Hydrophobic Amino Acid Substitutions Research Articles

Cell specific transformation by c-fms activating loop mutations is attributable to constitutive receptor degradation.

Expression of a receptor for human macrophage-colony stimulating factor (M-CSF or CSF-1), containing a point mutation which changes an aspartate to a valine at position 802 of the activating loop of the kinase domain, potently transforms the haemopoietic cell line FDC-P1 yet prevents Rat-2 fibroblast transformation. In order to understand this apparent paradox, aspartate 802 was changed by cassette mutagenesis to each of the other 19 amino acids. All hydrophobic amino acid substitutions were transforming when tested in FDC-P1 cells yet inactivating when tested in Rat-2 fibroblasts. These same amino acid substitutions also activated receptor degradation, strongly suggesting a causal relationship between receptor degradation and inactivation in fibroblasts. Point mutations or small deletions of Y708 within the kinase insert region of the mutant D802V receptor partly inhibited receptor degradation. The more stable D802V receptor derivatives were able to transform both FDC-P1 cells and Rat-2 fibroblasts, so establishing that the cell specific effect of the c-fmsD802V activating loop mutation is attributable to receptor degradation which accompanies kinase activation and prevents the transformation of Rat-2 but not of FDC-P1 cells.

Change in oligomerization specificity of the p53 tetramerization domain by hydrophobic amino acid substitutions.

The tumor suppressor function of the wild-type p53 protein is transdominantly inhibited by tumor-derived mutant p53 proteins. Such transdominant inhibition limits the prospects for gene therapy approaches that aim to introduce wild-type p53 into cancer cells. The molecular mechanism for transdominant inhibition involves sequestration of wild-type p53 subunits into inactive wild-type/mutant hetero-tetramers. Thus, p53 proteins, whose oligomerization specificity is altered so they cannot interact with tumor-derived mutant p53, would escape transdominant inhibition. Aided by the known three-dimensional structure of the p53 tetramerization domain and by trial and error we designed a novel domain with seven amino acid substitutions in the hydrophobic core. A full-length p53 protein bearing this novel domain formed homo-tetramers and had tumor suppressor function, but did not hetero-oligomerize with tumor-derived mutant p53 and resisted transdominant inhibition. Thus, hydrophobic core residues influence the oligomerization specificity of the p53 tetramerization domain.

Mutational analysis of fusion peptide-like regions in the mouse hepatitis virus strain A59 spike protein.

The coronavirus peplomer protein S is responsible for attachment and fusion during viral entry as well as for the induction of cell to cell fusion. While several regions within S have been shown to influence the ability to induce fusion, the region of the protein actually responsible for fusion, the fusion peptide, has not yet been identified. We identified two hydrophobic peptides (peptides #1 and #2) within MHV-A59 S2 as possible fusion domains. This was based on hydrophobicity, conservation among coronavirus S proteins and the prediction of a sided helix conformation. Using site directed mutagenesis and an in vitro cell to cell fusion assay we showed that substitution of hydrophobic amino acids with charged amino acids, within the predicted hydrophobic face of either of these two peptides eliminated fusion. Within peptide #1 substitution of the same hydrophobic amino acids with other hydrophobic amino acids or substitution of polar amino acids with charged or polar amino acids had little effect on fusion. Thus peptides #1 and #2 remain likely candidates for the MHV fusion peptide. A third previously identified peptide within S2 (Chambers et al., 1990) is unlikely as a fusion peptide as it is not well conserved among coronaviruses and substitution within the hydrophobic face with charged amino acids does not effect fusion.

Role of hydrophobic amino acid clusters in the transactivation activity of the human glucocorticoid receptor.

We have performed a mutagenesis analysis of the 58-amino-acid tau1-core peptide, which represents the core transactivation activity of the tau1 transactivation domain from the glucocorticoid receptor. Mutants with altered activity were identified by phenotypic screening in the yeast Saccharomyces cerevisiae. Most mutants with reduced activity had substitutions of hydrophobic amino acids. Most single-substitution mutants with reduced activity were localized near the N terminus of the tau1-core within a segment that has been shown previously to have a propensity for alpha-helix conformation, suggesting that this helical region is of predominant importance. The particular importance of hydrophobic residues within this region was confirmed by comparing the activities of alanine substitutions of the hydrophobic residues in this and two other helical regions. The hydrophobic residues were shown to be important for the transactivation activity of both the isolated tau1-core and the intact glucocorticoid receptor in mammalian cells. Rare mutations in helical regions I and II gave rise to increased transcriptional activation activity. These mutations increase the hydrophobicity of hydrophobic patches on each of these helices, suggesting a relationship between the hydrophobicity of the patches and transactivation activity. However, certain nonhydrophobic residues are also important for activity. Interestingly, helical region I partially matches a consensus motif found in the retinoic acid receptor, VP16, and several other activator proteins.

Lipid membrane permeability of modified c[D-Pen2, D-Pen5]enkephalin peptides.

Permeability coefficients of a series of analogues of a potent opioid peptide, c[D-Pen2, D-Pen5]enkephalin, were measured in a model membrane system. The analogues included hydrophobic amino acid substitutions on position 3. Liposomes of a mixed composition consisting of zwitterionic lipids and cholesterol served as the model membranes. The obtained permeability coefficients range between 0.38 x 10(-12) and 2.9 x 10(-12) cm/s. These data were correlated with the hydrophobicity scale of Nozaki and Tanford (J. Biol. Chem. 246, 1971, 2211-2217) (correlation coefficient = 0.9933) and with determinations of lipid order perturbation by differential scanning calorimetry (correlation coefficient = -0.9779). The reasonably good correlation obtained within the family of analogues substituted on position 3 (Gly, Ala, Leu, Phe) indicates that changes in permeabilities are primarily related to increases in the partition coefficient of the peptide. However, Phe residue added on the N-terminal end of the peptide (position 0) does not appear to follow the observed trend, showing stronger lipid perturbation and lower permeability compared to the Phe3 analog. This observation demonstrates that each class of peptide modifications requires a new basis of permeability analysis and predictions.

Adaptability at the protein-DNA interface is an important aspect of sequence recognition by bZIP proteins.

The related AP-1 and ATF/CREB families of transcriptional regulatory proteins bind as dimers to overlapping or adjacent DNA half-sites by using a bZIP structural motif. Using genetic selections, we isolated derivatives of yeast GCN4 that affect DNA-binding specificity at particular positions of the AP-1 target sequence. In general, altered DNA-binding specificity results from the substitution of larger hydrophobic amino acids for GCN4 residues that contact base pairs. However, in several cases, DNA binding by the mutant proteins cannot be simply explained in terms of the GCN4-AP-1 structure; movement of the protein and/or DNA structural changes are required to accommodate the amino acid substitutions. The quintet of GCN4 residues that make base-pair contacts do not entirely determine DNA-binding specificity because these residues are highly conserved in the bZIP family, yet many of the bZIP proteins bind to distinct DNA sites. The alpha-helical fork between the GCN4 DNA-binding and dimerization surfaces is important for half-site spacing preferences, because mutations in the fork alter the relative affinity for AP-1 and ATF/CREB sites. The basic region in the protein-DNA complex is a long isolated alpha-helix, with no constraints from other parts of a folded domain. From all of these considerations, we suggest that small shifts in position and orientation or local deformations in the alpha-helical backbone distinguish one bZIP complex from another.

Substitutions of hydrophobic amino acids reduce the amyloidogenicity of Alzheimer's disease βA4 peptides

The deposition of amyloid protein aggregates in brain is the main pathological feature of Alzheimer's disease. Their principal constituent is a peptide termed βA4, which comprises up to 43 amino acid residues. It is highly insoluble under physiological conditions and aggregates into filaments that form very dense clusters in vivo and in vitro. Based on a βA4 prototype sequence spanning residues 10 to 42 or 43, we have designed analogues in which hydrophobic amino acid residues in position 17 to 20 were substituted by more hydrophilic residues. Depending on the kind of newly introduced amino acids and their position within the sequence, the substitution of only two residues led to variants exhibiting a broad spectrum of different properties. Common to them was a reduced β-sheet content after solubilization in water and in the solid state. Some of the variants showed significantly reduced amyloidogenicity: although still forming filaments, they did not aggregate into the highly condensed depositions that are typical for amyloid. In addition, they could be solubilized in 200 m M-NaCl and KCl. When mixed with βA4 peptides bearing the natural sequence, two of the analogues could inhibit the formation of filaments in vitro. These results demonstrate that a well-preserved hydrophobic core around residues 17 to 20 of βA4 is crucial for the formation of β-sheet structure and the amyloid properties of βA4. The introduction of structural alterations within this region may guide the development of reagents for the therapy of Alzheimer's disease.

Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: evidence for mutational effects on the free energy of the denatured state.

In order to quantitate the contributions of the polar, uncharged amino acids to the stability of the native state of staphylococcal nuclease, each of the 13 alanines, 9 glycines, 9 threonines, 6 prolines, 6 glutamines, 6 asparagines, and 3 serines was substituted, either with both alanine and glycine or with 1 of these 2 amino acids plus valine. For each mutant, the stability to reversible denaturation (delta GH2O) was quantitated by determining the Kapp for this reaction as a function of guanidine hydrochloride concentration. In addition, the parameter mGuHCl (= d(delta G)/d[GuHCl]) was calculated from the data. To identify the local structural features responsible for the relatively large and variable changes in delta GH2O and mGuHCl observed for the same type of substitution at different locations in nuclease, statistical correlations were sought between delta GH2O, mGuHCl, and a number of descriptors of the local structure. As with substitutions of the large hydrophobic amino acids [Shortle, D., Stites, W. E., & Meeker, A. K. (1990) Biochemistry 29, 8033-8041], mutation of polar, uncharged residues to Gly leads to a change in stability that, on average, correlates well with the degree to which the wild-type residue is buried. This correlation is especially significant for threonine, an amino acid with both polar and hydrophobic character, but is not demonstrated for the more typically hydrophobic residue alanine. As reported in the previous study of alanine/glycine substitutions of hydrophobic residues, a significant correlation between changes in stability and changes in the value of mGuHCl is again observed, strengthening the conclusion that the putative structural changes in the denatured state which lead to increases or decreases in mGuHCl are responsible for a significant fraction of the stability loss for an average mutant. The existence of this correlation is consistent with the denatured state of wild-type staphylococcal nuclease having evolved to a relatively high free energy via optimization of a balance between a maximal exposure of hydrophobic surface and a minimal gain in chain entropy. On average, mutations are less stable in proportion to the extent of which they perturb this balance. A new and puzzling correlation is reported between the extent of buriedness of a residue in the wild-type native state versus the difference in mGuHCl between the Ala mutation and the Gly mutation at that position.