Motohisa Oobatake

ProTherm, version 2.0: thermodynamic database for proteins and mutants

Release 4.0 of ProTherm, thermodynamic database for proteins and mutants, contains approximately 14,500 numerical data (approximately 450% of the first version) of several thermodynamic parameters along with experimental methods and conditions, and structural, functional and literature information. The sequence and structural information of proteins is connected with thermodynamic data through links between entries in Protein Data Bank, Protein Information Resource and SWISS-PROT and the data in ProTherm. We have separated the Gibbs free energy change obtained at extrapolated temperature from the data on denaturation temperature measured by the thermal denaturation method. We have added the statistics of amino acid replacements and links to homologous structures to each protein. Further, we have improved the search and display options to enhance search capability through the web interface. ProTherm is freely available at http://gibk26. bse.kyutech.ac.jp/jouhou/Protherm/protherm.html.

Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins

Understanding the role of various interactions in enhancing the thermostability of proteins is important not only for clarifying the mechanism of protein stability but also for designing stable proteins. In this work, we have analyzed the thermostability of 16 different families by comparing mesophilic and thermophilic proteins with 48 various physicochemical, energetic and conformational properties. We found that the increase in shape, s (location of branch point in side chain) increases the thermostability, whereas, an opposite trend is observed for Gibbs free energy change of hydration for native proteins, GhN, in 14 families. A good correlation is observed between these two properties and the simultaneous increases of -GhN and s is necessary to enhance the thermostability from mesophile to thermophile. The increase in shape, which tends to increase with increasing number of carbon atoms both for polar and non-polar residues, may generate more packing and compactness, and the position of beta and higher order branches may be important for better packing. On the other hand, the increase in -GhN in thermophilic proteins increases the solubility of the proteins. This tendency counterbalances the increases in insolubility and unfolding heat capacity change due to the increase in the number of carbon atoms. Thus, the present results suggest that the stability of thermophilic proteins may be achieved by a balance between better packing and solubility.

Salt‐dependent monomer–dimer equilibrium of bovine β‐lactoglobulin at pH 3

Although bovine β‐lactoglobulin assumes a monomeric native structure at pH 3 in the absence of salt, the addition of salts stabilizes the dimer. Thermodynamics of the monomer–dimer equilibrium dependent on the salt concentration were studied by sedimentation equilibrium. The addition of NaCl, KCl, or guanidine hydrochloride below 1 M stabilized the dimer in a similar manner. On the other hand, NaClO4 was more effective than other salts by about 20‐fold, suggesting that anion binding is responsible for the salt‐induced dimer formation, as observed for acid‐unfolded proteins. The addition of guanidine hydrochloride at 5 M dissociated the dimer into monomers because of the denaturation of protein structure. In the presence of either NaCl or NaClO4, the dimerization constant decreased with an increase in temperature, indicating that the enthalpy change (ΔHD) of dimer formation is negative. The heat effect of the dimer formation was directly measured with an isothermal titration calorimeter by titrating the monomeric β‐lactoglobulin at pH 3.0 with NaClO4. The net heat effects after subtraction of the heat of salt dilution, corresponding to ΔHD, were negative, and were consistent with those obtained by the sedimentation equilibrium. From the dependence of dimerization constant on temperature measured by sedimentation equilibrium, we estimated the ΔHD value at 20°C and the heat capacity change (ΔCp) of dimer formation. In both NaCl and NaClO4, the obtained ΔCp value was negative, indicating the dominant role of burial of the hydrophobic surfaces upon dimer formation. The observed ΔCp values were consistent with the calculated value from the X‐ray dimeric structure using a method of accessible surface area. These results indicated that monomer–dimer equilibrium of β‐lactoglobulin at pH 3 is determined by a subtle balance of hydrophobic and electrostatic effects, which are modulated by the addition of salts or by changes in temperature.

RELATIONSHIP BETWEEN AMINO ACID PROPERTIES AND PROTEIN STABILITY : BURIED MUTATIONS

In order to understand the mechanism of protein stability and to develop a simple method for predicting mutation-induced stability changes, we analyzed the relationship between stability changes caused by buried mutations and changes in 48 amino acid properties. As expected from the importance of hydrophobicity, properties reflecting hydrophobicity are strongly correlated with the stability of proteins. We found that subgroup classification based on secondary structure increased correlations significantly, and mutations within β-strand segments correlated better than did those in α-helical segments, which may result from stronger hydrophobicity of the β-strands. Multiple regression analyses incorporating combinations of three properties from among all possible combinations of the 48 properties increased the correlation coefficient to 0.88 and by an average of 13% for all data sets. Analyzing the stability of tryptophan synthase mutants with Glu49 replaced by all other residues except Arg revealed that combining buriedness, solvent-accessible surface area for denatured protein, and unfolding Gibbs free energy change increased the correlation to 0.95. Consideration of sequence and structural information (neighboring residues in sequence and in space) did not significantly strengthen the correlations in buried mutations, suggesting that nonspecific interactions dominate in the interior of proteins.

pH-Dependent thermostabilization of Escherichia coli ribonuclease HI by histidine to alanine substitutions

Thermal stabilities of mutant ribonuclease HI proteins from Escherichia coli, in which each of five histidine residues was replaced with alanine, were examined at various pHs. Increases in the Tm values were observed at pH 3.0 for four of the mutant proteins, in which each of the four histidine residues exposed to the solvent was mutated, as compared to the Tm of the wild-type protein. The thermostabilization of three of the mutant proteins was dependent on pH, and only observed at low pH. The thermostabilizing effects of the His-->Ala substitutions were cumulative. The temperature of the midpoint of the transition in the thermal unfolding curves, Tm, of the most stable mutant enzyme, in which His 62, His 83, His 124, and His 127 were replaced by Ala, was 5.5 degrees C higher than that of the wild-type enzyme at pH 3.0. The stability of the wild-type protein decreased as the pH was lowered below pH 4, a condition favoring the protonation of carboxyl groups, probably due to unfavorable electrostatic interactions introduced by the increase in positive charges on the protein. Since imidazole groups are positively charged at pH 3.0, it seems likely that thermal stabilization at pH 3.0 by a His-->Ala substitution would be the result of a reduction in such unfavorable electrostatic interactions. These results suggest that amino acid substitutions that cause a decrease in the number of positive charges on the surface of a protein can be used as a general strategy to enhance protein stability at pH values below pH 4.

Importance of surrounding residues for protein stability of partially buried mutations.

Abstract For understanding the factors influencing protein stability, we have analyzed the relationship between changes in protein stability caused by partially buried mutations and changes in 48 physicochemical, energetic and conformational properties of amino acid residues. Multiple regression equations were derived to predict the stability of protein mutants and the efficiency of the method has been verified with both back-check and jack-knife tests. We observed a good agreement between experimental and computed stabilities. Further, we have analyzed the effect of sequence window length from 1 to 12 residues on each side of the mutated residue to include the sequence information for predicting protein stability and we found that the preferred window length for obtaining the highest correlation is different for each secondary structure; the preferred window length for helical, strand and coil mutations are, respectively, 0, 9 and 4 residues on both sides of the mutant residues. However, all the secondary structures have significant correlation for a window length of one residue on each side of the mutant position, implying the role of short- range interactions. Extraction of surrounding residue information for various distances (3 to 20Å) around the mutant position showed the highest correlation at 8Å, 6Å and 7Å, respectively, for mutations in helical, strand and coil segments. Overall, the information about the surrounding residues within the sphere of 7 to 8Å, may explain better the stability in all subsets of partially buried mutations implying that this distance is sufficient to accommodate the residues influenced by major intramolecular interactions for the stability of protein structures.

Hydration of Apomyoglobin in Native, Molten Globule, and Unfolded States by Using Microwave Dielectric Spectroscopy

The high resolution dielectric spectra of semidilute solutions of apomyoglobin in native (N, pH = 5), acid-induced molten globule (A, pH = 4), and unfolded (U(A), pH = 3) states have been measured in the range from 0.2 to 20 GHz. Based on a two-component mixture theory, we obtained the following hydration numbers per protein molecule: 590 +/- 65 for N, 630 +/- 73 for A, and 1110 +/- 67 for U(A). There was no clear difference between N and A states in contrast to the 25% reduction of helix content and the 50% reduction of heat capacity change upon unfolding. This suggests that the association of hydrophobic moieties might follow the disruption of secondary structures from N to A states. The measured hydration number of U(A) was close to that of the accessible water number (1340) of a protein molecule calculated for a fully extended structure, indicating that the structure of U(A) is extended but somewhat more compact than that of a fully extended state.

Thermodynamic databases for proteins and protein-nucleic acid interactions

Thermodynamic data regarding proteins and their interactions are important for understanding the mechanisms of protein folding, protein stability, and molecular recognition. Although there are several structural databases available for proteins and their complexes with other molecules, databases for experimental thermodynamic data on protein stability and interactions are rather scarce. Thus, we have developed two electronically accessible thermodynamic databases. ProTherm, Thermodynamic Database for Proteins and Mutants, contains numerical data of several thermodynamic parameters of protein stability, experimental methods and conditions, along with structural, functional, and literature information. ProNIT, Thermodynamic Database for Protein-Nucleic Acid Interactions, contains thermodynamic data for protein-nucleic acid binding, experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data have been incorporated into 3DinSight, an integrated database for structure, function, and properties of biomolecules. A WWW interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions. These thermodynamic databases, together with structural databases, help researchers gain insight into the relationship among structure, function, and thermodynamics of proteins and their interactions, and will become useful resources for studying proteins in the postgenomic era.

De novo design and creation of a stable artificial protein

Protein de novo design has been performed, as an exercise of the inverse folding problem. A beta/alpha-barrel protein was designed and synthesized using the Escherichia coli expression system for the structural characterization. A tertiary model with a two-fold symmetry was built, based upon the geometrical parameters extracted from X-ray crystal structures of several beta/alpha-barrel proteins. Amino acid frequencies at each position on the alpha- and beta-structures were investigated, and an amino acid sequence with 201 residues was designed. The associated gene was chemically synthesized and the fusion protein with human growth hormone was expressed in Escherichia coli. The purified protein after being cleaved and refolded was found to be stable and globular with the large amount of secondary structures. However, it has similar characteristics to the molten globules of natural proteins, with loose packing of side-chains. The approach for the tight packing is discussed.

Anatomy of specific interactions between λ repressor and operator DNA

Recognition of specific DNA sequences by proteins is essential for regulation of gene expression. To fully understand the recognition mechanism, it is necessary to understand not only the structure of the specific protein–DNA interactions but also the energetics. We therefore performed a computer analysis in which a phage DNA‐binding protein, λ repressor, was used to examine the changes in binding free energy (ΔΔG) and its energy components caused by single base mutations. We then determined which of the calculated energy components best correlated with the experimental data. The experimental ΔΔG values were well reproduced by the calculations. Component analysis revealed that the electrostatic and hydrogen bond energies were most strongly correlated with the experimental data. Among the 51 single base‐substitution mutants examined, positive ΔΔG values, corresponding to weakened binding, were caused by the loss of favorable electrostatic interactions and hydrogen bonds, the introduction of steric collisions and electrostatic repulsion, the loss of favorable interactions with a thymine methyl group, and the increase of unfavorable hydration energy from isolated DNA. This analysis also showed distinct patterns of recognition at A‐T and G‐C positions, as different combinations of energy components were involved in ΔΔG caused by the two substitution types. We have thus been able to identify the energy components that most strongly correlate with sequence‐dependent ΔΔG and determine their contribution to the specificity of DNA sequence recognition by the λ repressor. Application of this method to other systems should provide additional insight into the molecular mechanism of protein–DNA recognition. Proteins 2003.