Functional drift of sequence attributes in the FK506-binding proteins (FKBPs)

Diverse members of the FK506-binding proteins (FKBPs) group and their complexes with different macrocyclic ligands of fungal origins such as FK506, rapamycin, ascomycin, and their immunosuppressive and nonimmunosuppressive derivatives display a variety of cellular and biological activities. The functional relatedness of the FKBPs was estimated from the following attributes of their aligned sequences: 1 degrees conservation of the consensus sequence; 2 degrees sequence similarity; 3 degrees pI; 4 degrees hydrophobicity; 5 degrees amino acid hydrophobicity and bulkiness profiles. Analyses of the multiple sequence alignments and intramolecular interaction networks calculated from a series of structures of the FKBPs revealed some variations in the interaction clusters formed by the AA residues that are crucial for sustaining peptidylprolyl cis/trans isomerases (PPIases) activity and binding capacity of the FKBPs. Fine diversification of the sequences of the multiple paralogues and orthologues of the FKBPs encoded in different genomes alter the intramolecular interaction patterns of their structures and allowed them to gain some selectivity in binding to diverse targets (functional drift).     

Involvement of some large immunophilins and their ligands in the protection and regeneration of neurons: a hypothetical mode of action

The powerful immunosuppressive drugs such as FK506 and its derivatives induce some regeneration and protection of neurons from ischaemic brain injury and some other neurological disorders. The drugs form complexes with diverse FKBPs but apparently the FKBP52/FK506 complex was shown to be involved in the protection and regeneration of neurons. We used several different sequence attributes in searching diverse genomic databases for similar motifs as those present in the FKBPs. A Fortran library of algorithms (Par_Seq) has been designed and used in searching for the similarity of sequence motifs extracted from the multiple sequence alignments of diverse groups of proteins (query motifs) and the target motifs which are encoded in various genomes. The following sequence attributes were used in the establishment of the degree of convergence between: (A) amino acid (AA) sequence similarity (ID) of the query/target motifs and (B) their: (1) AA composition (AAC); (2) hydrophobicity (HI); (3) Jensen-Shannon entropy; and (4) AA propensity to form a particular secondary structure. The sequence hallmark of two different groups of peptidylprolyl cis/trans isomerases (PPIases), namely tetratricopetide repeat (TPR) motifs, which are present in the heat-shock cyclophilins and in the large FK506-binding proteins (FKBPs) were used to search various genomic databases. The Par_Seq algorithm has revealed that the TPR motifs have similar sequence attributes as a number of hydrophobic sequence segments of functionally unrelated membrane proteins, including some of the TMs from diverse G protein-coupled receptors (GPCRs). It is proposed that binding of the FKBP52/FK506 complex to the membranes via the TPR motifs and its interaction with some membrane proteins could be in part responsible for some neuro-regeneration and neuro-protection of the brain during some ischaemia-induced stresses.     

Effects of oxygen and antioxidants on the <Emphasis Type="Italic">cis-trans</Emphasis>-isomerization of unsaturated fatty acids caused by thiyl radicals

The interaction of unsaturated compounds methyllinoleate and β-carotene with thiyl radicals occurred in exchange radical reactions with mercaptoethanol. β-Carotene was shown to be an effective thiyl radical acceptor. In the case of methyllinoleate, thiyl radicals catalyze cis/trans isomerization, which can be reduced by the natural antioxidant α-tocopherol; the cis/trans isomerization rate decreases in an oxygen atmosphere.     

The Molecular Basis of the Interaction of Cyclophilin A with α-Synuclein

Peptidylprolyl isomerases (PPIases) catalyze cis/trans isomerization of prolines. The PPIase CypA colocalizes with the Parkinson's disease (PD)-associated protein α-synuclein in cells and interacts with α-synuclein oligomers. Herein, we describe atomic insights into the molecular details of the α-synuclein/CypA interaction. NMR spectroscopy shows that CypA catalyzes isomerization of proline 128 in the C-terminal domain of α-synuclein. Strikingly, we reveal a second CypA-binding site formed by the hydrophobic sequence ⁴⁷GVVHGVATVA⁵⁶, termed PreNAC. The 1.38 Å crystal structure of the CypA/PreNAC complex displays a contact between alanine 53 of α-synuclein and glutamine 111 in the catalytic pocket of CypA. Mutation of alanine 53 to glutamate, as found in patients with early-onset PD, weakens the interaction of α-synuclein with CypA. Our study provides high-resolution insights into the structure of the PD-associated protein α-synuclein in complex with the most abundant cellular cyclophilin.     

Molecular chaperones, folding catalysts, and the recovery of active recombinant proteins fromE. coli

The high-level expression of recombinant gene products in the gramnegative bacteriumEscherichia coli often results in the misfolding of the protein of interest and its subsequent degradation by cellular proteases or its deposition into biologically inactive aggregates known as inclusion bodies. It has recently become clear that in vivo protein folding is an energy-dependent process mediated by two classes of folding modulators. Molecular chaperones, such as the DnaK-DnaJ-GrpE and GroEL-GroES systems, suppress off-pathway aggregation reactions and facilitate proper folding through ATP-coordinated cycles of binding and release of folding intermediates. On the other hand, folding catalysts (foldases) accelerate rate-limiting steps along the protein folding pathway such as thecis/trans isomerization of peptidyl-prolyl bonds and the formation and reshuffling of disulfide bridges. Manipulating the cytoplasmic folding environment by increasing the intracellular concentration of all or specific folding modulators, or by inactivating genes encoding these proteins, holds great promise in facilitating the production and purification of heterologous proteins. Purified folding modulators and artificial systems that mimic their mode of action have also proven useful in improving the in vitro refolding yields of chemically denatured polypeptides. This review examines the usefulness and limitations of molecular chaperones and folding catalysts in both in vivo and in vitro folding processes.     

Structural Investigations of 13-O-Demethyl-FK506 and Its Isomers Generated by in vitro Metabolism of FK506 Using Human-Liver Microsomes

FK506 is currently under investigation as immunosuppressant after organ transplantation and in immune diseases. The structure of a demethylated metabolite 1 of FK506 isolated after in vitro metabolism by human-liver microsomes was established using two-dimensional homo- and heteronuclear NMR experiments. The demethylation position was found to be at O? C(13) using HMBC spectra. In contrast to FK506, 7 different isomers could be differentiated in COSY, HMBC, and HMQC spectra. The intensity of their signals was 50:18:11:9:6:6 (one isomer could not be quantified). This isomerization may be explained by epimerization at C(10) or alternative formations of the hemiketal ring between C(10) and C(13) or C(9) and C(13), in addition to cis/trans-isomerism about the amide bond (see Scheme). The structural variation is possible by participation of the OH group at C(13) formed after demethylation and could be derived from HMBC spectra. Chemical exchange evidenced by ROESY spectra proved the rotational isomerism. NMR investigation of the structure of 13-O-demethyl-FK 506 ( 1 ) revealed at least seven isomers.     

The Molecular Basis of the Interaction of Cyclophilin A with α‐Synuclein

Peptidylprolyl isomerases (PPIases) catalyze cis/trans isomerization of prolines. The PPIase CypA colocalizes with the Parkinson's disease (PD)‐associated protein α‐synuclein in cells and interacts with α‐synuclein oligomers. Herein, we describe atomic insights into the molecular details of the α‐synuclein/CypA interaction. NMR spectroscopy shows that CypA catalyzes isomerization of proline 128 in the C‐terminal domain of α‐synuclein. Strikingly, we reveal a second CypA‐binding site formed by the hydrophobic sequence ⁴⁷GVVHGVATVA⁵⁶, termed PreNAC. The 1.38 Å crystal structure of the CypA/PreNAC complex displays a contact between alanine 53 of α‐synuclein and glutamine 111 in the catalytic pocket of CypA. Mutation of alanine 53 to glutamate, as found in patients with early‐onset PD, weakens the interaction of α‐synuclein with CypA. Our study provides high‐resolution insights into the structure of the PD‐associated protein α‐synuclein in complex with the most abundant cellular cyclophilin.     

Solvent Effects on the Energetics of Prolyl Peptide Bond Isomerization

Racemic Ac-Gly-[β,δ-(13)C]Pro-OMe was synthesized, and the kinetics and thermodynamics of the isomerization of its prolyl peptide bond were determined in nine solvents by using NMR and IR spectroscopy. The free energy of activation is 1.3 kcal/mol larger in water than in aprotic solvents, and correlates with the ability of a solvent to donate a hydrogen bond but not with solvent polarity. These results are consistent with conventional pictures of amide resonance, which require transfer of charge between oxygen and nitrogen during isomerization. Similar medium effects may modulate the stability of planar peptide bonds in the active site of peptidyl-prolyl cis-trans isomerases (PPIases) and during the folding, function, or lysis of proteins.     

Enzymes catalyzing protein folding and their cellular functions

In live cells, protein folding often cannot occur spontaneously, but requires the participation of helper proteins - molecular chaperones and foldases. The mechanisms employed by chaperones markedly increase the effectiveness of protein folding, but have no bearing on the rate of this process, whereas foldases actually accelerate protein folding by exerting a direct influence on the rate-limiting steps of the overall reaction. Two types of foldases are known, using different principles of action. Peptidyl-prolyl cis/trans isomerase and protein-disulfide isomerase catalyze the folding of every protein that needs isomerization of prolyl peptide bonds or formation and isomerization of disulfide bonds for proper folding. By contrast, some foldases operating in the periplasm of bacterial cells are specifically designed to help in the folding of substrate proteins whose primary structure does not contain sufficient information for correct folding. In this review, we discuss recent data on the catalytic mechanisms of both types of foldases, focusing specifically on how a catalyst provides the structural information required for the folding of a target protein. Comparative analysis of the mechanisms employed by two different periplasmic foldases is used to substantiate the notion that combinations of a protein which is unable to fold independently and a specific catalyst delivering the necessary steric information are probably designed to achieve some particular biological purposes. The review also covers the problem of participation of peptidyl-prolyl cis/trans isomerase in different cellular functions, highlighting the role of this enzyme in conformational rearrangements of folded native proteins.     

Crystallographic proof for an extended hydrogen-bonding network in small prolyl isomerases

Parvulins compose a family of small peptidyl-prolyl isomerases (PPIases) involved in protein folding and protein quality control. A number of amino acids in the catalytic cavity are highly conserved, but their precise role within the catalytic mechanism is unknown. The 0.8 ? crystal structure of the prolyl isomerase domain of parvulin Par14 shows the electron density of hydrogen atoms between the D74, H42, H123, and T118 side chains. This threonine residue has previously not been associated with catalysis, but a corresponding T152A mutant of Pin1 shows a dramatic reduction of catalytic activity without compromising protein stability. The observed catalytic tetrad is strikingly conserved in Pin1- and parvulin-type proteins and hence constitutes a common feature of small peptidyl prolyl isomerases.     

Epimerization and deuterium exchange studies in selected cis,trans-1-alkyl-2-aryl(alkyl)-3-aroylaziridines

A series of base catalyzed reactions performed on selected cis, trans-1-alkyl-2-aryl(alkyl)-3-aroylaziridines at room temperature reveal the cis isomer to be of greater thermodynamic stability. Furthermore, base catalyzed deuterium exchange studies suggest this to be the case. Solvent effects on the isomeric cis/trans ratios are also presented and discussed.     

Enantioselective Synthesis of a Tricyclic,sp3-Rich Diazatetradecanedione: an Amino Acid-Based Natural Product-Like Scaffold

6-, 7-, and 8-membered rings are assembled from a linear precursor by successive cyclisation reactions to construct a tricyclic diazatricyclo[6.5.1.0^{4, 9}]-tetradecanedione scaffold. Advanced building blocks based on d -aspartic acid and l -pyroglutamic acid were combined by a sp³−sp² Negishi coupling. A carbamate-guided syn-diastereoselective epoxidation followed by an intramolecular epoxide opening allowed the construction of the piperidine ring. An efficient one-pot hydroxyl-group protection twofold deprotection reaction prepared the ground for the cyclisation to the bicycle. A final deprotection of the orthogonal protecting groups and lactamisation led to the novel, sp³-rich tricycle. The final compound is a substrate mimic of peptidyl-prolyl cis-trans isomerases featuring a locked trans-amide bond. Cheminformatic analysis of 179 virtual derivatives indicates favourable physicochemical properties and drug-like characteristics. As proof of concept we, show a low micromolar activity in a fluorescence polarisation assay towards the FK506-binding protein 12.     

Steric and Electronic Effects of Bidentate Phosphine Ligands on Ruthenium(II)‐Catalyzed Hydrogenation of Carbon Dioxide

The reactivity difference between the hydrogenation of CO₂ catalyzed by various ruthenium bidentate phosphine complexes was explored by DFT. In addition to the ligand dmpe (Me₂PCH₂CH₂PMe₂), which was studied experimentally previously, a more bulky diphosphine ligand, dmpp (Me₂PCH₂CH₂CH₂PMe₂), together with a more electron‐withdrawing diphosphine ligand, PN^MeP (Me₂PCH₂N^MeCH₂PMe₂), have been studied theoretically to analyze the steric and electronic effects on these catalyzed reactions. Results show that all of the most favorable pathways for the hydrogenation of CO₂ catalyzed by bidentate phosphine ruthenium dihydride complexes undergo three major steps: cis–trans isomerization of ruthenium dihydride complex, CO₂ insertion into the Ru?H bond, and H₂ insertion into the ruthenium formate ion. Of these steps, CO₂ insertion into the Ru?H bond has the lowest barrier compared with the other two steps in each preferred pathway. For the hydrogenation of CO₂ catalyzed by ruthenium complexes of dmpe and dmpp, cis–trans isomerization of ruthenium dihydride complex has a similar barrier to that of H₂ insertion into the ruthenium formate ion. However, in the reaction catalyzed by the PN^MePRu complex, cis–trans isomerization of the ruthenium dihydride complex has a lower barrier than H₂ insertion into the ruthenium formate ion. These results suggest that the steric effect caused by the change of the outer sphere of the diphosphine ligand on the reaction is not clear, although the electronic effect is significant to cis–trans isomerization and H₂ insertion. This finding refreshes understanding of the mechanism and provides necessary insights for ligand design in transition‐metal‐catalyzed CO₂ transformation.     

Initiation of Radical Chain Reactions of Thiol Compounds and Alkenes without any Added Initiator: Thiol‐Catalyzed cis/trans Isomerization of Methyl Oleate

A kinetic study of the dodecanethiol‐catalyzed cis/trans isomerization of methyl oleate (cis‐ 2 ) without added initiator was performed by focusing on the initiation of the radical chain reaction. The reaction orders of the rate of isomerization were 2 and 0.5 for 1 and cis‐ 2 , respectively, and an overall kinetic isotope effect k_H/k_D of 2.8 was found. The initiation was shown to be a complex reaction. The electron‐donor/‐acceptor (EDA) complex of dodecanethiol ( 1 ) and cis‐ 2 formed in a pre‐equilibrium reacts with thiol 1 to give a stearyl and a sulfuranyl radical through molecule‐assisted homolysis (MAH) of the sulfur–hydrogen bond. Fragmentation of the latter gives the thiyl radical, which catalyzes the cis/trans isomerization. A computational study of the EDA complex, MAH reaction, and the sulfuranyl radical calculated that the activation energy of the isomerization was in good agreement with the experimental result of E_A=82 kJ M ^?1. Overall, the results may explain that the thermal generation of thiyl radicals without any initiator is responsible for many well‐known thermally initiated addition reactions of thiol compounds to alkenes and their respective polymerizations and for the low shelf‐life stability of cis‐unsaturated thiol compounds and of mixtures of alkenes and thiol compounds.     

Thermal- and UV-induced cis/trans isomerization of undoped polyacetylene films. An ESR and IR investigation

The UV- and thermal-induced cis→trans isomerization of undoped polyacetylene (PA) films has been investigated. The results have shown that temperature and UV light promote the isomerization of PA with a similar mechanism. We suggest that the formation of paramagnetic defects in trans PA takes place by bond rehybridization, in agreement with previous hypotheses, and that both spin concentration and spin delocalization depend on the temperature of isomerization. It was found that under UV irradiation thermal cis→trans isomerization of polyacetylene also takes place at temperatures at which the sole thermal treatment isomerization is much lower or nil, and we suggest that the possibility of preparing trans PA under relatively mild conditions may lead to a better material.     

Evidence for the Preservation of Native Inter- and Intra-Molecular Hydrogen Bonds in the Desolvated FK-Binding Protein·FK506 Complex Produced by Electrospray Ionization

It is now well established that electrospray ionization (ESI) is capable of introducing noncovalent protein assemblies into a desolvated environment, thereby allowing their analysis by mass spectrometry. The degree to which native interactions from the solution phase are preserved in this environment is less clear. Site-directed mutagenesis of FK506-binding protein (FKBP) has been employed to probe specific intra- and inter-molecular interactions within the complex between FKBP and its ligand FK506. Collisional activation of wild-type and mutant-FKBP?FK506 ions, generated by ESI, demonstrated that removal of native protein-ligand interactions formed between residues Asp37, Tyr82, and FK506 significantly destabilized the complex. Mutation of Arg42 to Ala42, or Tyr26 to Phe26 also resulted in lower energy dissociation of the FKBP·FK506 complex. Although these residues do not form direct H-bonds to FK506, they interact with Asp37, ensuring its correct orientation to associate with the ligand. Comparison with solution-based affinity measurements of these mutants has been discussed, including the stabilization afforded by ordered water molecules. Ion mobility spectrometry (IMS) has been employed to provide gas-phase structural information on the unfolding of the complexes. The [M + 6H](6+) complexes of the wild-type and mutants have been shown to resist unfolding and retain compact conformations. However, removal of the basic Arg42 residue was found to induce significant structural weakening of the [M + 7H](7+) complex when raised to dissociation-level energies. Overall, destabilization of the FKBP·FK506 complex, resulting from targeted removal of specific H-bonds, provides evidence for the preservation of these interactions in the desolvated wild-type complex.     

Photochemistry and photophysics of stilbene dendrimers and related compounds

The syntheses and reactions of photoresponsive dendrimers are described. Dendrimers with photoreversible stilbene cores undergo mutual cis–trans isomerization in organic solvents to give photostationary state mixtures of cis- and trans-isomers. Even stilbene dendrimers with molecular weights as high as 6500 underwent mutual cis–trans isomerization within the lifetime of the excited singlet state. The large dendron group surrounding the photoreactive core may affect the excited state properties of the core to induce the efficiency of photoisomerization and/or reduce the fluorescence efficiency. The photochemistry of stilbene dendrimers, with various types of dendron groups, azobenzene dendrimers and other photoresposive dendrimers is discussed.     

Electronic control of amide cis-trans isomerism via the aromatic-prolyl interaction

The cis-trans isomerization of prolyl amide bonds results in large structural and functional changes in proteins and is a rate-determining step in protein folding. We describe a novel electronic strategy to control cis-trans isomerization, based on the demonstration that interactions between aromatic residues and proline are tunable by aromatic electronics. A series of peptides of sequence TXPN, X = Trp, pyridylalanine, pentafluorophenylalanine, or 4-Z-phenylalanine derivatives (Z = electron-donating, electron-withdrawing, or electron-neutral substituents), was synthesized and Ktrans/cis analyzed by NMR. Electron-rich aromatic residues stabilized cis amide bond formation, while electron-poor aromatics relatively favored trans amide bond formation. A Hammett correlation between aromatic electronics and cis-trans isomerization was observed. These results indicate that the interaction between aromatic residues and proline, which is observed to stabilize cis amide bonds and is also a general stabilizing interaction ubiquitous in proteins and protein-protein complexes, is not stabilized exclusively by a classical hydrophobic effect. To a large extent, the aromatic-prolyl interaction is driven and controllable by an electronic effect between the aromatic ring pi-electrons and the proline ring, consistent with a C-H-pi interaction as the key stabilizing force. The aromatic-prolyl interaction is electronically tunable by 0.9 kcal/mol and is enthalpic in nature. In addition, by combining aromatic ring electronics and stereoelectronic effects using 4-fluoroprolines, we demonstrate broad tuning (2.0 kcal/mol) of cis-trans isomerism in tetrapeptides. We demonstrate a simple tetrapeptide, TWflpN, that exhibits 60% cis amide bond and adopts a type VIa1 beta-turn conformation.     

Light-induced cis/trans isomerization of cis-[Pd(L-S,O)2] and cis-[Pt(L-S,O)2] complexes of chelating N,N-dialkyl-N′-acylthioureas: key to the formation and isolation of trans isomers

Irradiation cis-[M(Lⁿ-S,O)₂] complexes (M = Pt^II, Pd^II) derived from N,N-dialkyl-N′-benzoylthioureas (HLⁿ) with various sources of intense visible polychromatic or monochromatic light with λ < 500 nm leads to light-induced cis?→?trans isomerization in organic solvents. In all cases, white light derived from several sources or monochromatic blue-violet laser 405 nm light, efficiently results in substantial amounts of the trans isomer appearing in solution, as shown by ¹H NMR and/or reversed-phase HPLC separation in dilute solutions at room temperature. The extent and relative rates of cis/trans isomerization induced by in situ laser light (λ = 405 nm) of cis-[Pd(L²-S,O)₂] was directly monitored by ¹H NMR and ¹⁹⁵Pt NMR spectroscopy of selected cis-[Pt(L-S,O)₂] compounds in chloroform-d; both with and without light irradiation allows the δ(¹⁹⁵Pt) chemical shifts cis/trans isomer pairs to be recorded. The cis/trans isomers appear to be in a photo-thermal equilibrium between the thermodynamically favored cis isomer and its trans counterpart. In the dark, the trans isomer reverts back to the cis complex in what is probably a thermal process. The light-induced cis/trans process is the key to preparing and isolating the rare trans complexes which cannot be prepared by conventional synthesis as confirmed by the first example of trans-[Pd(L-S,O)₂] characterized by single-crystal X-ray diffraction, deliberately prepared after photo-induced isomerization in acetonitrile solution.     

Synthesis and epimerization of 1-Alkyl-2-carbomethoxy-4-methyl (or phenyl)azetidines

A number of 1-alkyl-2-carbomethoxyazetidines have been prepared from the reaction of primary amines with α,γ-dibromoearbonyl compounds. A series of base catalyzed reactions performed on selected cis, trans-1-alkyl-2-carbomethoxy-4-alkyl(aryl)azetidines reveal the cis isomer to be of greater thermodynamic stability. Furthermore, base catalyzed deuterium exchange studies suggest this to be the case.