Photoinduced aggregation of a model antibody-drug conjugate.

During synthesis, purification, and especially storage, antibody-drug conjugates (ADCs) may be exposed to various types of light. Several of the drugs commonly conjugated to antibodies contain photosensitive functional groups. Exposure to light could generate an excited state of the drug that subsequently triggers drug and/or protein degradation. To mimic and study photoinduced ADC degradation, we designed a model ADC in which the monoclonal antibody (mAb) trastuzumab was treated with the amine-reactive probe eosin-5-isothiocyanate to yield an antibody-eosin conjugate (T-EO). Photoinduced degradation was monitored by size exclusion chromatography (SEC), dynamic light scattering (DLS), SDS-PAGE under reducing and nonreducing conditions, and MS/MS analysis. SEC analysis of the model ADC showed the formation of higher molecular weight species directly following a 20 W-hr/m(2) exposure of UVA light. DLS analysis of these samples showed the formation of larger soluble particles, and precipitate was observed 24 h post light exposure. These results were not seen in control samples of the model ADC that were shielded from light. Furthermore, these results were not seen in control samples containing mAb alone, suggesting that aggregation was the result of light exposure of the conjugate. Importantly, when eosin-5-isothiocyanate was added separately to solutions containing mAb (i.e., without conjugation), the extent of photoinduced aggregation was substantially less, indicating that the conjugation of the photosensitizer to the mAb specifically promoted photoinduced aggregation. Reducing and nonreducing SDS-PAGE suggested that photoinduced interchain covalent cross-linking occurred through a mechanism other than disulfide formation. Using peptide mapping and MS/MS analysis, we identified key peptides in the T-EO sequence that undergo photodegradation. Finally, we also show that cross-linking products formed in as little as 1 h of exposure to ambient light. These findings suggest that precautions should be taken to ensure minimal exposure to light during the synthesis, purification, and storage of ADCs containing photosensitive drugs.

New paradigm for allosteric regulation of Escherichia coli aspartate transcarbamoylase.

For nearly 60 years, the ATP activation and the CTP inhibition of Escherichia coli aspartate transcarbamoylase (ATCase) has been the textbook example of allosteric regulation. We present kinetic data and five X-ray structures determined in the absence and presence of a Mg(2+) concentration within the physiological range. In the presence of 2 mM divalent cations (Mg(2+), Ca(2+), Zn(2+)), CTP does not significantly inhibit the enzyme, while the allosteric activation by ATP is enhanced. The data suggest that the actual allosteric inhibitor of ATCase in vivo is the combination of CTP, UTP, and a divalent cation, and the actual allosteric activator is a divalent cation with ATP or ATP and GTP. The structural data reveals that two NTPs can bind to each allosteric site with a divalent cation acting as a bridge between the triphosphates. Thus, the regulation of ATCase is far more complex than previously believed and calls many previous studies into question. The X-ray structures reveal that the catalytic chains undergo essentially no alternations; however, several regions of the regulatory chains undergo significant structural changes. Most significant is that the N-terminal region of the regulatory chains exists in different conformations in the allosterically activated and inhibited forms of the enzyme. Here, a new model of allosteric regulation is proposed.

ViewMotions Rainbow: a new method to illustrate molecular motions in proteins.

The biological functions of many enzymes are often coupled with significant conformational changes. The end states of these conformational changes can often be determined by X-ray crystallography. These X-ray structures are snapshots of the two extreme conformations in which the macromolecule exists, but the dynamic movements between the states are not easily visualized in a two-dimensional illustration. Here we have developed a new method to visualize macromolecular motions called a ViewMotions Rainbow diagram. These diagrams show the initial and final states overlaid along with approximately 30 intermediate structures calculated by linear interpolation of the backbone coordinates of the initial and final states. This group of structures is then spectrally colored from the initial structure in blue to the final structure in red. ViewMotions Rainbow diagrams provide the reader with a much easier way to understand the macromolecular motions using a single two-dimensional illustration. Since producing these diagrams requires a number of different software packages, we have setup the ViewMotions Web Server (http://viewmotions.bc.edu) to automatically generate these diagrams from two Protein Data Bank files or from the Database of Macromolecular Movements (http://molmovdb.org).

Selectivity of the highly preorganized tetradentate ligand 2,9-di(pyrid-2-yl)-1,10-phenanthroline for metal ions in aqueous solution, including lanthanide(III) ions and the uranyl(VI) cation.

Some metal ion complexing properties of DPP (2,9-Di(pyrid-2-yl)-1,10-phenanthroline) are reported with a variety of Ln(III) (Lanthanide(III)) ions and alkali earth metal ions, as well as the uranyl(VI) cation. The intense π-π* transitions in the absorption spectra of aqueous solutions of 10(-5) M DPP were monitored as a function of pH and metal ion concentration to determine formation constants of the alkali-earth metal ions and Ln(III) (Ln = lanthanide) ions. It was found that log K(1)(DPP) for the Ln(III) ions has a peak at Ln(III) = Sm(III) in a plot of log K(1) versus 1/r(+) (r(+) = ionic radius for 8-coordination). For Ln(III) ions larger than Sm(III), there is a steady rise in log K(1) from La(III) to Sm(III), while for Ln(III) ions smaller than Sm(III), log K(1) decreases slightly to the smallest Ln(III) ion, Lu(III). This pattern of variation of log K(1) with varying size of Ln(III) ion was analyzed using MM (molecular mechanics) and DFT (density functional theory) calculations. Values of strain energy (∑U) were calculated for the [Ln(DPP)(H(2)O)(5)](3+) and [Ln(qpy)(H(2)O)(5)](3+) (qpy = quaterpyrdine) complexes of all the Ln(III) ions. The ideal M-N bond lengths used for the Ln(III) ions were the average of those found in the CSD (Cambridge Structural Database) for the complexes of each of the Ln(III) ions with polypyridyl ligands. Similarly, the ideal M-O bond lengths were those for complexes of the Ln(III) ions with coordinated aqua ligands in the CSD. The MM calculations suggested that in a plot of ∑U versus ideal M-N length, a minimum in ∑U occurred at Pm(III), adjacent in the series to Sm(III). The significance of this result is that (1) MM calculations suggest that a similar metal ion size preference will occur for all polypyridyl-type ligands, including those containing triazine groups, that are being developed as solvent extractants in the separation of Am(III) and Ln(III) ions in the treatment of nuclear waste, and (2) Am(III) is very close in M-N bond lengths to Pm(III), so that an important aspect of the selectivity of polypyridyl type ligands for Am(III) will depend on the above metal ion size-based selectivity. The selectivity patterns of DPP with the alkali-earth metal ions shows a similar preference for Ca(II), which has the most appropriate M-N lengths. The structures of DPP complexes of Zn(II) and Bi(III), as representative of a small and of a large metal ion respectively, are reported. [Zn(DPP)(2)](ClO(4))(2) (triclinic, P1, R = 0.0507) has a six-coordinate Zn(II), with each of the two DPP ligands having one noncoordinated pyridyl group appearing to be π-stacked on the central aromatic ring of the other DPP ligand. [Bi(DPP)(H(2)O)(2)(ClO(4))(2)](ClO(4)) (triclinic, P1, R = 0.0709) has an eight-coordinate Bi, with the coordination sphere composed of the four N donors of the DPP ligand, two coordinated water molecules, and the O donors of two unidentate perchlorates. As is usually the case with Bi(III), there is a gap in the coordination sphere that appears to be the position of a lone pair of electrons on the other side of the Bi from the DPP ligand. The Bi-L bonds become relatively longer as one moves from the side of the Bi containg the DPP to the side where the lone pair is thought to be situated. A DFT analysis of [Ln(tpy)(H(2)O)(n)](3+) and [Ln(DPP)(H(2)O)(5)](3+) complexes is reported. The structures predicted by DFT are shown to match very well with the literature crystal structures for the [Ln(tpy)(H(2)O)(n)](3+) with Ln = La and n = 6, and Ln = Lu with n = 5. This then gives one confidence that the structures for the DPP complexes generated by DFT are accurate. The structures generated by DFT for the [Ln(DPP)(H(2)O)(5)](3+) complexes are shown to agree very well with those generated by MM, giving one confidence in the accuracy of the latter. An analysis of the DFT and MM structures shows the decreasing O--O nonbonded distances as one progresses from La to Lu, with these distances being much less than the sum of the van der Waals radii for the smaller Ln(III) ions. The effect that such short O--O nonbonded distances has on thermodynamic complex stability and coordination number is then discussed.

Metal ion involvement in the allosteric mechanism of Escherichia coli aspartate transcarbamoylase.

Escherichia coli aspartate transcarbamoylase (ATCase) allosterically regulates pyrimidine nucleotide biosynthesis. The enzyme is inhibited by CTP and can be further inhibited by UTP, although UTP alone has little or no influence on activity; however, the mechanism for the synergistic inhibition is still unknown. To determine how UTP is able to synergistically inhibit ATCase in the presence of CTP, we determined a series of X-ray structures of ATCase·nucleotide complexes. Analysis of the X-ray structures revealed that (1) CTP and dCTP bind in a very similar fashion, (2) UTP, in the presence of dCTP or CTP, binds at a site that does not overlap the CTP/dCTP site, and (3) the triphosphates of the two nucleotides are parallel to each other with a metal ion, in this case Mg(2+), coordinated between the ß- and γ-phosphates of the two nucleotides. Kinetic experiments showed that the presence of a metal ion such as Mg(2+) is required for synergistic inhibition. Together, these results explain how the binding of UTP can enhance the binding of CTP and why UTP binds more tightly in the presence of CTP. A mechanism for the synergistic inhibition of ATCase is proposed in which the presence of UTP stabilizes the T state even more than CTP alone. These results also call into question many of the past kinetic and binding experiments with ATCase with nucleotides as the presence of metal contamination was not considered important.

A second allosteric site in Escherichia coli aspartate transcarbamoylase.

Escherichia coli aspartate transcarbamoylase is feedback inhibited by CTP and UTP in the presence of CTP. Here, we show by X-ray crystallography that UTP binds to a unique site on each regulatory chain of the enzyme that is near but not overlapping with the known CTP site. These results bring into question all of the previously proposed mechanisms of allosteric regulation in aspartate transcarbamoylase.

Crystallographic snapshots of the complete catalytic cycle of the unregulated aspartate transcarbamoylase from Bacillus subtilis.

Here, we report high-resolution X-ray structures of Bacillus subtilis aspartate transcarbamoylase (ATCase), an enzyme that catalyzes one of the first reactions in pyrimidine nucleotide biosynthesis. Structures of the enzyme have been determined in the absence of ligands, in the presence of the substrate carbamoyl phosphate, and in the presence of the bisubstrate/transition state analog N-phosphonacetyl-L-aspartate. Combining the structural data with in silico docking and electrostatic calculations, we have been able to visualize each step in the catalytic cycle of ATCase, from the ordered binding of the substrates, to the formation and decomposition of the tetrahedral intermediate, to the ordered release of the products from the active site. Analysis of the conformational changes associated with these steps provides a rationale for the lack of cooperativity in trimeric ATCases that do not possess regulatory subunits.

Enhanced metal ion selectivity of 2,9-di-(pyrid-2-yl)-1,10-phenanthroline and its use as a fluorescent sensor for cadmium(II).

The metal ion complexing properties of the ligand DPP (2,9-di-(pyrid-2-yl)-1,10-phenanthroline) were studied by crystallography, fluorimetry, and UV-visible spectroscopy. Because DPP forms five-membered chelate rings, it will favor complexation with metal ions of an ionic radius close to 1.0 A. Metal ion complexation and accompanying selectivity of DPP is enhanced by the rigidity of the aromatic backbone of the ligand. Cd2+, with an ionic radius of 0.96 A, exhibits a strong CHEF (chelation enhanced fluorescence) effect with 10(-8) M DPP, and Cd2+ concentrations down to 10(-9) M can be detected. Other metal ions that cause a significant CHEF effect with DPP are Ca2+ (10(-3) M) and Na+ (1.0 M), whereas metal ions such as Zn2+, Pb2+, and Hg2+ cause no CHEF effect with DPP. The lack of a CHEF effect for Zn2+ relates to the inability of this small ion to contact all four donor atoms of DPP. The structures of [Cd(DPP)2](ClO4)2 (1), [Pb(DPP)(ClO4)2H2O] (2), and [Hg(DPP)(ClO4)2] (3) are reported. The Cd(II) in 1 is 8-coordinate with the Cd-N bonds to the outer pyridyl groups stretched by steric clashes between the o-hydrogens on these outer pyridyl groups and the central aromatic ring of the second DPP ligand. The 8-coordinate Pb(II) in 2 has two short Pb-N bonds to the two central nitrogens of DPP, with longer bonds to the outer N-donors. The coordination sphere around the Pb(II) is completed by a coordinated water molecule, and two coordinated ClO4(-) ions, with long Pb-O bonds to ClO4(-) oxygens, typical of a sterically active lone pair on Pb(II). The Hg(II) in 3 shows an 8-coordinate structure with the Hg(II) forming short Hg-N bonds to the outer pyridyl groups of DPP, whereas the other Hg-N and Hg-O bonds are rather long. The structures are discussed in terms of the fit of large metal ions to DPP with minimal steric strain. The UV-visible studies of the equilibria involving DPP and metal ions gave formation constants that show that DPP has a higher affinity for metal ions with an ionic radius close to 1.0 A, particularly Cd(II), Gd(III), and Bi(III), and low affinity for small metal ions such as Ni(II) and Zn(II). The complexes of several metal ions, such as Cd(II), Gd(III), and Pb(II), showed an equilibrium involving deprotonation of the complex at remarkably low pH values, which was attributed to deprotonation of coordinated water molecules according to: [M(DPP)(H2O)]n+ <==> [M(DPP)(OH)](n-1)+ + H+. The tendency to deprotonation of these DPP complexes at low pH is discussed in terms of the large hydrophobic surface of the coordinated DPP ligand destabilizing the hydration of coordinated water molecules and the build-up of charge on the metal ion in its DPP complex because of the inability of the coordinated DPP ligand to hydrogen bond with the solvent.