Structure based library approach to photosynthesis inhibitors:Combinatorial synthesis of hydrouracil library

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Solid-phase assembly and in situ screening of protein tyrosine phosphatase inhibitors

A highly efficient solid-phase strategy for assembly of small molecule inhibitors against protein tyrosine phosphatase 1B (PTP1B) is described. The method is highlighted by its simplicity and product purity. A 70-member combinatorial library of analogues of a known PTP1B inhibitor has been synthesized, which upon direct in situ screening revealed a potent inhibitor ( Ki = 7.0 microM) against PTP1B.     

(iPr3P)6Rh6H12]2+: a high-hydride content octahedron that bridges the gap between late and early transition metal clusters

Treatment of [(iPr3P)2Rh(nbd)][Y] {nbd = norbornadiene, Y = B{3,5-(CF3)2C6H3}4- [B(ArF)4] or 1-H-closo-CB11Me11-} with H2 (ca. 4 atm) results in the isolation, in moderate yield, of the octahedral cluster complex [(iPr3P)6Rh6H12][Y]2 1. The cluster (for both anions) has been characterized by NMR, mass spectroscopy, and X-ray crystallography. These show 1 to have 12 edge-bridging hydrogen atoms, and the structure bears more resemblance to clusters of the early transition metals with pi-donor ligands than those of the late transition metals with pi-acceptor ligands. Intermediate complexes on the route to 1, namely, the nonclassical dihydrogen complexes [(iPr3P)2Rh(H)2(eta2-H2)x][B(ArF)4] (x = 1 or 2), have been observed spectroscopically. The high hydride content of 1 makes it a possible model for nanocluster colloidal Rh(0) catalysts that are used in olefin and arene hydrogenation.     

Discovery of potential M2 channel inhibitors based on the amantadine scaffold via virtual screening and pharmacophore modeling

The M2 channel protein on the influenza A virus membrane has become the main target of the anti-flu drugs amantadine and rimantadine. The structure of the M2 channel proteins of the H3N2 (PDB code 2RLF) and 2009-H1N1 (Genbank accession number GQ385383) viruses may help researchers to solve the drug-resistant problem of these two adamantane-based drugs and develop more powerful new drugs against influenza A virus. In the present study, we searched for new M2 channel inhibitors through a combination of different computational methodologies, including virtual screening with docking and pharmacophore modeling. Virtual screening was performed to calculate the free energies of binding between receptor M2 channel proteins and 200 new designed ligands. After that, pharmacophore analysis was used to identify the important M2 protein-inhibitor interactions and common features of top binding compounds with M2 channel proteins. Finally, the two most potential compounds were determined as novel leads to inhibit M2 channel proteins in both H3N2 and 2009-H1N1 influenza A virus.     

Didepside Formation by the Nonreducing Polyketide Synthase Preu6 of Preussia isomera Requires Interaction of Starter Acyl Transferase and Thioesterase Domains

Orsellinic acid (OA) derivatives are produced by filamentous fungi using nonreducing polyketide synthases (nrPKSs). The chain-releasing thioesterase (TE) domains of such nrPKSs were proposed to also catalyze dimerization to yield didepsides, such as lecanoric acid. Here, we use combinatorial domain exchanges, domain dissections and reconstitutions to reveal that the TE domain of the lecanoric acid synthase Preu6 of Preussia isomera must collaborate with the starter acyl transferase (SAT) domain from the same nrPKS. We show that artificial SAT-TE fusion proteins are highly effective catalysts and reprogram the ketide homologation chassis to form didepsides. We also demonstrate that dissected SAT and TE domains of Preu6 physically interact, and SAT and TE domains of OA-synthesizing nrPKSs may co-evolve. Our work highlights an unexpected domain–domain interaction in nrPKSs that must be considered for the combinatorial biosynthesis of unnatural didepsides, depsidones, and diphenyl ethers.     

Probing the phosphopeptide specificities of protein tyrosine phosphatases,SH2 and PTB domains with combinatorial library methods

Protein tyrosine phosphatases, SH2 and PTB domains are crucial elements for cellular signal transduction and regulation. Much effort has been directed towards elucidating their specificity in the past decade using a variety of approaches. Combinatorial library methods have contributed significantly to the understanding of substrate and ligand specificity of phosphoprotein recognizing domains. This review gives a brief overview of the structural characteristics of protein tyrosine phosphatases, SH2 and PTB domains and their binding to phosphopeptides. The chemical synthesis of peptides containing phosphotyrosine or phosphotyrosine mimics and the various formats of synthesis and deconvolution of combinatorial libraries are explained in detail. Examples are given as how different combinatorial libraries have been used to study the interaction of phosphopeptides with SH2 domains and phosphatases. The intrinsic advantages and difficulties of library synthesis, screening and deconvolution are pointed out. Finally, some experimental results on the substrate specificity of protein tyrosine phosphatase 1B and the SH2 domain of the adaptor protein Grb-2 are summarized and discussed.     

Synthesis, characterization, and reactivity of Fe complexes containing cyclic diazadiphosphine ligands: the role of the pendant base in heterolytic cleavage of H2

The iron complexes CpFe(P(Ph)(2)N(Bn)(2))Cl (1-Cl), CpFe(P(Ph)(2)N(Ph)(2))Cl (2-Cl), and CpFe(P(Ph)(2)C(5))Cl (3-Cl)(where P(Ph)(2)N(Bn)(2) is 1,5-dibenzyl-1,5-diaza-3,7-diphenyl-3,7-diphosphacyclooctane, P(Ph)(2)N(Ph)(2) is 1,3,5,7-tetraphenyl-1,5-diaza-3,7-diphosphacyclooctane, and P(Ph)(2)C(5) is 1,4-diphenyl-1,4-diphosphacycloheptane) have been synthesized and characterized by NMR spectroscopy, electrochemical studies, and X-ray diffraction. These chloride derivatives are readily converted to the corresponding hydride complexes [CpFe(P(Ph)(2)N(Bn)(2))H (1-H), CpFe(P(Ph)(2)N(Ph)(2))H (2-H), CpFe(P(Ph)(2)C(5))H (3-H)] and H(2) complexes [CpFe(P(Ph)(2)N(Bn)(2))(H(2))]BAr(F)(4), [1-H(2)]BAr(F)(4), (where BAr(F)(4) is B[(3,5-(CF(3))(2)C(6)H(3))(4)](-)), [CpFe(P(Ph)(2)N(Ph)(2))(H(2))]BAr(F)(4), [2-H(2)]BAr(F)(4), and [CpFe(P(Ph)(2)C(5))(H(2))]BAr(F)(4), [3-H(2)]BAr(F)(4), as well as [CpFe(P(Ph)(2)N(Bn)(2))(CO)]BAr(F)(4), [1-CO]Cl. Structural studies are reported for [1-H(2)]BAr(F)(4), 1-H, 2-H, and [1-CO]Cl. The conformations adopted by the chelate rings of the P(Ph)(2)N(Bn)(2) ligand in the different complexes are determined by attractive or repulsive interactions between the sixth ligand of these pseudo-octahedral complexes and the pendant N atom of the ring adjacent to the sixth ligand. An example of an attractive interaction is the observation that the distance between the N atom of the pendant amine and the C atom of the coordinated CO ligand for [1-CO]BAr(F)(4) is 2.848 ?, considerably shorter than the sum of the van der Waals radii of N and C atoms. Studies of H/D exchange by the complexes [1-H(2)](+), [2-H(2)](+), and [3-H(2)](+) carried out using H(2) and D(2) indicate that the relatively rapid H/D exchange observed for [1-H(2)](+) and [2-H(2)](+) compared to [3-H(2)](+) is consistent with intramolecular heterolytic cleavage of H(2) mediated by the pendant amine. Computational studies indicate a low barrier for heterolytic cleavage of H(2). These mononuclear Fe(II) dihydrogen complexes containing pendant amines in the ligands mimic crucial features of the distal Fe site of the active site of the [FeFe]-hydrogenase required for H-H bond formation and cleavage.     

Accelerated screening of phage-display output with alkaline phosphatase fusions

When using multiple targets and libraries, selection of affinity reagents from phage-displayed libraries is a relatively time-consuming process. Herein, we describe an automation-amenable approach to accelerate the process by using alkaline phosphatase (AP) fusion proteins in place of the phage ELISA screening and subsequent confirmation steps with purified protein. After two or three rounds of affinity selection, the open reading frames that encode the affinity selected molecules (i.e., antibody fragments, engineered scaffold proteins, combinatorial peptides) are amplified from the phage or phagemid DNA molecules by PCR and cloned en masse by a Ligation Independent Cloning (LIC) method into a plasmid encoding a highly active variant of E. coli AP. This time-saving process identifies affinity reagents that work out of context of the phage and that can be used in various downstream enzyme linked binding assays. The utility of this approach was demonstrated by analyzing single-chain antibodies (scFvs), engineered fibronectin type III domains (FN3), and combinatorial peptides that were selected for binding to the Epsin N-terminal Homology (ENTH) domain of epsin 1, the c-Src SH3 domain, and the appendage domain of the gamma subunit of the clathrin adaptor complex, AP-1, respectively.     

Chemical synthesis and molecular recognition of phosphatase-resistant analogues of phosphatidylinositol-3-phosphate

The remodeling of phosphatidylinositol polyphosphates in cellular membranes by phosphatases and kinases orchestrates the signaling by these lipids in space and time. To provide chemical tools to study the changes in cell physiology mediated by these lipids, three new metabolically stabilized (ms) analogues of phosphatidylinositol-3-phosphate (PtdIns(3)P) were synthesized. We describe herein the total asymmetric synthesis of 3-methylphosphonate, 3-(monofluoromethyl)phosphonate and 3-phosphorothioate analogues of PtdIns(3)P. From differentially protected D-myo-inositol key intermediates, a versatile phosphoramidite reagent was employed in the synthesis of PtdIns(3)P analogues with diacylglyceryl moieties containing dioleoyl, dipalmitoyl, and dibutyryl chains. In addition, we introduce a new phosphorylation reagent, (monofluoromethyl)phosphonyl chloride, which has general applications for the preparation of "pKa-matched" monofluorophosphonates. These ms-PtdIns(3)P analogues exhibited reduced binding activities with 15N-labeled FYVE and PX domains, as significant 1H and 15N chemical shift changes in the FYVE domain were induced by titrating ms-PtdIns(3)P analogues into membrane-mimetic dodecylphosphocholine micelles. In addition, the PtdIns(3)P analogues with dioleoyl and dipalmitoyl chains were substrates for the 5-kinase enzyme PIKfyve; the corresponding phosphorylated ms-PI(3,5)P2 products were detected by radio-TLC analysis.     

Engineering temperature-sensitive SH3 domains.

BACKGROUND: The ability to control specific protein-protein interactions conditionally in vivo would be extremely helpful for analyzing protein-protein interaction networks. SH3 (Src homology 3) modular protein binding domains are found in many signaling proteins and they play a crucial role in signal transduction by binding to proline-rich sequences. RESULTS: Random in vitro mutagenesis coupled with yeast two-hybrid screening was used to identify mutations in the second SH3 domain of Nck that render interaction with its ligand temperature sensitive. Four of the mutants were functionally temperature sensitive in mammalian cells, where temperature sensitivity was correlated with a pronounced instability of the mutant domains at the nonpermissive temperature. Two of the mutations affect conserved residues in the hydrophobic core (Val133 and Val160), suggesting a general strategy for engineering temperature-sensitive SH3-containing proteins. Indeed mutagenesis of the corresponding positions in another SH3 domain, that of Crk-1, rendered the full-length Crk-1 protein temperature sensitive for function and stability in mammalian cells. CONCLUSIONS: Construction of temperature-sensitive SH3 domains is a novel approach to regulating the function of SH3 domains in vivo. Such mutants will be valuable in dissecting SH3-mediated signaling pathways. Furthermore, the methodology described here to isolate temperature-sensitive domains should be widely applicable to any domain involved in protein-protein interactions.     

Parallel synthesis of a vitamin D(3) library in the solid-phase.

A highly efficient synthesis of the vitamin D(3) system on solid support is described. Two synthetic strategies for the solid-phase synthesis of vitamin D(3) were developed. One is for 11-hydroxy analogues, and the other is for most other synthetic analogues. In the latter strategy, the sulfonate-linked CD-ring 58 was initially immobilized on PS-DES resin to give solid-supported CD-ring 63 (Scheme 10). Similarly, solid-supported CD-ring 63 was prepared by attachment of the CD-ring 10 to the chlorosulfonate resin 64. The vitamin D(3) system was synthesized by Horner-Wadsworth-Emmons reaction of the A-ring phosphine oxide to a solid-supported CD-ring, followed by simultaneous introduction of the side chain and cleavage from resin with a Cu(I)-catalyzed Grignard reagent. Parallel synthesis of the vitamin D(3) analogues was accomplished by a split and pool methodology utilizing radio frequency encoded combinatorial chemistry, and a manual parallel synthesizer for side chain diversification and deprotection. Additionally, we demonstrated the synthesis of various A-rings in a similar protocol for efficient preparation of building blocks.     

Hydroxamate-based iron chelators: combinatorial syntheses of desferrioxamine B analogues and evaluation of binding affinities

This article describes the solid-phase combinatorial methods developed for the synthesis of polyhydroxamate-based siderophores. This strategy was applied to generate several libraries of structural DFO (1a) analogues that include DFO variants, non-amide analogues, C-terminal modified analogues, reverse-amide analogues, and hybrid analogues. To assess the relative iron-binding affinities of these compounds, a high-throughput spectrophotometric screening method based on competition with 8-hydroxyquinoline-5-sulfonic acid was developed. Some of the promising candidates containing various terminal functional groups were identified and prepared on large scale to enable future studies in animal models for iron-overload diseases.     

Catalytic and biochemical features of a monoclonal antibody heavy chain, JN1-2, raised against a synthetic peptide with a hemagglutinin molecule of influenza virus

It has long been an important issue to produce a catalytic antibody that possesses the ability to lose the infectivity of a bacteria or virus. The monoclonal antibody JN1-2 was generated using a synthetic peptide (TGLRNGITNKVNSVIEKAA) conjugated with human IgG. The peptide sequence includes the conserved region of the hemagglutinin molecule (HA(1) and HA(2) domains), which locates on the envelope of the influenza virus and plays an important role in influenza A virus infection. The monoclonal antibody specifically reacted with the HA2 domain, not only of H2 but also of an H1 strain of the H1N1 subtype (H1 strain). The heavy chain (JN1-2-H) isolated from the parent antibody showed catalytic activity cleaving the above antigenic peptide with very high turnover (kcat = 26 min(-1)), and it could slowly degrade the recombinant HA(2) domain by the catalytic function. Interestingly, the heavy chain exhibited the ability to reduce the infectivity of type A H1N1 but not type B, indicating specificity to type A. This characteristic monoclonal catalytic antibody heavy chain could suppress the infection of the influenza virus in vitro assays.     

A double-functionalized cyclen with carbamoyl and dansyl groups (cyclen = 1,4,7,10-tetraazacyclododecane): a selective fluorescent probe for Y(3+) and La(3+).

A cyclen (=1,4,7,10-tetraazacyclododecane) doubly functionalized with three carbamoylmethyl groups and one dansylaminoethyl (dansyl = 2-(5-(dimethylamino)-1-naphthalenesulfonyl) group (L(2) = 1-(2-(5-(dimethylamino)-1-naphthalenesulfonylamido)ethyl)-4,7,10-tris(carbamoylmethyl)-cyclen) was synthesized and characterized. Potentiometrtic pH titration and UV spectrophotometric titration of L(2) served to determine deprotonation of the pendant dansylamide (L(2) --> H(-1)L(2)) with a pK(a) value of 10.6, while the fluorometric titration disclosed a pK(a) value of 8.8 +/- 0.2, which was assigned to the dansyl deprotonation in the excited state. The 1:1 M(3+)-H(-1)L(2) complexation constants (log K(app) = 6.0 for Y(3+) and 5.2 for La(3+), where K(app)(M-H(-1)L(2)) = [M(3+)-H(-1)L(2)]/[M(3+)](free)[L(2)](free) (M(-1)) at pH 7.4) were determined by potentiometric pH titration and UV and fluorescence spectrophotometric titrations (excitation at 335 nm and emission at 520 nm) in aqueous solution (with I = 0.1 (NaNO(3))) and 25 degrees C. The X-ray structure analysis of the Y(3+)-H(-1)L complex showed nine-coordinated Y(3+) with four nitrogens of cyclen, three carbamoyl oxygens, and the deprotonated nitrogen and a sulfonyl oxygen of the dansylamide. The crystal data are as follow: formula C(28)H(49)N(11)O(13.5)SY (Y(3+)-H(-1)L(2) x 2(NO(3)(-)) x 2.5H(2)O), M(r) = 876.73, monoclinic, space group P2(1)/n (No. 14), a = 18.912(3) A, b = 17.042(3) A, c = 24.318(4) A, beta = 95.99(1) degrees, V = 7794(2) A(3), Z = 8, R1 = 0.099. Upon M(3+)-H(-1)L(2) complexation, the dansyl fluorescence greatly increased (8.6 and 3.8 times for Y(3+) and La(3+), respectively) in aqueous solution at pH 7.4. Other lanthanide ions also yielded Ln(3+)-H(-1)L(2) complexes with similar K(app) values, although all the dansyl fluorescences were weakly quenched. On the other hand, zinc(II) formed only a 1:1 Zn(2+)-L(2) complex at neutral pH with negligible fluorescence change. The X-ray crystal structure of the Zn(2+)-L(2) complex confirmed the pendant dansylamide being noncoordinating. The crystal data are as follow: formula C(28)H(51)N(11)O(14)SZn (Zn(2+)-L(2) x 2(NO(3)(-)) x 3H(2)O), M(r) = 863.22, monoclinic, space group C2/n (No. 15), a = 35.361(1) A, b = 13.7298(5) A, c = 18.5998(6) A, beta = 119.073(2) degrees, V = 7892.3(5) A(3), Z = 8, R1 = 0.084. Other divalent metal ions did not interact with L(2) at all (e.g., Mg(2+) and Ca(2+)) or interacted with L(2) with the dansyl fluorescence quenched (e.g., Cu(2+)).     

1-H2N-CB11F11]---synthesis and reactions of a functionalized fluorinated carbadodecaborate anion

In anhydrous hydrogen fluoride, K[1-H2N-CB11H11] is fluorinated with elemental fluorine to produce K[1-H2N-CB11F11]. Under strong alkaline conditions, two fluorine atoms of the [1-H2N-CB11F11]- anion are regioselectively exchanged, yielding the [1-H2N-4,6-(HO)2-CB11F9]- anion via [1-H2N-6-HO-CB11F10]- as an intermediate. Both hydroxycarborate anions were isolated as [Ph4P]+ salts. All of the species were characterized by IR, Raman, and multi-NMR spectroscopy, thermal analysis (DSC) as well as by mass spectrometry (MALDI). The assignment of the NMR signals was supported by DFT calculations. Solid-state structures of K[1-H2N-CB11F11], [BzPh3P][1-H2N-CB11F11], [Ph4P][1-H2N-4,6-(HO)2-CB11F9], [Ph4P][1-H2N-6-HO-CB11F10], and [BzPh3P][1-H2N-CB11H11] were determined by single-crystal X-ray diffraction.     

Crown compounds for anions: sandwich and half-sandwich complexes of cyclic trimetric perfluoro-o-phenylenemercury with polyhedral closo-[B10H10]2- and closo-[B12H12]2- anions

It has been shown by IR and NMR spectroscopy that cyclic trimeric perfluoro-o-phenylenemercury (o-C6F4-Hg)3 (1) is capable of binding closo-[B10H10]2- and closo-[B12H12]2- anions to form complexes [[(o-C6F4Hg)3](B10-H10)]2- (2), [[(o-C6F4Hg)3]2(B10H10)]2-(3), [[(o-C6F4Hg)3](B12H12)]2- (4), and [[(o-C6F4Hg)3]2(B12H12)]2- (5). According to IR data, the bonding of the [B10H10]2- and [B12H12]2- ions to the macrocycle in these complexes is accomplished through the formation of B-H-Hg bridges. Complexes 2, 3, and 5 have been isolated in analytically pure form and have been characterized by spectroscopic means. X-ray diffraction studies of 3 and 5 have revealed that these compounds have unusual sandwich structures, in which the polyhedral di-anion is located between the planes of two molecules of 1 and is bonded to each of them through two types of B-H-Hg bridges. One type is the simultaneous coordination of a B-H group to all three Hg atoms of the macrocycle. The other type is the coordination of a B-H group to a single Hg atom of the cycle. According to X-ray diffraction data, complex 2 has an analogous but half-sandwich structure. The obtained complexes 2-5 are quite stable; their stability constants in THF/acetone (1:1) at 20 degrees C have been determined as 1.0 x 10(2)Lmol(-1), 2.6 x 10(3)L(2)mol(2), 0.7 x 10(2)Lmol(-1), and 0.98 x 10(3)L(2)mol(-2), respectively.     

Small Heteroborane Cluster Systems. 6. Mössbauer Effect Study of Iron Substituted Small Metallaborane Clusters

The M?ssbauer effect spectra for a series of small [Fe(eta(5)-C(5)H(5))(CO)(x)()] substituted metallaborane complexes are reported, where x = 1 or 2. The pentaborane cage in compounds [Fe(eta(5)-C(5)H(5))(CO)(2)B(5)H(7)P(C(6)H(5))(2)] (1), [Fe(eta(5)-C(5)H(5))(CO)(2)B(5)H(8)] (2), and [(Fe(eta(5)-C(5)H(5))(CO)(2))(2)B(5)H(7)] (3) was found to act as a significantly better donor ligand than the ligands in a comparison group of previously reported [Fe(eta(5)-C(5)H(5))(CO)LX] complexes, where L = CO or PPh(3) and X = halide, pseudohalide, or alkyl ligands. These metallaborane complexes were found to most resemble their silyl analogues in M?ssbauer spectral parameters and the electronic distribution around the iron centers. In addition, the M?ssbauer data showed that the [&mgr;-2,3-(P(C(6)H(5))(2)B(5)H(7)](-) ligand was a superior donor to the corresponding unsubstituted [B(5)H(8)](-) ligand. The M?ssbauer spectral results for the metallaborane complexes studied were found to be in general agreement with the anticipated donor and accepting bonding considerations for the cage ligands based upon their infrared and (11)B NMR spectra and X-ray structural features. The M?ssbauer data for the [Fe(eta(5)-C(5)H(5))(CO)B(4)H(6)(P(C(6)H(5))(2))] (4) and [Fe(eta(5)-C(5)H(5))(CO)B(3)H(7)(P(C(6)H(5))(2))] (5) complexes, in comparison with compound 1, showed that as the borane cage becomes progressively smaller, it becomes a poorer donor ligand. A qualitative relationship was found between the observed M?ssbauer isomer shift data and the number of boron cage vertices for the structurally related [Fe(eta(5)-C(5)H(5))(CO)(x)B(y)H(z)P(C(6)H(5))(2)] complexes, where x = 1 or 2, y = 3-5, and z = 6 or 7. The X-ray crystallographic data for compounds 1, 2, 5, and [Fe(eta(5)-C(5)H(5))(CO)B(5)H(8)] (6) were also found to agree with the trends observed in the M?ssbauer spectra which showed that the s-electron density on the iron nucleus increases in the order 5 < 6 < 2 < 1. The X-ray crystal structure of complex 2 is also reported. Crystallographic data for 2: space group P2(1)/c (No. 14, monoclinic), a = 6.084(3) ?, b = 15.045(8) ?, c = 13.449(7) ?, beta = 99.69(5) degrees, V = 1213(1) ?(3), Z = 4 molecules/cell.     

Domain-specific incorporation of noninvasive optical probes into recombinant proteins

An integrated approach is described that allows the domain-specific incorporation of optical probes into large recombinant proteins. The strategy is the combination of two existing techniques, expressed protein ligation (EPL) and in vivo amino acid replacement of tryptophans with tryptophan (Trp) analogues. The Src homology 3 (SH3) domain from the c-Crk-I adaptor protein has been labeled with a Trp analogue, 7-azatryptophan (7AW), using Escherichia coli Trp auxotrophs. Structural, biochemical, and thermodynamic studies show that incorporation of 7AW does not significantly perturb the structure or function of the isolated domain. Ligation of the 7AW-labeled SH3 domain to the c-Crk-I Src homology 2 (SH2) domain, via EPL, generated the multidomain protein, c-Crk-I, with a domain-specific label. Studies of this labeled protein show that the biochemical and thermodynamic properties of the SH3 domain do not change within the context of a larger multidomain protein. The technology described here is likely to be a useful tool in enhancing our understanding of the behavior of modular domains in their natural context, within multidomain proteins.     

Formation of functional heterologous complexes using subunits from the picromycin, erythromycin and oleandomycin polyketide synthases

BACKGROUND: Recently developed tools for the genetic manipulation of modular polyketide synthases (PKSs) have advanced the development of combinatorial biosynthesis technologies for drug discovery. Although many of the current techniques involve engineering individual domains or modules of the PKS, few experiments have addressed the ability to combine entire protein subunits from different modular PKSs to create hybrid polyketide pathways. We investigated this possibility by in vivo assembly of heterologous PKS complexes using natural and altered subunits from related macrolide PKSs. RESULTS: The pikAI and pikAII genes encoding subunits 1 and 2 (modules 1-4) of the picromycin PKS (PikPKS) and the eryAIII gene encoding subunit 3 (modules 5-6) of the 6-deoxyerythronolide B synthase (DEBS) were cloned in two compatible Streptomyces expression vectors. A strain of Streptomyces lividans co-transformed with the two vectors produced the hybrid macrolactone 3-hydroxynarbonolide. Co-expression of the same pik genes with the gene for subunit 3 of the oleandomycin PKS (OlePKS) was also successful. A series of hybrid polyketide pathways was then constructed by combining PikPKS subunits 1 and 2 with modified DEBS3 subunits containing engineered domains in modules 5 or 6. We also report the effect of junction location in a set of DEBS-PikPKS fusions. CONCLUSIONS: We show that natural as well as engineered protein subunits from heterologous modular PKSs can be functionally assembled to create hybrid polyketide pathways. This work represents a new strategy that complements earlier domain engineering approaches for combinatorial biosynthesis in which complete modules or PKS protein subunits, in addition to individual enzymatic domains, are used as building blocks for PKS engineering.     

Structural basis for efficient chromophore communication and energy transfer in a constructed didomain protein scaffold

The construction of useful functional biomolecular components not currently part of the natural repertoire is central to synthetic biology. A new light-capturing ultra-high-efficiency energy transfer protein scaffold has been constructed by coupling the chromophore centers of two normally unrelated proteins: the autofluorescent protein enhanced green fluorescent protein (EGFP) and the heme-binding electron transfer protein cytochrome b(562) (cyt b(562)). Using a combinatorial domain insertion strategy, a variant was isolated in which resonance energy transfer from the donor EGFP to the acceptor cyt b(562) was close to 100% as evident by virtually full fluorescence quenching on heme binding. The fluorescence signal of the variant was also sensitive to the reactive oxygen species H(2)O(2), with high signal gain observed due to the release of heme. The structure of oxidized holoprotein, determined to 2.75 ? resolution, revealed that the two domains were arranged side-by-side in a V-shape conformation, generating an interchromophore distance of ～17 ? (14 ? edge-to-edge). Critical to domain arrangement is the formation of a molecular pivot point between the two domains as a result of different linker sequence lengths at each domain junction and formation of a predominantly polar interdomain interaction surface. The retrospective structural analysis has provided an explanation for the basis of the observed highly efficient energy transfer through chromophore arrangement in the directly evolved protein scaffold and provides an insight into the molecular principles by which to design new proteins with coupled functions.