Targeted alteration of the substrate specificity of peptide synthetases by rational module swapping

Analysis of the primary structure of peptide synthetases involved in the non-ribosomal synthesis of peptide antibiotics has revealed a highly conserved and ordered modular arrangement. A module contains at least two domains, involved in ATP-dependent substrate activation and thioester formation. The occurrence and arrangement of these functional building blocks is associated with the number and order of the amino acids incorporated in the peptide product. In this study, we present data on the targeted exchange of the leucine-activating module within the three-module surfactin synthetase 1 (SrfA-A) of Bacillus subtilis. This was achieved by engineering several hybrid srfA-A genes, which were introduced into the surfactin biosynthesis operon by in vivo recombination. We examined the hybrid genes for expression and investigated the enzymatic activities of the resulting recombinant peptide synthetases. For the first time, we demonstrate directly that an individual minimal module, of bacterial or fungal origin, confers its amino acid-specific activity on a multi-modular peptide synthetase. Furthermore, it is shown that directed incorporation of ornithine at the second position of the peptide chain induces a global alteration in the conformation of surfactin and may result in premature cyclization or a branched cyclic structure. Received: 10 July 1997 / Accepted: 11 September 1997     

Identification of amino acid residues involved in substrate specificity of plant acyl-ACP thioesterases using a bioinformatics-guided approach

Background  

The large amount of available sequence information for the plant acyl-ACP thioesterases (TEs) made it possible to use a bioinformatics-guided approach to identify amino acid residues involved in substrate specificity. The Conserved Property Difference Locator (CPDL) program allowed the identification of putative specificity-determining residues that differ between the FatA and FatB TE classes. Six of the FatA residue differences identified by CPDL were incorporated into the FatB-like parent via site-directed mutagenesis and the effect of each on TE activity was determined. Variants were expressed in E. coli strain K27 that allows determination of enzyme activity by GCMS analysis of fatty acids released into the medium.     

Probing protein-tyrosine phosphatase substrate specificity using a phosphotyrosine-containing phage library

Protein tyrosine phosphatases (PTPs) play important, highly dynamic roles in signaling. Currently about 90 different PTP genes have been described. The enzymes are highly regulated at all levels of expression, and it is becoming increasingly clear that substrate specificity of the PTP catalytic domains proper contributes considerably to PTP functionality. To investigate PTP substrate selectivity, we have set up a procedure to generate phage libraries that presents randomized, phosphotyrosine-containing peptides. Phages that expressed suitable substrates were selected by immobilized, substrate-trapping GST-PTP fusion proteins. After multiple rounds of selection, positive clones were confirmed by SPOT analysis, dephosphorylation by wild-type enzyme, and Km determinations. We have identified distinct consensus substrate motifs for PTP1B, Sap-1, PTP-beta, SHP1, and SHP2. Our results confirm substrate specificity for individual PTPs at the peptide level. Such consensus sequences may be useful both for identifying potential PTP substrates and for the development of peptidomimetic inhibitors.     

A survey of furin substrate specificity using substrate phage display.

The substrate specificity of furin, a mammalian enzyme involved in the cleavage of many constitutively expressed protein precursors, was studied using substrate phage display. In this method, a multitude of substrate sequences are displayed as fusion proteins on filamentous phage particles and ones that are cleaved can be purified by affinity chromatography. The cleaved phage are propagated and submitted to additional rounds of protease selection to further enrich for good substrates. DNA sequencing of the cleaved phage is used to identify the substrate sequence. After 6 rounds of sorting a substrate phage library comprising 5 randomized amino acids (xxxxx), virtually all clones had an RxxR motif and many had Lys, Arg, or Pro before the second Arg. Nine of the selected sequences were assayed using a substrate-alkaline phosphatase fusion protein system. All were cleaved after the RxxR, and some substrates with Pro or Thr in P2 were also found to be cleaved as efficiently as RxKR or RxRR. To further elaborate surrounding determinants, we constructed 2 secondary libraries (xxRx(K/R)Rx and xxRxPRx). Although no consensus developed for the latter library, many of the sequences in the the former library had the 7-residue motif (L/P)RRF(K/R)RP, suggesting that the furin recognition sequence may extend over more than 4 residues. These studies further clarify the substrate specificity of furin and suggest the substrate phage method may be useful for identifying consensus substrate motifs in other protein processing enzymes.     

Structure-based approach to alter the substrate specificity of Bacillus subtilis aminopeptidase

Aminopeptidases can selectively catalyze the cleavage of the N-terminal amino acid residues from peptides and proteins. Bacillus subtilis aminopeptidase (BSAP) is most active toward p-nitroanilides (pNAs) derivatives of Leu, Arg, and Lys. The BSAP with broad substrate specificity is expected to improve its application. Based on an analysis of the predicted structure of BSAP, four residues (Leu 370, Asn 385, Ile 387, and Val 396) located in the substrate binding region were selected for saturation mutagenesis. The hydrolytic activity toward different aminoacyl-pNAs of each mutant BSAP in the culture supernatant was measured. Although the mutations resulted in a decrease of hydrolytic activity toward Leu-pNA, N385L BSAP exhibited higher hydrolytic activities toward Lys-pNA (2.2-fold) and Ile-pNA (9.1-fold) than wild-type BSAP. Three mutant enzymes (I387A, I387C and I387S BSAPs) specially hydrolyzed Phe-pNA, which was undetectable in wild-type BSAP. Among these mutant BSAPs, N385L and I387A BSAPs were selected for further characterized and used for protein hydrolysis application. Both of N385L and I387A BSAPs showed higher hydrolysis efficiency than the wild-type BASP and a combination of the wild-type and N385L and I387A BSAPs exhibited the highest hydrolysis efficiency for protein hydrolysis. This study will greatly facilitate studies aimed on change the substrate specificity and our results obtained here should be useful for BSAP application in food industry.     

Designing recombinant vaccines with viral properties: a rational approach to more effective vaccines

One of the great demands and challenges for vaccination is to successfully target the pathogens responsible for much of mankind's chronic disease burden including: AIDS, infectious hepatitis, tuberculosis and malaria. Another is realizing the potential of therapeutic immunization to cure diseases such as cancer, allergy and inflammatory autoimmunity. To achieve these objectives, the fundamental insights gained from immunology, genomics, molecular-cellular biology and vaccinology must be implemented in order to develop more effective, better defined and safer vaccines. As an illustrative example of this we examine the key features of viruses that are known to be responsible for eliciting superb host immune responses. These insights have formed a basis for understanding the effectiveness of existing vaccines and provide a framework for designing and developing new vaccines better able to meet pressing unmet medical needs. The key immunogenic properties of viruses that are understood to date and are currently being applied include: their particulate nature, their highly repetitive and ordered structures, their ability to induce innate immunity with consequent conditioning of adaptive responses and the kinetics and distribution of viral antigens during infection. Vaccines and vaccine-formulations recently registered for use in humans already incorporate some of these elements. Of great anticipation is the progress of the next-generation vaccines now advancing through the various stages of research and development. Vaccines which, by way of rational design, incorporate viral properties to induce tailored responses and thus have the potential to provide safer and more effective prophylaxis and therapies.     

Probing the substrate specificity of Escherichia coli RNase E using a novel oligonucleotide-based assay

Endoribonuclease RNase E has a central role in both processing and decay of RNA in Escherichia coli, and apparently in many other organisms, where RNase E homologs were identified or their existence has been predicted from genomic data. Although the biochemical properties of this enzyme have been already studied for many years, the substrate specificity of RNase E is still poorly characterized. Here, I have described a novel oligonucleotide-based assay to identify specific sequence determinants that either facilitate or impede the recognition and cleavage of RNA by the catalytic domain of the enzyme. The knowledge of these determinants is crucial for understanding the nature of RNA–protein interactions that control the specificity and efficiency of RNase E cleavage and opens new perspectives for further studies of this multi-domain protein. Moreover, the simplicity and efficiency of the proposed assay suggest that it can be a valuable tool not only for the characterization of RNase E homologs but also for the analysis of other site-specific nucleases.     

Analysis of the substrate specificity of tyrosylprotein sulfotransferase using synthetic peptides

Tyrosylprotein sulfotransferase (TPST) catalyzes the sulfation of proteins at tyrosine residues. We have analyzed the substrate specificity of TPST from bovine adrenal medulla with a novel assay, using synthetic peptides as substrates. The peptides were modeled after the known, or putative, tyrosine sulfation sites of the cholecystokinin precursor, chromogranin B (secretogranin I) and vitronectin, as well as the tyrosine phosphorylation sites of alpha-tubulin and pp60src. Varying the sequence of these peptides, we found that (i) the apparent Km of peptides with multiple tyrosine sulfation sites decreased exponentially with the number of sites; (ii) acidic amino acids were the major determinant for tyrosine sulfation, acidic amino acids adjacent to the tyrosine being more important than distant ones; (iii) a carboxyl terminally located tyrosine residue may be sulfated. Moreover, TPST catalyzed the sulfation of a peptide corresponding to the tyrosine autophosphorylation site of pp60v-src (Tyr-416) but not of a peptide corresponding to the non-autophosphorylation site of pp60c-src (Tyr-527). These results experimentally define structural determinants for the substrate specificity of TPST and show that this enzyme and certain autophosphorylating tyrosine kinases have overlapping substrate specificities in vitro.     

Investigation on the substrate specificity of human plasmin using tripeptidyl-p-nitroanilide substrates

The hydrolysis of 35 tripeptidyl-p-nitroanilides was studied with human plasmin and the kinetic parameters were determined. The individual contribution of the various side chains to the kinetic parameters was calculated by regression analysis. Considering Km, substrates having Z-D-Ile-Phe-Lys as well as H-D-Ile-Phe-Lys sequences were found to be the best, while Bz-Ile-Leu-Lys and pGlu-Leu-Lys sequences are the best for kcat. The Km values of substrates protected at N-terminus are lower, their kcat values are higher than those of the unprotected ones with the same sequence.     

Changing the substrate specificity of cytochrome c peroxidase using directed evolution

5-Lipoxygenase (5-LO) is a key enzyme involved in the synthesis of leukotrienes from arachidonic acid, and its activation is usually followed by translocation to the nuclear envelope. The details of mechanisms involved in the translocation of 5-LO are not well understood, though Ca(2+) is known to be essential. Here we show that ionomycin, a Ca(2+) ionophore, induces 5-LO translocation and necrotic cell death in Rat-2 fibroblasts, suggesting a potential relationship between activation of 5-LO and cell death. These effects were markedly attenuated in Rat2-Rac(N17) cells expressing a dominant negative Rac1 mutant. Pretreatment with SB203580, a specific inhibitor of p38 MAP kinase, or EGTA, a Ca(2+) chelator, likewise diminished ionomycin-induced 5-LO translocation and cell death, but PD98059, a MEK inhibitor, did not. Thus, Rac and p38 MAP kinase appear to be components in a Ca(2+)-dependent pathway leading to 5-LO translocation and necrotic cell death in Rat-2 fibroblasts.     

Designing a connected nature reserve using a network flow theory approach

Establishing nature conservation reserves is an effective and widely accepted practice to protect biodiversity. In order to promote the effectiveness and efficiency of the reserve, spatial attributes of the reserve should be considered. Connectedness (contiguity) is one of these important spatial attributes. Currently in the biological literature there are only a few formal/exact optimization approaches to endogenously designing a connected nature reserve. This article adds a new approach by adapting a spatial unit allocation model to the reserve design problem. Using concepts from network flow theory, the model defines a sink site from which no flow directs out and ensures contiguity by specifying the outflow and inflow relationship of the potential sites. Computational performance of the model is tested using hypothetical problems with various sizes including up to 400 potential sites. Results show that the time needed to solve the problem to optimality increases exponentially both as number of potential sites increases and as species distribution gets more sparse. An empirical application involving 80 potential sites and 15 bird species in part of Fox River watershed, Illinois USA is presented. Factors influencing an IP model’s computational performance and potential extensions of the model were discussed.     

TRPV1 modulators: structure-activity relationships using a rational combinatorial approach

A discrete library of linear and hydantoin-containing dipeptide derivatives, based on the Lys-Trp(Nps) scaffold, was prepared by solid-phase synthesis. SAR studies indicated that potency for TRPV1 blockade and selectivity towards NMDA is mainly dictated by the side-chain length and the basic nature of α, ω-groups in the N-terminal residue. The 2-Nps moiety at position 2 of Trp indole ring is preferred over the 2-pyridine one.     

Designing connected nature reserve networks using a graph theory approach

Habitat fragmentation has been cited as one of the critical reasons for biodiversity loss. Establishing connected nature reserve networks is an effective way to reduce habit fragmentation. However, the resources devoted to nature reserves have always been scarce. Therefore it is important to allocate our scarce resources in an optimal way. The optimal design of a reserve network which is effective both ecologically and economically has become an important research topic in the reserve design literature. The problem of optimal selection of a subset from a larger group of potential habitat sites is solved using either heuristic or formal optimization methods. The heuristic methods, although flexible and computationally fast, can not guarantee the solution is optimal therefore may lead to scarce resources being used in an ineffective way. The formal optimization methods, on the other hand, guarantees the solution is optimal, but it has been argued that it would be difficult to model site selection process using optimization models, especially when spatial attributes of the reserve have to be taken into account. This paper presents a linear integer programming model for the design of a minimal connected reserve network using a graph theory approach. A connected tree is determined corresponding to a connected reserve. Computational performance of the model is tested using datasets randomly generated by the software GAMS. Results show that the model can solve a connected reserve design problem which includes 100 potential sites and 30 species in a reasonable period of time. As an empirical application, the model is applied to the protection of endangered and threatened bird species in the Cache River basin area in Illinois, US. Two connected reserve networks are determined for 13 bird species.     

Designing connected nature reserve networks using a graph theory approach

Habitat fragmentation has been cited as one of the critical reasons for biodiversity loss. Establishing connected nature reserve networks is an effective way to reduce habit fragmentation. However, the resources devoted to nature reserves have always been scarce. Therefore it is important to allocate our scarce resources in an optimal way. The optimal design of a reserve network which is effective both ecologically and economically has become an important research topic in the reserve design literature. The problem of optimal selection of a subset from a larger group of potential habitat sites is solved using either heuristic or formal optimization methods. The heuristic methods, although flexible and computationally fast, can not guarantee the solution is optimal therefore may lead to scarce resources being used in an ineffective way. The formal optimization methods, on the other hand, guarantees the solution is optimal, but it has been argued that it would be difficult to model site selection process using optimization models, especially when spatial attributes of the reserve have to be taken into account. This paper presents a linear integer programming model for the design of a minimal connected reserve network using a graph theory approach. A connected tree is determined corresponding to a connected reserve. Computational performance of the model is tested using datasets randomly generated by the software GAMS. Results show that the model can solve a connected reserve design problem which includes 100 potential sites and 30 species in a reasonable period of time. As an empirical application, the model is applied to the protection of endangered and threatened bird species in the Cache River basin area in Illinois, US. Two connected reserve networks are determined for 13 bird species.     

Investigation of the substrate specificity of thylakoid protein kinase using synthetic peptides

Synthetic peptide analogues of the N-terminal region of the light harvesting chlorophyll a/b binding polypeptide of photosystem II (LHC II) were used to probe the effect of charged groups on the protein kinase activity of pea (Pisum sativum) thylakoid membranes. The effectiveness of the synthetic peptides as substrates for protein kinase activity or as inhibitors of LHC II phosphorylation was correlated with their net positive charge, which ranged between +2 and +5. The effects of the synthetic peptides on phosphorylation of other, non-LHC II, thyakoid polypeptides are also discussed.     

Analysis of human cytochrome P450 2C8 substrate specificity using a substrate pharmacophore and site-directed mutants

The structural determinants of substrate specificity of human liver cytochrome P450 2C8 (CYP2C8) were investigated using site-directed mutants chosen on the basis of a preliminary substrate pharmacophore and a three-dimensional (3D) model. Analysis of the structural features common to CYP2C8 substrates exhibiting a micromolar K(m) led to a substrate pharmacophore in which the site of oxidation by CYP2C8 is 12.9, 8.6, 4.4, and 3.9 A from features that could establish ionic or hydrogen bonds, and hydrophobic interactions with protein amino acid residues. Comparison of this pharmacophore with a 3D model of CYP2C8 constructed using the X-ray structure of CYP2C5 suggested potential CYP2C8 amino acid residues that could be involved in substrate recognition. Twenty CYP2C8 site-directed mutants were constructed and expressed in yeast to compare their catalytic activities using five CYP2C8 substrates that exhibit different structures and sizes [paclitaxel, fluvastatin, retinoic acid, a sulfaphenazole derivative (DMZ), and diclofenac]. Mutation of arginine 241 had marked effects on the hydroxylation of anionic substrates of CYP2C8 such as retinoic acid and fluvastatin. Serine 100 appears to be involved in hydrogen bonding interactions with a polar site of the CYP2C8 substrate pharmacophore, as shown by the 3-4-fold increase in the K(m) of paclitaxel and DMZ hydroxylation after the S100A mutation. Residues 114, 201, and 205 are predicted to be in close contact with substrates, and their mutations lead either to favorable hydrophobic interactions or to steric clashes with substrates. For instance, the S114F mutant was unable to catalyze the 6alpha-hydroxylation of paclitaxel. The S114F and F205A mutants were the best catalysts for retinoic acid and paclitaxel (or fluvastatin) hydroxylation, respectively, with k(cat)/K(m) values 5 and 2.1 (or 2.4) times higher, respectively, than those found for CYP2C8. Preliminary experiments of docking of the substrate into the experimentally determined X-ray structure of substrate-free CYP2C8, which became available quite recently [Schoch, G. A., et al. (2004) J. Biol. Chem. 279, 9497], were consistent with key roles for S100, S114, and F205 residues in substrate binding. The results suggest that the effects of mutation of arginine 241 on anionic substrate hydroxylation could be indirect and result from alterations of the packing of helix G with helix B'.     

Pressure swing reactor for converting suspension of solid substrate p-hydroxyphenylhydantoin by immobilized d-hydantoinase

A reactor consisting of filter-separated two stirred compartments was developed to carry out the conversion of suspension of solid substrate d,l-p-hydroxyphenyl-hydantoin (pHPH) into d-n-carbamoyl-p-hydroxyphenylglycine (d-CpHPG) by immobilized d-hydantoinase (IDH). The immobilized enzyme and substrate suspensions were separated by a 60?μm filter to prevent the IDH from contamination with the insoluble impurities present in the substrate. The poor mass transfer between the two compartments limited the overall enzymatic reaction. It took 180?min for this reactor to accomplish the hydrolysis of 4% (w/v) pHPH. However, it took only 45?min for the reactor without using the filter to separate the two stirred compartments. The performance of the filter-separated reactor was significantly improved by applying pressure swing to the system. The pressure swing was generated by cyclically pressurizing the substrate compartment with nitrogen that caused the solution of the two compartments to flow back and forth through the filter. The reaction time for accomplishing the 4% (w/v) pHPH hydrolysis was reduced to 90?min when the pressure swing was applied with a frequency of 20?cycles/hr. The conversion of pHPH suspension of concentration as high as 15% (w/v) was easily accomplished in this pressure swing operated reactor. The used IDH of this reactor showed the same appearance as the fresh one. On the other hand, the used IDH in conventional stirred tank reactor was fouled with insoluble impurities present in the substrate.     

The study of the substrate specificity of rat-brain fucosyltransferase using synthetic acceptors

The substrate specificity of fucosyltransferase (FT) from rat forebrain and cerebellum was studied using synthetic acceptors. Of 16 acceptors tested, only those containing the Galβ1-4GlcNAcβ1-R fragment were subjected to enzymic fucosylation. The isomer with a 1–3 bond as well as lactose and oligosaccharides with an additional Neu5Ac residue attached to Gal or a Fuc residue attached to GlcNAc were not fucosylated, whereas Fucα1-2Galβ1-4GlcNAc displayed the same substrate properties as Galβ1-4GlcNAc. FT from the cerebellum and forebrain was shown to have a specificity similar to that of mammalian FT IV. The activity of the cerebellum FT with all types of substrates was higher than that of FT isolated from the forebrain, the specificity profiles being similar. This communication is dedicated to the 70th birthday of Prof. A.Ya. Khorlin.