Plasmonics for the study of metal ion–protein interactions

Metal-protein solution interactions investigated using model systems: Thermodynamic and spectroscopic methods

The first-row D-block metal ions are essential for the physiology of living organisms, functioning as cofactors in metalloproteins or structural components for enzymes: almost half of all proteins require metals to perform the biological function. Understanding metal-protein interactions is crucial to unravel the mysteries behind molecular biology, understanding the effects of metal imbalance and toxicity or the diseases due to disorders in metal homeostasis. Metal-protein interactions are dynamic: they are noncovalent and affected by the environment to which the system is exposed. To reach a complete comprehension of the system, different conditions must be considered for the experimental investigation, in order to get information on the species distribution, the ligand coordination modes, complex stoichiometry and geometry. Thinking about the whole environment where a protein acts, investigations are often challenging, and simplifications are required to study in detail the mechanisms of metal interaction. This chapter is intended to help researchers addressing the problem of the complexity of metal-protein interactions, with particular emphasis on the use of peptides as model systems for the metal coordination site. The thermodynamic and spectroscopic methods most widely employed to investigate the interaction between metal ions and peptides in solution are here covered. These include solid-phase peptide synthesis, potentiometric titrations, calorimetry, electrospray ionization mass spectrometry, UV-Vis spectrophotometry, circular dichroism (CD), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). Additional experimental methods, which can be employed to study metal complexes with peptides, are also briefly mentioned. A case-study is finally reported providing a practical example of the investigation of metal-protein interaction by means of thermodynamic and spectroscopic methods applied to peptide model systems.

THE USE OF MASS SPECTROMETRY TO STUDY ZN-METALLOPROTEASE-SUBSTRATE INTERACTIONS

Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the development of several different diseases. For this reason, in recent years, many analytical approaches have been applied for studying the interaction between ZnMPs and their substrates and how environmental factors can affect enzyme activities. In this scenario, mass spectrometric methods occupy a very important role in elucidating different aspects of ZnMPs-substrates interaction. These range from identification of cleavage sites to quantitation of kinetic parameters. In this work, an overview of all the main achievements regarding the application of mass spectrometric methods to investigating ZnMPs-substrates interactions is presented. A general experimental protocol is also described which may prove useful to the study of similar interactions. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Biophysical approaches for the study of metal-protein interactions

Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.

FT-IR Spectroscopy for the Identification of Binding Sites and Measurements of the Binding Interactions of Important Metal Ions with Bovine Serum Albumin

Proteins play crucial roles in the transportation and distribution of therapeutic substances, including metal ions in living systems. Some metal ions can strongly associate, while others show low affinity towards proteins. Consequently, in the present work, the binding behaviors of Ca2+, Ba2+, Ag+, Ru3+, Cu2+ and Co2+ with bovine serum albumin (BSA) were screened. BSA and the metal ions were allowed to interact at physiological pH and their binding interactions were screened by using FT-IR spectroscopy. Spectra were collected by using hydrated films over a range of 4000–400 cm−1. The interaction was demonstrated by a significant reduction in the spectral intensities of the amide I (C=O stretching) and amide II bands (C–N stretching coupled to NH bending) of the protein after complexation with metal ions. The binding interaction was further revealed by spectral shifting of the amide I band from 1651 cm−1 (free BSA) to 1653, 1654, 1649, 1655, 1655, and 1654 cm−1 for BSA–Ca2+, BSA–Ba2+, BSA–Ag+, BSA–Ru3+, BSA–Cu2+ and BSA–Co2+ complexes, respectively. The shifting of the amide I band was due to the interactions of metal ions with the O and N atoms of the ligand protein. Estimation of the secondary protein structure showed alteration in the protein conformation, characterized by a marked decrease (12.9–40.3%) in the α-helix accompanied by increased β-sheet and β-turn after interaction with the metal ions. The interaction results of this study were comparable with those reported in our previous investigation of metal ion–BSA interactions using affinity capillary electrophoresis (ACE), which has proven the accuracy of the FT-IR technique in the measurement of interactions between proteins and metal ions.

Fingerprints of Calcium-Binding Protein Conformational Dynamics Monitored by Surface Plasmon Resonance

Surface plasmon resonance (SPR) spectroscopy is widely used to probe interactions involving biological macromolecules by detecting changes in the refractive index in a metal/dielectric interface following the dynamic formation of a molecular complex. In past years, SPR-based experimental approaches were developed to monitor conformational changes induced by the binding of small analytes to proteins coupled to the surface of commercially available sensor chips. A significant contribution to our understanding of the phenomenon came from the study of several Ca(2+)-sensor proteins operating in diverse cellular scenarios, in which the conformational switch is triggered by specific Ca(2+) signals. Structural and physicochemical analyses demonstrated that the SPR signal not only depends on the change in protein size upon Ca(2+)-binding but likely originates from variations in the hydration shell structure. The resulting changes in the dielectric properties of water or of the protein-water interface eventually reflect different crowding conditions on the SPR sensor chip, which mimic the cellular environment. SPR could hence be used to monitor conformational transitions in proteins, especially when a significant variation in the hydrophobicity of the solvent-exposed protein surface occurs, thus leading to changes in the dielectric milieu of the whole sensor chip surface. We review recent work in which SPR has been successfully employed to provide a fingerprint of the conformational change dynamics in proteins under native and altered conditions, which include post-translational modifications, copresence of competing analytes, and point mutations of single amino acids associated with genetic diseases.

Metal complexes and metalloproteases: targeting conformational diseases

In recent years many metalloproteases (MPs) have been shown to play important roles in the development of various pathological conditions. Although most of the literature is focused on matrix MPs (MMPs), many other MPs have been demonstrated to be involved in the degradation of peptides or proteins whose accumulation and dyshomeostasis are considered as being responsible for the development of conformational diseases, i.e., diseases where non-native protein conformations lead to protein aggregation. It seems clear that, at least in principle, it must be possible to control the levels of many aggregation-prone proteins not only by reducing their production, but also by enhancing their catabolism. Metal complexes that can perform this function were designed and tested according to at least two different strategies: (i) intervening on the endogenous MPs by directly or indirectly modulating their activity; (ii) acting as artificial MPs, replacing or synergistically functioning with endogenous MPs. These two different bioinorganic approaches are widely represented in the current literature and the aim of this review is to rationally organize and discuss both of them so as to give a critical insight into these approaches and highlighting their limitations and future perspectives.

Monitoring the biomolecular interactions and the activity of Zn-containing enzymes involved in conformational diseases: experimental methods for therapeutic purposes

Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the development of several different diseases. For this reason, in recent years, many analytical approaches have been applied for studying the interaction between ZnMPs and their substrates/inhibitors and how environmental factors can affect enzyme activities. In this scenario, nuclear magnetic resonance, X-ray diffraction, mass spectrometric (MS), and optical methods occupy a very important role in elucidating different aspects of the ZnMPs-substrates/inhibitors interaction, ranging from identification of cleavage sites to quantitation of kinetic parameters and inhibition constants. Here, an overview of all the main achievements in the application of different experimental approaches with special attention to MS methods to the investigation of ZnMPs-substrates/inhibitors interaction is given. A general MS experimental protocol which has been proved to be useful to study such interactions is also described.