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Biomedical subjects

J Kyte

Publications and source records attributed to J Kyte.

At least 19 recordsLinked to original sources
PubMed1999

Dimerization of the extracellular domain of the receptor for epidermal growth factor containing the membrane-spanning segment in response to treatment with epidermal growth factor.

A recombinant fragment of the human receptor for epidermal growth factor containing both its extracellular domain and its membrane-spanning segment, when dissolved with Triton X-100, was observed to dimerize in response to addition of epidermal growth factor (EGF) even at the lowest concentration of this fragment that could be assayed (4 nM). Consequently, the dissociation constant for the dimer of this fragment is at least 10,000-fold smaller than that for dimers of soluble, recombinant forms of the extracellular domain lacking the membrane-spanning segment. The second-order rate constant for dimerization of the fragment containing the extracellular domain and the membrane-spanning segment was estimated to be greater than 0.3 nM(-1) min(-1), more than 10-fold that of the native enzyme under the same conditions. This result suggests that the cytoplasmic domain of the intact enzyme sterically hinders its dimerization. When EGF is removed from the dimer of the fragment, the rate constant for its dissociation is greater than 0.2 min(-1), more than 40-fold that of the native enzyme. This result suggests that interfaces between cytoplasmic domains of intact EGF receptor impart significant stabilization to the dimer of the enzyme.

Amino Acid Sequence↗
PubMed1999

Kinetics of activation of the tyrosine kinase of a deletion mutant of epidermal growth factor receptor missing the sites of self-phosphorylation.

The addition of epidermal growth factor (EGF) to epidermal growth factor receptor (EGF receptor) dissolved in a solution of the detergent Triton X-100 results in the activation of its protein tyrosine kinase. To investigate the importance of the sites for self-phosphorylation on the enzyme in this process, the kinetics of activation of a deletion mutant missing the last 195 amino acids of the protein, including all of the sites for self-phosphorylation, were followed by monitoring the initial velocity at which the enzyme catalyzes the phosphorylation of the exogenous substrate RRKGSTAENAEYLRV. The activation of the enzymatic activity of this deletion mutant of EGF receptor displays kinetics that are second-order with respect to the concentration of the enzyme as does wild-type EGF receptor. The second-order rate constant for its activation is 36 +/- 10 microM-1 min-1, which is only 3-fold greater than the second-order rate constant for the activation of wild-type EGF receptor under the same conditions (13 +/- 2 microM-1 min-1). These results suggest that the mechanism by which the protein tyrosine kinase of the deletion mutant is activated is the same as that for the activation of the wild-type receptor and that the sites of self-phosphorylation in the wild-type EGF receptor do not participate in the mechanism of activation of the enzyme.

Amino Acid Sequence↗
PubMed1998

Lysine-691 of the anion exchanger from human erythrocytes is located on its cytoplasmic surface.

A combination of vectorial modification and site-directed immunochemistry has been used to determine the disposition, with respect to the membrane, of Lys-691 of the anion exchanger from human erythrocytes. Intact erythrocytes and inside-out vesicles were vectorially modified in the same container with pyridoxal phosphate and sodium [3H]borohydride. The modified inside-out vesicles were separated from erythrocytes by differential centrifugation and the vesicles and erythrocyte membranes were treated with alkali and digested with trypsin and thermolysin to liberate the peptides IVSKPER and IVSK¿Nepsilon-[4'-(5'-phospho-[4-3H]pyridoxyl)]¿PER. These peptides, containing the unmodified and modified versions of Lys-691, were retrieved from the digests by site-directed immunochemistry and were identified by HPLC and liquid scintillation spectroscopy. Both the inside-out vesicles and the intact erythrocytes contained the peptide IVSKPER, however, the 3H-label from the phosphopyridoxylated peptide could be detected only in the inside-out vesicles. The incorporation of 3H into Lys-691 of the anion exchanger from inside-out vesicles was at least 30-fold greater than the incorporation into Lys-691 of the anion exchanger from intact erythrocytes. It follows that Lys-691 of the anion exchanger is located on the cytoplasmic surface of the plasma membrane.

Anion Exchange Protein 1, Erythrocyte↗
PubMed1996

Identification of an active site residue of the R1 subunit of ribonucleotide reductase from Escherichia coli: characterization of substrate-induced polypeptide cleavage by C225SR1.

Incubation of the C225S mutant of the R1 subunit of ribonucleotide reductase from Escherichia coli with the R2 subunit and nucleoside diphosphates leads to fragmentation of the polypeptide backbone of R1 [Mao, S. S., Holler, T. P., Bollinger, J.M., Jr., Yu, G. X., Johnston, M.I., & Stubbe, J. (1992) Biochemistry 31, 9744--9751]. The 26 and 60 kDa cleavage fragments were purified to homogeneity. The 26 kDa polypeptide was digested with Lys-C, and the peptides were partially purified by RP-HPLC. Mass spectrometric analysis (MALDI-TOF) of the HPLC fractions allowed the identification of the C-terminal peptide. The molecular mass of this peptide (2176) revealed that serine-224 constitutes its C-terminus, and further analysis of the distribution of its monoisotopic masses by FAB-MS indicated that Ser224 possesses a carboxamide rather than a carboxylate group. Treatment of the 60 kDa cleavage fragment with cyanogen bromide and subsequent MALDI-TOF analysis of the partially RP-HPLC purified peptides yielded a fraction containing its N-terminal peptide. This peptide was digested with trypsin, and the digestion mixture was purified by HPLC. Analysis of the fractions by MALDI-TOF identified the N-terminal peptide and determined a mass of 2222. This mass suggested valine 226 was the N-terminal residue (modified by an adduct of 28 mass units). Larger amounts of the C-terminal tetrapeptide of the 60 kDa fragment (V226LIE229) were obtained by complete digestion of the crude reaction mixture with endoproteinase Glu-C. The peptide mixture was then purified on an immunoadsorbent column containing immobilized antibodies raised against a synthetic peptide with the sequence KVLIE. After elution of the affinity-bound peptide, it was analyzed by CID-MS verifying that an adduct of 28 mass units was attached to valine 226. These results indicated that the amino group of Val226 is formylated. The localization of the residues at the cleavage site of C225SR1 provides a biochemical identification of the active site region of the R1 subunit of RDPR from E.coli. The details of the mechanism of cleavage remain to be elucidated.

Amino Acid Sequence↗
PubMed1996

Activation of epidermal growth factor receptor by epidermal growth factor.

The binding of epidermal growth factor (EGF) to epidermal growth factor receptor (EGF receptor) induces dimerization of the receptor and activation of its protein tyrosine kinase. Each of these three steps was followed as a function of the concentrations of EGF and of EGF receptor. Binding of EGF was followed by sedimentation of the complex between [3H]EGF and EGF receptor, dimerization was measured by quantitative cross-linking with glutaraldehyde, and the activation of the protein tyrosine kinase was monitored under the same conditions by following the initial velocity of the phosphorylation of peptides containing tyrosine. The binding of epidermal growth factor to its receptor was measured as a function of the concentration of epidermal growth factor, and the relationship was sigmoid with an average value of 1.7 for the Hill coefficient. Both dimerization and the activation of the tyrosine kinase displayed saturation as a function of the concentration of EGF. The ranges of the concentrations of EGF where dimerization and activation of the tyrosine kinase activity were half-maximal were 15-30 and 50-200 nM, respectively, but the value for the concentration of EGF at the half-maximum for the activation of the tyrosine kinase was a complex function of the concentration of EGF receptor. The observed behavior of the binding of EGF, the dimerization of EGF receptor, and the activation of the tyrosine kinase were used as criteria against which to test mechanisms for the process of activation. Equations were derived for various reversible and irreversible mechanisms and used to calculate the theoretical behaviors of the three properties. In direct comparisons of the experimental and the theoretical data, several of the previously proposed reversible and irreversible mechanisms for the activation of EGF receptor were found to be inadequate, but a reasonable mechanism was formulated that was compatible with the experimental data. In this mechanism, dimeric EGF receptor must be occupied by two molecules of EGF for enzymatic activity to be expressed.

Amino Acid Sequence↗
PubMed1990

[The demonstration of an extramembranous location for the putative amphipathic helix of the acetylcholine receptor].

It has been demonstrated that the lysyl residues at the centers of the potential amphipathic helices of the alpha- and beta-subunits could be readily labeled in native acetylcholine receptor with anionic electrophiles. This result indicates that the regions in the sequences of the alpha- and beta-polypeptides which patterns of hydropathy are those of amphipathic helices are fully exposed on the surface of the native protein and do not span the membrane.

Amino Acid Sequence↗
PubMed1989

Assessment of the number of free cysteines and isolation and identification of cystine-containing peptides from acetylcholine receptor.

The number of free cysteines in each polypeptide of acetylcholine receptor from the electric organ of Torpedo californica has been assessed by alkylating the native protein with N-ethylmaleimide and iodoacetamide during homogenization of the tissue and alkylating the polypeptides with N-ethylmaleimide as they were unfolded in solutions of dodecyl sulfate. The cysteines unavailable for alkylation could be accounted for as specific cystines, connecting positions in the amino acid sequences of the individual polypeptides. Unreduced, alkylated polypeptides of acetylcholine receptor were digested with thermolysin or trypsin. Cystine-containing peptides in the chromatograms of the digests were identified electrochemically by the use of a dual gold/mercury electrode. Three thermolytic peptides and three tryptic peptides have been isolated from these digests and shown to contain intact cystines that were originally present in the native protein. The majority of these peptides contained an intact, intramolecular cystine connecting two cysteines in locations homologous to cysteines 128 and 142 from the alpha polypeptide. Each of these cystines from each of the polypeptides of acetylcholine receptor was isolated in at least one peptide, respectively. Each of these cystine-containing peptides also contained glucosamine. It can be concluded that each asparagine in the sequence Asn-Cys-Thr/Ser, which occurs in the respective, homologous location in every polypeptide, is glycosylated even though a cystine sits between the asparagine and the threonine or serine. In addition, the existence of the cystine connecting the adjacent cysteines, alpha 192 and alpha 193, in the alpha subunit of acetylcholine receptor [Kao, P. N., & Karlin, A. (1986) J. Biol. Chem. 261, 8085-8088] has been confirmed.

Amino Acid Sequence↗
PubMed1989

Nucleophilic behavior of lysine-501 of the alpha-polypeptide of sodium and potassium ion activated adenosinetriphosphatase consistent with a role in binding adenosine triphosphate.

An immunoadsorbent specific for the carboxy-terminal sequence -GAPER, which comprises residues 502-506 of the alpha-polypeptide of ovine sodium and potassium ion activated adenosinetriphosphatase [(Na+ + K+)-ATPase], was used to isolate the products of the reaction between the lysine immediately preceding this sequence in the intact protein and either [3H]acetic anhydride or fluorescein 5'-isothiocyanate. Changes in the apparent nucleophilicity of this lysine, Lys501, were observed with both reagents when ATP was bound by the intact, native enzyme poised in the E1 conformation or when the structure of the enzyme was changed from the E1 conformation into the E2-P conformation. With both reagents, a decrease of more than 4-fold in the yield of incorporation occurred during the former change, but a decrease of only 2-fold occurred during the latter. Because a much larger decrease occurred when ATP was bound in the absence of a conformational change than occurred when a major conformational change took place in the absence of the occupation of the active site, these changes in the incorporation of [3H]acetyl suggest that Lys501 from the alpha polypeptide is directly involved in binding ATP within the active site of (Na+ + K+)-ATPase. The immunochemical reactions between the specific polyclonal antibodies raised against the sequence-GAPER and denatured or enzymically active (Na+ + K+)-ATPase were also investigated. Western blots and the inhibition of enzymic activity caused by the antibody have shown that it can bind to both the denatured and the native form of the alpha-polypeptide, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetic Anhydrides↗
PubMed1987

Demonstration that lysine-501 of the alpha polypeptide of native sodium and potassium ion activated adenosinetriphosphatase is located on its cytoplasmic surface.

Evidence that the peptide HLLVMKGAPER, which can be released from intact sodium and potassium ion activated adenosinetriphosphatase by tryptic digestion, is located on the cytoplasmic surface of the native enzyme has been obtained. An immunoadsorbent directed against the carboxy-terminal sequence of this tryptic peptide has been constructed. The peptide KGAPER was synthesized by solid-phase techniques. Antibodies against the sequence -GAPER were purified by immunoadsorption, using the synthetic peptide attached to agarose beads. These antibodies, in turn, were coupled to agarose beads to produce an immunoadsorbent. Sealed, right-side-out vesicles, prepared from canine kidneys, were labeled with pyridoxal phosphate and sodium [3H]borohydride in the absence or presence of saponin, respectively. A tryptic digest of these labeled vesicles was passed over the immunoadsorbent. Large increases in the incorporation of radioactivity into the peptides bound by the immunoadsorbent were observed in the digests obtained from the vesicles exposed to saponin. From the results of several control experiments examining the labeling reaction as applied to these vesicles, it could be concluded that this increase in incorporation resulted only from the access that the reagents gained to the inside of the vesicles in the presence of saponin and that the increase in the extent of modification was due to the cytoplasmic disposition of this segment in the native enzyme.

Amino Acid Sequence↗
PubMed1986

One-dimensional crystals of (Na+ + K+)-ATPase dimers.

Preparations of purified (Na+ + K+)-ATPase contain both fragments of membranes and long and undulating cylindrical structures. These structures have been described as edgeways of membrane fragments. We have analyzed these structures using negative staining, thin sectioning and freeze-fracture-etch electron microscopy and describe their structure for the first time. Each cylinder is 12-19 nm in width and is comprised of an unstained core from which rows of distinct particles spaced 5-6 nm apart project on both sides. Each cylindrical structure was interpreted as a linear polymer of (alpha beta)2 dimers of (Na+ + K+)-ATPase molecules. Therefore, the particles that project from both sides are the cytoplasmic domains of the molecules of the enzyme, whereas the membrane-spanning domains form the unstained core of the cylinder. From considerations of the packing of the dimers in the cylinder we conclude that the cross-sectional area of the cytoplasmic domain should be larger than that of the membrane-spanning domain. Our results are consistent with the hypothesis that the (alpha beta) protomer is the native state of the enzyme. The (alpha beta)2 dimers observed in the fractions are the result of a secondary aggregation process occurring during the purification procedure.

Animals↗
PubMed1984

Structural organization of (Na+ + K+)-ATPase in purified membranes.

The structural organization of crystalline, membrane-bound (Na+ + K+)-ATPase was studied by negative staining and thin sectioning. The enzyme molecules were induced to form crystalline arrays within fragments of membrane by incubation in defined ionic conditions. The enzyme remained fully active after crystallization. Negative staining and computer processing of images of the crystalline specimens identified two discrete crystalline arrays. The dimensions of the unit cell of one of the arrays were large enough to accommodate an alpha beta protomer; those of the other array, an (alpha beta)2 diprotomer . Thin sections of the crystalline fraction contained a unique membrane complex that was formed from two apposed plasma membranes. The paired membranes in this complex were separated by a center-to-center space of 15 nm containing evenly spaced septa that connected the membrane surfaces; the overall thickness of the entire structure was 22-25 nm. The agglutinin from Ricinus communis, a lectin that binds to the carbohydrate moiety of the beta-subunit of (Na+ + K+)-ATPase, decorated the free surfaces of the complex. Therefore, this complex of paired membranes is the result of interactions between the cytoplasmic domains of the enzyme. From measurements of the dimensions of these structures, we estimate the overall length of the enzyme to be approximately 11.5 nm along the axis perpendicular to the plane of the membrane, and the molecular protrudes more (approximately 5 nm) on the cytoplasmic surface than on the extracytoplasmic surface (approximately 2 nm).

Animals↗
PubMed1983

A discontinuous electrophoretic system for separating peptides on polyacrylamide gels.

An electrophoretic system for separating, with high resolution, peptides 25-250 residues in length is described. The peptides are stacked by discontinuous electrophoresis to form very sharp bands at the origin. They are then separated on a matrix of 20% polyacrylamide, 8 M urea, and 0.1% dodecyl sulfate. Through this combination, high resolution and clean separation, based on polymer length, are achieved.

Animals↗
PubMed1981

Molecular considerations relevant to the mechanism of active transport.

A small group of closely related proteins is responsible for all active transport in animal cells, and inorganic cations are the only substances transported by these enzymes. They share a common kinetic mechanism in which two fundamental conformations participate, each receiving and dispatching substrates from its unique side of the membrane. During transport, the cations must pass through their enzyme to cross the membrane and intense interest is currently focused on the possibility that the path which they follow lies within the interface between two discrete subunits in a dimeric structure. Although 'half-of-sites' behaviour, consistent with this hypothesis, has been reported, it is now known that systematic errors were responsible for this mistaken conclusion. The number of protomers which comprise a functional unit of active transport has not been determined.

Adenosine Triphosphatases↗
PubMed1980

Stoichiometry and molecular weight of the minimum asymmetric unit of canine renal sodium and potassium ion-activated adenosine triphosphatase.

Sodium and potassium ion-activated adenosine triphosphatase is known to be composed of at least two different polypeptides, alpha and beta. When a detergent-treated supernatant preparation of the enzyme is reacted with the cross-linking reagent, cupric phenanthroline, a single, covalent heterodimer is formed. This product is formed from one of each of the two polypeptides. The remaining, unreacted alpha and beta chains maintain a constant ratio to each other throughout the reaction. The same heterodimer is formed in membrane-bound enzyme when reacted with several other cross-linking reagents. The protein mass ratio between the chains in the native enzyme, determined by two methods, is 2.15 +/- 0.16. Using this value and a value of 121,000 +/- 6,000 for the molecular weight of the larger polypeptide, a molecular weight of 56,000 +/- 7,000 can be calculated for the protein portion of the smaller polypeptide. Upon removal of a substantial portion of the carbohydrate from the smaller polypeptide, a change in its electrophoretic mobility is observed, while that of the larger polypeptide remains unaffected. The apparent length of this unglycosylated small chain is 450 residues, corresponding to a molecular weight of 51,000. Taken together, these results demonstrated that the two polypeptides of the (Na+ + K+)-ATPase exist in an equimolar, noncovalent association in the native enzyme, and that the protein molecular weight of the minimum asymmetric unit is 177,000 +/- 13,000, Previous results which address the question of the quaternary structure of the ATPase are re-examined in light of these determinations.

Animals↗
PubMed1979

Examination of intramolecular heterogeneity of plasma membrane protein degradation in canine renal tubular epithelial cells and in rat liver.

We have examined the hypothesis that hydrophilic portions of membrane-bound proteins which lie on either side of the phospholipid bilayer may be degraded at a different rate than are the hydrophobic portions of membrane proteins which are within the bilayer. Plasma membrane fractions from cells of the Maden-Darby canine kidney cell line and rat liver were digested with papain and pronase to cleave a mixture of peptides which is enriched in hydrophilic amino acids. It is proposed that these peptides are derived from regions of membrane-bound proteins which lie outside the bilayer. The residual particulate protein is enriched in hydropholic amino acids and presumably contains the portion of membrane-bound proteins which are in direct contact with the bilayer. A double-isotope method was used to assess the relative degradation rates of these two protein fractions. There was no measurable difference in protein degradation rates between the two fractions and the initial plasma membranes. These results suggest that the intramolecular heterogeneity which results from insertion of membrane-bound proteins into a bilayer is not a factor in their degradation.

Animals↗