Hydrophobic residues 382-386 of antithrombin III, Ala-Ala-Ala-Ser-Thr, serve as the epitope for an antibody which facilitates hydrolysis of the inhibitor by thrombin.

In the presence of a monoclonal antibody raised against the human thrombin-antithrombin III complex, the reaction between thrombin and antithrombin III proceeded to form preferentially a two-chain form of the inhibitor rather than to follow the major pathway of stable acyl complex formation. We thus propose the term "switching antibody" for an antibody that switches the enzyme-inhibitor reaction (Asakura, S., Matsuda, M., Yoshida, N., Terukina, S., and Kihara, H. (1989) J. Biol. Chem. 264, 13736-13739). By analyzing a CNBr fragment of the thrombin-antithrombin III complex that reacts with the antibody we localized the epitope for the antibody to a strongly hydrophobic residue 382-386 peptide segment, Ala-Ala-Ala-Ser-Thr, of the inhibitor, which is also contiguous with a hydrophobic amino acid Ala at its carboxyl terminus. This particular region should be cryptic in nascent antithrombin III, but could have been exposed to provide the reactive site for the antibody at an early stage of the reaction. Thereby a conformational change may have been induced at or near the reactive site of the complex, facilitating hydrolysis of the inhibitor by the enzyme. Interestingly, this hydrophobic region is highly conserved among members of the serpin family.     

Caffeine derivatives of haematin compounds

1. Caffeine reacts with haematin to form a caffeine-haematin compound that has a characteristic absorption spectrum. 2. Graphical analysis of the titration of haematin with caffeine shows that 2mol.prop. of caffeine split the dimeric haematin. 3. Thermodynamic parameters suggest that the reaction involves the making and breaking of hydrophobic bonds. 4. Graphical analysis shows dimeric haem to be split by 2mol.prop. of caffeine to yield a compound with an unusual multibanded absorption in the Soret region. 5. It is postulated that the linkage between the haem groups of dimeric haem and the haematin groups of dimeric haematin is essentially hydrophobic in nature.     

Prebiotic phosphate: a problem insoluble in water ? ]

It is well-known that in water phosphate readily reacts with calcium, precipitating as insoluble apatite. How phosphorus could have been available for prebiotic reactions is still an open problem. We suggest that phosphorus-containing compounds might have accumulated in a hydrophobic medium, since the absence of calcium ions would have prevented them from precipitating as apatite. Hydrophobic compounds may have been synthesized on the early Earth through the polymerization of methane or through Fischer-Tropsch-type reactions. Moreover, hydrophobic compounds would have been delivered to the early Earth by extraterrestrial infall. In previous articles (Morchio and Traverso [1999], Morchio et al. [2001]) we suggested that such hydrophobic material would have formed a hydrophobic layer on the surface of the sea, which would have provided an environment thermodynamically more suitable than water for the concentration and polymerization of organic molecules fundamental to life, particularly amino acids and (pyrimidine) bases. It may be hypothesized that elemental phosphorus or phosphorus-containing compounds (such as phosphite) deriving from volcanic eruptions would have ended up raining down into the hydrophobic layer, accumulating due to the absence of calcium ions, in an environment protected against hydrolysis. Phosphorus-containing compounds might have interacted with hydrophobic molecules in the layer giving rise to polymers. In particular, phosphite might have reacted with the hydrophobic amino acids, giving rise to phosphoamino acids, which, in turn, might have interacted with pyrimidine bases (relatively abundant in the layer) giving rise to peptides and oligonucleotide-like polymers. Indeed, it has been experimentally shown (Zhou et al. [1996]) that, in an anhydrous organic medium (pyridine), dialkilphosphite reacts with amino acids to form phosphoamino acids, which interact with pyrimidine nucleosides to give nucleotides, short oligonucleotides and phosphoryl peptides.     

Beta-Ketoacyl-acyl carrier protein synthetase. Characterization of the acyl-enzyme intermediate.

Beta-Ketoacyl-acyl carrier protein (ACP) synthetase catalyzes the condensation reaction of fatty acid synthesis in Escherichia coli. The homogeneous enzyme reacts with hexanoyl-CoA to form hexanoyl-enzyme which was isolated and characterized. Hexanoyl-enzyme contains 2 mol of hexanoate/mol of enzyme (molecular weight 66,000); it is liable at alkaline pH, and it reacts with neutral hydroxylamine to form hexanoyl hydroxamic acid. Hexanoate was cleaved from the enzyme when hexanoyl-enzyme was subjected to performic acid oxidation. These properties indicate that hexanoyl-enzyme is a thioester. Studies of the circular dichroism spectra of fully acylated and nonacylated forms of the enzyme indicated that the secondary structure of the enzyme is relatively unperturbed by the presence of the hexanoyl groups. An alpha helical content of 65% was estimated for the enzyme from the circular dichroism spectrum. Hexanoyl-enzyme is active in both partial reactions that comprise the beta-ketoacyl-ACP synthetase reaction; it reacts with ACP to form hexanoyl-ACP and with malonyl-ACP to form beta-ketooctanoyl-ACP. Although the hexanoate of hexanoyl-enzyme is transferred very rapidly to ACP, the physiological acceptor in this reaction, it is also transferred very slowly to CoA, dithiothreitol, and 2-mercaptoethanol, indicating that the enzyme can react nonspecifically with a number of unrelated mercaptans.     

Multiple pathways of the reaction of 2,2-diphenyl-1-picrylhydrazyl radical (DPPH·) with (+)-catechin: evidence for the formation of a covalent adduct between DPPH· and the oxidized form of the polyphenol

The pathways of the reaction of 2,2-diphenyl picrylhydrazyl radicals (DPPH·) with (+)-catechin were studied in alcoholic solvents. The reaction mixtures were analysed by using reversed-phase liquid chromatography (HPLC) and electrospray ionization mass spectrometry (ESI-MS). The intermediate o-quinone of catechin, yellow dimers, trimers and, interestingly, an adduct of the oxidized form of catechin with DPPH radicals were identified. The mass of this adduct was 681 Da, suggesting that one molecule of the DPPH radical complexes with the oxidized form of catechin. It is concluded that once the intermediate o-quinone is formed, the reaction proceeds in two pathways, either the o-quinone reacts with catechin to form a hydrophilic dimer (type B), which is further oxidized to hydrophobic dimers (type A) and consequently to oligomers of higher molecular weights; or the A-ring of the o-quinone is further oxidized by a DPPH radical and that this oxidized intermediate then reacts with another DPPH radical to form the observed adduct. The identification of the latter mechanism could explain the contradictory results reported in the literature for the reaction of polyphenols with DPPH radicals.     

Reactivity of ubiquinone and ubiquinol with superoxide and the hydroperoxyl radical: implications for in vivo antioxidant activity

Endogenous ubiquinones (UQ) such as coenzyme Q(10) are essential electron carriers in the mitochondrial respiratory chain, and the reduced ubiquinol form (UQH(2)) is a chain-breaking antioxidant, decreasing oxidative damage caused by lipid peroxidation within mitochondria. Consequently, exogenous UQ are used as therapies to decrease mitochondrial oxidative damage. The proximal radical produced during mitochondrial oxidative stress is superoxide (O(2)(.-)) and the reaction between UQ and O(2)(.-) to form the ubisemiquinone radical anion (UQ(.-)) may also be important for the scavenging of O(2)(.-) by exogenous UQ. The situation in vivo is that many UQ are predominantly located in the hydrophobic membrane core, from which O(2)(.-) will be excluded but its conjugate acid, HOO(.), can enter. The reactivity of UQ or UQH(2) with HOO(.) has not been reported previously. Here a pulse radiolysis study on the reactions between UQ/UQH(2) and O(2)(.-)/HOO(.) in water and in solvent systems mimicking the surface and core of biological membranes has been undertaken. O(2)(.-) reacts very rapidly with UQ, suggesting that this may contribute to the scavenging of O(2)(.-) in vivo. In contrast, UQH(2) reacts relatively slowly with HOO(.), but rapidly with other oxygen- and carbon-centered radicals, indicating that the antioxidant role of UQH(2) is mainly in preventing lipid peroxidation.     

Requirements for Sod Mimics Operating In Vitro to Work Also In Vivo

When an efficient SOD mimic operating in vitro is introduced into cells, the following requirements are needed in order that this compound will catalyze O^?₂ dismutation efficiently: it should be non toxic, stable, has a long metabolic half life, does not form ternary complexes with the cell components, its reduced form reacts slowly with molecular oxygen. should be able to cross cell membranes and also to reach lipophilic or hydrophobic regions. Thus, it seems that finding an efficient compound that has high SOD-like activity in vivo will not be easily achieved.     

Conformational flexibility and structure of creatine kinase

The structural flexibility of creatine kinase has been investigated with the covalent hydrophobic probe 2-[4′-(2″-iodoacetamido) phenyl] aminonaphthalene-6-sulfonic acid (IAANS) which reacts at vastly different rates with the two subunits to give a protein conjugate with fluorescence characteristic of reaction with a site in a hydrophobic cleft. Binding of purine nucleotides greatly enhances the probe fluorescence while pyrimidine nucleotides quench the fluorescence. Small anions bind to nucleotide-free creatine kinase near the location of the transferable phosphoryl group and quench both the IAANS fluorescence of modified creatine kinase and the tryptophan fluorescence of native creatine kinase. Chloride and nitrate non-competitively inhibit MgADP binding both with and without creatine. Fluorescence energy transfer demonstrates that the active sites of creatine kinase are well separated and become further apart after the nucleotide-induced conformational change.     

The origin of enantioselectivity in aldolase antibodies: crystal structure, site-directed mutagenesis, and computational analysis

Catalytic aldolase antibodies, generated by reactive immunization, catalyze the aldol reaction with the efficiency of natural enzymes, but accept a much broader range of substrates. Two separate groups of aldolase antibodies that catalyze the same aldol reactions with antipodal selectivity were analyzed by comparing their amino acid sequences with their crystal structures, site-directed mutagenesis data, and computational docking of the transition states of the aldol reaction. The crystal structure of aldolase antibody 93F3 Fab' at 2.5A resolution revealed a combining site with two lysine residues, including LysL89 that reacts to form the covalent enamine intermediate. In contrast, antibody 33F12 has one active site lysine, LysH93. The reactive lysine residues in each group of antibodies are differentially located on the heavy and light chain variable regions in pseudo-symmetric opposite orientations, but both within highly hydrophobic environments. Thus, the defining feature for the observed enantioselectivities of these aldolase antibody catalysts is the respective location and relative disposition of the reactive lysine residues within the active sites of these catalysts.     

Morphogenetic behavior of tropical marine yeast Yarrowia lipolytica in response to hydrophobic substrates

The morphogenetic behavior of a tropical marine Yarrowia lipolytica strain on hydrophobic substrates was studied. Media containing coconut oil or palm kernel oil (rich in lauric and myristic acids) prepared in distilled water or seawater at a neutral pH supported 95% of the cells to undergo a transition from the yeast form to the mycelium form. With potassium laurate, 51% of the cells were in the mycelium form, whereas with myristate, 32% were in the mycelium form. However, combinations of these two fatty acids in proportions that are present in coconut oil or palm kernel oil enhanced the mycelium formation to 65%. The culture also produced extracellular lipases during the morphogenetic change. The yeast cells were found to attach to the large droplets of the hydrophobic substrates during the transition, while the mycelia were associated with the aqueous phase. The alkane-grown yeast partitioned more efficiently in the hydrophobic phases when compared with the coconut oil-grown mycelia. A fatty acid analysis of the mycelial form revealed the presence of lauric acid in addition to the long-chain saturated and unsaturated fatty acids observed in the yeast form. The mycelia underwent a rapid transition to the yeast form with n-dodecane, a medium-chain aliphatic hydrocarbon. Thus, the fungus displayed a differential behavior towards the two types of saturated hydrophobic substrates.     

Naphthalene Black Staining of Granules of Eosinophilic Granulocytes: Proposed Mechanism of Action Using Chemical Blockade and Computer Graphics

Histochemical staining of the granules of eosinophilic granulocytes and subsequent blockade of the reaction by alkaline benzil was strongly suggestive that in its purified form, the diazo dye naphthalene black reacts with tissue sites containing high concentrations of arginine residues. Computer graphics modelling indicated that the sulfonate group of the dye reacts electrostatically with the guanidino functional group of arginine. This acid-base type reaction likely has a stoichiometric ratio of 2:1 in favor of the amino acid.     

Yeast cystathionine beta-synthase reacts with L-allothreonine, a non-natural substrate, and L-homocysteine to form a new amino acid, 3-methyl-L-cystathionine

Our studies of the reaction mechanism of cystathionine beta-synthase from yeast (Saccharomyces cerevisiae) are facilitated by the spectroscopic properties of the pyridoxal phosphate coenzyme. The enzyme catalyzes the reaction of L-serine with L-homocysteine to form L-cystathionine through a series of pyridoxal phosphate intermediates. In this work, we explore the substrate specificity of the enzyme by use of substrate analogues combined with kinetic measurements under pre-steady-state conditions and with circular dichroism and fluorescence spectroscopy under steady-state conditions. Our results show that L-allothreonine, but not L-threonine, serves as an effective substrate. L-Allothreonine reacts with the pyridoxal phosphate cofactor to form a stable 3-methyl aminoacrylate intermediate that absorbs maximally at 446 nm. The rapid-scanning stopped-flow results show that the binding of L-allothreonine as the external aldimine is faster than formation of the 3-methyl aminoacrylate intermediate. The 3-methyl aminoacrylate intermediate reacts with L-homocysteine to form a new amino acid, 3-methyl-L-cystathionine, which was characterized by nuclear magnetic resonance spectroscopy. This new amino acid may be a useful analogue of L-cystathionine.     

4,4(')-Dianilino-1,1(')-binaphthyl-5,5(')-disulfonate: report on non-beta-sheet conformers of Alzheimer's peptide beta(1-40)

The venerable fluorescent probe of protein hydrophobic regions, 4,4(')-dianilino-1,1(')-binaphthyl-5,5(')-disulfonate (bis-ANS), unexpectedly increases in fluorescence with soluble beta(1-40) in acidic buffer solutions but reacts weakly with amyloid fibrils while other hydrophobic probes react with the fibrils. CD analysis correlates reaction with the probe with random coil/mixed conformations and alpha-helical forms of beta(1-40) in buffer solutions but less so with soluble beta-sheet forms or amyloid fibrils. The kinetics of the fluoroalcohol-induced interconversion of conformers can be followed by changes in bis-ANS fluorescence. Formation of the beta-sheet form in aqueous buffer is limited by a slow component (minutes) while fluoroalcohol-promoted changes between beta-sheet and alpha-helix occur over seconds. Variants of beta(1-40) such as beta(1-42) or the Dutch E22Q mutation of beta(1-40) and fragments beta(1-28), beta(12-28), beta(10-20 amide), and beta(10-35 amide) react with bis-ANS under conditions that do not support fibril formation. Primary amino acid sequence is important as beta(1-11) does not cause bis-ANS fluorescence while beta(1-16) does, but hydrophobicity is not as beta(25-35) and beta(15-20 amide) are unreactive. bis-ANS is a useful biophysical tool for characterizing particular, but not all, soluble Abeta conformations distinct from the fibrillar form of amyloid peptides detected by Thioflavin T.     

Proteolytic Cleavage of Subunits of the Nucleocapsid of the Paramyxovirus Simian Virus 5

The protein subunits of the nucleocapsid of the parainfluenza virus simian virus 5 isolated from infected cells after dispersion with trypsin, chymotrypsin, or ficin are cleaved proteolytically. The molecular weights of the subunits which result from cleavage depend on the enzyme used, but are around 43,000, compared to the native subunit of 61,000. In most instances cleavage of the subunit appears to be due to the protease used to disperse the cell, and follows cell disruption. Nucleocapsids composed of native, uncleaved subunits can frequently be obtained from infected cells dispersed without a proteolytic enzyme; however, cleavage occasionally occurs even under those conditions, indicating that cellular proteases can at times cleave this protein. Nucleocapsids containing uncleaved subunits can be isolated from cells persistently infected with simian virus 5, indicating that persistent infection is not invariably associated with intracellular cleavage of this protein. Nucleocapsids composed of native subunits are hydrophobic, whereas those composed of the cleaved subunit can be dispersed in aqueous solution. It is suggested that the portion of the molecule removed by cleavage may be responsible for a specific interaction during virus assembly between the nucleocapsid and those areas of plasma membrane which contain the non-glycosylated viral membrane protein, which is also hydrophobic. An amino acid analysis of native and cleaved subunits has been done. The portion of the subunit removed by cleavage does not have a high proportion of hydrophobic residues, suggesting that those present are arranged together to form a hydrophobic domain.The N termini of both the native and cleaved subunits are blocked. This suggests that the portion of the molecule which is externally disposed and removed by cleavage contains the C terminus, and the cleaved subunit which reacts with the viral RNA contains the N terminus.     

Multiple pathways of the reaction of 2,2-diphenyl-1-picrylhydrazyl radical (DPPH and the oxidized form of the polyphenol

The pathways of the reaction of 2,2-diphenyl picrylhydrazyl radicals (DPPH) with (+)-catechin were studied in alcoholic solvents. The reaction mixtures were analysed by using reversed-phase liquid chromatography (HPLC) and electrospray ionization mass spectrometry (ESI-MS). The intermediate o-quinone of catechin, yellow dimers, trimers and, interestingly, an adduct of the oxidized form of catechin with DPPH radicals were identified. The mass of this adduct was 681 Da, suggesting that one molecule of the DPPH radical complexes with the oxidized form of catechin. It is concluded that once the intermediate o-quinone is formed, the reaction proceeds in two pathways, either the o-quinone reacts with catechin to form a hydrophilic dimer (type B), which is further oxidized to hydrophobic dimers (type A) and consequently to oligomers of higher molecular weights; or the A-ring of the o-quinone is further oxidized by a DPPH radical and that this oxidized intermediate then reacts with another DPPH radical to form the observed adduct. The identification of the latter mechanism could explain the contradictory results reported in the literature for the reaction of polyphenols with DPPH radicals.     

Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.

We present a model for the hydrophobic interaction in globular proteins that is based entirely on an analysis of known X-ray structures. This structure-derived hydrophobic force is identified as the strongest among the non-covalent interactions that stabilize native folds. The functional form of the hydrophobic interaction is found to be linear, corresponding to a constant force along the observable distance range (5 to 70 A). The parameters of the hydrophobic amino acid pair potentials yield a structure-derived hydrophobicity scale that correlates strongly with scales derived by a variety of complementary approaches. We demonstrate that the structure-derived hydrophobic interaction alone is able to distinguish a substantial number of native conformations from a large pool of misfolded structures.     

Formation of a TBA reaction product from crown ether in the presence of KO2.

Potassium superoxide (KO2), which can be dissolved in dimethyl sulfoxide containing crown ether, has been used as a source of O2-. for superoxide reaction systems. We have found that crown ether reacts with thiobarbituric acid (TBA) in the presence of KO2 to form a red pigment, which is a well-known reaction product of lipoperoxide.     

The crystal structure of the 1:1 complex of beta-cyclodextrin with trans-cinnamic acid

The crystal structure of the 1:1 complex of beta-cyclodextrin (cyclomaltoheptaose) with trans-cinnamic acid was studied by X-ray diffraction. Two beta-cyclodextrin molecules related by a twofold crystal axis form dimers in the hydrophobic cavity of which, two guest molecules are entirely buried. The complex crystallizes in the monoclinic C2 space group with channel-type molecular packing. The oxygen atoms of the carboxylate group of the trans-cinnamic acid molecule form strong hydrogen bonds with two water molecules lying in the interdimeric space of the hydrophobic channel.     

Crystal structures of branched-chain amino acid aminotransferase complexed with glutamate and glutarate: true reaction intermediate and double substrate recognition of the enzyme

Branched-chain amino acid aminotransferase (BCAT), which has pyridoxal 5'-phosphate as a cofactor, is a key enzyme in the biosynthetic pathway of hydrophobic amino acids (leucine, isoleucine, and valine). The enzyme reversibly catalyzes the transfer of the amino group of a hydrophobic amino acid to 2-oxoglutarate to form a 2-oxo acid and glutamate. Therefore, the active site of BCAT should have a mechanism to enable recognition of an acidic amino acid as well as a hydrophobic amino acid (double substrate recognition). The three-dimensional structures of Escherichia coli BCAT (eBCAT) in complex with the acidic substrate (glutamate) and the acidic substrate analogue (glutarate) have been determined by X-ray diffraction at 1.82 and 2.15 A resolution, respectively. The enzyme is a homo hexamer, with the polypeptide chain of the subunit folded into small and large domains, and an interdomain loop. The eBCAT in complex with the natural substrate, glutamate, was assigned as a ketimine as the most probable form based upon absorption spectra of the crystal complex and the shape of the residual electron density corresponding to the cofactor-glutamate bond structure. Upon binding of an acidic substrate, the interdomain loop approaches the substrate to shield it from the solvent region, as observed in the complex with a hydrophobic substrate. Both the acidic and the hydrophobic side chains of the substrates are bound to almost the same position in the pocket of the enzyme and are identical in structure. The inner side of the pocket is mostly hydrophobic to accommodate the hydrophobic side chain but has four sites to coordinate with the gamma-carboxylate of glutamate. The mechanism for the double substrate recognition observed in eBCAT is in contrast to those in aromatic amino acid and histidinol-phosphate aminotransferases. In an aromatic amino acid aminotransferase, the acidic side chain is located at the same position as that for the aromatic side chain because of large-scale rearrangements of the hydrogen bond network. In the histidinol-phosphate aminotransferase, the acidic and basic side chains are located at different sites and interact with different residues of the disordered loop.     

Engineering, expression, and purification of “soluble” human cytochrome P45017α and its functional characterization

To engineer a "soluble" form of membrane-bound cytochrome P45017alpha (CYP17)--a key enzyme in steroid hormone biosynthesis--in the present work we have built a computer model of the tertiary structure of the hemeprotein, identified the surface hydrophobic amino acid residues, substituted these residues for more hydrophilic ones, and expressed and purified hydrophilized forms of CYP17. We have constructed and purified the following mutant forms of human CYP17: CYP17dH (CYP17 with deleted hydrophobic N-terminal sequence (Delta(23))) and CYP17mod (CYP17dH with substituted cluster of hydrophobic amino acid residues in the region of the FG-loop). Removal of the N-terminal sequence responsible for interaction with the membrane does not dramatically change the association of the protein with the membrane. However, CYP17mod containing hydrophilic FG-loop is mostly localized in the cytosolic fraction. Thus, in the present work we for the first time engineered a "soluble" form of the usually membrane-bound human CYP17 that is not bound to membrane. The expression degree of CYP17mod is approximately 900 nmol/liter of culture. The hemeprotein can be purified to apparent homogeneity without using detergents at any purification step. It is shown that replacement of hydrophobic amino acid residues in the FG-loop region does not change the metabolic profile during hydroxylation of steroids that is characteristic for wild type CYP17. Besides, the modification of the hemeprotein does not affect the affinity of CYP17 to steroid substrates. The engineered "soluble" form of human CYP17 is used as a subject for crystallization of the hemeprotein.