Conformations of lasalocid A-lithium complexes in acetonitrile

The interaction of the ionophore antibiotic lasalocid-A with lithium perchlorate in acetonitrile has been studied by circular dichroism (c.d.) and 1H, 13C and 7Li nuclear magnetic resonance (n.m.r.) techniques. Analysis of the c.d. data has shown that both the 2:1 sandwich (ionophore-cation-ionosphore) complex and 1:1 complex coexist in solution. The n.m.r. data are consistent with a conformational model in which the carbonyl oxygen, he tetrahydrofuran and the tetrahydropyran ring oxygen atoms, two hydroxyl group oxygens and either a water or a solvent molecule coordinate to the lithium ion.

Solution structure of O-glycosylated C-terminal leucine zipper domain of human salivary mucin (MUC7)

Solution structures of a 23 residue glycopeptide II (KIS* RFLLYMKNLLNRIIDDMVEQ, where * denotes the glycan Gal-beta-(1-3)-alpha-GalNAc) and its deglycosylated counterpart I derived from the C-terminal leucine zipper domain of low molecular weight human salivary mucin (MUC7) were studied using CD, NMR spectroscopy and molecular modeling. The peptide I was synthesized using the Fmoc chemistry following the conventional procedure and the glycopeptide II was synthesized incorporating the O-glycosylated building block (N alpha-Fmoc-Ser-[Ac-4,-beta-D-Gal-(1,3)-Ac(2)alpha-D-GalN(3)]-OPfp) at the appropriate position in stepwise assembly of peptide chain. Solution structures of these glycosylated and nonglycosylated peptides were studied in water and in the presence of 50% of an organic cosolvent, trifluoroethanol (TFE) using circular dichroism (CD), and in 50% TFE using two-dimensional proton nuclear magnetic resonance (2D H-1 NMR) spectroscopy. CD spectra in aqueous medium indicate that the apopeptide I adapts, mostly, a beta-sheet conformation whereas the glycopeptide II assumes helical structure. This transition in the secondary structure, upon glycosylation, demonstrates that the carbohydrate moiety exerts significant effect on the peptide backbone conformation. However, in 50% TFE both the peptides show pronounced helical structure. Sequential and medium range NOEs, C alpha H chemical shift perturbations, (3)J(NH:C alpha H) couplings and deuterium exchange rates of the amide proton resonances in water containing 50% TFE indicate that the peptide I adapts alpha-helical structure from Ile2-Val21 and the glycopeptide II adapts alpha-helical structure from Ser3-Glu22. The observation of continuous stretch of helix in both the peptides as observed by both NMR and CD spectroscopy strongly suggests that the C-terminal domain of MUC7 with heptad repeats of leucines or methionine residues may be stabilized by dimeric leucine zipper motif. The results reported herein may be invaluable in understanding the aggregation (or dimerization) of MUC7 glycoprotein which would eventually have implications in determining its structure-function relationship.

Lipid-amphotericin B complex structure in solution: A possible first step in the aggregation process in cell membranes

The interactions between the polyene antibiotic amphotericin B with dipalmitoylphosphatidylcholine were investigated in vesicles (using circular dichroism) and in chloroform solution (using circular dichroism and IH, I3C, and 31P nuclear magnetic resonance). The results show that amphotericin B readily aggregates in vesicles and that the extent of aggregation depends on the 1ipid:drug concentration ratio. Introduction of sterol molecules into the membrane hastens the process of aggregation of amphotericin B. In chloroform solutions amphotericin B strongly interacts with phospholipid molecules to form a stoichiometric complex. The results suggest that there are interactions between the conjugated heptene stretch of amphotericin B and the methylene groups of lipid acyl chains, while the sugar moiety interacts with the phosphate head group by the formation of a hydrogen bond. A model is proposed for the lipid-amphotericin B complex, in which amphotericin B interacts equally well with the two lipid acyl chains, forming a 1:l complex.

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

Calcium ionophore, A23187 and its amino acid complexes: spectroscopic and molecular modeling studies.

The circular dichroism, fluorescence, Nuclear Magnetic Resonance and BLM conductance studies indicate that A23187 forms a stable complex with amino acids at low ionophore concentrations (<10(-4)M). However, A23187 prefers to be in a dimeric structure with no significant binding to amino acids, at concentrations higher than 10(-4)M. It was also observed that at lower concentrations, at which the amino acids bind to the ionophore, the affinity for calcium ions was several orders of magnitude lower than that at higher ionophore concentrations. We have also conducted molecular modeling studies to examine the structure of the A23187 dimer and its amino acid complexes. The results of these modeling studies strongly support our experimental results and validate the formation of a hydrogen bonded and energetically stable A23187 dimer and its amino acid complexes.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages.

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation. © 2013 Elsevier Ltd.

In situ circular dichroic electrochemical study of bilirubin and bovine serum albumin complex

The electrooxidation of bilirubin (BR) and bovine serum albumin (BSA) complexes was studied by in situ circular dichroism (CD) spectroelectrochemistry. The result showed that the mechanism of the whole electrooxidation process of this complex corresponded to electrochemical processes (EE mechanism) in aqueous solution. Some parameters of the process were obtained by double logarithm method, differential method and nonlinear regression method. In visible region, CD spectra of the two enantiomeric components of the complex and their fraction distribution against applied potentials were obtained by singular value decomposition least-square (SVDLS) method. Meanwhile, the distribution of the five components of secondary structure was also obtained by the same method in far-UV region. The peak potential gotten from EE mechanism corresponds to a turning point for the component transition, beyond which the whole reaction reaches a new equilibrium. Under applied positive potentials, the enantiomeric equilibrium between M and P form is broken and M form transfers to its enantiomer of P, while the fraction of alpha-helix increases and that improves the transition to P form.

Investigation of ergosterol in situ circular dichroic spectroelectrochemistry

In the present paper, the electrochemical behavior of ergosterol has been investigated by in situ circular dichroism (CD) spectroelectrochemistry with long path-length thin layer cell. E-0 (1.02V), alpha n(alpha) (0.302) of the electroxidation process of ergosterol were obtained from the CD spectroelectrochemical data. The mechanism of the electroxidation process of ergosterol is suggested.

Engineering new strategies to improve pharmacokinetics of therapeutic proteins

Tese de doutoramento, Farmácia (Biotecnologia Farmacêutica), Universidade de Lisboa, Faculdade de Farmácia, 2014

Novos polímeros conjugados baseados em calixarenos contendo fontes quirais de origem natural: síntese, propriedades e aplicações sensoriais

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Química e Biológica

Identification of a novel determinant for membrane association in hepatitis C virus nonstructural protein 4B.

Nonstructural protein 4B (NS4B) plays an essential role in the formation of the hepatitis C virus (HCV) replication complex. It is a relatively poorly characterized integral membrane protein predicted to comprise four transmembrane segments in its central portion. Here, we describe a novel determinant for membrane association represented by amino acids (aa) 40 to 69 in the N-terminal portion of NS4B. This segment was sufficient to target and tightly anchor the green fluorescent protein to cellular membranes, as assessed by fluorescence microscopy as well as membrane extraction and flotation analyses. Circular dichroism and nuclear magnetic resonance structural analyses showed that this segment comprises an amphipathic alpha-helix extending from aa 42 to 66. Attenuated total reflection infrared spectroscopy and glycosylation acceptor site tagging revealed that this amphipathic alpha-helix has the potential to traverse the phospholipid bilayer as a transmembrane segment, likely upon oligomerization. Alanine substitution of the fully conserved aromatic residues on the hydrophobic helix side abrogated membrane association of the segment comprising aa 40 to 69 and disrupted the formation of a functional replication complex. These results provide the first atomic resolution structure of an essential membrane-associated determinant of HCV NS4B.

The Synthesis and Coordination Chemistry of Two Families of Polydentate Ligands - Exploring Their Potential for the Preparation of Molecule-Based Magnets

The synthesis and studies of two classes of poly dentate ligands are presented as two projects. In project 1, four new carboxamide ligands have been synthesised via the condensation of 2,2',6,6'-tetrachloroformyl-4,4'-bipyridine or 2,6-dichloroformyl pyridine together with heterocyclic amines containing pyridine or pyrazole substituents. The coordination chemistry of these ligands has been investigated and studies have shown that with a Cu(II) salt, two carboxamide ligands LJ and L2 afford large clusters with stoichiometries [Cu8(L1)4Cl16].CHCl3.5H2O.7CH3OH (I) and [Cu9(L2)6Cl6].CH3OH.5H2O.(C2H5)3N (II) respectively. [molecular diagram availabel in pdf]. X-ray diffraction studies of cluster (I) reveal that it has approximate S4 symmetry and is comprised of four ligands and eight copper (II) centers. Here, coordination takes place via amide 0 atoms, and pyrazole nitrogens. This complex is the first reported example of an octanuclear copper cluster with a saddle-shaped structure. The second cluster comprises nine copper ions that are arranged in a cyclic array. Each ligand coordinates three copper centers and each copper ion shares two ligands to connect six ligands with nine copper ions. The amide nitrogens are completely deprotonated and both amide Nand 0 atoms coordinate the metal centres. The cluster has three-fold symmetry. There are six chloride ions, three of which are bridging two neighbouring Cu(II) centres. Magnetic studies of (I) and (II) reveal that both clusters display weak antiferromagnetic interactions between neighbouring Cu(II) centers at low temperature. In the second project, three complexes with stoichiometries [Fe[N302](SCN)2]2 (III), R,R-[Fe[N3O2](SCN)2 (IV) and R,R-]Fe[N3O2](CN)2] (V) were prepared and characterized, where [N302] is a pentadentate macrocycle. Complex (III) was prepared via the metal templated Schiff-base condensation of 2,2',6,6'-tetraacetyl-4,4'-bipyridine together with 3,6-dioxaoctane-I,8-diamine and comprises of a dimeric macro cycle where the two Fe(II) centres are in a pentagonal-bipyramidal environment with the [N302] ligands occupying the equatorial plane and two axial NCS ligands. Complexes (IV) and (V) were prepared via the condensation of 2,6-diacetylpyridine together with a chiral diamine in the presence of FeCh. The synthetic strategy for the preparation of the chiral diamine (4R,5R)-4,5-diphenyl-3,6-dioxa-I,8-octane-diamine was elucidated. The chirality of both macrocycles (IV) and (V) was probed by circular dichroism spectroscopy. The crystal structure of (IV) at 200 K contains two independent molecules in the unit cell, both of which contain a hepta-coordinated Fe(II) and axial NCS ligands. Variable temperature magnetic susceptibility and structural studies are consistent with a high spin Fe(II) complex and show no evidence of any spin crossover behaviour. In contrast, the bis cyanide derivative (V) crystallizes with two independent molecules in the unit cell, both of which have different coordination geometries consistent with different spin states for the two Fe(II) centres. At 250 K, the molecular structure of (V) shows the presence of both 7- and a 6-coordinate Fe(II) complexes in the crystal lattice. As the temperature is lowered, the molecules undergo a structural change and at 100 K the structural data is consistent with a 6- and 5-coordinate Fe(II) complex in the unit cell. Magnetic studies confirm that this complex undergoes a gradual, thermal, spin crossover transition in the solid state. Photomagnetic measurements indicate this is the first chiral Fe (II) sea complex to exhibit a LIESST.

Ligand Design for Dual Property Single Molecule Magnets

This thesis describes two different approaches for the preparation of polynuclear clusters with interesting structural, magnetic and optical properties. Firstly, exploiting p-tert-butylcalix[4]arene (TBC4) macrocycles together with selected Ln(III) ions for the assembly of emissive single molecule magnets, and secondly the preparation and coordination of a chiral mpmH ligand with selected 3d transition metal ions, working towards the discovery of chiral polynuclear clusters. In Project 1, the coordination chemistry of the TBC4 macrocycle together with Dy(III) and Tb(III) afforded two Ln6[TBC4]2 complexes that have been structurally, magnetically and optically characterized. X-ray diffraction studies reveal that both complexes contain an octahedral core of Ln6 ions capped by two fully deprotonated TBC4 macrocycles. Although the unit cells of the two complexes are very similar, the coordination geometries of their Ln(III) ions are subtly different. Variable temperature ac magnetic susceptibility studies reveal that both complexes display single molecule magnet (SMM) behaviour in zero dc field and the energy barriers and associated pre-exponential factors for each relaxation process have been determined. Low temperature solid state photoluminescence studies reveal that both complexes are emissive; however, the f-f transitions within the Dy6 complex were masked by broad emissions from the TBC4 ligand. In contrast, the Tb(III) complex displayed green emission with the spectrum comprising four sharp bands corresponding to 5D4 → 7FJ transitions (where J = 3, 4, 5 and 6), highlighting that energy transfer from the TBC4 macrocycle to the Tb(III) ion is more effective than to Dy. Examples of zero field Tb(III) SMMs are scarce in the chemical literature and the Tb6[TBC4]2 complex represents the first example of a Tb(III) dual property SMM assembled from a p-tert-butylcalix[4]arene macrocycle with two magnetically derived energy barriers, Ueff of 79 and 63 K. In Project 2, the coordination of both enantiomers of the chiral ligand, α-methyl-2-pyridinemethanol (mpmH) to Ni(II) and Co(II) afforded three polynuclear clusters that have been structurally and magnetically characterized. The first complex, a Ni4 cluster of stoichiometry [Ni4(O2CCMe3)4(mpm)4]·H2O crystallizes in a distorted cubane topology that is well known in Ni(II) cluster chemistry. The final two Co(II) complexes crystallize as a linear mixed valence trimer with stoichiometry [Co3(mpm)6]·(ClO4)2, and a Co4 mixed valence complex [Co(II)¬2Co(III)2(NO3)2(μ-mpm)4(ONO2)2], whose structural topology resembles that of a defective double cubane. All three complexes crystallize in chiral space groups and circular dichroism experiments further confirm that the chirality of the ligand has been transferred to the respective coordination complex. Magnetic susceptibility studies reveal that for all three complexes, there are competing ferro- and antiferromagnetic exchange interactions. The [Co(II)¬2Co(III)2(NO3)2(μ-mpm)4(ONO2)2] complex represents the first example of a chiral mixed valence Co4 cluster with a defective double cubane topology.