Glucose-sensitive insulin with attenuation of hypoglycaemia.

The risk of inducing hypoglycaemia (low blood glucose) constitutes the main challenge associated with insulin therapy for diabetes. Insulin doses must be adjusted to ensure that blood glucose values are within the normal range, but matching insulin doses to fluctuating glucose levels is difficult because even a slightly higher insulin dose than needed can lead to a hypoglycaemic incidence, which can be anything from uncomfortable to life-threatening. It has therefore been a long-standing goal to engineer a glucose-sensitive insulin that can auto-adjust its bioactivity in a reversible manner according to ambient glucose levels to ultimately achieve better glycaemic control while lowering the risk of hypoglycaemia.

Nonspecificity fingerprints for clinical-stage antibodies in solution.

Monoclonal antibodies (mAbs) have successfully been developed for the treatment of a wide range of diseases. The clinical success of mAbs does not solely rely on optimal potency and safety but also require good biophysical properties to ensure a high developability potential. In particular, nonspecific interactions are a key developability parameter to monitor during discovery and development.

Non-specificity as the sticky problem in therapeutic antibody development.

Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins.

Surface patches induce nonspecific binding and phase separation of antibodies.

Nonspecific interactions are a key challenge in the successful development of therapeutic antibodies. The tendency for nonspecific binding of antibodies is often difficult to reduce by rational design, and instead, it is necessary to rely on comprehensive screening campaigns. To address this issue, we performed a systematic analysis of the impact of surface patch properties on antibody nonspecificity using a designer antibody library as a model system and single-stranded DNA as a nonspecificity ligand.

Diboronate Fluorophore for the Measurement of l-Glucose and Other Carbohydrates and Its Interaction with Albumin.

l-Glucose has recently been investigated as an artificial sweetener, but no facile method is established for the measurement of l-glucose. The commercial probe Eversense employs a fluorescent diboronate in a small device for the optical monitoring of d-glucose in people with diabetes. Being achiral, the Eversense probe should be able to detect l-glucose as well as native d-glucose, but the probe is designed for fixation under the skin, and our attempts to use the probe at laboratory conditions failed, as the probe was resetting when moved between compartments.

An integrated platform approach enables discovery of potent, selective and ligand-competitive cyclic peptides targeting the GIP receptor.

In any drug discovery effort, the identification of hits for further optimisation is of crucial importance. For peptide therapeutics, display technologies such as mRNA display have emerged as powerful methodologies to identify these desired hit ligands against targets of interest. The diverse peptide libraries are genetically encoded in these technologies, allowing for next-generation sequencing to be used to efficiently identify the binding ligands.

(Dis)similarity Index To Compare Correlated Motions in Molecular Simulations.

Molecular dynamics (MD) simulations are widely used to complement or guide experimental studies in the characterization of protein dynamics, thanks to improvements in force-field accuracy, along with in the software and hardware to sample the conformational landscape of proteins. Among the different applications of MD simulations, the study of correlated motions is largely employed for different purposes. Several metrics have been developed to describe correlated motions in the MD ensemble, such as methods based on Pearson Correlation or Mutual Information.

The Toxic Effects of Pathogenic Ataxin-3 Variants in a Yeast Cellular Model.

Ataxin-3 (AT3) is a deubiquitinating enzyme that triggers an inherited neurodegenerative disorder, spinocerebellar ataxia type 3, when its polyglutamine (polyQ) stretch close to the C-terminus exceeds a critical length. AT3 variants carrying the expanded polyQ are prone to associate with each other into amyloid toxic aggregates, which are responsible for neuronal death with ensuing neurodegeneration. We employed Saccharomyces cerevisiae as a eukaryotic cellular model to better clarify the mechanism by which AT3 triggers the disease.

Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops.

ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains.

The role of salt bridges on the temperature adaptation of aqualysin I, a thermostable subtilisin-like proteinase.

Differences in salt bridges are believed to be a structural hallmark of homologous enzymes from differently temperature-adapted organisms. Nevertheless, the role of salt bridges on structural stability is still controversial. While it is clear that most buried salt bridges can have a functional or structural role, the same cannot be firmly stated for ion pairs that are exposed on the protein surface.

PyInteraph: a framework for the analysis of interaction networks in structural ensembles of proteins.

In the last years, a growing interest has been gathering around the ability of Molecular Dynamics (MD) to provide insight into the paths of long-range structural communication in biomolecules. The knowledge of the mechanisms related to structural communication helps in the rationalization in atomistic details of the effects induced by mutations, ligand binding, and the intrinsic dynamics of proteins. We here present PyInteraph, a tool for the analysis of structural ensembles inspired by graph theory.

Interactions of ataxin-3 with its molecular partners in the protein machinery that sorts protein aggregates to the aggresome.

Ataxin-3 (AT3) is the protein that triggers the inherited neurodegenerative disorder spinocerebellar ataxia type 3 when its polyglutamine (polyQ) stretch close to the C-terminus exceeds a critical length. AT3 consists of the N-terminal globular Josephin domain (JD) and the C-terminal disordered one. It cleaves isopeptide bonds between ubiquitin monomers, an event involved in protein quality control mechanisms.

Different ataxin-3 amyloid aggregates induce intracellular Ca(2+) deregulation by different mechanisms in cerebellar granule cells.

This work aims at elucidating the relation between morphological and physicochemical properties of different ataxin-3 (ATX3) aggregates and their cytotoxicity. We investigated a non-pathological ATX3 form (ATX3Q24), a pathological expanded form (ATX3Q55), and an ATX3 variant truncated at residue 291 lacking the polyQ expansion (ATX3/291Δ). Solubility, morphology and hydrophobic exposure of oligomeric aggregates were characterized.

The conformational ensemble of the disordered and aggregation-protective 182-291 region of ataxin-3.

Background: Intrinsically disordered proteins (IDPs) are an emerging part of structural biology that has challenged the classic paradigm of structure-function relationship. Indeed, IDPs have been associated with different physiological functions and associated with several pathologies, such as polyglutamine (polyQ) related diseases. Ataxin-3 (AT3) is the smallest polyQ protein, composed by the N-terminal folded Josephin domain (JD), which is amyloidogenic on its own, and a C-terminal unstructured part.

Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted homodimeric enzyme. A case study of the Vibrio alkaline phosphatase.

Background: Protein dynamics influence protein function and stability and modulate conformational changes. Such motions depend on the underlying networks of intramolecular interactions and communicating residues within the protein structure. Here, we provide the first characterization of the dynamic fingerprint of the dimeric alkaline phosphatase (AP) from the cold-adapted Vibrio strain G15-21 (VAP), which is among the APs with the highest known kcat at low temperatures.

The relationship between aggregation and toxicity of polyglutamine-containing ataxin-3 in the intracellular environment of Escherichia coli.

Several neurodegenerative diseases are triggered by proteins containing a polyglutamine (polyQ) stretch expanded beyond a critical threshold. Among these, ataxin-3 (AT3) is the causative agent of spinocerebellar ataxia type-3. We expressed three authentic AT3 variants in Escherichia coli: one normal (AT3-Q24), one expanded (AT3-Q55) and one truncated immediately upstream of the polyQ (AT3-291Δ).

Protein aggregation: mechanisms and functional consequences.

Understanding the mechanisms underlying protein misfolding and aggregation has become a central issue in biology and medicine. Compelling evidence show that the formation of amyloid aggregates has a negative impact in cell function and is behind the most prevalent human degenerative disorders, including Alzheimer's Parkinson's and Huntington's diseases or type 2 diabetes. Surprisingly, the same type of macromolecular assembly is used for specialized functions by different organisms, from bacteria to human.

The role of the central flexible region on the aggregation and conformational properties of human ataxin-3.

Aggregation of human ataxin-3 (AT3) into amyloid fibrils is responsible for spinocerebellar ataxia type 3. This protein consists of a folded N-terminal domain (Josephin domain, residues 1-182), a central flexible region (residues 183-291), a poly-glutamine sequence of variable length and a short C-terminal flexible region. Very little is known about the influence of the central flexible region on the conformational and aggregation properties of this protein.

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies.

A major role for side-chain polyglutamine hydrogen bonding in irreversible ataxin-3 aggregation.

The protein ataxin-3 consists of an N-terminal globular Josephin domain (JD) and an unstructured C-terminal region containing a stretch of consecutive glutamines that triggers the neurodegenerative disorder spinocerebellar ataxia type 3, when it is expanded beyond a critical threshold. The disease results from misfolding and aggregation, although the pathway and structure of the aggregation intermediates are not fully understood. In order to provide insight into the mechanism of the process, we monitored the aggregation of a normal (AT3Q24) ataxin-3, an expanded (AT3Q55) ataxin-3, and the JD in isolation.

Conformational plasticity of the calcium-binding pocket in the Burkholderia glumae lipase: remodeling induced by mutation of calcium coordinating residues.

Most bacterial lipases bind one or more Ca²+ atoms at different locations and are a suitable case of study for investigating structural effects related to calcium binding, depletion, or mutation of calcium-binding sites. Generally Ca²+ in microbial lipases can play a crucial role in the stabilization of the whole three-dimensional structure by mediating long-range effects. It has been recently demonstrated that calcium binding influences thermal stability of Burkholderia glumae lipase (BGL) through the restriction of conformational plasticity of specific regions.

Conformational diseases: structural studies of aggregation of polyglutamine proteins.

Protein misfolding and aggregation into insoluble amyloid deposits are often associated with neurodegenerative disorders. In particular, the polyglutamine (polyQ) diseases are inherited disorders triggered by the expansion of the polyQ tract over its physiological length in the involved protein. The molecular mechanism of aggregation from the native protein into amyloids involves several steps including protein misfolding, aggregation into oligomers, which seems to be the most toxic species, and, finally rearrangements into mature fibrils.

Relevance of metal ions for lipase stability: structural rearrangements induced in the Burkholderia glumae lipase by calcium depletion.

We have studied the accessibility of the structural calcium ion in the Burkholderia glumae lipase and the consequences of its removal on the protein conformation by different biophysical techniques (circular dichroism, fluorimetry, and mass spectrometry) and by molecular-dynamics simulations. We show that, in the native protein, calcium is not accessible unless specific flexible loops are displaced, for example, by a temperature increase. Such movements concern the whole calcium-binding pocket and particularly the environment of the coordinating aspartate residue 241.

Deactivation and unfolding are uncoupled in a bacterial lipase exposed to heat, low pH and organic solvents.

The lipase from Burkholderia glumae (BGL) was incubated at variable temperature, pH and concentration of organic solvents, and the decrease of enzymatic activity was compared to changes in the molecular structure as monitored by ESI-mass spectrometry. We observed that deactivation is not strictly related to structural instability in the assay conditions, in fact (i) thermal deactivation preceded denaturation; (ii) acid-induced deactivation arose at higher pH than partial or global protein unfolding; and (iii) activity in most organic solvents decreased at solvent concentrations where conformation was fully retained. In particular, no denaturation at all could be elicited by dimethyl formamide (DMF), isopropanol, and dimethyl sulfoxide (DMSO) up to 80%, in spite of a reduction of enzyme activity to 60-75%.