Crystallization of immunoglobulin Fab fragments specific for DNA

The purification and crystallization of Fab fragments of two mouse monoclonal immunoglobulins specific for different DNA structures are described. In each case, papain digestion of the immunoglobulins produced a mixture of Fab species differing in their isoelectric points. Purification of one of these species was required to obtain suitable crystals. One of these antibodies, Jel 72, is specific for right-handed duplex poly(dG).poly(dC). An Fab fragment of Jel 72 with a pI of 8.8 was purified by anion-exchange chromatography and used to obtain crystals from 56% saturated ammonium sulfate and 50 mM sodium acetate, pH 4.2, that diffract to 2.6-A resolution. They belong to the orthorhombic space group P2(1)2(1)2(1), with cell dimensions of a = 94.6, b = 102.6, c = 92.4 A. The other antibody, Jel 318, binds triple-stranded DNA poly[d(Tm5C)].poly[d(GA)].poly[d(m5C + T)]. Jel 318 Fab fragments with isoelectric points of 7.6 and 7.8 were also purified by anion-exchange chromatography, and crystals were obtained from 12% polyethylene glycol 8000, 50 mM NaCl, and 10 mM Tris.HCl, pH 7.8. These crystals diffract to about 2.4-A resolution and also belong to the orthorhombic space group P2(1)2(1)2(1), with cell dimensions of a = 82.4, b = 139.5, and c = 42.0 A. For both Fab fragments, crystal size and quality improved dramatically upon purification of an individual isoelectric species.     

Characterization of matrix-bound Band 3, the anion transport protein from human erythrocyte membranes

Band 3 (Mr = 95,000), the anion transport protein of human erythrocyte membranes exists primarily as a dimer in solutions of nonionic detergents such as octaethylene glycol mono-n-dodecyl ether (C12E8). The role of the oligomeric structure of Band 3 in the binding of [14C]4-benzamido-4'-aminostilbene-2,2'-disulfonate (BADS), an inhibitor of anion transport (Ki = 1-2 microM), was studied by characterizing the interaction of BADS with dimers and monomers of Band 3 covalently attached to p-mercuribenzoate-Sepharose 4B. BADS bound to matrix-bound Band 3 dimers with an affinity of approximately 3 microM at a stoichiometry of 1 BADS molecule/Band 3 monomer, in agreement with the BADS binding characteristic of Band 3 in the membrane and in solutions of C12E8. Band 3 dimers could be attached to the matrix via one subunit by limiting the amount of p-chloromercuribenzoate on the Sepharose bead. Matrix-bound monomers were formed by dissociation of the dimers with dodecyl sulfate or guanidine hydrochloride. Complete removal of the denaturants allowed formation of refolded Band 3 monomers since the matrix-bound subunits could not reassociate. These refolded Band 3 monomers were unable to bind BADS. Release of the monomers from the matrix with 2-mercaptoethanol allowed reformation of dimers with recovery of the BADS binding sites. These results suggest that the dimeric structure of Band 3 is required for BADS binding and that the BADS binding sites may be at the interface between the two halves of the Band 3 dimer.     

mtDNA diversity in rhesus monkeys reveals overestimates of divergence time and paraphyly with neighboring species

Reconstructions of the human-African great ape phylogeny by using mitochondrial DNA (mtDNA) have been subject to considerable debate. One confounding factor may be the lack of data on intraspecific variation. To test this hypothesis, we examined the effect of intraspecific mtDNA diversity on the phylogenetic reconstruction of another Plio- Pleistocene radiation of higher primates, the fascicularis group of macaque (Macaca) monkey species. Fifteen endonucleases were used to identify 10 haplotypes of 40-47 restriction sites in M. mulatta, which were compared with similar data for the other members of this species group. Interpopulational, intraspecific mtDNA diversity was large (0.5%- 4.5%), and estimates of divergence time and branching order incorporating this variation were substantially different from those based on single representatives of each species. We conclude that intraspecific mtDNA diversity is substantial in at least some primate species. Consequently, without prior information on the extent of genetic diversity within a particular species, intraspecific variation must be assessed and accounted for when reconstructing primate phylogenies. Further, we question the reliability of hominoid mtDNA phylogenies, based as they are on one or a few representatives of each species, in an already depauperate superfamily of primates.      

Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis

The first three-dimensional structure of phenylalanine ammonia lyase (PAL) has been determined at 2.1 A resolution for PAL from Rhodosporidium toruloides. The enzyme is structurally similar to the mechanistically related histidine ammonia lyase (HAL), with PAL having an additional approximately 160 residues extending from the common fold. We propose that catalysis (including lowering the pK(a) of nonacidic C3 of l-phenylalanine for an E1cb mechanism) is potentially governed by dipole moments of seven alpha helices associated with the PAL active site (six positive poles and one negative pole). Cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) resides atop the positive poles of three helices, for increasing its electrophilicity. The helix dipoles appear fully compatible with a model of phenylalanine docked in the active site of PAL having the first covalent bond formed between the amino group of substrate and the methylidene group of MIO: 12 highly conserved residues (near the N termini of helices for enhancing function) are poised to serve roles in substrate recognition, MIO activation, product separation, proton donation, or polarizing electrons from the phenyl ring of substrate for activation of C3; and a highly conserved His residue (near the C terminus of the one helix that directs its negative pole toward the active site to increase the residue's basicity) is positioned to act as a general base, abstracting the pro-S hydrogen from C3 of substrate. A similar mechanism is proposed for HAL, which has a similar disposition of seven alpha helices and similar active-site residues. The helix dipoles appear incompatible with a proposed mechanism that invokes a carbocation intermediate.     

Crystallization and preliminary X-ray crystallographic analysis of verotoxin-1 B-subunit

The B-subunit of verotoxin-1, which is believed to form a pentamer (monomer Mr = 7691), has been crystallized by vapor diffusion over a wide range of conditions. The best crystals, obtained with polyethylene glycol 8000 as the precipitant, belong to the orthorhombic space group P2(1)2(1)2(1), with cell dimensions a = 59.2 A, b = 102.7 A, c = 56.3 A. The cell dimensions are consistent with one B-subunit pentamer per asymmetric unit, and the crystals diffract to at least 2.0 A resolution. Data collected using synchrotron radiation at a wavelength of 2.070 A may allow the structure to be solved using the anomalous signal from three sulfur atoms in the monomer, combined with averaging over the non-crystallographic symmetry.     

The binary phase behavior of 1, 3-dipalmitoyl-2-stearoyl-sn-glycerol and 1, 2-dipalmitoyl-3-stearoyl-sn-glycerol

The binary phase behavior of purified 1, 3-dipalmitoyl-2-stearoyl-sn-glycerol (PSP) and 1, 2-dipalmitoyl-3-stearoyl-sn-glycerol (PPS) was investigated at a very slow (0.1 °C/min) and a relatively fast (3.0 °C/min) cooling rate. Mixtures with molar fractions of 0.1 increments were studied in terms of melting and crystallization, polymorphism, solid fat content (SFC), hardness and microstructure. Only the α-form of a double chain length (DCL) structure was detected for all mixtures in both experiments. The kinetic phase diagram, constructed using heating DSC thermograms, displayed two distinct behaviors separated by a singularity at the 0.5_PSP composition: a eutectic in the X_PSP ≤ 0.5 and a monotectic in the X_PSP ≤ 0.5 concentration region. The singularity was attributed to the formation of a 1:1 (mol:mol) molecular compound. Apart from the segment from 0.0_PSP to the eutectic point, X_E, the simulation of the liquidus line using a model based on the Hildebrand equation suggested that the molecular interactions are strong and tend to favor the formation of unlike pairs in the liquid state and that the miscibility is not significantly dependent on cooling rate. The kinetic effects are manifest in all measured properties, particularly dramatically in the X_PSP ≤ X_E concentration region. An analysis of induction time as measured by pulse nuclear magnetic resonance (pNMR) showed that PPS retards crystal growth, an effect which can explain the peculiarity of this concentration region. At both cooling rates, fit of the SFC (%) versus time curves to a modified form of the Avrami model revealed two common growth modes for all the mixtures. The polarized light microscope (PLM) of the PSP-PPS mixtures revealed networks made of spherulitic crystallites of size, growth direction and boundaries that are varied and sensitive to composition and cooling rate. The change in the microstructure and final SFC (%), particularly noticeable at compositions close to the eutectic, explain in part the differences seen in relative hardness.     

An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1

The Ser/Thr protein kinase PINK1 phosphorylates the well‐folded, globular protein ubiquitin (Ub) at a relatively protected site, Ser65. We previously showed that Ser65 phosphorylation results in a conformational change in which Ub adopts a dynamic equilibrium between the known, common Ub conformation and a distinct, second conformation wherein the last β‐strand is retracted to extend the Ser65 loop and shorten the C‐terminal tail. We show using chemical exchange saturation transfer (CEST) nuclear magnetic resonance experiments that a similar, C‐terminally retracted (Ub‐CR) conformation also exists at low population in wild‐type Ub. Point mutations in the moving β5 and neighbouring β‐strands shift the Ub/Ub‐CR equilibrium. This enabled functional studies of the two states, and we show that while the Ub‐CR conformation is defective for conjugation, it demonstrates improved binding to PINK1 through its extended Ser65 loop, and is a superior PINK1 substrate. Together our data suggest that PINK1 utilises a lowly populated yet more suitable Ub‐CR conformation of Ub for efficient phosphorylation. Our findings could be relevant for many kinases that phosphorylate residues in folded protein domains.     

The binary phase behavior of 1,3-dilauroyl-2-stearoyl-sn-glycerol and 1,2-dilauroyl-3-stearoyl-sn-glycerol

The binary phase behavior of purified 1,3-dilauroyl-2-stearoyl-sn-glycerol (LSL) and 1,2-dilauroyl-3-stearoyl-sn-glycerol (LLS) was investigated at a slow (0.1 °C/min) and a relatively fast (3.0 °C/min) cooling rate in terms of melting and crystallization, polymorphism, solid fat content (SFC), hardness and microstructure. Much of the behavior of the system is explained by its polymorphism and the influence of thermal processing. The α-form and the β′-form of a double chain length structure were detected in the mixtures cooled at 3.0 °C/min, whereas only the β′-form was detected in those cooled at 0.1 °C/min. X-ray diffraction data as well as thermodynamic data propose that the most stable phases are promoted by the symmetrical LSL. The measured trends in structural characteristics, thermal properties, SFC, relative hardness and microstructure delimit three groups of mixtures which imply a competition between the stabilizing effect of LSL and disordering introduced by kinetic effects: (a) LLS-rich mixtures with LSL molar fractions (X_LSL) less than 0.3, (b) mixtures with X_LSL clustered around 0.5 and (c) LSL-rich mixtures with X_LSL ≥ 0.7. The balance between ordering and kinetic effects determines the polymorphism of the mixtures, which in turn determines the behavior of the LSL/LLS system. The kinetic phase diagram of the LSL/LLS binary system constructed using heating differential scanning calorimetry thermograms displayed a singularity at the 0.5_LSL molar fraction which delimits two distinct behaviors: eutectic behavior in one region and monotectic behavior in the other. The molecular interactions, as depicted by a non-ideality parameter of mixing obtained from a thermodynamic model based on the Hildebrand equation, suggests an almost ideal mixing behavior and a moderate tendency to the formation of unlike-pairs in the liquid state.