Bulky Amino Acid Residues Research Articles

Dimethylthiazolidine Carboxylic Acid as a Rigid P3 Unit in Inhibitors of Serine Proteases: Application to Two Targets†

Serine proteases are a very large class of enzymes, many of which represent important targets for therapeutic agents against a wide variety of disease states. The similarity in active site architecture for these proteases has often allowed inhibitor design strategies for a particular target to be successfully applied to other enzymes in the class. In many cases, the presence of a bulky P3 amino acid residue in peptide-based inhibitors is central to conferring an extended peptide conformation, critical to binding of the ligands to serine protease active sites. The dimethylthiazolidine carboxylic acid 'residue' was found to be effective as a novel P3 replacement in peptidomimetic inhibitors of two distinct serine proteases, the hepatitis C NS3 protease and the human cytomegalovirus maturational protease. An array of NMR methods was used to confirm that the dimethylthiazolidine carboxylic acid unit indeed confers conformational and dynamic properties very similar to that of the rigidified parent structures.

Effect of mutagenesis at the region upstream from the G(Q/E) motif of three types of geranylgeranyl diphosphate synthase on product chain-length

(All-E) geranylgeranyl diphosphate synthases have been classified into three types based on the characteristic sequences around the first aspartate rich motif, which is highly conserved among the enzymes. In type I geranylgeranyl diphosphate synthases, which consist of archaeal enzymes, a bulky amino acid residue at the 5th position upstream from the motif plays a main role in the product determination, by blocking further elongation of prenyl chain as the bottom of the reaction cavity. On the other hand, type III geranylgeranyl diphosphate synthases, which consist of the enzymes from eukaryotes except for plants, use a bulky amino acid residue at the 2nd position upstream from the conserved G(Q/E) motif for product chain-length determination. Thus we introduced mutations into the region upstream from the G(Q/E) motif of geranylgeranyl diphosphate synthases of the three different types to confirm the importance of the region for the product chain-length determination. The results of the mutational analyses indicated that not only the 2nd but also the 3rd position upstream from the G(Q/E) motif is involved in the product chain-length determination mechanism in types I and III geranylgeranyl diphosphate synthases, while the amino acid substitution in this region did not affect the chain-length of the products of type II geranylgeranyl diphosphate synthase, which consist of the enzymes from bacteria and plants. The region upstream from the G(Q/E) motif possibly contributes to the product determination in the wide range of geranylgeranyl diphosphate synthases, as well as that around the first aspartate rich motif.

Modulation of Substrate Preference ofThermusMaltogenic Amylase by Mutation of the Residues at the Interface of a Dimer

To elucidate the relationship between the substrate size and geometric shape of the catalytic site of Thermus maltogenic amylase, Gly50, Asp109, and Val431, located at the interface of the dimer, were replaced with bulky amino acids. The k(cat)/K(m) value of the mutant for amylose increased significantly, whereas that for amylopectin decreased as compared to that of the wild-type enzyme. Thus, the substituted bulky amino acid residues modified the shape of the catalytic site, such that the ability of the enzyme to distinguish between small and large molecules like amylose and amylopectin was enhanced.

Unique Peroxidase Reaction Mechanism in Prostaglandin Endoperoxide H Synthase-2: COMPOUND I IN PROSTAGLANDIN ENDOPEROXIDE H SYNTHASE-2 CAN BE FORMED WITHOUT ASSISTANCE BY DISTAL GLUTAMINE RESIDUE

Prostaglandin-endoperoxide H synthase-2 (PGHS-2) shows peroxidase activity to promote the cyclooxygenase reaction for prostaglandin H2, but one of the highly conserved amino acid residues in peroxidases, distal Arg, stabilizing the developing negative charge on the peroxide through a hydrogen-bonding interaction, is replaced with a neutral amino acid residue, Gln. To characterize the peroxidase reaction in PGHS-2, we prepared three distal glutamine (Gln-189) mutants, Arg (Gln-->Arg), Asn (Gln-->Asn), and Val (Gln-->Val) mutants, and examined their peroxidase activity together with their structural characterization by absorption and resonance Raman spectra. Although a previous study (Landino, L. M., Crews, B. C., Gierse, J. K., Hauser, S. D., and Marnett, L. (1997) J. Biol. Chem. 272, 21565-21574) suggested that the Gln residue might serve as a functionally equivalent residue to Arg, our current results clearly showed that the peroxidase activity of the Val and Asn mutants was comparable with that of the wild-type enzyme. In addition, the Fe-C and C-O stretching modes in the CO adduct were almost unperturbed by the mutation, implying that Gln-189 might not directly interact with the heme-ligated peroxide. Rather, the peroxidase activity of the Arg mutant was depressed, concomitant with the heme environmental change from a six-coordinate to a five-coordinate structure. Introduction of the bulky amino acid residue, Arg, would interfere with the ligation of a water molecule to the heme iron, suggesting that the side chain volume, and not the amide group, at position 189 is essential for the peroxidase activity of PGHS-2. Thus, we can conclude that the O-O bond cleavage in PGHS-2 is promoted without interactions with charged side chains at the peroxide binding site, which is significantly different from that in typical plant peroxidases.

Purification of serine carboxypeptidase from the hepatopancreas of Japanese common squid Todarodes pacificus and its application for elimination of bitterness from bitter peptides

An acidic serine carboxypeptidase (CPase Tpa) from the hepatopancreas of Japanese common squid Todarodes pacificus was purified. Purified CPase Tpa had a molecular mass of 36 kDa on sodium dodecylsulfate-polyacrylamide gel electrophoresis, and an isoelectric point of 6.0. The optimum pH of CPase Tpa was pH 4.0. In investigating the specificity of CPase Tpa for several peptide substances, it was found that peptides with hydrophobic or bulky amino acid residues at the P1 position reacted well. The enzymatic activity was almost completely inhibited by p-chloromercuribenzoic acid, monoiodoacetic acid, diisopropylfluorophosphate and HgCl2. This is the basis for its grouping in the serine carboxypeptidase family (EC 3. 4. 16. 5). The substrate specificity of CPase Tpa can be used to eliminate the bitterness of bitter peptides. In this study, the bitterness-reductive effect using bitter peptides prepared by hydrolyzing soy protein, casein and corn gluten with pepsin or trypsin was tested. The bitterness of soy peptide digested with pepsin was completely eliminated by treatment with CPase Tpa, whereas the bitterness of casein digested with trypsin and corn peptide digested with pepsin were somewhat less efficient. On the basis of these results, it is anticipated that CPase Tpa would be effective in eliminating the bitterness of some bitter peptides.

Site-specific Conformational Studies of Prion Protein (PrP) Amyloid Fibrils Revealed Two Cooperative Folding Domains within Amyloid Structure

Despite the ability of most proteins to form amyloid, very little is know about amyloid fibril structures and the factors that govern their stability. Using amyloid fibrils produced from full-length prion protein (PrP), we describe a reliable approach for determining both site-specific and global conformational stability of the fibrillar form. To measure site-specific stability, we produced six variants of PrP by replacing the residues at positions 88, 98, 127, 144, 196, and 230 with cysteine, labeled the new cysteines with the fluorescent dye acrylodan, and investigated their conformational status within the amyloid form in guanidine hydrochloride-induced denaturation experiments. We found that the fibrils labeled at positions 127, 144, 196, and 230 displayed cooperative unfolding and showed a very high C1/2 value similar to that observed for the global unfolding of the amyloid structure. The unfolding at residue 98 was also cooperative; however, it showed a C1/2 value substantially lower than that of global unfolding, whereas the unfolding of fibrils labeled at residue 88 was non-cooperative. These data illustrate that there are at least two independent cooperative folding domains within the amyloid structure of the full-length PrP. In addition, kinetic experiments revealed only a partial overlap between the region that constituted the fibrillar cross-beta core and the regions that were involved in nucleation. This result illustrates that separate PrP regions accounted for the nucleation and for the formation of the conformationally most stable fibrillar core.

Quantitative structure‐activity relationship study of bitter di‐ and tri‐peptides including relationship with angiotensin I‐converting enzyme inhibitory activity

Bitterness represents a major challenge in industrial application of food protein hydrolysates or bioactive peptides and is a major factor that controls the flavor of formulated therapeutic products. The aim of this work was to apply quantitative structure-activity relationship modeling as a tool to determine the type and position of amino acids that contribute to bitterness of di- and tri-peptides. Datasets of bitter di- and tri-peptides were constructed using values from available literature, followed by modeling using partial least square (PLS) regression based on the three z-scores of 20 coded amino acids. Prediction models were validated using cross-validation and permutation tests. Results showed that a single-component model could explain 52 and 50% of the Y variance (bitterness threshold) of bitter di- and tri-peptides, respectively. Using PLS regression coefficients, it was determined that hydrophobic amino acids at the carboxyl-terminus and bulky amino acid residues adjacent to the carboxyl terminal are the major determinants of the intensity of bitterness of di- and tri-peptides. However, there was no significant (p > 0.05) correlation between bitterness of di- and tri-peptides and their angiotensin I-converting enzyme-inhibitory properties.

Crystal Structure of Type-III Geranylgeranyl Pyrophosphate Synthase from Saccharomyces cerevisiae and the Mechanism of Product Chain Length Determination

Geranylgeranyl pyrophosphate synthase (GGPPs) catalyzes a condensation reaction of farnesyl pyrophosphate with isopentenyl pyrophosphate to generate C(20) geranylgeranyl pyrophosphate, which is a precursor for carotenoids, chlorophylls, geranylgeranylated proteins, and archaeal ether-linked lipid. For short-chain trans-prenyltransferases that synthesize C(10)-C(25) products, bulky amino acid residues generally occupy the fourth or fifth position upstream from the first DDXXD motif to block further elongation of the final products. However, the short-chain type-III GGPPs in eukaryotes lack any large amino acid at these positions. In this study, the first structure of type-III GGPPs from Saccharomyces cerevisiae has been determined to 1.98 A resolution. The structure is composed entirely of 15 alpha-helices joined by connecting loops and is arranged with alpha-helices around a large central cavity. Distinct from other known structures of trans-prenyltransferases, the N-terminal 17 amino acids (9-amino acid helix A and the following loop) of this GGPPs protrude from the helix core into the other subunit and contribute to the tight dimer formation. Deletion of the first 9 or 17 amino acids caused the dissociation of dimer into monomer, and the Delta(1-17) mutant showed abolished enzyme activity. In each subunit, an elongated hydrophobic crevice surrounded by D, F, G, H, and I alpha-helices contains two DDXXD motifs at the top for substrate binding with one Mg(2+) coordinated by Asp(75), Asp(79), and four water molecules. It is sealed at the bottom with three large residues of Tyr(107), Phe(108), and His(139). Compared with the major product C(30) synthesized by mutant H139A, the products generated by mutant Y107A and F108A are predominantly C(40) and C(30), respectively, suggesting the most important role of Tyr(107) in determining the product chain length.

High-resolution powder diffraction study of purple membrane with a large Guinier-type camera

X-ray diffraction patterns from a film of oriented purple membranes, which comprise two-dimensional crystals of bacteriorhodopsin (BR) trimers, were recorded with a 1 m-pathlength Guinier-type camera at SPring-8 BL40B2. A well focused X-ray beam and a camera with a high angular resolution of 0.024 degrees enabled a powder diffraction profile with very sharp and well separated peaks to be obtained up to a resolution of 2.3 A. Using integrated diffraction intensities up to a Bragg spacing of 4.2 A, a cluster of bulky amino acid residues and the head group of the BR chromophore are apparent in the electron density map projected along the membrane normal. Thus, a combination of synchrotron X-rays and large Guinier camera can be used for analyzing the conformational changes of BR in the intact state. In addition, the method might be extended to the structural analysis of film materials composed of two-dimensional arrays of nanoparticles.

Catalytic Residues and Substrate Specificity of Recombinant Human Tripeptidyl Peptidase I (CLN2)

Tripeptidyl peptidase I (TTP-I), also known as CLN2, a member of the family of serine-carboxyl proteinases (S53), plays a crucial role in lysosomal protein degradation and a deficiency in this enzyme leads to fatal neurodegenerative disease. Recombinant human TPP-I and its mutants were analyzed in order to clarify the biochemical role of TPP-I and its mechanism of activity. Ser280, Glu77, and Asp81 were identified as the catalytic residues based on mutational analyses, inhibition studies, and sequence similarities with other family members. TPP-I hydrolyzed most effectively the peptide Ala-Arg-Phe*Nph-Arg-Leu (*, cleavage site) (k(cat)/K(m) = 2.94 microM(-1).s(-1)). The k(cat)/K(m) value for this substrate was 40 times higher than that for Ala-Ala-Phe-MCA. Coupled with other data, these results strongly suggest that the substrate-binding cleft of TPP-I is composed of only six subsites (S(3)-S(3)'). TPP-I prefers bulky and hydrophobic amino acid residues at the P(1) position and Ala, Arg, or Asp at the P(2) position. Hydrophilic interactions at the S(2) subsite are necessary for TPP-I, and this feature is unique among serine-carboxyl proteinases. TPP-I might have evolved from an ancestral gene in order to cleave, in cooperation with cathepsins, useless proteins in the lysosomal compartment.

Study of the specificity of thrombin with tripeptidyl-p-nitroanilide substrates.

The kinetic behaviour of human thrombin has been studied with 26 tripeptidyl-p-nitroanilide substrates protected at the N terminus and with 9 unprotected ones. By the regression analysis of experimentally determined 1/Km, kcat and kcat/Km values the individual contribution of each side chain of the various substrates to the kinetic parameters was calculated. The contributions to the kinetic parameters of the best substrates provide information about the structure of the binding site. The interaction of subsites S1 and P1, which determines primary specificity, proved to be marginal on the basis of contribution values, though it depends upon this contact whether the substrate is hydrolyzed at all. At subsite S2 proline appeared to be favourable. Subsite S3 plays an important role in efficiency. The best parameters were obtained here with the D configurations of bulky amino acid residues. The aromatic protecting groups applied did not improve the properties of substrates. BZDPhe-Pro-Arg-Nan was predicted by calculation to be better than the protected substrates assayed. The compound was synthesized and tested. Its experimentally determined 1/Km, 55.1 mM-1, was in good agreement with 50.9 mM-1 found by calculation.

Mutations within the Protein Z-Dependent Protease Inhibitor (ZPI) Gene Are Associated with Venous Thromboembolic Disease: A New Form of Thrombophilia.

ZPI is a recently characterised inhibitory serpin present in plasma. In vitro studies have shown that ZPI inhibits both factor Xa (in the presence of protein Z) and factor XIa. Deficiency of ZPI is predicted to enhance coagulation and may be a risk factor for venous thrombosis. To test this hypothesis we carried out mutation screening within the coding region of the ZPI gene in a cohort of 150 patients with a history of DVT or PE (first event before the age of 60 years) and 150 matched controls. Five PCR products were produced for each subject. Heteroduplex analysis was performed using dHPLC and the PCR products were sequenced directly if a heteroduplex mismatch was identified.Sixteen mutations/polymorphisms were identified within the coding region of the ZPI gene. Two mutations were regarded as functionally significant as they produced stop codons at arginine 67 and tryptophan 303 and would be expected to result in the loss of ZPI activity. These stop codon mutations were found in 8 patients and 2 controls. Based on these results, a power calculation was performed that showed that an additional 100 patients and controls would be necessary to confirm that the stop codon mutations were statistically significant risk factors for thrombosis. Bidirectional allele specific PCR was developed to rapidly identify these stop codon mutations and a further 100 patients and 100 controls were examined using this technique. The stop codon mutations were found in 11 patients (W303X n=8: R67X n=3) and only 2 controls (R67X n=2) (two sided Fishers exact p=0.02) with an odds ratio = 5.7 (95%CI, 1.25 to 26.0). In addition two further non-conservative mutations were identified in two other thrombosis patients. These resulted in a serine to tyrosine (codon 122) and a phenylalanine to leucine (codon 124) change in the region homologous to the D helix of other heparin activated serpins. These changes, involving bulky aromatic amino acid residues, have the potential to disrupt the structure and function of the D helix.We identified a further 12 mutations/polymorphisms (C454G, C574T, A603G, A647G, G752A, A947T, C1276T, G1277A, G1438A, A1617C, G1789T and C1811T (italics: not previously described)). The significance of these mutations is uncertain. We have identified mutations causing stop codons, which will result in loss of ZPI function, in 4.4% of patients who present with venous thrombosis before the age of 60 years, compared with an incidence of only 0.8% in controls. Further studies are ongoing to measure the plasma concentration of ZPI in the affected individuals. Our results support an association between mutations in the ZPI gene and venous thrombosis. We propose that ZPI deficiency as a result of these mutations is potentially a new form of thrombophilia.

Dissecting the Structural Rearrangement and Activation of αIIbβ3 Integrin with a Disulfide Bridge.

Platelet αIIbβ3 integrin undergoes extensive structural rearrangement upon activation. Crystallographic and high-resolution electron microscopic observation revealed that integrins could assume multiple conformers under physiological conditions. However, functional assignment of each conformer has not been clearly determined. It is postulated that transition from the bent to the extended conformer (switchblade-like movement) and widening of the angle between the βA and the β hybrid domains (swing-out of the hybrid domain) that accompanies the extension is the critical event for integrin activation. To examine the authenticity of this hypothesis, we created and characterized mutant αIIbβ3 of which conformation was fixed in a specific conformer with an artificially introduced disulfide bridge. A double cysteine mutation βV332C/βS674C was designed to ligate βA and βTD, thus it is expected to fix integrin in a bent conformer by stabilizing the βA/βTD interface. Another mutation αD319C/βV359C was designed to ligate α β-propeller and the β hybrid domains. This mutation is expected to prevent the swing-out of the hybrid domain and the possible α/β headpiece dissociation. When expressed in CHO cells, both mutants were unable to bind fibrinogen, unless the disulfide bridge had been disrupted by DTT treatment. The LIBS epitope expression in βV332C/βS674C was significantly impaired and did not respond to induction by RGD peptide. The binding of ligand-mimetic mAb OP-G2 was also significantly impaired. By contrast, αD319C/βV359C showed comparable LIBS epitope expression and OP-G2 binding as wild-type αIIbβ3. The RGD peptide induced LIBS epitope expression, albeit slightly weaker than wild-type. Consistently, the βG327C/βV419C mutation that was designed to ligate βA and β hybrid domains, thus fix integrin headpiece in closed conformer by preventing the swing-out of the hybrid domain without affecting the α/β head interface, specifically blocked fibrinogen binding without affecting the binding of anti-LIBS or OP-G2. These results indicate that βV332C/βS674C is absolutely inactive and incapable of undergoing structural rearrangements associated with activation, while the αD319C/βV359C and βG327C/βV419C are capable of doing so upon binding to ligand-mimetic RGD peptide. Disruption of the βA/βTD interface by introducing a bulky amino acid residue in the interface or by deletion of the CD loop in the βTD did not induce integrin activation. However, introducing a bulky N-glycan at βV332 or at βS674 in the βA/βTD interface significantly potentiated ligand binding. Notably, the effects of the two N-glycans were synergistic. In summary, these results suggest, 1) that the bent conformer represents an inactive conformer, 2) that the contribution of the putative βA/βTD interface interaction in restraining integrin in the bent conformer is minimal, 3) that increasing the distance between the βA and the βTD, i.e. decreasing the angle of the bend, makes integrin highly susceptible to activation, 4) integrin with closed headpiece represents low affinity conformer, but it is capable of undergoing structural rearrangement upon ligand binding. Taken together, our results are consistent with the switchblade model. Conformational change other than the swing-out of the hybrid domain may trigger the structural rearrangement from bent to extended conformer upon ligand binding.

Interaction interface of human flap endonuclease-1 with its DNA substrates.

Flap endonuclease-1 or FEN-1 is a structure-specific and multifunctional nuclease critical for DNA replication, repair, and recombination; however, its interaction with DNA substrates has not been fully understood. In the current study, we have defined the borders of the interaction between the FEN-1 protein and its DNA substrates and identified six clusters of conserved positively charged amino acid residues, which are in direct contact with DNA substrate. To map further the corresponding interactions between FEN-1 residues and DNA substrates, we performed biochemical assays employing a series of flap DNA substrates lacking some structural components and a series of binding-deficient point mutants of FEN-1. It was revealed that Arg(47), Arg(70), and Lys(326)-Arg(327) of FEN-1 interact with the upstream duplex of DNA substrates, whereas Lys(244)-Arg(245) interact with the downstream duplex. This result indicates the orientation of the FEN-1-DNA interaction. Moreover, Arg(70) and Arg(47) were determined to interact with the sites around the 2nd nucleotide (Arg(70)) or the 5th/6th nucleotide (Arg(47)) of the template strand in the upstream duplex portion counting from the nick point of the flap substrate. Together with previously published data and the crystallographic ainformation from the FEN-1.DNA complex that we published recently (Chapados, B. R., Hosfield, D. J., Han, S., Qiu, J., Yelent, B., Shen, B., Tainer, J. A. (2004) Cell 116, 39-50) we are able to propose a reasonable model for how the human FEN-1 protein interacts with its DNA substrates.

Identification of Novel ERK2 Substrates through Use of an Engineered Kinase and ATP Analogs

The mitogen-activated protein kinases are key regulators of cellular organization and function. To understand the mechanisms(s) by which these ubiquitous kinases affect specific cellular changes, it is necessary to identify their diverse and numerous substrates in different cell contexts and compartments. As a first step in achieving this goal, we engineered a mutant ERK2 in which a bulky amino acid residue in the ATP binding site (glutamine 103) is changed to glycine, allowing this mutant to utilize an analog of ATP (cyclopentyl ATP) that cannot be used by wild-type ERK2 or other cellular kinases. The mutation did not inhibit ERK2 kinase activity or substrate specificity in vitro or in vivo. This method allowed us to detect only ERK2-specific phosphorylations within a mixture of proteins. Using this ERK2 mutant/analog pair to phosphorylate ERK2-associated proteins in COS-1 cells, we identified the ubiquitin ligase EDD (E3 identified by differential display) and the nucleoporin Tpr (translocated promoter region) as two novel substrates of ERK2, in addition to the known ERK2 substrate Rsk1. To further validate the method, we present data that confirm that ERK2 phosphorylates EDD in vitro and in vivo. These results not only identify two novel ERK2 substrates but also provide a framework for the future identification of numerous cellular targets of this important signaling cascade.

Alteration of reaction and substrate specificity of a bacterial type III polyketide synthase by site-directed mutagenesis.

RppA, which belongs to the type III polyketide synthase family, catalyses the synthesis of 1,3,6,8-tetrahydroxynaphthalene (THN), which is the key intermediate of melanin biosynthesis in the bacterium Streptomyces griseus. The reaction of THN synthesis catalysed by RppA is unique in the type III polyketide synthase family, in that it selects malonyl-CoA as a starter substrate. The Cys-His-Asn catalytic triad is also present in RppA, as in plant chalcone synthases, as revealed by analyses of active-site mutants having amino acid replacements at Cys(138), His(270) and Asn(303) of RppA. Site-directed mutagenesis of the amino acid residues that are likely to form the active-site cavity revealed that the aromatic ring of Tyr(224) is essential for RppA to select malonyl-CoA as a starter substrate, since substitution of Tyr(224) by amino acids other than Phe and Trp abolished the ability of RppA to accept malonyl-CoA as a starter, whereas the mutant enzymes Y224F and Y224W were capable of synthesizing THN via the malonyl-CoA-primed reaction. Of the site-directed mutants generated, A305I was found to produce only a triketide pyrone from hexanoyl-CoA as starter substrate, although wild-type RppA synthesizes tetraketide and triketide pyrones in the hexanoyl-CoA-primed reaction. The kinetic parameters of Ala(305) mutants and identification of their products showed that the substitution of Ala(305) by bulky amino acid residues restricted the number of elongations of the growing polyketide chain. Both Tyr(224) (important for starter substrate selection) and Ala(305) (important for intermediate elongation) were found to be conserved in three other RppAs from Streptomyces antibioticus and Streptomyces lividans.

The B′ Helix Determines Cytochrome P450nor Specificity for the Electron Donors NADH and NADPH

Nitric oxide reductase (Nor) cytochrome P450nor (P450nor) is unique because it is catalytically self-sufficient, receiving electrons directly from NADH or NADPH. However, little is known about the direct binding of NADH to cytochrome. Here, we report that oxidized pyridine nucleotides (NAD(+) and NADP(+)) and an analogue induce a spectral perturbation in bound heme when mixed with P450nor. The P450nor isoforms are classified according to electron donor specificity for NADH or NADPH. One type (Fnor, a P450nor of Fusarium oxysporum) utilizes only NADH. We found that NAD(+) induced a type I spectral change in Fnor, whereas NADP(+) induced a reverse type I spectral change, although the K(d) values for both were comparable. In contrast, NADP(+) as well as NAD(+) caused a type I spectral change in Tnor, a P450nor isozyme from Trichosporon cutaneum that utilizes both NADH and NADPH as electron donors. The B' helix region of Tnor ((73)SAGGKAAA(80)) contains some Ala and Gly residues, whereas the sequence is replaced at a few sites with more bulky amino acid residues in Fnor ((73)SASGKQAA(80)). A single mutation (S75G) significantly improved the NADPH- dependent Nor activity of Fnor, and the overall activity was accelerated via the NADPH-enhanced reduction step. These results showed that pyridine nucleotide cofactors can bind P450nor and that only a few residues in the B' helix region determine cofactor specificity. We further showed that a poor electron donor (NADPH) could also bind Fnor, but an appropriate configuration for electron transfer is blocked by steric hindrance mainly by Ser(75) against the 2'-phosphate moiety. The present results along with previous observations together revealed a novel motif for cofactor binding.

Systematic site-directed mutagenesis of human protein SRP54: interactions with signal recognition particle RNA and modes of signal peptide recognition.

The amino acid residues of human protein SRP54 which are required for binding to SRP RNA were identified by generating 40 nonoverlapping tri-alanine alterations within its methionine-rich M-domain (SRP54M). The mutant polypeptides were expressed in Escherichia coli, and their ability to bind to human and Methanococcus jannaschii SRP RNA were determined in vitro. Residues at positions 379-387, 394-396, 400-405, and 409-411 of human SRP54 were within the predicted RNA binding site, and their alteration abolished the binding activities of the mutant polypeptides as expected. Changes at positions 418-423 had intermediate effects. Polypeptides containing mutations of 328-TLR-330 were inactive although these residues were far away from the presumed RNA binding site in the crystal structure of the free protein. Using the structures of the E. coli Ffh/4.5S core and of the human SRP54m dimer as templates, a molecular model of the complex between human SRP RNA helix 8 and a single SRP54M molecule was constructed in which Leucine 329 was positioned in closer proximity to the RNA binding domain. This representation was supported by studies of the SRP54m monomer/dimer ratio using gel filtration. The results were consistent with a change in the shape of the signal peptide binding groove upon binding of SRP54 to SRP RNA. We propose that the SRP RNA and a small region centered at a bulky nonpolar amino acid residue at position 329 of protein SRP54 play a critical role in the SRP-dependent binding and release of signal peptides.

Substrate specificity of carp hepatopancreatic cathepsin S for peptides and myofibrillar proteins

SUMMARY: From 250 g of carp hepatopancreas, 0.29 mg of the purified enzyme was obtained. The bond specificity of cathepsin S for α-neoendorphin and neurotensin was 6Arg-7Lys and 3Tyr-4Glu, respectively. The cleavage sites for insulin B-chain were estimated to be the bonds at 3Asn-4Gln, 6Leu-7Cys, 12Val-13Glu, 13Glu-14Ala, 16Tyr-17Leu, 22Arg-23Gly, 24Phe-25Phe and 26Tyr-27Thr. P2 position on these peptides were bulky and hydrophobic amino acid residues such as Phe or Leu, small amino acid residues such as Gly, Ala and Val were also accepted in these positions. Regarding the protein substrates, cathepsin S degraded carp α-actinin, actin, tropomyosin and troponins T and I although the proteolyzing speeds were distinct from one another.

Photochromic and photoresponsive properties of optically active poly(methacrylate)s with pendantL-leucine,L-valine andL-proline residues connected to 4-aminoazobenzene moieties

The photochromic behaviour of optically active methacrylic polymers containing in the side chains a bulky chiral amino acid residue interposed between the backbone and the azobenzene chromophore through amido groups, such as poly[(S)-4-(2-methacryloylamino-4-methylpentanoylamino)azobenzene] [poly(MLEA)], poly[(S)-4-(2-methacryloylamino-3-methylbutanoylamino)azobenzene] [poly(MVA)] and poly[(S)-4-(N-methacryloyl-2-pyrrolidinoylamino)azobenzene] [poly(MPA)] was investigated in comparison with the corresponding low molecular weight model compounds. The photoresponsive properties of the above polymers were also evaluated by circular dichroism measurements at various extent of photoisomerization and in solvents with different polarity. All the results are discussed in terms of structural requirements of the macromolecules.