of the 123 amino acid residues in the small subunit, and 467 of the 475 residues in the large subunit. The R-value for this model is 0.24, with relatively small deviations from ideal stereochemistry. Subunit interactions in the L8S8 molecule have been analysed and are described. The interface areas between the subunits are extensive, and bury almost half of the accessible surface areas of both the large and the small subunit. A number of conserved interaction areas that may be of functional significance have been identified and are described, and biochemical and mutagenesis data are discussed in the structural framework of the model.

Extreme differences in charge changes during protein evolution

The maintenance of a proper distribution of charged amino acid residues might be expected to be an important factor in protein evolution. We therefore compared the inferred changes in charge during the evolution of 43 protein families with the changes expected on the basis of random base substitutions. It was found that certain proteins, like the eye lens crystallins and most histones, display an extreme avoidance of changes in charge. Other proteins, like phospholipase A2 and ferredoxin, apparently have sustained more charged replacements than expected, suggesting a positive selection for changes in charge. Depending on function and structure of a protein, charged residues apparently can be important targets for selective forces in protein evolution. It appears that actual biased codon usage tends to decrease the proportion of charged amino acid replacements. The influence of nonrandomness of mutations is more equivocal. Genes that use the mitochondrial instead of the universal code lower the probability that charge changes will occur in the encoded proteins.

Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity

The four half-transamination reactions [the pyridoxal form of Escherichia coli aspartate aminotransferase (AspAT) with aspartate or glutamate and the pyridoxamine form of the enzyme with oxalacetate or 2-oxoglutarate] were followed in a stopped-flow spectrometer by monitoring the absorbance change at either 333 or 358 nm. The reaction progress curves in all cases gave fits to a monophasic exponential process. Kinetic analyses of these reactions showed that each half-reaction is composed of the following three processes: (1) the rapid binding of an amino acid substrate to the pyridoxal form of the enzyme; (2) the rapid binding of the corresponding keto acid to the pyridoxamine form of the enzyme; (3) the rate-determining interconversion between the two complexes. This mechanism was supported by the findings that the equilibrium constants for half- and overall-transamination reactions and the steady-state kinetic constants (Km and kcat) agreed well with the predicted values on the basis of the above mechanism using pre-steady-state kinetic parameters. The significant primary kinetic isotope effect observed in the reaction with deuterated amino acid suggests that the withdrawal of the alpha-proton of the substrates is rate determining. The pyridoxal form of E. coli AspAT reacted with a variety of amino acids as substrates. The Gibbs free energy difference between the transition state and the unbound state (unbound enzyme plus free substrate), as calculated from the pre-steady-state kinetic parameters, showed a linear relationship with the accessible surface area of amino acid substrate bearing an uncharged side chain.(ABSTRACT TRUNCATED AT 250 WORDS)

Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: protein unfolding effects

Using the heat capacity values for amino acid side-chains and the peptide unit determined in the accompanying paper, we calculated the partial heat capacities of the unfolded state for four proteins (apomyoglobin, apocytochrome c, ribonuclease A, lysozyme) in aqueous solution in the temperature range from 5 to 125 degrees C, with an assumption that the constituent amino acid residues contribute additively to the integral heat capacity of a polypeptide chain. These ideal heat capacity functions of the extended polypeptide chains were compared with the calorimetrically determined heat capacity functions of the heat and acid-denatured proteins. The average deviation of the experimental functions from the calculated ideal ones in the whole studied temperature range does not exceed the experimental error (5%). Therefore, the heat-denatured state of a protein, in solutions with acidic pH preventing aggregation, approximates well the completely unfolded state of this macromolecule. The heat capacity change caused by hydration of amino acid residues upon protein unfolding was also determined and it was shown that this is the major contributor to the observed heat capacity effect of unfolding. Its value is different for different proteins and correlates well with the surface area of non-polar groups exposed upon unfolding. The heat capacity effect due to the configurational freedom gain by the polypeptide chain was found to contribute only a small part of the overall heat capacity change on unfolding.

Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: hydration effect

The partial molar heat capacities of various peptides and various organic compounds that model the amino acid side-chains or their parts in aqueous solution have been determined by precise scanning microcalorimetry in the temperature range from 5 to 125 degrees C. This provides an estimate of the partial molar heat capacity of the peptide--CHCONH--group and the side-chains of all amino acid residues. The values obtained are compared with the values found for these substances in the gaseous phase, in order to define the hydration effect. It has been shown that the partial heat capacity of the non-polar groups is positive at low temperature (5 degrees C) and decreases with increasing temperature, while for the polar and charged groups it is negative at low temperature, becomes zero at room temperature and increases further with increasing temperature. This leads to a hydrophobicity scale of the amino acid side-chains based upon the temperature dependences of their heat capacities. Due to the observed specificity in the temperature dependence, at room temperature, the heat capacities of amino acid side-chains correlate well with the non-polar surface areas.

Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution

The amino acid sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum has been fitted to the electron density maps. The resulting protein model has been refined to a nominal resolution of 1.7 A using the constrained-restrained least-squares refinement program of Sussman and the restrained least-squares refinement program of Hendrickson & Konnert. The crystallographic refinement, based on 76,452 reflections with F greater than sigma (F) in the resolution range 5.5 to 1.7 A resulted in a crystallographic R-factor of 18.0%. The asymmetric unit contains one dimeric ribulose-1,5-biphosphate carboxylase molecule, consisting of 869 amino acid residues and 736 water molecules. The geometry of the refined model is close to ideal, with root-mean-square deviations of 0.018 A in bond lengths and 2.7 degrees in bond angles. Two loop regions, comprising residues 54 to 63 and 324 to 335, and the last ten amino acid residues at the C terminus are disordered in our crystals. The expected trimodal distribution is obtained for the side-chain chi 1-angles with a marked preference for staggered conformation. The hydrogen-bonding pattern in the N-terminal beta-sheet and the parallel sheet in the beta/alpha-barrel is described. A number of hydrogen bonds and salt bridges are involved in domain-domain and subunit-subunit interactions. The subunit-subunit interface in the dimer covers an area of 2800 A2. Considerable deviations from the local 2-fold symmetry are found at both the N terminus (residues 2 to 5) and the C terminus (residues 422 to 457). Furthermore, loop 8 in the beta/alpha-barrel domain has a different conformation in the two subunits. A number of amino acid side-chains have different conformations in the two subunits. Most of these residues are located at the surface of the protein. An analysis of the individual temperature factors indicates a high mobility of the C-terminal region and for some of the loops at the active site. The positions and B-factors for 736 solvent sites have been refined (average B: 45.9 A2). Most of the solvent molecules are bound as clusters to the protein. The active site of the enzyme, especially the environment of the activator Lys191 in the non-activated enzyme is described. Crystallographic refinement at 1.7 A resolution clearly revealed the presence of a cis-proline at the active site. This residue is part of the highly conserved region Lys166-Pro167-Lys168.