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Results for “Protein Conformation, alpha-Helical”

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At least 19 recordsLinked to original sources
PubMed2026

Evolutionary history and recombination in the mitochondrial carrier SLC25 superfamily analyzed by similarities in the exon and transmembrane α-helix sequences.

Mitochondrial carriers (MCs), which constitute a superfamily also called the solute carrier family 25 (SLC25), are characterized by conserved signature motif sequences and a six-transmembrane α-helical transporter domain. They transport a wide variety of substrates ranging from protons, inorganic ions, citric acid cycle intermediates, and amino acids to nucleotides and cofactors. The superfamily members can be divided into subfamilies, each with a distinct substrate specificity. In an attempt to understand how different subfamilies have evolved, we analyzed the protein sequences of the exons (with conserved boundaries) and the six transmembrane α-helices of MCs from highly diverged organisms. The results show that some MC subfamilies have all exons and transmembrane α-helices most similar to a closely related subfamily, which is consistent with a scenario of gene duplication and mutational divergence from a last common ancestor. However, several MC subfamilies appear to be mosaics of exons and transmembrane α-helices most similar to different and distant subfamilies, which in some cases could be explained by recombination between the superfamily genes during evolution. It seems that this latter mechanism could have played a role in the formation of new subfamilies with different substrate specificities by the combination of MC transporter domain segments that had been optimized previously for binding specific portions of the substrates. This study presents novel evolutionary relationships between MC subfamilies and may provide clues for how protein superfamilies have expanded and how to investigate their evolution.

Evolution, Molecular↗
PubMed1976

Physical studies of the nonhistone chromosomal proteins HMG-U and HMG-2.

The nonhistone chromosomal proteins, HMG-1 and HMG-2, have a folded conformation, with a high alpha-helical content, over a wide pH range. At high and low pH values, the molecules unfold. Both molecules contain cysteine and tryptophan. The tryptophans appear to be buried in the folded form. HMG-1 shows aggregation at pH 5.7, as does HMG-2 at pH 9.0. The folded form is insensitive to high concentrations of salt, suggesting that charge-charge interaction plays no role in stabilizing the tertiary structure.

Animals↗
PubMedDate not supplied

Metal complexes of poly(alpha-amino acids). A potentiometric and circular dichroism investigation of Cu(II) complexes of poly(L-lysine), poly(L-ornithine), and poly(L-diaminobutyric acid).

The conformational properties of cupric complexes of poly(L-lysine), poly(L-ornithine), and poly(L-diaminobutyric acid) have been investigated by potentiometric, visible and UV absorption, and circular dichroism (CD) techniques. The three polymers form two kinds of complexes stable at pH less than 8.5 (type I complexes) and at pH less than 8.5 (type II complexes). It has been found that in the low pH complexes of poly(L-diaminobutyric acid) at least one deprotonated amido nitrogen is coordinated to cupric ions. Type II complexes involve always amide nitrogens in the coordination sphere of Cu(II). Evidence is presented that the structure of such complexes is not compatible with the alpha-helical conformation of the peptide backbone.

Aminobutyrates↗
PubMed1977

Studies on the catalytic action of poly-alpha-amino acids. VII. Stereospecificity in the enzyme-like hydrolysis of benzoyl-L-(D)-arginine-p-nitroanilides by copoly (Cys, Glu).

The substrate specificity in the hydrolysis of L-, DL-, and D-BAPA (benzoylarginine-p-nitro-anilide) by copoly (L-Cys, L-Glu) and copoly (D-Cys, D-Glu) was studied, and enzyme-like stereospecific hydrolyses by poly-alpha-amino acids were identified for the first time. The L-type copolymer hydrolyzed L-BAPA faster than D-BAPA and the rates (v) of BAPA hydrolyses by L-type copolymer were found to be in the order vL greater than vDL greater than vD. On the other hand, the D-type copolymer hydrolysed D-BAPA faster than L-BAPA and the rates of BAPA hydrolyses by D-type copolymer were in the order vD greater than vDL greater than vL. In all cases, the reaction followed Michaelis-Menten kinetics when the substrate concentration was corrected, and the optimum conditions of the reaction were pH 6.0 and 40 degrees. The activity appeared after a certain amount of BAPA had combined with the polymer. D- and L-substrates combine competitively with the polymer and the different rates of hydrolysis are presumably due to the different substrate configurations in relation to the conformation of the active site in the polymer. The polymer shows activity near the range of random coil conformation, where some alpha-helical conformation is still present. Only some of the cysteine residues in the copolymer are involved in the hydrolytic activity.

Arginine↗
PubMed1976

Cooperative reactions of poly-L-lysine-heme complex with molecular oxygen, carbon monoxide, or cyanide ion.

The interaction of the alpha-helical poly-L-lysine-heme complex with molecular oxygen, carbon monoxide, or cyanide ion was studied. Binding equilibrium curve and activation parameters for the reactions were determined. Sigmoid responses were observed for the absorption of molecular oxygen or carbon monoxide by the complex and the cooperative parameter was found to be 2.1. This indicated a cooperative interaction between hemes situated on a cylindrical alpha-helix of poly-L-lysine. But those of other polymer-ligand-heme complexes were 1.0. The cooperative reaction mechanism, in which an alpha-helical poly-L-lysine plays an important role, was suggested.

Binding Sites↗
PubMed1976

Glutamine synthetase adenylyltransferase from Escherichia coli: purification and physical and chemical properties.

The glutamine synthetase adenylyltransferase (EC 2.7.7.42), WHIch catalyzes the adenylylation and deadenylylation of glutamine synthetase in E. coli, has been stabilized and purified 2200-fold to apparent homogeneity. Sedimentation and electrophoresis studies show that the native enzyme is a single polypeptide chain of 115,000 +/- 5000 molecular weight with an isoelectric pH (PL) OF 4.98, a sedimentation coefficient (S20.w0) of 5.6S, and a molar frictional coefficient (f/f0) of 1.52. An alpha-helical content of approximately equal to 25% and approximately equal to 28% beta-pleated sheet and approximately equal to 47% random coil structures were estimated from circular dichroism measurements. The amino acid composition of the protein has been determined. The intrinsic tryptophanyl residue flourescence of adenylyltransferase is two fold greater than that of L-tryptophan; this property has been used to monitor ligand-induced conformational changes in the enzyme. Activators of the adenylylation reaction (ATP, L-glutamine, or the E. coli PII regulatory protein) produced an enhancement of fluorescence; alpha-ketoglutarate, an inhibitor of adenylylation and an activator of deadenulylation, caused a net decrease in fluorescence. The adenylytransferase has separate interaction sites for L-glutamine and the regulatory PII protein.

Amino Acids↗
PubMed1978

The effects of pH and temperature on the circular dichroism of human erythrocyte membranes.

The effects of pH and temperature on the structure of human erythrocyte membranes were studied by circular dichroism (CD). The results obtained demonstrate that the membrane CD spectra undergo significant changes when the pH of the solution deviates from its native pH range of 7 to 8. Spectral changes in the acidic pH region include drastic reductions and slight shifts in the CD signal which may reflect a decrease in alpha-helical content of the proteins and/or an increase in optical artifacts, both of which are irreversible. In the alkaline pH region, dramatic increases in ellipticity and blue-shifts in the spectra are observed between pH 8 and 10. In addition, the spectra more closely resemble those reported for membrane samples where the spectral distortions have been removed. The changes in the alkaline region are demonstrated to be only partially reversible and may be due to conformational alterations in the membrane proteins and/or to a reduction in optical distortions. Thermal stability studies reinforce the irreversible behavior of the membrane samples.

Cell Membrane↗
PubMed1978

Interstrain variation of the major internal structural component (p30gag) of two murine oncornaviruses: comparative immunochemical, biochemical, and biophysical analysis.

The major internal structural protein (p30(gag)) of the Moloney leukemia virus and the endogenous Y-1 murine oncornavirus was examined for biochemical and biophysical manifestations of interstrain antigenic variation. Although the two viral proteins share murine group-specific antigenic determinants, the Y-1 virus p30 appeared to have both a lower relative number of such determinants and a decreased affinity at the cross-reactive sites for Moloney virus p30 monospecific antibodies. Further, immunological analysis indicated the presence of unique antigenic sites on the Moloney virus p30 not shared by the analogous Y-1 virus molecule. The two polypeptides copurified and had similar isoelectric points (pH 6.2 to 6.3) and sedimentation coefficients (2.47S). However, equilibrium sedimentation yielded a significant mass difference between the two proteins, 28,300 +/- 600 and 31,000 +/- 300 daltons for the Moloney and Y-1 virus molecules, respectively. Amino acid analysis indicated a concomitant increase in total residues for the Y-1 virus p30, although a number of residues appeared to have been conserved between the two viral proteins. Conformational studies and hydrodynamic calculations demonstrated marked secondary and tertiary structural differences; with the Y-1 virus p30 being an asymmetric prolate ellipsoid containing 27 to 28% alpha-helix and Moloney virus p30 being somewhat more spherical and possessing an alpha-helical content of 50 to 55%. Two-dimensional mapping of (125)I-labeled tryptic peptides of each p30 suggested that considerable sequence heterogeneity is responsible for many of the biophysical, biochemical, and immunochemical differences in these two analogous structural proteins.

Amino Acids↗
PubMed1976

Physical and kinetic properties of homogenous bovine lens aldose reductase.

Aldose reductase from calf lens was purified 15,000-fold. The homogeneity of the final preparation was demonstrated by molecular sieve chromatography, analytical ultracentrifugation, sodium dodecyl sulfate gel electrophoresis, Ouchterlony immunodiffusion, and polyacrylamide gel electrophoresis at three pH values. The monomeric nature of the enzyme is suggested by the molecular weight of 37,000 from both molecular sieve chromatography and sodium dodecyl sulfate-gel electrophoresis with beta-mercaptoethanol. This closely corresponds with a molecular weight of 40,400 estimated by using calculate physical constants in the Svedberg equation. The S20,w was 3.6 to 3.7 as determined from ultracentrifuge and sucrose density gradient data. The Stokes radius was found to be 2.5 +/- 0.2 nm and 2.75 +/- 0.15 nm by two different methods. The diffusion constant D20,w is (7.8 +/- 10(-7) +/- 0.45 X 10(-7) cm2/s). The molecule is nearly spherical as indicated by a frictional ratio f/fo = 1.14. The alpha-helical content was estimated from circular dichroism data to be 5% and did not change in the presence of added substrates, products, and some enzyme inhibitors. Homotropic cooperative effects were observed as shown by the concave downward curvature of the reciprocal plots.

Alcohol Oxidoreductases↗
PubMed1979

Thermal stability of soluble mitochondrial H+-ATPase.

ATPase melting has been studied by circular dichroism and differential scanning microcalorimetry. Decomposition of the alpha-helix of H+-ATPase (in which about 80% of the peptide groups of the enzyme are involved) following thermal treatment is shown to proceed gradually, beginning with room temperature. Effect of nucleotides upon melting is detected in the range of 20 degrees--40 degrees C. Above 40 degrees C, the pattern of thermal decomposition of the three-dimensional structure of H+-ATPase is independent of the nature of nucleotides present. Highly stable alpha-helical sites have been found in the enzyme molecule. Possible mechanism of formation of such sites is discussed, and the results obtained are compared with data on thermal stability of ATPase from thermophilic bacteria. Structural changes in the molecule following thermal treatment are compared with ATPase activity changes under similar experimental conditions.

Adenosine Triphosphatases↗
PubMed1977

[Diffuse x-ray wide-angle scattering of polyglutamic acid in solution].

The diffuse wide angle x-ray scattering (WAXS) of polyglutamic acid (PGA) in solution was studied using an x-ray diffractometer with small aperture of the primary beam. The scattering curve was recorded at an angular interval from (article: see text). The experimental scattering intensity of PGA with alpha-helical CD spectrum showed a maximum at 14.4 nm-1. Unordered PGA in solution yielded no maximum at this scattering angle. The studies have proved that the scattering theory can be applied to globular proteins in solution as well as to chain molecules in solution in this angular interval. The differences between the calculated scattering curves and the experimental curves indicate minor movements of the side chains of PGA in solutions and slight structuring of the solvent at the surface of the polypeptide chain.

Glutamates↗
PubMed1976

Structure and fluctuation of a Streptomyces subtilisin inhibitor.

The kinetics of the hydrogen-deuterium exchange reaction in a subtilisin inhibitor from Streptomyces albogriseolus has been examined by infrared absorption measurement in aqueous solutions at various pH values and temperatures. In the analysis of each piece of kinetic data, it was assumed that the total 104 peptide hydrogen atoms are classified into three kinetic classes A, B1, and B2, and that the sizes of these classes are 72, 15, and 17, respectively at every pH and at every temperature examined. On the basis of the peak position determined for the amide II band in each stage of the exchange reaction, an approximate assignment was suggested of the A, B1 and B2 respectively to an unordered structure, a beta-structure,and an alpha-helical structure in the molecule. This assignment was supported by infrared absorption measurement of a film of this protein and by circular dichroic study of the solutions. On the basis of the temperature effect on the hydrogen-exchange rate constants and on the basis of ultraviolet absorption study in the higher temperature region (40 to 90 degrees C), a discussion has been made on the nature of the fluctuation of the molecular structure of this protein.

Bacterial Proteins↗
PubMed1978

Studies on erythrocruorin. VII. Reconstitution of earthworm erythrocruorin from the apoprotein.

Apoerythrocruorin prepared from the giant respiratory hemoprotein of the earthworm (60 S, Mr = 3 X 10(-6)) is an electrophoretically homogeneous molecule which sediments as a single peak of low molecular weight (3.5 S) and has a lower alpha-helical content (approx. 30%) than the native protein. Titration of globin with ferric heme indicates the presence of different binding sites; however, after purification by ion exchange chromatography, the reconstitution product contains 1 haem/23 000 g of protein as the native molecule. Reconstituted ferric erythrocruorin is a low molecular weight hemichrome with the same optical and physicochemical properties of the hemichrome formed by natural ferric erythrocruorin. Reconstituted ferrous erythrocruorin reacquires the alpha-helical content and the quaternary structure of the native molecule. Reassociation into 10-S speices (1/12 of the whole molecules) is fast and easy, while that into whole molecules is slow and somewhat erratic. The functional properties of reconstituted ferrous erythrocruorin (oxygen affinity, cooperativity in oxygen binding, magnitude of Bohr effect) are very similar to those of the "stable" low cooperativity form of the undissociated protein.

Apoproteins↗
PubMed1975

Desmosomes, filaments, and keratohyaline granules: their role in the stabilization and keratinization of the epidermis.

Components of desmosomes, filaments, and keratohyaline granules were studied by electron microscope and biochemical methods to clarify their role in the stabilization and keratinization of the epidermis. Isolated desmosomes are composed of 76% protein, 17% carbohydrate, and 10% lipid. The bulk of protein consists of a "spectrin"-like fibrous protein, presumably present in the plaque, and of glycoproteins in the desmosomal interspace. The main component of filaments, prekeratin, is a low-sulfur alpha-protein composed of a pair of three-chain subunits with non-alpha-helical segments separated by 200 A-long alpha-helical regions. The major component of isolated keratohyaline granules, the amorphous particulate material, is formed by a high-sulfur protein with a single-type of polypeptide chain. Polypeptide chains comparable to those found in prekeratin and keratohyaline granules were recovered from extracts of horny cells. Within the living part of the epidermis, filaments hypothetically form a cytoskeletal system which is anchored to desmosomes by a filamentous plaque protein. Glycoproteins are involved in the formation of strong junctions between the cells which enable the living part of the epidermis to respond as a whole to mechanical stress. The stratum corneum is stabilized by a similar system in a consolidated state which is less extensible. Horny cells are enveloped by a thickened membrane and the interfilamentous spaces are filled with various proteins including the sulfur-rich amorphous protein found in keratohyaline granules.

Animals↗
PubMed1976

Isolation and characterization of human plasma alpha 1-proteinase inhibitor and a conformational study of its interaction with proteinases.

1. alpha 1-Proteinase inhibitor was isolated from human plasma by a five-step procedure. Isoelectric focusing showed that six components focused between pH4.85 and 4.95. 2. The mol.wt. of the inhibitor was 52000 by sedimentation equilibrium and sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. The amino acid and carbohydrate compositions of the inhibitor were also determined. 3. The far-u.v.c.d. (circular-dichroism) spectrum indicated that the inhibitor had about 36% alpha-helical content. 4. The loss of proteinase-inhibitory activity when the inhibitor was exposed to pH values less than 5.0 or greater than 10.5 was accompanied by small changes in the far-u.v.c.d. spectrum and large changes in the near-u.v.c.d. spectrum. The change at alkaline pH was associated with ionization of tyrosine residues. 5. Interaction of inhibitor with chymotrypsin caused perturbation of the c.d. spectrum and this was used to follow the interaction and show a 1:1 stoicheiometry. 6. C.d., electrophoresis and isoelectric focusing showed that the inhibitor-enzyme complex is degraded by free enzyme. 7. Parallel studies with trypsin indicated that it too forms a 1:1 complex with inhibitor and is degraded by excess of enzyme.

Amino Acids↗
PubMed1977

Mammalian epidermal keratin: isolation and characterization of the alpha-helical proteins from newborn rat.

Neutral buffer-insoluble proteins extracted from newborn rat epidermis with alkaline urea have been purified by chromatography on Sephadex G-150 columns run in the presence of sodium dodecyl sulfate. Two proteins with apparent molecular weights of 60 000 and 68 000, respectively have been isolated and characterized. Spectropolarimetric studies show both of them to be alpha-helical in contrast to the non-helical heavier and lighter species also solubilized with alkaline urea. The amino acid composition of the two proteins, their electrophoretic behavior and their immunological characteristics are essentially identical. Both proteins appear to be major constituents of rat epidermal tonofilaments.

Amino Acids↗
PubMed1977

The secondary structure of myelin basic protein extracted by deoxycholate.

Because of the implication of myelin basic protein in some neurological diseases its in vivo structure is of particular interest. The protein is usually isolated using organic solvents and acid solutions and has previously been shown to contain little alpha-helical or beta-structure; but it is not known how the extraction methods influence the structure. Following recent observations that deoxycholate generally causes minimal structural perturbation when used to dissolve membrane proteins, this detergent has been used to extract the basic protein from bovine myelin. The protein contained in deoxycholate washes of myelin has been purified by gel chromatography and its secondary structure examined by circular dichroism spectroscopy. This protein and conventionally prepared bovine and human basic protein to which 1% deoxycholate has been added appear to have the same structure: they contain 8-14% more helical structure than the chloroform/methanol-extracted protein in pH 4.8 acetate buffer or in pH 9.15 Tris buffer. This conformational change is unaffected by addition of 0.25 M NaCl. The helical content will approach the upper limit if, as is expected, these ordered segments are short. It is suggested that basic protein may adopt this more ordered structure in myelin and possess activity not apparent in its water-soluble unordered conformation. Retention of its encephalitogenic activity following severe treatment may result from an ability to rapidly refold to the original conformation rather than from this activity being inherent in the unordered form.

Animals↗
PubMed1978

Chymotrypsin inhibitors from hemolymph of the silkworm, Bombyx mori.

Three new protease inhibitors were isolated and purified about 200-fold from hemolymph of silkworm larvae, Bombyx mori, using ion-exchange and affinity chromatography. Two of the three inhibitors were basic proteins (SCI-I had pI 9.4 and SCI-II had pI 9.6) and one was acidic (SCI-III had pI 4.0). The molecular weight of each inhibitor was determined to be 7,000 by the sedimentation equilibrium method. The amino acid composition of the inhibitors were similar except for the contents of Asp, Glu, Ile, Leu, and Lys. Val, His, and Trp were not present in the inhibitors and Met appeared only in SCI-III. The CD spectra of the inhibitors were all similar and indicated a low content of alpha-helical structure (10% at most). Each inhibitor could inhibit the protease and esterase activities of bovine alpha-chymotrypsin at a one-to-one molar ratio, and the dissociation constants were 3.1 X 10(-9)M for SCI-I and II and 1.3 X 10(-8)M for SCI-III. Only SCI-II showed a weak inhibitory activity against bovine trypsin. Subtilisin BPN' and papain were not inhibited by these inhibitors.

Amino Acids↗