Mutation matrices and physical-chemical properties: Correlations and implications

To investigate how the properties of individual amino acids result in proteins with particular structures and functions, we have examined the correlations between previously derived structure-dependent mutation rates and changes in various physical-chemical properties of the amino acids such as volume, charge, α-helical and β-sheet propensity, and hydrophobicity. In most cases we found the ΔG of transfer from octanol to water to be the best model for evolutionary constraints, in contrast to the much weaker correlation with the ΔG of transfer from cyclohexane to water, a property found to be highly correlated to changes in stability in site-directed mutagenesis studies. This suggests that natural evolution may follow different rules than those suggested by results obtained in the laboratory. A high degree of conservation of a surface residue's relative hydrophobicity was also observed, a fact that cannot be explained by constraints on protein stability but that may reflect the consequences of the reverse-hydrophobic effect. Local propensity, especially α-helical propensity, is rather poorly conserved during evolution, indicating that non-local interactions dominate protein structure formation. We found that changes in volume were important in specific cases, most significantly in transitions among the hydrophobic residues in buried locations. To demonstrate how these techniques could be used to understand particular protein families, we derived and analyzed mutation matrices for the hypervariable and framework regions of antibody light chain V regions. We found a surprisingly high conservation of hydrophobicity in the hypervariable region, possibly indicating an important role for hydrophobicity in antigen recognition. Proteins 27:336–344, 1997. © 1997 Wiley-Liss, Inc.     

Hydrophobicity of amino acid subgroups in proteins

Protein folding studies often utilize areas and volumes to assess the hydrophobic contribution to conformational free energy (Richards, F.M. Annu. Rev. Biophys. Bioeng. 6:151-176, 1977). We have calculated the mean area buried upon folding for every chemical group in each residue within a set of X-ray elucidated proteins. These measurements, together with a standard state cavity size for each group, are documented in a table. It is observed that, on average, each type of group buries a constant fraction of its standard state area. The mean area buried by most, though not all, groups can be closely approximated by summing contributions from three characteristic parameters corresponding to three atom types: (1) carbon or sulfur, which turn out to be 86% buried, on average; (2) neutral oxygen or nitrogen, which are 40% buried, on average; and (3) charged oxygen or nitrogen, which are 32% buried, on average.     

Polar and nonpolar atomic environments in the protein core: Implications for folding and binding

Hydrophobic interactions are believed to play an important role in protein folding and stability. Semi-empirical attempts to estimate these interactions are usually based on a model of solvation, whose contribution to the stability of proteins is assumed to be proportional to the surface area buried upon folding. Here we propose an extension of this idea by defining an environment free energy that characterizes the environment of each atom of the protein, including solvent, polar or nonpolar atoms of the same protein or of another molecule that interacts with the protein. In our model, the difference of this environment free energy between the folded state and the unfolded (extended) state of a protein is shown to be proportional to the area buried by nonpolar atoms upon folding. General properties of this environment free energy are derived from statistical studies on a database of 82 well-refined protein structures. This free energy is shown to be able to discriminate misfolded from correct structural models, to provide an estimate of the stabilization due to oligomerization, and to predict the stability of mutants in which hydrophobic residues have been substituted by site-directed mutagenesis, provided that no large structural modifications occur. © 1994 Wiley-Liss, Inc.     

Solvent-induced organization: A physical model of folding myoglobin

The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by solvent-induced hydrophobic forces. A quantitative model of these forces is developed and compared with experimental and theoretical results. The model is then tested by being employed in a simulation scheme designed to mimic solvent effects. Realistic dynamic trajectories of myoglobin are shown as it folds from an extended conformation to a close approximation of the native state. Various suggestive features of the process are discussed. The tenets of the model are further tested by folding the single-chain plant protein leghemoglobin. © 1994 Wiley-Liss, Inc.     

Enumerating Designing Sequences in the HP Model

The hydrophobic/polar HP model on the square lattice has been widely used toinvestigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the number of contacts, the upper limit on the chain length N has been 18–20 because of the rapid exponential growth of thenumbers of conformations and sequences. We show how a few optimizations push this limit by about 5 units. Based on these calculations, we study the statistical distribution of hydrophobicity along designing sequences. We find that the average number of hydrophobic and polar clumps along the chains is larger for designing sequences than for random ones, which is in agreement with earlier findings for N 18 and with results for real enzymes. We also show that this deviation from randomness disappears if the calculations are restricted to maximally compact structures.     

Molecular modeling of the amphipathic helices of the plasma apolipoproteins.

In this paper we propose a classification of the amphipathic helical repeats occurring in the plasma apolipoprotein sequences. It is based upon the calculation of the molecular hydrophobicity potential around the helical segments. The repeats were identified using a new autocorrelation matrix, based upon similarities of hydrophobic and hydrophilic properties of the amino acid residues within the apolipoprotein sequences. The helices were constructed by molecular modeling, the molecular hydrophobicity potential was calculated, and isopotential contour lines drawn around the helices yielded a three-dimensional visualization of the hydrophobicity potential. Two classes of apolipoproteins could be differentiated by comparing the hydrophobic angles obtained by projection of the isopotential contour lines on a plane perpendicular to the long axis of the helix. The isopotential contour lines around apo AI, AIV, and E are more hydrophilic than hydrophobic, whereas they are of similar intensity for apo AII, CI, and CIII. In both cases discoidal lipid-protein complexes are generated, with the amphipathic helices around the edge of the lipid core. The long axis of the helices is oriented parallel to the phospholipid acyl chains and the hydrophilic side of the helix toward the aqueous phase. As a result of the differences in hydrophobicity potential, the contact between the hydrophobic side of the helices and the phospholipid acyl chains is larger for apo AII, CI, and CIII than for the other apolipoproteins. This might account for the greater stability of the discoidal complexes generated between phospholipids and these apoproteins.     

信号肽疏水性的提高促进青霉素G酰化酶分泌

设计和合成了一段具有连续１０仆亮氨酸强疏水核心的信号肽（ａｒｔｉｆｉｃｉａｌ ｓｉｇｎａｌ ｐｅｐｔｉｄｅ,ＡＳＰ）,由ＥｃｏＲＩ－ＫｐｎＩ位点融合到青霉素Ｇ酰化酶（ｐｅｎｉｃｉｌｌｉｎ Ｇａｃｙｌａｓｅ,ＰＡＣ）信号肽（ｗｉｌｄ ｔｙｐｅｓｉｇｎａｌ ｐｅｐｔｉｄｅ,ＷＴＳＰ）的－４Ｐｒｏ位点,分别构建了ＰＡＣ表达质粒：ｐＫＫｐａｃ△ＳＰ,ｐＫＫｐａｃＷＴＳＰ,ｐＫＫｐａｃＡＳＰ,ｐＥＴｐａｃ     

Reductive Biotransformation of Benzaldehyde Derivatives by Baker's Yeast in Non-Conventional Media: Effect of Substrate Hydrophobicity on the Biocatalytic Reaction

The reduction of six derivatives of benzaldehyde, α,α,α-trifluorotolualdehyde, nitrobenzaldehyde, anisaldehyde, fluorobenzaldehyde, tolualdehyde, chlorobenzaldehyde, each of which was substituted in the ortho-, meta- and para-positions, was investigated in whole cell yeast biotransformations conducted in non-conventional media. Correlation between hydrophobic (π) and electronic (σ) parameters of the substituent of the substrate and biocatalytic activity in organic solvent media (hexane containing 2% v/v water) was evaluated. While catalytic activity in general decreased as the substituent hydrophobicity (π) increased, the trend was more pronounced for ortho- substituents compared to meta- and para-. When the electronic parameters (σ) of the meta- and para- substituents were correlated with the catalytic activity, the opposite was observed, namely the catalytic activity increased as the electronic parameter of the substituent increased. This observation was similar for meta- and para- substituents.

Preliminary studies on the relationships between solvent and substrate polarity on the one hand and catalytic activity on the other are also presented and discussed.     

Honeybees have Hydrophobic Wings that Enable Them to Fly through Fog and Dew

Honeybees have received public attention for their remarkable performance in low-altitude flying and their outstanding airborne hovering capability.However,minimal attention has been given to their capability to fly through the harshest climatic conditions.In this study,we used a high-speed camera and recorded an interesting phenomenon in which honeybees (Apis mellifera ligustica) flew effortlessly through mists or drizzling rain.To identify the mechanism behind honeybees flying through mists,the microstructure of their wings was examined via atomic force microscopy and scanning electron microscopy.Experimental results showed that the surface of a honeybee wing was rough,with bristles distributed on both the dorsal and ventral sides.The measurement results of the contact angle proved that the surface of honeybee wings was hydrophobic.Furthermore,hydrophobic proteins,which contained at least one hydrophobic tetra-peptide (i.e.,AAPA/V),were obtained.The rugged surface and hydrophobic proteins caused the hydrophobicity of honeybee wings.These results identify the hydrophobic mechanism of honeybee wings,which will be useful in designing hydrophobic structures.     

Interaction between leukocytic elastase and Kunitz-type inhibitors from bovine spleen

The four Kunitz-type protease inhibitors purified from bovine spleen, which include the basic pancreatic trypsin inhibitor (BPTI), form stable complexes with human leukocytic elastase. The values of the affinity constants of these complexes are similar, in agreement with the great structural similarity of the four inhibitors, but are lower than those measured for the complexes with other serine proteases. Two main factors appear to be responsible for the stability of these complexes, i.e., hydrophobic interactions and ionization phenomena that take place during complex formation. These two factors have been analyzed in terms of the general model previously used for describing the interaction between the serine proteases and their natural inhibitors.