Biomedical subjects

T C Terwilliger

Publications and source records attributed to T C Terwilliger.

11 recordsLinked to original sources

PubMed1991

Approaches to predicting effects of single amino acid substitutions on the function of a protein.

The relative activities of 313 mutants of the gene V protein of bacteriophage f1, assayed in vivo, have been used to evaluate two approaches to predicting the effects of single amino acid substitutions on the function of a protein. First, we tested methods that only depend on the properties of the wild-type and substituting amino acids. None of the properties or measures of the functional equivalence of amino acids we tested, including the frequency of exchange of amino acids among homologous proteins as well as changes in side-chain size, hydrophobicity, and charge, were found to be more than weakly correlated with the activities of mutants. The principal reason for this poor correlation was found to be that the effect of a particular substitution varies considerably from site to site. We then tested an approach using the activities of several mutants with substitutions at a site to predict the activity of another mutant, and we find that this is a relatively good indicator of whether the other mutant at that site will be functional. A predictive scheme was developed that combines the weak information from the models depending on the properties of the wild-type and substituting amino acids with the stronger information from the tolerance of a site to substitution. Although this scheme requires no knowledge of the structure of a mutant protein, it is useful in predicting the activities of mutants.

Amino Acids↗

PubMed1991

Isolation and in vitro characterization of temperature-sensitive mutants of the bacteriophage f1 gene V protein.

In vivo selections were used to isolate 43 temperature-sensitive gene V mutants of the bacteriophage f1 from a collection of mutants constructed by saturation mutagenesis of the gene. The sites of temperature-sensitive substitutions are found in both the beta-sheets and the turns of the protein, and some sites are exposed to the solvent while others are not. Thirteen of the variant proteins were purified and characterized to evaluate their free energy changes upon unfolding and their affinities for single-stranded DNA, and eight were tested for their tendencies to aggregate at 42 degrees C. Each of the three temperature-sensitive mutants at buried sites and six of ten at surface sites had free energy changes of unfolding substantially lower (less stabilizing) than the wild-type at 25 degrees C. A seventh mutant at a surface site had a substantially altered unfolding transition and its free energy of unfolding was not estimated. The affinities of the mutant proteins for single-stranded DNA varied considerably, but two mutants at a surface site, Lys69, had much weaker binding to single-stranded DNA than any of the other mutants, while two mutants at another surface site, Glu30, had the highest DNA-binding affinities. The wild-type gene V protein is stable at 42 degrees C, but six of the eight mutants tested aggregated within a few minutes and the remaining two aggregated within 30 minutes at this temperature. Overall, each of the temperature-sensitive proteins tested had a tendency to aggregate at 42 degrees C, and most also had either a low free energy of unfolding (at 25 degrees C), or weak DNA binding. We suggest that any of these properties can lead to a temperature-sensitive gene V phenotype.

Codon↗

PubMed1991

Reversible denaturation of the gene V protein of bacteriophage f1.

The guanidine hydrochloride (GuHCl)-induced denaturation of the gene V protein of bacteriophage f1 has been studied, using the chemical reactivity of a cysteine residue that is buried in the folded protein and the circular dichroism (CD) at 211 and 229 nm as measures of the fraction of polypeptide chains in the folded form. It is found that this dimeric protein unfolds in a single cooperative transition from a folded dimer to two unfolded monomers. A folded, monomeric form of the gene V protein was not detected at equilibrium. The kinetics of unfolding of the gene V protein in 3 M GuHCl and the refolding in 2 M GuHCl are also consistent with a transition between a folded dimer and two unfolded monomers. The GuHCl concentration dependence of the rates of folding and unfolding suggests that the transition state for folding is near the folded conformation.

Coliphages↗

PubMed1991

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.

Calorimetry↗

PubMed1991

Repacking protein interiors.

Several goals of protein engineering may be achieved through redesign and repacking of protein interiors. The effects of interior apolar substitutions on protein stability depend strongly on the site of the substitution. One reason for this is that protein interiors have properties both of apolar liquids and of crystalline solids. Substitutions at interior sites affect the stability of a protein by changing the hydrophobicity, but each site in a protein has a characteristic energy associated with introducing packing changes, and the net stability depends on both of these factors.

Models, Chemical↗

PubMed1989

Influence of interior packing and hydrophobicity on the stability of a protein.

Protein interiors contain many tightly packed apolar atoms in a nearly crystalline state. Both shielding of apolar atoms from solvent and efficient interior packing arrangements affect protein stability, but their relative importance is unclear. To separate these effects, the stabilities of wild-type and mutant gene V proteins from bacteriophage fl were studied by measuring resistance to denaturation. The effects of subtle interior packing changes, both separate from and combined with changes in buried side chain hydrophobicity, were measured. For the interior apolar-to-apolar substitutions studied, the two effects were of the same magnitude and alteration of packing without accompanying hydrophobicity changes substantially destabilized the protein.

Calorimetry↗

PubMed1988

Construction of a synthetic variant of the bacteriophage f1 gene V by assembling oligodeoxynucleotides corresponding to only one strand of DNA.

A simple and widely applicable procedure for constructing synthetic variants of a gene, involving the synthesis of only one strand of DNA, has been developed. The method is suited for cases in which a cloned DNA with a sequence related to the gene to be constructed is available. First, a heteroduplex DNA which is single-stranded throughout the region of interest is made. This single-stranded region is then used as a template to correctly align and allow ligation of synthetic oligos corresponding to the entire gene. To favor the replication of the strand encoding the synthetic gene, a template strand containing some substitutions of deoxyuridine for deoxythymidine is used. This procedure was used to construct a synthetic bacteriophage f1 gene V which differs from the wild-type (wt) gene at 45 positions out of 298. The synthetic gene was designed to include nine restriction sites without altering the sequence of the encoded DNA-binding protein. The gene construction was found to be very efficient, and about 40% of the resulting plasmids contained the desired synthetic gene. The synthetic gene was found to be fully active and could substitute for the wt gene in bacteriophage f1.

Amino Acid Sequence↗

PubMed1988

Simple and highly efficient site-specific mutagenesis, by ligation of an oligodeoxyribonucleotide into gapped heteroduplex DNA in which the template strand contains deoxyuridine.

A simple and highly efficient procedure for oligodeoxynucleotide (oligo)-directed mutagenesis has been developed. In this procedure, a gapped heteroduplex DNA is first constructed and purified. The gapped heteroduplex consists of a circular 'template' strand of DNA, which contains some misincorporated deoxyuridine nucleotides, and a complementary strand which does not contain deoxyuridine, and which lacks a defined segment. Making a specific change in the sequence of the DNA within the gapped region then only requires ligation and transformation. An oligo, exactly the same length as the gap, and with the desired sequence, is synthesized, purified, and ligated directly into the gap in the heteroduplex. When this DNA is used to transform wt (ung+) Escherichia coli, about 80% of the resulting plasmids contain the sequence determined by the synthetic oligo. One gapped heteroduplex preparation can be used for many mutagenesis experiments, so that this procedure is well-suited for producing a series of defined mutations within a defined target region flanked by sites for restriction enzyme cleavage. As the method does not require a polymerase, the effects of primer displacement and polymerase infidelity are avoided.

DNA, Bacterial↗

PubMed1988

A genetic selection for temperature-sensitive variants of the gene V protein of bacteriophage f1.

Complementary negative and positive genetic selections based on the activity of a plasmid-encoded bacteriophage f1 gene V are developed. The negative selection is based on an activity of the gene V protein in E. coli cells which markedly reduces the infection of those cells by f1-related viruses. In order to select against cells expressing active gene V protein, the cells are infected with the p'age R386, a derivative of f1 which confers resistance to chloramphenicol, and are plated in the presence of the antibiotic. Those cells which contain gene V protein are infrequently infected with the virus and are unable to grow in the presence of chloramphenicol; those which do not contain the gene V protein are readily infected and can grow in the presence of the antibiotic. The positive genetic selection consists of excising the gene V sequences from the plasmids and using them to replace the gene V of a bacteriophage f1 derivative containing an amber mutation in gene V. Only those genes which encode an active gene V protein can support phage growth and yield plaques. The two genetic selections can be combined in order to yield a substantial enrichment for genes encoding temperature-sensitive gene V proteins.

Cloning, Molecular↗

PubMed1986

Kinetics of receptor modification. The multiply methylated aspartate receptors involved in bacterial chemotaxis.

A method for determining the extent of methyl esterification of each of the four potential sites on the aspartate receptors involved in chemotaxis in Escherichia coli and Salmonella typhimurium is presented. In this procedure, radioactive methyl esters are incorporated into the receptors, the receptors are cleaved by trypsin and the V8 protease from Staphylococcus aureus, and the four fragments containing sites of methylation are separated by high performance liquid chromatography. Using this technique, we find that the rate of methyl esterification increases at all four sites after stimulation with the "attractant" aspartate, suggesting that all four sites of modification are involved in adaptation to aspartate. We also find that the rate of methyl esterification at each site is correlated with the homology between the protein sequence at that site and the "consensus" sequence, Glu-Glu-X-X-Ala-Thr/Ser.

Amino Acid Sequence↗

PubMed1986

Surface structure recognized for covalent modification of the aspartate receptor in chemotaxis.

The aspartate receptor involved in chemotaxis is modified by methyl esterification at four distinct glutamate residues during the adaptive response of this receptor. To explain the high degree of specificity of this modification, it has been proposed that the methyltransferase recognizes the sequence Glu-Glu-Xaa-Xaa-Ala-Ser/Thr in an alpha-helical conformation and methylates the second glutamate in this sequence. This hypothesis is strengthened here by localized mutagenesis studies. By reversing the alanine-threonine sequence to threonine-alanine at the principal site of methylation, Glu-309, a factor of 4 decrease in reactivity was achieved. Thus, the rate of methylation of this site is sensitive to the reversal of two residues of similar structure. These residues are somewhat distant in sequence from the glutamate that is modified but are adjacent in space if an alpha-helical structure is present. The other sites of modification, Glu-295, Glu-302, and Glu-491, are slightly increased in reactivity in the mutant. The 4-fold change in reactivity of the major site of methylation obtained with a relatively subtle change supports the recognition sequence hypothesis, including its structural implications. It is noted, in addition, that chemotaxis of bacteria expressing the mutant receptor does not seem to be greatly altered. This might be explained by the observation that the overall methylation levels of the mutant and wild-type receptors are similar.

Amino Acid Sequence↗