Biomedical subjects

R J Pinker

Publications and source records attributed to R J Pinker.

5 recordsLinked to original sources

PubMed1994

Stabilization of myoglobin by multiple alanine substitutions in helical positions.

We have carried out a series of multiple Xaa-->Ala changes at nonadjacent surface positions in the sequence of sperm whale myoglobin. Although the corresponding single substitutions do not increase the thermal stability of the protein, multiple substitutions enhance the stability of the resulting myoglobins. The effect observed is an increase in the observed Tm (midpoint unfolding temperature) relative to that predicted from assuming additivity of the free energy changes corresponding to single mutations. The stabilization occurs in the presence of urea, as measured by the dependence of the unfolding temperature on urea concentration. The sites that have been altered occur in different helices and are not close in sequence or in the native structure of myoglobin. The observed effect is consistent with a role of multiple alanines in residual interactions in the unfolded state of the mutant proteins.

Alanine↗

PubMed1994

Molten globular characteristics of the native state of apomyoglobin.

Apomyoglobin, myoglobin lacking the haem group, is a natural intermediate in biosynthesis of myoglobin, and has some structural features in common with the haem-containing native state. Unfolding or refolding studies of apomyoglobin have identified a molten globule intermediate at acid pH. We show here that both the native state of apomyoglobin and the molten globule intermediate have highly plastic structures. Substitution of single amino acids on the surface or in the interior of helices in the native protein produce dramatic changes in the helix content and tryptophan emission of apomyoglobin at neutral and acidic pH. The signals from the intermediate and native apomyoglobin correlate closely suggesting that apomyoglobin itself has a molten globule-like character, its structure representing a population of interconverting substates rather than a fixed conformation.

Animals↗

PubMed1993

Alpha-helix stability and the native state of myoglobin.

Native proteins fold to form structures that contain secondary-structure regular patterns in the peptide backbone, such as alpha-helix, beta-structure, and turns with high frequency. The role of this secondary structure in stabilizing the native folded state is presently unclear. Alanine substitutions at helical sites in myoglobin show no correlation with the helical propensity of the side chains involved. In an effort to demonstrate a relationship between the effect of a side chain on stabilizing secondary structure and the native structure, we have carried out site-directed changes in the sequence of the helical protein sperm whale myoglobin. Fully buried hydrophobic side chains were exchanged for similar side chains at sites corresponding to midhelical positions in the native state. The results show a positive correlation between the alpha-helix-forming ability of the substituted side chain and the stability of the mutant proteins, when differences between the size of the side chains are taken into account. If, in addition, each type of amino acid substitution is averaged over different sites, the helix propensities of the amino acids account for much of the residual variation. This implies that the stability of the native state of a protein is coupled to that of secondary structural elements in the structure. In magnitude, the net contribution of propensity differences is smaller than hydrophobic effects, but not negligible in terms of the net free energy of unfolding.

Mutagenesis, Site-Directed↗

PubMed1993

Capping interactions in isolated alpha helices: position-dependent substitution effects and structure of a serine-capped peptide helix.

The influence of an amino acid on the stability of alpha-helical structure depends on the position of the residue in the helix with respect to the ends. Short alpha helices in proteins are stabilized both by H-bonding of the main-chain NH and CO groups and by capping interactions between side chains and unfulfilled peptide groups at the N and C termini. Peptide models based on consensus position-dependent helix sequences allow one to model capping effects in isolated helices and to establish a base line for these interactions in proteins. We report here an extended series of substitutions in the cap positions of our peptide models and the solution structure of peptide S3, with serine at the N-cap position defined as the N-terminal residue with partly helix and partly coil conformation. The resulting model, determined by 2D 1H NMR, is consistent with a structure at the N-cap involving H-bonding between the serine gamma oxygen and the peptide NH of the glutamic acid residue three amino acids toward the C terminus. A bifurcated H-bond of Ser O gamma with the NH of Asp5 is possible also, since this group is within interacting distance. This provides direct evidence that specific side-chain interactions with the main chain stabilize isolated alpha-helical structure.

Amino Acid Sequence↗

PubMed1993

Effects of alanine substitutions in alpha-helices of sperm whale myoglobin on protein stability.

The peptide backbones in folded native proteins contain distinctive secondary structures, alpha-helices, beta-sheets, and turns, with significant frequency. One question that arises in folding is how the stability of this secondary structure relates to that of the protein as a whole. To address this question, we substituted the alpha-helix-stabilizing alanine side chain at 16 selected sites in the sequence of sperm whale myoglobin, 12 at helical sites on the surface of the protein, and 4 at obviously internal sites. Substitution of alanine for bulky side chains at internal sites destabilizes the protein, as expected if packing interactions are disrupted. Alanine substitutions do not uniformly stabilize the protein, either in capping positions near the ends of helices or at mid-helical sites near the surface of myoglobin. When corrected for the extent of exposure of each side chain replaced by alanine at a mid-helix position, alanine replacement still has no clear effect in stabilizing the native structure. Thus linkage between the stabilization of secondary structure and tertiary structure in myoglobin cannot be demonstrated, probably because of the relatively small free energy differences between side chains in stabilizing isolated helix. By contrast, about 80% of the variance in free energy observed can be accounted for by the loss in buried surface area of the native residue substituted by alanine. The differential free energy of helix stabilization does not account for any additional variation.

Alanine↗