Effect of temperature on viscosity properties of some alpha-amino acids in aqueous urea solutions

Viscosities for solutions of glycine, DL-alpha-alanine, DL-alpha-amino-n-butyric acid, DL-valine, DL-leucine and L-serine in 5 mol kg(-1) aqueous urea have been determined at 278.15, 288.15, 298.15 and 308.15 K. The viscosity B-coefficients for the amino acids in the aqueous urea solution have been calculated at different temperatures. The effect of temperature on the B-coefficients is discussed on the basis of the Feakins equation. The contribution of solute to the activation parameters (delta mu0*2, deltaH0*2, deltaS0*2) for viscous flow of the solution have been calculated, together with the Gibbs energy, enthalpy and entropy of transfer for the amino acids from the ground-state solvent to the hypothetical viscous transition state solvent. The contributions of the charged end group (NH3+, COO-) and CH2 groups of the amino acids to B-coefficient and delta mu0*2 have been also estimated using the linear correlations between B-coefficient or delta mu0*2 and the number of carbon atoms in the alkyl chains of the amino acids. All the activation parameters are discussed in terms of the solute-solvent interactions in the ground and transition states.     

Partial molar volumes of some alpha-amino acids in aqueous sodium acetate solutions at 308.15 K

The apparent molar volumes V(2,phi) have been determined for glycine, DL-alpha-alanine, DL-alpha-amino-n-butyric acid, DL-valine and DL-leucine in aqueous solutions of 0.5, 1.0, 1.5 and 2.0 mol kg(-1) sodium acetate by density measurements at 308.15 K. These data have been used to derive the infinite dilution apparent molar volumes V(0)(2,phi) for the amino acids in aqueous sodium acetate solutions and the standard volumes of transfer, Delta(t)V(0), of the amino acids from water to aqueous sodium acetate solutions. It has been observed that both V(0)(2,phi) and Delta(t)V(0) vary linearly with increasing number of carbon atoms in the alkyl chain of the amino acids. These linear correlations have been utilized to estimate the contributions of the charged end groups (NH(3)(+), COO(-)), CH(2) group and other alkyl chains of the amino acids to V(0)(2,phi) and Delta(t)V(0). The results show that V(0)(2,phi) values for (NH(3)(+), COO(-)) groups increase with sodium acetate concentration, and those for CH(2) are almost constant over the studied sodium acetate concentration range. The transfer volume increases and the hydration number of the amino acids decreases with increasing electrolyte concentrations. These facts indicate that strong interactions occur between the ions of sodium acetate and the charged centers of the amino acids. The volumetric interaction parameters of the amino acids with sodium acetate were calculated in water. The pair interaction parameters are found to be positive and decreased with increasing alkyl chain length of the amino acids, suggesting that sodium acetate has a stronger dehydration effect on amino acids which have longer hydrophobic alkyl chains. These phenomena are discussed by means of the co-sphere overlap model.     

Calmodulin binding to the C-terminus of the small-conductance Ca2+-activated K+ channel hSK1 is affected by alternative splicing

We identified three splice variants of hSK1 whose C-terminal structures are determined by the independent deletion of two contiguous nucleotide sequences. The upstream sequence extends 25 bases in length, is initiated by a donor splice site within exon 8, and terminates at the end of the exon. The downstream sequence consists of nine bases that compose exon 9. When the upstream sequence (hSK1(-)(25b)) or both sequences (hSK1(-)(34b)) are deleted, truncated proteins are encoded in which the terminal 118 amino acids are absent. The binding of calmodulin to these variants is diminished, particularly in the absence of Ca2+ ions. The first 20 amino acids of the segment deleted from hSK1(-)(25b) and hSK1(-)(34b) contain a 1-8-14 Ca2+ calmodulin binding motif, and synthetic oligopeptides based on this region bind calmodulin better in the presence than absence of Ca2+ ions. When the downstream sequence (hSK1(-)(9b)) alone is deleted, only the three amino acids A452, Q453, and K454 are removed, and calmodulin binding is not reduced. On the basis of the relative abundance of mRNA encoding each of the four isoforms, the full-length variant appears to account for most hSK1 in the human hippocampus, while hSK1(-)(34b) predominates in reticulocytes, and hSK1(-)(9b) is especially abundant in human erythroleukemia cells in culture. We conclude that the binding of calmodulin by hSK1 can be modulated through alternative splicing.     

Interaction of water vapour with twenty different poly-L-amino acids and their excess hydration in presence of sodium chloride

Using the isopiestic vapour pressure technique, the magnitudes of excess binding of water and NaCl per mole of twenty different poly-L-amino acid residues, respectively in the presence of different bulk molefractions (X2) of NaCl have been evaluated from the mathematical expressions for the Gibbs surface excesses. At certain high ranges of NaCl concentration, the plot of -Gamma1 (2) versus X1/X2 becomes linear, so that moles of water and NaCl, respectively bound per mole of amino acid residue can be evaluated. -Gamma(2)1 is the excess moles of H20 per mole of amino acid residue and X1 and X2 stand for mole fractions of the water and NaCl, respectively in the sample system. Also, using the integrated form of the Gibbs absorption equation, the values of standard free energy change (deltaG(0)) for the excess adsorption of NaCl per kg of poly-L-amino acids have been evaluated. These values are all positive as a result of positive excess hydration of polyamino acids. The standard free energy of excess hydration deltaG(0)hy (equal to -deltaG(0)) is negative due to spontaneous excess hydration of polyamino acid in the presence of a salt.     

Alignment of the peptides derived from acid-catalyzed cleavage of an aspartylprolyl bond in the major internal structural polypeptide of avian retroviruses

The major internal structural polypeptide (p27) of Rous sarcoma virus (RSV), and the analogous polypeptide (P27(0)) OF Rous-associated virus-O (RAV-O), an endogenous virus released spontaneously by some chicken cells) have been cleaved selectively at a single aspartylprolyl peptide bond to yield two fragments. The NH2- and COOH-terminal amino acid sequences of p27 and p27(0) and their mild acid-cleavage fragments have been determined. These results show the existence of an identical cleavage site and a similar NH2- and COOH-terminal amino acid sequence in both the polypeptides. Furthermore they indicate that the difference in the molecular weights of p27 and p27(0) results from an insertion of amino acids in the COOH-terminal peptide of p27(0) rather than a shift in the scission site of the precursor molecule.     

Synthetic, biologically active amphiphilic peptides

Amphiphilic peptides typically consist of a peptide portion that may be 5-25 (or more) amino acids in length. The hydrophobic portion may be a single fatty acid residue, but can also be more elaborate. The main focus of this article lies on the family of synthetic anion binders (SATs) of the general structure (R(1))(2)N-COCH(2)OCH(2)CO-(Aaa)(n)-OR(3). The most-common R(1) group is the octadecyl (C(18)H(37)) group. The most studied peptide sequence in this family is (Gly)(3)-Pro-(Gly)(3), although different sequences (and longer and shorter peptides) have been prepared as well. The C-terminal ester residue providing the most effective anion release from liposomes is heptyl (C(7)H(15)), although many others have been examined. The compound (C(18)H(37))(2)N-COCH(2)OCH(2)CO-(Gly)(3)-Pro-(Gly)(3)-OBn (Bn=benzyl) was found to mediate Cl(-) transport in mouse epithelial cells.     

L-type amino acids stimulate gastric acid secretion by activation of the calcium-sensing receptor in parietal cells

Parietal cells are the primary acid secretory cells of the stomach. We have previously shown that activation of the calcium-sensing receptor (CaSR) by divalent (Ca(2+)) or trivalent (Gd(3+)) ions stimulates acid production in the absence of secretagogues by increasing H(+),K(+)-ATPase activity. When overexpressed in HEK-293 cells, the CaSR can be allosterically activated by L-amino acids in the presence of physiological concentrations of extracellular Ca(2+) (Ca(o)(2+); 1.5-2.5 mM). To determine whether the endogenously expressed parietal cell CaSR is allosterically activated by L-amino acids, we examined the effect of the amino acids L-phenylalanine (L-Phe), L-tryptophan, and L-leucine on acid secretion. In ex vivo whole stomach preparations, exposure to L-Phe resulted in gastric luminal pH significantly lower than controls. Studies using D-Phe (inactive isomer) failed to elicit a response on gastric pH. H(+)-K(+)-ATPase activity was monitored by measuring the intracellular pH (pH(i)) of individual parietal cells in isolated rat gastric glands and calculating the rate of H(+) extrusion. We demonstrated that increasing Ca(o)(2+) in the absence of secretagogues caused a dose-dependent increase in H(+) extrusion. These effects were amplified by the addition of amino acids at various Ca(o)(2+) concentrations. Blocking the histamine-2 receptor with cimetidine or inhibiting system L-amino acid transport with 2-amino-2-norbornane-carboxylic acid did not affect the rate of H(+) extrusion in the presence of L-Phe. These data support the conclusion that amino acids, in conjunction with a physiological Ca(o)(2+) concentration, can induce acid secretion independent of hormonal stimulation via allosteric activation of the stomach CaSR.     

Genetic engineering of the Fusarium solani pisi lipase cutinase for enhanced partitioning in PEG-phosphate aqueous two-phase systems

The Fusarium solani pisi lipase cutinase has been genetically engineered to investigate the influence of C-terminal peptide extensions on the partitioning of the enzyme in PEG-salt based aqueous two-phase bioseparation systems. Seven different cutinase lipase variants were constructed containing various C-terminal peptide extensions including tryptophan rich peptide tags ((WP)(2) and (WP)(4)), positively ((RP)(4)) and negatively ((DP)(4)) charged tags as well as combined tags with tryptophan together with either positively ((WPR)(4)) or negatively ((WPD)(4)) charged amino acids. The modified cutinase variants were stably produced in Escherichia coli as secreted to the periplasm from which they were efficiently purified by IgG-affinity chromatography employing an introduced N-terminal IgG-binding ZZ affinity fusion partner present in all variants. Partitioning experiments performed in a PEG 4000/sodium phosphate aqueous two-phase system showed that for variants containing either (WP)(2) or (WP)(4) peptide extensions, 10- to 70-fold increases in the partitioning to the PEG rich top-phase were obtained, when compared to the wild type enzyme. An increased partitioning was also seen for cutinase variants tagged with both tryptophans and charged amino acids, whereas the effect of solely charged peptide extensions was relatively small. In addition, when performing partitioning experiments from cell disintegrates, the (WP)(4)-tagged cutinase showed a similarly high PEG-phase partitioning, indicating that the effect from the peptide tag was unaffected by the background of the host proteins. Taken together, the results show that the partitioning of the recombinantly produced cutinase model enzyme could be significantly improved by relatively minor genetic engineering and that the effects observed for purified proteins are retained also in an authentic whole cell disintegrate system. The results presented should be of general interest also for the improvement of the partitioning properties of other industrially interesting proteins including bulk enzymes.     

Dissociation constants of protonated methionine species in NaCl media

The sulfur-containing amino acid, methionine, has a role in the physiological environment because of its strong interactions with metals. To understand these interactions of metals with methionine, one needs reliable dissociation constants for the protonated methionine species (NH(3)(+)CH(CH(2)CH(2)SCH(3))COOH; H(2)B(+)). The values of stoichiometric dissociation constants, pK(i)*, for protonated methionine species (H(2)B(+) if H(+)+HB, K(1); HB if H(+)+B(-), K(2)) were determined from potentiometric measurements in NaCl solutions as a function of ionic strength, 0.25-6.0 mol (kg H(2)O)(-1) and temperature (5-45 degrees C). The results were extrapolated to pure water using the Pitzer equations to estimate the activity of H(+), H(2)B(+), HB and B(-) as a function of ionic strength and temperature. The resulting thermodynamic values of K(1) and K(2) were fit to the equations (T/K): ln K(1)=69.0013-3496.58/(T/K)-10.9153 ln (T/K); ln K(2)=116.4162-10638.02/(T/K)-18.0553 ln (T/K) with standard errors of 0.003 and 0.033, respectively, for ln K(1)* and ln K(2)*. Pitzer interaction parameters (lambda(HB-Na) and zeta(HB-Na-Cl)) for the neutral HB were determined from literature data. The Pitzer parameters (beta(0)(H(2)BCl), beta(1)(H(2)BCl) and C(phi)(H(2)BCl)) for the interactions of H(2)B(+) with Cl(-) and Na(+) with and B(2-) (beta(0)(NaB), beta(1)(NaB) and C(phi)(NaB)) were also determined. These coefficients can be used to make reasonable estimates of the activity coefficients of methionine species and the pK(i)(*) for the dissociation of methionine in physiological solutions, composed mostly of NaCl over a wide range of temperature and ionic strength.     

Ternary copper(II) complexes involving 2-(aminomethyl)-benzimidazole and some bio-relevant ligands. Equilibrium studies and kinetics of hydrolysis for glycine methyl ester under complex formation

Formation equilibria of copper(II) complexes of 2-(aminomethyl)-benzimidazole (AMBI) and the ternary complexes Cu(AMBI)L (L = amino acid, amide, dicarboxylic acid or DNA constituents) have been investigated. Ternary complexes of amino acids or amides are formed by a simultaneous mechanism. Amino acids form the complex Cu(AMBI)L, whereas amides form two complex species Cu(AMBI)L and Cu(AMBI)(LH₋₁). The ternary complexes of copper(II) with AMBI and dicarboxylic acids or DNA units are formed by a stepwise mechanism, whereby binding of copper(II) to AMBI is followed by ligation of the dicarboxylic acids or DNA components. The values of Δ log K indicate that the ternary complexes containing aromatic amino acids are significantly more stable than the complexes containing alkyl- and hydroxyalkyl-substituted amino acids. This may be taken as an evidence for a stacking interaction between the aromatic moiety of AMBI and the aromatic side chains of the bio-active ligands. The solid complexes Cu(AMBI)L where L = 1,1-cyclobutanedicarboxylic acid (CBDCA) and malonic acid were separated and identified by elemental analysis and infrared spectroscopy and magnetic moment. The decomposition course and steps for the isolated complexes were analyzed and the kinetic parameters of the non-isothermal decomposition were calculated. The hydrolysis of glycine methyl ester (MeGly) is catalyzed by the Cu(AMBI)²⁺ complex. The kinetic data is fitted assuming that the hydrolysis reaction proceeds in two steps. The first step, involving coordination of the amino acid ester by the amino and carbonyl groups, is followed by rate-determining attack by OH⁻ ion. The second step involves the equilibrium formation of the hydroxo-complex Cu(AMBI)(MeGly)(OH) followed by intramolecular OH⁻ attack.     

Effect of temperature on thrombin- and trypsin-catalyzed hydrolysis of synthetic substrates

A comparative analysis of the temperature effect on the thrombin- and trypsin-catalyzed hydrolysis of synthetic substrates which are derivatives of A(alpha)-chain of fibrinogen has been carried out. The substrates have general formula: Tos-P2-Arg-OCH3 and Tos-P3-P2-Arg-OCH3, where P2-Gly, Val, MeVal; P3 = Gly, Sar. The activation parameters delta G not equal to, delta H not equal to and delta S not equal to are determined. Thrombin is shown to split the most effectively tripeptide containing amino acids sequence Gly-Gly at the subsites of P3 and P2. It is suggested to be caused by an ability of the above compound to take a bent conformation at the active site of thrombin.     

Sublethal effects of copper on the freshwater crab Potamonautes warreni

The mass specific rates of oxygen consumption (M (O(2)) M(b)(-1)), ammonia excretion (M (NH(4)-N) M(b)(-1)) and carbon dioxide production (M (CO(2)) M(b)(-1)) were measured after 7, 14 and 21 days exposure of adult Potamonautes warreni to a sublethal concentration of 1.0 mg Cu l(-1) (15.75 micromol l(-1)). Under control (non-copper-exposed) conditions M (O(2)) M(b)(-1) was 35.7+/-8.5 micromol kg(-1)min(-1) (mean+/-S.D.), M (NH(4)-N) M(b)(-1) 2.92+/-0.26 micromol kg(-1)min(-1) and M (CO(2)) M(b)(-1) 25.6+/-9.0 micromol kg(-1)min(-1). The oxygen:nitrogen (O:N) ratio and respiratory quotient (RQ) were 24.5+/-3.0 and 0.80+/-0.06, respectively. M (O(2)) M(b)(-1) of copper-exposed crabs showed a significant increase after 7 and 14 days, but decreased significantly by 40% after 21 days. From the increased O:N ratio and RQ below 0.7, it is clear that crabs exposed to 1 mg Cul(-1) metabolize lipids during the entire 21-day exposure period. Free fatty acids in the midgut gland were determined by GC-MS, and showed increases of up to 600% in some C14 to C18 fatty acids. It is proposed that the excess lipids inhibit the pyruvate dehydrogenase complex, leading to the acceleration of the gluco- and glyco-neogenic pathways. Increased glyconeogenesis results in elevated glycogen concentrations in all tissues after 21 days. Experiments on acutely exposed P. warreni show increased incorporation of 14C-labelled lactate into glycogen.     

Two-electron reduction of quinones by rat liver NAD(P)H:quinone oxidoreductase: quantitative structure-activity relationships

Mammalian NAD(P)H:quinone oxidoreductase (NQO1, DT-diaphorase, EC 1.6.99.2) catalyzes the two-electron reduction of quinones and plays one of the main roles in the bioactivation of quinoidal drugs. In order to understand the enzyme substrate specificity, we have examined the reactions of rat NQO1 with a number of quinones with available potentials of single-electron (E(1)(7)) reduction and pK(a) of their semiquinones. The hydride transfer potentials (E(7)(H(-))) were calculated from the midpoint potentials of quinones and pK(a) of hydroquinones. Our findings imply that benzo- and naphthoquinones with a van der Waals volume (VdWvol) < or = 200 A(3) are much more reactive than glutathionyl-substituted naphthoquinones, polycyclic quinones, and FMN (VdWvol>200 A(3)) with the same reduction potentials. The entropies of activation (DeltaS(not equal)) in the reduction of "fast" oxidants are equal to -84 to -76 J mol(-1) K(-1), whereas in the reduction of "slow" oxidants Delta S(not equal)=-36 to -11 J mol(-1) K(-1). The large negative Delta S(not equal) in the reduction of fast oxidants may be explained by their better electronic coupling with reduced FAD or the formation of charge-transfer complexes, since fast oxidants bind at the dicumarol binding site, whereas the binding of some slow oxidants outside it has been demonstrated. The reactivity of quinones may be equally well described in terms of the three-step (e(-),H(+),e(-)) hydride transfer, using E(1)(7), pK(a)(QH*), and VdWvol as correlation parameters, or in terms of single-step (H(-)) hydride transfer, using E(7)(H(-)) and VdWvol in the correlation. The analysis of NQO1 reactions with single-electron acceptors and quinones using an "outer-sphere" electron transfer model points to the possibility of a three-step hydride transfer.     

Synthesis, micellar properties, DNA binding and antimicrobial studies of some surfactant-cobalt(III) complexes

A new class of surfactant-cobalt(III) complex ions of the type, cis-[Co(X)(2)(C(14)H(29)NH(2))Cl](2+) (where X=ethylenediamine (en), or 2,2'-bipyridyl (bpy), or 1,10-phenanthroline (phen)) and cis-[Co(trien)(C(14)H(29)NH(2))Cl](2+) (trien=triethylenetetramine) were synthesized and characterized by IR, NMR, UV-visible electronic absorption spectra, elemental analysis and metal analysis. The critical micelle concentration (CMC) values of these surfactant-cobalt(III) complexes in aqueous solution were obtained from conductance measurements. Specific conductivity data (at 298, 308, 318 and 328 K) served for the evaluation of the temperature-dependent CMC and the thermodynamics of micellization (DeltaG(0)(m), DeltaH(0)(m) and DeltaS(0)(m)). Interactions between calf thymus DNA and the surfactant-cobalt(III) complexes in aqueous solution have been investigated by electronic absorption spectroscopy, emission spectroscopy and viscosity measurements. The electrostatic interactions, van der Waals interactions and/or partial intercalative binding have been observed in these systems. The surfactant-cobalt(III) complexes were screened for their antibacterial and antifungal activities against various microorganisms. The results were compared with the standard drugs, Ciprofloxacin and Fluconazole respectively.     

Reaction of a model siderophore with Ni(II), Co(II) and Zn(II) in aqueous solution: kinetics and spectroscopy

A spectroscopic study was performed showing that the [Fe(III)(L(2-))(2)](1-) (L(2-)=dopacatecholate) complex reacts with Ni(II), Co(II) and Zn(II) in an aqueous solution containing S(2)O(3)(2-) resulting in the soluble [M(L(1-))(3)](1-) (L(1-)=dopasemiquinone; M=Ni(II), Co(II) or Zn(II) complex species. The Raman and IR spectra of the [CTA][M(L(1-))(3)] complexes, CTA=hexadecyltrimethylammonium cation, in the solid state were obtained. The kinetic constants for the metal substitution reactions were determined at four different temperatures, providing values for DeltaH(not equal), DeltaS(not equal) and DeltaG(not equal). The reactions were slow (k=10(-11) Ms(-1)) and endothermic. The system investigated can be considered as a simplified model to explain some aspects of siderophore chemistry.     

Different roles for basic and aromatic amino acids in conserved region 2 of Escherichia coli sigma(70) in the nucleation and maintenance of the single-stranded DNA bubble in open RNA polymerase-promoter complexes.

Amino acid residues in region 2 of final sigma(70) have been shown to play an important role in the strand separation step that is necessary for formation of the functional or open RNA polymerase-promoter complex. Here we present a comparison of the roles of basic and aromatic amino acids in the accomplishment of this process, using RNA polymerase bearing alanine substitutions for both types of amino acids in region 2. We determined the effects of the substitutions on the kinetics of open complex formation, as well as on the ability of the RNA polymerase to form complexes with single-stranded DNA, and with forked DNA duplexes carrying a single-stranded overhang consisting of bases in the -10 region. We concluded that two basic amino acids (Lys(414) and Lys(418)) are important for promoter binding and demonstrated distinct roles, at a subsequent step, for two aromatic amino acids (Tyr(430) and Trp(433)). It is likely that these four amino acids, which are close to each other in the structure of final sigma(70), together are involved in the nucleation of the strand separation process.     

The contribution of amino acid region ASP695-TYR698 of factor V to procofactor activation and factor Va function

There is strong evidence that a functionally important cluster of amino acids is located on the COOH-terminal portion of the heavy chain of factor Va, between amino acid residues 680 and 709. To ascertain the importance of this region for cofactor activity, we have synthesized five overlapping peptides representing this amino acid stretch (10 amino acids each, HC1-HC5) and tested them for inhibition of prothrombinase assembly and function. Two peptides, HC3 (spanning amino acid region 690-699) and HC4 (containing amino acid residues 695-704), were found to be potent inhibitors of prothrombinase activity with IC(50) values of approximately 12 and approximately 10 microm, respectively. The two peptides were unable to interfere with the binding of factor Va to active site fluorescently labeled Glu-Gly-Arg human factor Xa, and kinetic analyses showed that HC3 and HC4 are competitive inhibitors of prothrombinase with respect to prothrombin with K(i) values of approximately 6.3 and approximately 5.3 microm, respectively. These data suggest that the peptides inhibit prothrombinase because they interfere with the incorporation of prothrombin into prothrombinase. The shared amino acid motif between HC3 and HC4 is composed of Asp(695)-Tyr-Asp-Tyr-Gln(699) (DYDYQ). A pentapeptide with this sequence inhibited both prothrombinase function with an IC(50) of 1.6 microm (with a K(D) for prothrombin of 850 nm), and activation of factor V by thrombin. Peptides HC3, HC4, and DYDYQ were also found to interact with immobilized thrombin. A recombinant factor V molecule with the mutations Asp(695) --> Lys, Tyr(696) --> Phe, Asp(697) --> Lys, and Tyr(698) --> Phe (factor V(2K2F)) was partially resistant to activation by thrombin but could be readily activated by RVV-V activator (factor Va(RVV)(2K2F)) and factor Xa (factor Va(Xa)(2K2F)). Factor Va(RVV)(2K2F) and factor Va(Xa)(2K2F) had impaired cofactor activity within prothrombinase in a system using purified reagents. Our data demonstrate for the first time that amino acid sequence 695-698 of factor Va heavy chain is important for procofactor activation and is required for optimum prothrombinase function. These data provide functional evidence for an essential and productive contribution of factor Va to the activity of prothrombinase.     

Exceptional pairs of amino acid neighbors in alpha-helices

Amino acids seem to have specific preferences for various locations in alpha-helices. These specific preferences, called singlet local propensity (SLP), have been determined by calculating the preference of occurrence of each amino acid in different positions of the alpha-helix. We have studied the occurrence of amino acids, single or pairs, in different positions, singlet or doublet, of alpha-helices in a database of 343 non-homologous proteins representing a unique superfamily from the SCOP database with a resolution better than 2.5 A from the Protein Data Bank. The preference of single amino acids for various locations of the helix was shown by the relative entropy of each amino acid with respect to the background. Based on the total relative entropy of all amino acids occurring in a single position, the N(cap) position was found to be the most selective position in the alpha-helix. A rigorous statistical analysis of amino acid pair occurrences showed that there are exceptional pairs for which, the observed frequency of occurrence in various doublet positions of the alpha-helix is significantly different from the expected frequency of occurrence in that position. The doublet local propensity (DLP) was defined as the preference of occurrences of amino acid pairs in different doublet positions of the alpha-helix. For most amino acid pairs, the observed DLP (DLP(O)) was nearly equal to the expected DLP (DLP(E)), which is the product of the related SLPs. However, for exceptional pairs of amino acids identified above, the DLP(O) and DLP(E) values were significantly different. Based on the relative values of DLP(O) and DLP(E), exceptional amino acid pairs were divided into two categories. Those, for which the DLP(O) values are higher than DLP(E), should have a strong tendency to pair together in the specified position. For those pairs which the DLP(O) values are less than DLP(E), there exists a hindrance in neighboring of the two amino acids in that specific position of the alpha-helix. These cases have been identified and listed in various tables in this paper. The amount of mutual information carried by the exceptional pairs of amino acids was significantly higher than the average mutual information carried by other amino acid pairs. The average mutual information conveyed by amino acid pairs in each doublet position was found to be very small but non-zero.     

Peptidase specificity characterization of C- and N-terminal catalytic sites of angiotensin I-converting enzyme

Quenched fluorescence peptides were used to investigate the substrate specificity requirements for recombinant wild-type angiotensin I-converting enzyme (ACE) and two full-length mutants bearing a single functional active site (N- or C-domain). We assayed two series of bradykinin-related peptides flanked by o-aminobenzoic acid (Abz) and N-(2,4-dinitrophenyl)ethylenediamine (EDDnp), namely, Abz-GFSPFXQ-EDDnp and Abz-GFSPFRX-EDDnp (X = natural amino acids), in which the fluorescence appeared when Abz/EDDnp are separated by substrate hydrolysis. Abz-GFSPFFQ-EDDnp was preferentially hydrolyzed by the C-domain while Abz-GFSPFQQ-EDDnp exhibits higher N-domain specificity. Internally quenched fluorescent analogues of N-acetyl-SDKP-OH were also synthesized and assayed. Abz-SDK(Dnp)P-OH, in which Abz and Dnp (2,4-dinitrophenyl) are the fluorescent donor-acceptor pair, was cleaved at the D-K(Dnp) bond with high specificity by the ACE N-domain (k(cat)/K(m) = 1.1 microM(-)(1) s(-)(1)) being practically resistant to hydrolysis by the C-domain. The importance of hydroxyl-containing amino acids at the P(2) position for N-domain specificity was shown by performing the kinetics of hydrolysis of Abz-TDK(Dnp)P-OH and Abz-YDK(Dnp)P-OH. The peptides Abz-YRK(Dnp)P-OH and Abz-FRK(Dnp)P-OH which were hydrolyzed by wild-type ACE with K(m) values of 5.1 and 4.0 microM and k(cat) values of 246 and 210 s(-)(1), respectively, have been shown to be excellent substrates for ACE. The differentiation of the catalytic specificity of the C- and N-domains of ACE seems to depend on very subtle variations on substrate-specific amino acids. The presence of a free C-terminal carboxyl group or an aromatic moiety at the same substrate position determines specific interactions with the ACE active site which is regulated by chloride and seems to distinguish the activities of both domains.