Analytical Workflows to Unlock Predictive Power in Biotherapeutic Developability.

PURPOSE: Forming accurate data models that assist the design of developability assays is one area that requires a deep and practical understanding of the problem domain. We aim to incorporate expert knowledge into the model building process by creating new metrics from instrument data and by guiding the choice of input parameters and Machine Learning (ML) techniques. METHODS: We generated datasets from the biophysical characterisation of 5 monoclonal antibodies (mAbs). We explored combinations of techniques and parameters to uncover the ones that better describe specific molecular liabilities, such as conformational and colloidal instability. We also employed ML algorithms to predict metrics from the dataset. RESULTS: We found that the combination of Differential Scanning Calorimetry (DSC) and Light Scattering thermal ramps enabled us to identify domain-specific aggregation in mAbs that would be otherwise overlooked by common developability workflows. We also found that the response to different salt concentrations provided information about colloidal stability in agreement with charge distribution models. Finally, we predicted DSC transition temperatures from the dataset, and used the order of importance of different metrics to increase the explainability of the model. CONCLUSIONS: The new analytical workflows enabled a better description of molecular behaviour and uncovered links between structural properties and molecular liabilities. In the future this new understanding will be coupled with ML algorithms to unlock their predictive power during developability assessment.

Juggling cadmium detoxification and zinc homeostasis: A division of labour between the two C. elegans metallothioneins.

The chemical properties of toxic cadmium and essential zinc are very similar, and organisms require intricate mechanisms that drive selective handling of metals. Previously regarded as unspecific "metal sponges", metallothioneins (MTLs) are emerging as metal selectivity filters. By utilizing C. elegans mtl-1 and mtl-2 knockout strains, metal accumulation in single worms, single copy fluorescent-tagged transgenes, isoform specific qPCR and lifespan studies it was possible to demonstrate that the handling of cadmium and zinc by the two C. elegans metallothioneins differs fundamentally: the MTL-2 protein can handle both zinc and cadmium, but when it becomes unavailable, either via a knockout or by elevated cadmium exposure, MTL-1 takes over zinc handling, leaving MTL-2 to sequester cadmium. This division of labour is reflected in the folding behaviour of the proteins: MTL-1 folded well in presence of zinc but not cadmium, the reverse was the case for MTL-2. These differences are in part mediated by a zinc-specific mononuclear His3Cys site in the C-terminal insertion of MTL-1; its removal affected the entire C-terminal domain and may shift its metal selectivity towards zinc. Overall, we uncover how metallothionein isoform-specific responses and protein properties allow C. elegans to differentiate between toxic cadmium and essential zinc.

Metallothioneins: unparalleled diversity in structures and functions for metal ion homeostasis and more.

Metallothioneins have been the subject of intense study for five decades, and have greatly inspired the development of bio-analytical methodologies including multi-dimensional and multi-nuclear NMR.With further advancements in molecular biology, protein science, and instrumental techniques, recent years have seen a renaissance of research into metallothioneins. The current report focuses on in vitro studies of so-called class II metallothioneins from a variety of phyla, highlighting the diversity of metallothioneins in terms of structure, biological functions, and molecular functions such as metal ion specificity, thermodynamic stabilities, and kinetic reactivity. We are still far from being able to predict any of these properties, and further efforts will be required to generate the knowledge that will enable a better understanding of what governs the biological and chemical properties of these unusual and intriguing small proteins.

Zinc transfer from the embryo-specific metallothionein E(C) from wheat: a case study.

The direct observation of binding and release of spectroscopically silent metal ions such as Zn(2+) and Ca(2+) by proteins has been challenging before the advent of native electrospray ionisation mass spectrometry. This report highlights the powerful capability of ESI-MS to provide insight into metalloprotein speciation that is independent of any spectroscopic property. Using the zinc-binding plant metallothionein E(C) from wheat as a study case, we show that ESI-MS is unique amongst other techniques in capturing intermediary metallospecies that evolve during the course of metal transfer to the chelator EDTA, as a model reaction to mimic the biological function of the protein as a zinc donor. Zinc release from the two-domain protein E(C) appears to be extremely rapid and non-cooperative, and progresses with loss of one zinc ion from the fully loaded Zn(6) species, and a transient build-up of Zn(5) and Zn(4) species, which further react to give species with 0-3 zinc ions bound. (1)H NMR data has provided further insights into the different behaviour of the two domains upon metal depletion.

Toward a property/function relationship for metallothioneins: histidine coordination and unusual cluster composition in a zinc-metallothionein from plants.

Early cysteine labeled (E(C)) proteins are plant metallothioneins, which were first identified in wheat embryos and are thought to be seed-specific. An exhaustive analysis of expressed sequence tag (EST) entries reveals that homologs are expressed in embryos of both classes of flowering plants (monocotyledons and dicotyledons), but also occur in conifers (gymnosperms) and seed-free spike moss (lycophyta). Mass spectrometric and elemental analysis results indicate that, contrary to the widely propagated number of five, E(C) binds predominantly six zinc ions in at least two zinc-thiolate clusters. 1H and 111Cd NMR experiments suggest that, in contrast to the majority of previously characterized metallothioneins, two conserved histidine residues participate in metal binding. The collected data is consistent with the presence of clusters unprecedented in metallothioneins so far. This novel cluster composition is accompanied by metal-binding properties that are substantially different from other metallothioneins; thus wheat E(C) binds zinc less strongly than either mammalian or cyanobacterial MTs. The unique biochemical properties of wheat E(C) render it ideally suited for a role in zinc donation to nascent proteins during seed development, a role that has been suggested based on the fact that E(C) is induced by the plant hormone abscisic acid, but not by heavy metals. Our results provide a step further toward developing a property/function relationship for metallothioneins.

Diversity and distribution of plant metallothioneins: a review of structure, properties and functions.

More than 30 years have passed since the discovery of the first plant metallothionein in wheat embryos, from which the emergence of a uniquely diverse metallothionein family with a fascinating array of structural nuances and molecular properties has been witnessed. Metallothioneins are not only constitutively expressed, but the production of different types of plant metallothionein is also stimulated by a myriad of endogenous and exogenous agents in both a temporally and spatially regulated manner. This ubiquitous, yet discrete expression of metallothioneins not only signifies their importance for plant survival and development, but also suggests a functional divergence for the individual plant metallothionein subfamilies. Understanding why one type of plant metallothionein has more advantageous structural and metal binding attributes over another for a given biological process is a crucial piece in the puzzle of assigning physiological functions to these proteins. In this review, we discuss how in vivo and in vitro studies have advanced our understanding of the structure-property-function relationship for the plant metallothionein family. In particular, we highlight the progress that has been made for the Type 4 plant metallothioneins.

Tools for metal ion sorting: in vitro evidence for partitioning of zinc and cadmium in C. elegans metallothionein isoforms.

In vitro evidence for the isoform-specific partitioning of cadmium and zinc ions between the two C. elegans metallothioneins is presented. This observation is discussed in terms of isoform-specific affinities towards zinc and cadmium and the implications of our study on the in vivo roles of C. elegans metallothioneins.

C. elegans metallothioneins: response to and defence against ROS toxicity.

The genome of the nematode Caenorhabditis elegans encodes for two multifunctional metal binding metallothioneins (MTs), CeMT-1 and CeMT-2. Here we applied qPCR to identify a transcriptional up-regulation following the exposure to free radical generators (ROS) paraquat or hydrogen peroxide, a trend that was confirmed with Pmtl::GFP expressing alleles. The deletion of the MT loci resulted in an elevation of in vivo levels of hydrogen peroxide and exposure to ROS caused a reduction in total egg production, growth and life span in wild type nematodes, effects that were particularly pronounced in the CeMT-2 and double knockout. Moreover, in vitro incubation of recombinant MTs with hydrogen peroxide demonstrated the presence of direct oxidation of the CeMTs, with zinc released from both isoforms and concomitant formation of intra-molecular disulfides. Finally, metabolic profiling (metabolomic) analysis of wild type and MT knockouts in the presence/absence of oxidative stressors, confirmed the overall trend described by the other experiments, and identified 2-aminoadipate as a potential novel small-molecule marker of oxidative stress. In summary, this study highlights that C. elegans metallothioneins scavenge and protect against reactive oxygen species and potentially against oxidative stress, with CeMT-2 being more effective than CeMT-1.

The two Caenorhabditis elegans metallothioneins (CeMT-1 and CeMT-2) discriminate between essential zinc and toxic cadmium.

The nematode Caenorhabditis elegans expresses two metallothioneins (MTs), CeMT-1 and CeMT-2, that are believed to be key players in the protection against metal toxicity. In this study, both isoforms were expressed in vitro in the presence of either Zn(II) or Cd(II). Metal binding stoichiometries and affinities were determined by ESI-MS and NMR, respectively. Both isoforms had equal zinc binding ability, but differed in their cadmium binding behaviour, with higher affinity found for CeMT-2. In addition, wild-type C. elegans, single MT knockouts and a double MT knockout allele were exposed to zinc (340 microm) or cadmium (25 microm) to investigate effects in vivo. Zinc levels were significantly increased in all knockout strains, but were most pronounced in the CeMT-1 knockout, mtl-1 (tm1770), while cadmium accumulation was highest in the CeMT-2 knockout, mtl-2 (gk125) and the double knockout mtl-1;mtl-2 (zs1). In addition, metal speciation was assessed by X-ray absorption fine-structure spectroscopy. This showed that O-donating, probably phosphate-rich, ligands play a dominant role in maintaining the physiological concentration of zinc, independently of metallothionein status. In contrast, cadmium was shown to coordinate with thiol groups, and the cadmium speciation of the wild-type and the CeMT-2 knockout strain was distinctly different to the CeMT-1 and double knockouts. Taken together, and supported by a simple model calculation, these findings show for the first time that the two MT isoforms have differential affinities towards Cd(II) and Zn(II) at a cellular level, and this is reflected at the protein level. This suggests that the two MT isoforms have distinct in vivo roles.