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Biomedical subjects

A Horovitz

Publications and source records attributed to A Horovitz.

At least 37 records · Page 2Linked to original sources
PubMed1995

Changes mimicking endometrial neoplasia in postmenopausal, tamoxifen-treated women with breast cancer: a transvaginal Doppler study.

In menopausal patients with breast cancer who receive tamoxifen therapy, transvaginal sonography may show an abnormal endometrium. Our objective was to evaluate the effects of prolonged tamoxifen therapy on endometrial blood flow in postmenopausal patients with breast cancer, and to correlate blood flow characteristics with the sonographic appearance of the endometrium and its pathology. Transvaginal color Doppler ultrasound examinations were performed on 45 postmenopausal women (age range 54-70 years) with breast cancer, who had been treated with tamoxifen for 1-3 years. Twenty women (Group 1) had a thick, irregular, cystic endometrium of > or = 5 mm, and 25 (Group 2) showed a thin endometrium of < 5 mm. The blood flow response was assessed by visualization of arterial waveforms in the endometrial and subendometrial regions with a transvaginal color flow imaging system. Resistance indexes (RI) were calculated for analysis and correlated with endometrial appearance and histology. The mean RI in Group 1 was 0.39 +/- 0.10 (range 0.32-0.54), while the mean RI in Group 2 was 0.79 +/- 0.10 (range 0.54-0.90; p < 0.001). On histology, 12 patients in Group 1 showed atrophic endometria confirmed by hysteroscopy, while in the remaining eight, endometrial polyps were found. In Group 2, all patients had scanty, atrophic endometria. Six of the eight patients with endometrial polyps had an RI of < 0.4 and none had malignant changes. These data suggest that tamoxifen therapy in women with postmenopausal breast cancer induces endometrial, morphological and blood flow changes, mimicking endometrial neoplasia.(ABSTRACT TRUNCATED AT 250 WORDS)

Aged↗
PubMed1994

Residue lysine-34 in GroES modulates allosteric transitions in GroEL.

The conserved residue Lys-34 in GroES was replaced by alanine and glutamic acid using site-directed mutagenesis. This residue is near the carboxy terminus of the mobile loop in GroES (residues 17-32) which becomes immobilized upon formation of the GroEL/GroES complex [Landry et al. (1993) Nature 364, 255-258]. Both charge neutralization (Lys-34-->Ala) and charge reversal (Lys-34-->Glu) at this position have little effect on the binding constant of GroES to GroEL, but they increase the enhancement by GroES of cooperativity in ATP hydrolysis by GroEL. This is reflected by a change in the Hill coefficient (at 10 mM K+) from 4.10 (+/- 0.22) in the presence of wild-type GroES to 5.17 (+/- 0.24) and 4.46 (+/- 0.14) in the presence of the GroES mutants Lys-34-->Ala and Lys-34-->Glu, respectively. The results are interpreted using the Monod-Wyman-Changeux (MWC) model for cooperativity [Monod et al. (1965) J. Mol. Biol. 12, 88-118]. They suggest that Lys-34 in GroES modulates the allosteric transition in GroEL by stabilizing a relaxed (R)-like state.

Adenosine Triphosphatases↗
PubMed1994

Two lines of allosteric communication in the oligomeric chaperonin GroEL are revealed by the single mutation Arg196-->Ala.

Sequence homology between GroEL and Escherichia coli DNA polymerase I, together with the fact that both proteins bind adenine nucleotides, suggested to us that they may have a similar nucleotide binding site. Arg196 in GroEL corresponds to Arg425 in DNA polymerase I, which is near its nucleotide binding site. Here, we report the striking effects of the mutation Arg196-->Ala in GroEL on its kinetic and allosteric properties with respect to ATP. The mutation reduces positive co-operativity in ATP hydrolysis found in wild-type GroEL. It also gives rise to strong substrate (ATP) inhibition, which is not apparent in the wild-type protein. The dual effect of the mutation reflects the presence of two lines of allosteric communication between ATP binding sites in GroEL and suggests the existence of nested co-operativity.

Adenosine Triphosphate↗
PubMed1994

Prediction of an inter-residue interaction in the chaperonin GroEL from multiple sequence alignment is confirmed by double-mutant cycle analysis.

A search for co-ordinated amino acid changes in the hsp60 family of chaperonins suggested that cysteine residues at positions 137 and 518 in the Escherichia coli chaperonin GroEL may interact with each other. In order to determine whether this interaction indeed exists we constructed a double-mutant cycle comprising wild-type GroEL, the single mutants Cys137-->Ser and Cys518-->Ser and the corresponding double mutant. The effects of the two mutations on the function of GroEL, in assisting the refolding of a non-folded protein substrate (rhodanese), are shown to be non-additive. It is also shown that ADP by itself specifically destabilizes the Cys518-->Ser mutant GroEL particle with this effect being suppressed in the double mutant. The observed pattern of co-ordinated mutations in the hsp60 family of chaperonins is thus shown to reflect a real interaction, though most likely indirect, between Cys137 and Cys518 in GroEL. Our study demonstrates that patterns of co-ordinated mutations combined with double-mutant cycle analysis can provide structural information on interactions in a protein without an available three-dimensional structure at atomic resolution.

Bacterial Proteins↗
PubMed1994

Direct demonstration that ATP is in contact with Cys-137 in chaperonin GroEL.

The nonhydrolyzable ATP analogue ATP gamma S (adenosine 5'-3-O-(thio)triphosphate) is affinity cross-linked to GroEL by formation of a disulfide bridge in a peroxide-promoted reaction. By replacing with serine each of 3 cysteine residues in GroEL, it is shown that ATP gamma S specifically cross-links to Cys-137. It is thus demonstrated that the ATP bound to GroEL is in direct contact with Cys-137.

Adenosine Triphosphate↗
PubMed1993

The N terminus of the molecular chaperonin GroEL is a crucial structural element for its assembly.

The Escherichia coli heat-shock protein GroEL is a member of the highly conserved family of tetradecameric chaperonins 60, which assist in the folding and assembly of other proteins. Using site-directed mutagenesis, it is shown that replacement of the absolutely conserved amino acid residue Lys-3 by arginine or isoleucine destabilizes the GroEL particle and that the replacement Lys-3-->Glu completely blocks its formation. The rank order of effects of these mutations on the stability of the GroEL particle correlates with the associated changes in net charge at that position. Our results show that the N terminus of GroEL is a crucial structural element for its assembly.

Amino Acid Sequence↗
PubMed1993

Mutation Ala2-->Ser destabilizes intersubunit interactions in the molecular chaperone GroEL.

The mutation Ala2-->Ser in the molecular chaperone GroEL increases positive co-operativity in ATP hydrolysis, as reflected by a change in the Hill coefficient from 2.36(+/- 0.23) for wild-type to 3.19(+/- 0.17) for the mutant. This amino acid replacement destabilizes the oligomeric structure of GroEL. It is shown that adenine nucleotides also have a specific destabilizing effect which is more pronounced in the case of the Ala2-->Ser mutant. Addition of GroES or the non-folded protein ligand rhodanese blocks the destabilizing effect of adenine nucleotides for both wild-type and mutant. The results are interpreted using the Monod-Wyman-Changeux (MWC) model for co-operativity.

Adenosine Triphosphatases↗
PubMed1992

Alpha-helix stability in proteins. II. Factors that influence stability at an internal position.

The solvent-exposed residue Ala32 in the second alpha-helix of barnase was replaced by all other naturally occurring amino acids and the concomitant effects on the protein stability were determined. The results are assumed to reflect both the distinct conformational preferences of the different amino acids and also possible intrahelical interactions. The conformational preferences may be fully rationalized by invoking only a few physical principles. The results agree well with recently experimentally determined rank-order of helix-forming tendencies determined on a model peptide. There is very weak correlation between the results and the experimental host-guest values. There is a weak correlation between our results and the statistical helix propensities and a slightly better correlation with the positional-dependent statistical parameters of J. S. Richardson, and D. C. Richardson.

Amino Acid Sequence↗
PubMed1992

Co-operative interactions during protein folding.

The theory for measuring co-operativity between interactions in proteins by protein engineering experiments is developed by introducing a procedure for analysing increasing orders of synergy in a protein with increasing numbers of residues. The (pairwise) interaction energy (delta 2Gint) between two side-chains may be measured experimentally by a double-mutant cycle consisting of the wild-type protein, the two single mutants and the double mutant. This procedure may be extended to three residues to give a value for delta 3Gint for a triple-mutant cube, and to higher orders using multi-dimensional mutant space. We now show that delta 3Gint is the excess energy of adding all three chains compared with the sum of all the pairwise values of delta 2Gint for each of the constituent double-mutant cycles and the sum of all the single addition energies. This physical interpretation extends to higher orders of mutation. delta nGint (i.e. the interaction energy for n residues), thus, reveals the layers of synergy in interactions as a protein is built up. This procedure is applied to measuring changes in synergy during the refolding of barnase for the triad of salt-linked residues Asp8, Asp12 and Arg110, which are mutated to alanine residues. The value of delta 3Gint in the folded structure is 0.77(+/- 0.06) kcal mol-1 (i.e. the triad is 0.77 kcal mol-1 more stable than expected from the sum of the individual pairwise interactions and single contributions). The value of delta 3Gint is still significant in the transition state for unfolding (0.60(+/- 0.07) kcal mol-1) and in the folding intermediate (0.60(+/- 0.13 kcal mol-1)). These results show that synergistic interactions exist in barnase, in its transition state for unfolding and in a refolding intermediate. A direct measurement of the change of co-operativity between the folded state and the transition state for unfolding shows a decrease of 0.17(+/- 0.04) kcal mol-1, suggesting that the initial stages of protein unfolding may be accompanied by some loosening of structure in parts that still interact. The similar extent of co-operativity in the transition state for unfolding and the intermediate in refolding suggests that the intermediate is homogeneous, at least in the region of the salt-linked triad, as heterogeneity would lower the co-operativity.

Bacterial Proteins↗
PubMed1992

Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida.

What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four-stranded beta-sheets, a scaffold on which to explore variations in loop topology; Grendel, a four-helical membrane anchor, ready for fusion to water-soluble functional domains; Finger-clasp, a dimer of interdigitating beta-beta-alpha units, the simplest variant of the "handshake" structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather--a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three-dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.

Algorithms↗
PubMed1991

Pathway and stability of protein folding.

We describe an experimental approach to the problem of protein folding and stability which measures interaction energies and maps structures of intermediates and transition states during the folding pathway. The strategy is based on two steps. First, protein engineering is used to remove interactions that stabilize defined positions in barnase, the RNAse from Bacillus amyloliquefaciens. The consequent changes in stability are measured from the changes in free energy of unfolding of the protein. Second, each mutation is used as a probe of the structure around the wild-type side chain during the folding process. Kinetic measurements are made on the folding and unfolding of wild-type and mutant proteins. The kinetic and thermodynamic data are combined and analysed to show the role of individual side chains in the stabilization of the folded, transition and intermediate states of the protein. The protein engineering experiments are corroborated by nuclear magnetic resonance studies of hydrogen exchange during the folding process. Folding is a multiphasic process in which alpha-helices and beta-sheet are formed relatively early. Formation of the hydrophobic core by docking helix and sheet is (partly) rate determining. The final steps involve the forming of loops and the capping of the N-termini of helices.

Amino Acid Sequence↗
PubMed1991

COSMIC analysis of the major alpha-helix of barnase during folding.

The structures of transition states and intermediates in protein folding may be analysed by protein engineering methods that remove simple interactions that stabilize the folded state. We have now extended the range and reliability of the procedure by using the COSMIC (Combination of Sequential Mutant Interaction Cycles) technique, in which a series of double-mutant cycles is constructed. In each cycle, the side-chains of two amino acid residues that interact in the folded state are mutated separately and together. Kinetic and equilibrium measurements on folding for each cycle show unambiguously whether or not two residues interact during protein folding. A series of such cycles has been constructed to leapfrog along the major alpha-helix of barnase, comprising residues 6 to 18. The helix is found to be intact from its C terminus to residue 12 but begins to unwind towards the N terminus in both the transition state for unfolding and in a folding intermediate.

Amino Acid Sequence↗
PubMed1990

Strength and co-operativity of contributions of surface salt bridges to protein stability.

Many of the interactions that stabilize proteins are co-operative and cannot be reduced to a sum of pairwise interactions. Such interactions may be analysed by protein engineering methods using multiple thermodynamic cycles comprising wild-type protein and all combinations of mutants in the interacting residues. There is a triad of charged residues on the surface of barnase, comprising residues Asp8, Asp12 and Arg110, that interact by forming two exposed salt bridges. The three residues have been mutated to alanine to give all the single, double and triple mutants. The free energies of unfolding of wild-type and the seven mutant proteins have been determined and the results analysed to give the contributions of the residues in the two salt bridges to protein stability. It is possible to isolate the energies of forming the salt bridges relative to the solvation of the separated ions by water. In the intact triad, the apparent contribution to the stabilization energy of the protein of the salt bridge between Asp12 and Arg110 is -1.25 kcal mol-1, whereas that of the salt bridge between Asp8 with Arg110 is -0.98 kcal mol-1. The strengths of the two salt bridges are coupled: the energy of each is reduced by 0.77 kcal mol-1 when the other is absent. The salt-linked triad, relative to alanine residues at the same positions, does not contribute to the stability of the protein since the favourable interactions of the salt bridges are more than offset by other electrostatic and non-electrostatic energy terms. Salt-linked triads occur in other proteins, for example, haemoglobin, where the energy of only the salt-bridge term is important and so the coupling of salt bridges could be of general importance to the stability and function of proteins.

Alanine↗
PubMed1990

Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles.

Coulombic interactions between charges on the surface of proteins contribute to stability. It is difficult, however, to estimate their importance by protein engineering methods because mutation of one residue in an ion pair alters the energetics of many interactions in addition to the coulombic energy between the two components. We have estimated the interaction energy between two charged residues, Asp-12 and Arg-16, in an alpha-helix on the surface of a barnase mutant by invoking a double-mutant cycle involving wild-type enzyme (Asp-12, Thr-16), the single mutants Thr----Arg-16 and Asp----Ala-12, and the double mutant Asp----Ala-12, Thr----Arg-16. The changes in free energy of unfolding of the single mutants are not additive because of the coulombic interaction energy. Additivity is restored at high concentrations of salt that shield electrostatic interactions. The geometry of the ion pair in the mutant was assumed to be the same as that in the highly homologous ribonuclease from Bacillus intermedius, binase, which has Asp-12 and Arg-16 in the native enzyme. The ion pair does not form a hydrogen-bonded salt bridge, but the charges are separated by 5-6 A. The mutant barnase containing the ion pair Asp-12/Arg-16 is more stable than wild type by 0.5 kcal/mol, but only a part of the increased stability is attributable to the electrostatic interaction. We present a formal analysis of how double-mutant cycles can be used to measure the energetics of pairwise interactions.

Amino Acid Sequence↗
PubMed1987

Non-additivity in protein-protein interactions.

The energy of binding between proteins may be seen as the sum of the contributions of the individual amino acid residues. These contributions are additive when the binding energy, due to different amino acid residues, is independent of the interactions between amino acids in the same polypeptide chain. A measure of non-additivity is the coupling free energy. In this communication it is shown that: (1) the coupling free energy is the sum of intramolecular and intermolecular contributions; and (2), when additivity exists, experimentally determined values for the free energy of transfer of amino acids from water to the hydrophobic protein-protein interface are a very good approximation of their contribution to the energy of binding. Additivity cycles can be useful in determining the precise conditions where this approximation holds.

Allosteric Site↗
PubMed1987

The saliva of the medicinal leech Hirudo medicinalis--I. Biochemical characterization of the high molecular weight fraction.

1. A method is described for obtaining dilute Hirudo medicinalis saliva by feeding leeches through a membrane on arginine/saline and squeezing them immediately after from the posterior end forwards. The process can be repeated at intervals. Yields are considerably higher than from salivary gland extracts. 2. Hirudo saliva contains hirudin, eglin, hyaluronidase, collagenase and apyrase. Leech collagenase and apyrase are here reported for the first time. 3. On gel filtration of lyophilized saliva, activity peaks were well defined. Approximate molecular weights were determined. Apyrase appears in two forms with optimum activity around pH 7.5. Collagenase was identified as belonging to the mammalian type.

Adenylate Kinase↗