Biophysical approaches for the study of metal-protein interactions

Intrinsically photoluminescent hydrogels to measure peptides‑copper binding affinities

NH2 decorated intrinsically photoluminescent hydrogels (IPH-NH2) were functionalized with the addition of various peptides via EDC/NHS coupling method. These peptidic devices bind copper with binding affinities depending on surface functionalization. Particularly, fluorescence analysis of copper titrations, alongside the determination of quenching efficiency and lifetime measurements, allowed to assess binding constants and to elucidate the underlying binding mechanism. Various peptides, having the same copper binding amino acidic residues (GHK) but different chain lengths, were tested and it was found that increasing the distance of the GHK sequence from the IPH-NH2 surface resulted in a decrease in the binding constant, as well as a reduction in quenching efficiency, whereas the binding mechanism remained unchanged as indicated by lifetime measurements. This method not only provides binding constants for peptides immobilized on biosensor surfaces or pre-fabricated devices without altering their structure, but also contributes to the optimization of biosensor design, tailoring it to its intended application.

PinMyMetal: a hybrid learning system to accurately model transition metal binding sites in macromolecules

Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural, catalytic, or regulatory roles. Modeling transition metal ions, especially in transient, reversible, and concentration-dependent regulatory sites, remains challenging. We present PinMyMetal (PMM), a hybrid machine learning system designed to accurately predict transition metal localization and environment in macromolecules, tailored to tetrahedral and octahedral geometries. PMM outperforms other predictors, achieving high accuracy in ligand and coordinate predictions. It excels in predicting regulatory sites (median deviation 0.36 Å), demonstrating superior accuracy in locating catalytic sites (0.33 Å) and structural sites (0.19 Å). Each predicted site is assigned a certainty score based on local structural and physicochemical features, independent of homologs. Interactive validation through our server, CheckMyMetal, expands PMM's scope, enabling it to pinpoint and validate diverse functional metal sites from different structure sources (predicted structures, cryo-EM, and crystallography). This facilitates residue-wise assessment and robust metal binding site design. The lightweight PMM system demands minimal computing resources and is available at https://PMM.biocloud.top . The PMM workflow can interrogate with protein sequence to characterize the localization of the most probable transition metals, which is often interchangeable and hard to differentiate by nature.

Biophysical characterization and structural insights of leptospiral complement regulator-acquiring protein A

Many pathogens establish a successful infection by evading the host complement system, an essential arm of innate immunity. Pathogenic Leptospira is reported to escape complement-mediated killing by recruiting the host complement regulators by lipoproteins or outer surface proteins. One of the outer surface proteins, Leptospiral complement regulator-acquiring protein A (LcpA), is known to recruit complement regulators, C4b-binding protein (C4BP), and Factor H (FH) on the bacterial surface. Mapping of interacting domains from C4BP and FH with the LcpA has already been reported. However, the region or structural part of the LcpA mediating the interaction is not known yet. Here, we report cloning, expression, refolding and purification of recombinant LcpA from an inclusion body of E. coli heterologous expression system. We also demonstrate the biophysical characterization of recombinant LcpA and reveal its secondary structure contents. Moreover, the protein displays a moderate thermostability. The change of intrinsic fluorescence and CD spectra demonstrate a change in the secondary structure of protein due to binding with Zn2+ ions. Molecular docking of LcpA with the complement regulators displays important interface residues from both the individual counterparts. Molecular dynamic simulation analysis demonstrates the stability of interactions between LcpA and C4BP. In our understanding, this is the first report on the large-scale purification of LcpA through refolding experiments and biophysical characterization of LcpA. This study may provide additional information on the structural basis of binding with the complement regulators.

Inhibitor binding to metal-substituted metalloenzyme: Sulfonamide affinity for carbonic anhydrase IX

Transition metal ions are structural and catalytic cofactors of many proteins including human carbonic anhydrase (CA), a Zn-dependent hydrolase. Sulfonamide inhibitors of CA recognize and form a coordination bond with the Zn ion located in the active site of the enzyme. The Zn ion may be removed or substituted with other metal ions. Such CA protein retains the structure and could serve as a tool to study metal ion role in the recognition and binding affinity of inhibitor molecules. We measured the affinities of selected divalent transition metal ions, including Mn, Fe, Co, Ni, Cu, Cd, Hg, and Zn to metal-free CA isozymes CA I, CA II, and CAIX by fluorescence-based thermal shift assay, prepared metal-substituted CAs, and determined binding of diverse sulfonamide compounds. Sulfonamide inhibitor binding to metal substituted CA followed a U-shape pH dependence. The binding was dissected to contributing binding-linked reactions and the intrinsic binding reaction affinity was calculated. This value is independent of pH and protonation reactions that occur simultaneously upon binding native CA and as demonstrated here, to metal substituted CA. Sulfonamide inhibitor binding to cancer-associated isozyme CAIX diminished in the order: Zn > Co > Hg > Cu > Cd > Mn > Ni. Energetic contribution of the inhibitor-metal coordination bond was determined for all above metals. The understanding of the principles of metal influence on ligand affinity and selectivity should help design new drugs targeting metalloenzymes.

Biochemical and biophysical interaction of rare earth elements with biomacromolecules: A comprehensive review

The growing utilization of rare earth elements (REEs) in industrial and technological applications has captured global interest, leading to the development of high-performance technologies in medical diagnosis, agriculture, and other electronic industries. This accelerated utilization has also raised human exposure levels, resulting in both favourable and unfavourable impacts. However, the effects of REEs are dependent on their concentration and molecular species. Therefore, scientific interest has increased in investigating the molecular interactions of REEs with biomolecules. In this current review, particular attention was paid to the molecular mechanism of interactions of Lanthanum (La), Cerium (Ce), and Gadolinium (Gd) with biomolecules, and the biological consequences were broadly interpreted. The review involved gathering and evaluating a vast scientific collection which primarily focused on the impact associated with REEs, ranging from earlier reports to recent discoveries, including studies in human and animal models. Thus, understanding the molecular interactions of each element with biomolecules will be highly beneficial in elucidating the consequences of REEs accumulation in the living organisms.

Characterization of four peptides from milk fermented with kombucha cultures and their metal complexes-in search of new biotherapeutics

The most common skin diseases include eczema, psoriasis, acne, and fungal infections. There is often no effective cure for them. Increasing antimicrobial drug resistance prompts us to search for new, safe, and effective therapeutics. Among such interesting candidates are peptides derived from milk fermented with specific lactic acid bacteria or with kombucha cultures, which are a potential treasure trove of bioactive peptides. Four of them are discussed in this article. Their interactions with zinc and copper ions, which are known to improve the well-being of the skin, were characterized by potentiometry, MS, ITC, and spectroscopic methods, and their cytostatic potential was analyzed. The results suggest that they are safe for human cells and can be used alone or in complexes with copper for further testing as potential therapeutics for skin diseases.

PinMyMetal: A hybrid learning system to accurately model metal binding sites in macromolecules

Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural (4-residue predominate), catalytic (3-residue predominate), or regulatory (2-residue predominate) roles. Computational tools for modeling metal ions in protein structures, especially for transient, reversible, and concentration-dependent regulatory sites, remain immature. We present PinMyMetal (PMM), a sophisticated hybrid machine learning system for predicting zinc ion localization and environment in macromolecular structures. Compared to other predictors, PMM excels in predicting regulatory sites (median deviation of 0.34 Å), demonstrating superior accuracy in locating catalytic sites (median deviation of 0.27 Å) and structural sites (median deviation of 0.14 Å). PMM assigns a certainty score to each predicted site based on local structural and physicochemical features independent of homolog presence. Interactive validation through our server, CheckMyMetal, expands PMM's scope, enabling it to pinpoint and validates diverse functional zinc sites from different structure sources (predicted structures, cryo-EM and crystallography). This facilitates residue-wise assessment and robust metal binding site design. The lightweight PMM system demands minimal computing resources and is available at https://PMM.biocloud.top. While currently trained on zinc, the PMM workflow can easily adapt to other metals through expanded training data.

M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings

MOTIVATION

Understanding metal-protein interaction can provide structural and functional insights into cellular processes. As the number of protein sequences increases, developing fast yet precise computational approaches to predict and annotate metal-binding sites becomes imperative. Quick and resource-efficient pre-trained protein language model (pLM) embeddings have successfully predicted binding sites from protein sequences despite not using structural or evolutionary features (multiple sequence alignments). Using residue-level embeddings from the pLMs, we have developed a sequence-based method (M-Ionic) to identify metal-binding proteins and predict residues involved in metal binding.

RESULTS

On independent validation of recent proteins, M-Ionic reports an area under the curve (AUROC) of 0.83 (recall = 84.6%) in distinguishing metal binding from non-binding proteins compared to AUROC of 0.74 (recall = 61.8%) of the next best method. In addition to comparable performance to the state-of-the-art method for identifying metal-binding residues (Ca2+, Mg2+, Mn2+, Zn2+), M-Ionic provides binding probabilities for six additional ions (i.e. Cu2+, Po43-, So42-, Fe2+, Fe3+, Co2+). We show that the pLM embedding of a single residue contains sufficient information about its neighbours to predict its binding properties.

AVAILABILITY AND IMPLEMENTATION

M-Ionic can be used on your protein of interest using a Google Colab Notebook (https://bit.ly/40FrRbK). The GitHub repository (https://github.com/TeamSundar/m-ionic) contains all code and data.

Comparative investigation on interaction between potent antimalarials and human serum albumin using multispectroscopic and computational approaches

This study performed a comparative investigation to explore the interaction mechanisms between two potential antimalarial compounds, JMI 346 and JMI 105, and human serum albumin (HSA), a vital carrier protein responsible for maintaining important biological functions. Our aim was to assess the pharmacological efficiency of these compounds while comprehensively analyzing their impact on the dynamic behavior and overall stability of the protein. A comprehensive array of multispectroscopic techniques, including UV-Vis. spectroscopy, steady-state fluorescence analysis, synchronous fluorescence spectroscopy, three-dimensional fluorescence and circular dichroism spectroscopy, docking studies, and molecular dynamics simulations, were performed to probe the intricate details of the interaction between the compounds and HSA. Our results revealed that both JMI 346 and JMI 105 exhibited promising pharmacological effectiveness within the context of malaria therapy. However, JMI 346 was found to exhibit a significantly higher affinity and only minor altered impact on HSA, suggesting a more favorable interaction with the protein on the dynamic behavior and overall stability of the protein in comparison to JMI 105. Further studies can build on these results to optimize the drug-protein interaction and enable the development of more potent and targeted antimalarial treatments.

An Overview of Scaffolds and Biomaterials for Skin Expansion and Soft Tissue Regeneration: Insights on Zinc and Magnesium as New Potential Key Elements

The utilization of materials in medical implants, serving as substitutes for non-functional biological structures, supporting damaged tissues, or reinforcing active organs, holds significant importance in modern healthcare, positively impacting the quality of life for millions of individuals worldwide. However, certain implants may only be required temporarily to aid in the healing process of diseased or injured tissues and tissue expansion. Biodegradable metals, including zinc (Zn), magnesium (Mg), iron, and others, present a new paradigm in the realm of implant materials. Ongoing research focuses on developing optimized materials that meet medical standards, encompassing controllable corrosion rates, sustained mechanical stability, and favorable biocompatibility. Achieving these objectives involves refining alloy compositions and tailoring processing techniques to carefully control microstructures and mechanical properties. Among the materials under investigation, Mg- and Zn-based biodegradable materials and their alloys demonstrate the ability to provide necessary support during tissue regeneration while gradually degrading over time. Furthermore, as essential elements in the human body, Mg and Zn offer additional benefits, including promoting wound healing, facilitating cell growth, and participating in gene generation while interacting with various vital biological functions. This review provides an overview of the physiological function and significance for human health of Mg and Zn and their usage as implants in tissue regeneration using tissue scaffolds. The scaffold qualities, such as biodegradation, mechanical characteristics, and biocompatibility, are also discussed.

Bioinorganic Chemistry of Micronutrients Related to Alzheimer's and Parkinson's Diseases

Metal ions are fundamental to guarantee the regular physiological activity of the human organism. Similarly, vitamins play a key role in many biological functions of the metabolism, among which are coenzymes, redox mediators, and antioxidants. Due to their importance in the human organism, both metals and vitamins have been extensively studied for their involvement in neurodegenerative diseases (NDs). However, the full potential of the interaction between vitamins and metal ions has not been fully explored by researchers yet, and further investigation on this topic is needed. The aim of this review is to provide an overview of the scientific literature on the implications of vitamins and selected metal ions in two of the most common neurodegenerative diseases, Alzheimer's and Parkinson's disease. Furthermore, vitamin-metal ion interactions are discussed in detail focusing on their bioinorganic chemistry, with the perspective of arousing more interest in this fascinating bioinorganic field.

Binding Investigation of Some Important Metal Ions Copper (I), Nickel (II), and Aluminium (III) with Bovine Serum Albumin Using Valid Spectroscopic Techniques

Studies based on the interaction of metals with proteins resulted in the development of promising metal-based compounds with encouraging medicinal potential. This study was aimed to utilize FT-IR and UV-Vis spectroscopic techniques to analyze the interactions of biologically significant metal ions, such as Al3+, Ni+2, and Cu+, with bovine serum albumin (BSA). Different concentrations of metal ions were interacted with BSA, and the complexes were analyzed using the two techniques. The change in the BSA secondary structure components such as β-sheet, β-antiparallel, α-helix, β-turn, and random coil were analyzed using second derivative resolution enhancement. The FT-IR spectroscopy suggested a marked decrease in the C=O stretching (corresponding to amide I) and C=N stretching (corresponding to amide II) intensities. Interestingly, upon complexation, a marked reduction (22.58–29.03%) in the α-helical component was observed with a considerable increase in the random coil component. The intensity of the absorption peak of BSA obtained using UV was observed to increase consecutively as the concentration of Cu+, Al3+, and Ni2+ ions increased. The binding constants for the BSA-Cu+, BSA-Ni+2, and BSA-Al+3 complexes were calculated to be 3.46 × 104 M−1, 1.28 × 104 M−1, and 2.08 × 104 M−1, respectively. It was concluded that the binding interaction decreased in the order Cu+ > Al3+ > Ni2+. These findings were similar to our previous findings using affinity capillary electrophoresis (ACE). Therefore, it can be inferred that the FT-IR and UV techniques might be utilised effectively to assess the metal-protein interaction and can have wide application in routine analysis. These techniques have several advantages in being simple, easy-to-perform, rapid, and affordable over other high-end techniques.

Characterization of novel nuclease and protease activities among Leptospiral immunoglobulin-like proteins

Bacterial immunoglobulin-like (BIg) domain containing proteins play a variety of biological functions. Leptospiral Immunoglobulin-like (Lig) proteins are well-known virulence factors located on the surface of the pathogenic Leptospira that act during adhesion, invasion, and immune evasion. The Lig proteins have many roles and have been designated as multifaceted proteins. However, the hydrolyzing function of Lig proteins is not yet investigated in detail. Here, we report novel in-vitro nuclease and protease activities in the Ig-like domain of LigA protein. All Ig-like domains were able to cleave DNA in the presence of a divalent ion, but not RNA. Site-directed mutagenesis revealed Mg⁺² binding residues in the Ig-like domain of LigA7. The basis of novel nuclease activity may be associated with protein adopting different conformation in the presence of divalent ions and substrate as investigated by change of intrinsic fluorescence. The docking of a stretch of double-strand DNA shows the binding on the positive surface of the protein. In addition, the protein is also observed to cleave a general protease substrate, β-casein, in our experimental condition. Our results proposed that the novel functions may be associated with neutrophil extracellular Trap (NET) evasion. Overall this study enhances the basic knowledge of non-nuclease proteins involved in the DNA cleavage activity and makes the foundation to explore its in-vivo activity in pathogenic Leptospira and other pathogens as well. Moreover, this information may be utilized to develop preventive strategies to interfere with Leptospira immune evasion.

A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level

Clear evidence has shown that metal ions strongly connect and delicately tune the dynamic homeostasis in living bodies. They have been proved to be associated with protein structure, stability, regulation, and function. Even small changes in the concentration of metal ions can shift their effects from natural beneficial functions to harmful. This leads to degenerative diseases, malignant tumors, and cancers. Accurate characterizations and predictions of metalloproteins at the residue level promise informative clues to the investigation of intrinsic mechanisms of protein-metal ion interactions. Compared to biophysical or biochemical wet-lab technologies, computational methods provide open web interfaces of high-resolution databases and high-throughput predictors for efficient investigation of metal-binding residues. This review surveys and details 18 public databases of metal-protein binding. We collect a comprehensive set of 44 computation-based methods and classify them into four categories, namely, learning-, docking-, template-, and meta-based methods. We analyze the benchmark datasets, assessment criteria, feature construction, and algorithms. We also compare several methods on two benchmark testing datasets and include a discussion about currently publicly available predictive tools. Finally, we summarize the challenges and underlying limitations of the current studies and propose several prospective directions concerning the future development of the related databases and methods.

Zn-Enhanced Asp-Rich Antimicrobial Peptides: N-Terminal Coordination by Zn(II) and Cu(II), Which Distinguishes Cu(II) Binding to Different Peptides

The antimicrobial activity of surfactant-associated anionic peptides (SAAPs), which are isolated from the ovine pulmonary surfactant and are selective against the ovine pathogen Mannheimia haemolytica, is strongly enhanced in the presence of Zn(II) ions. Both calorimetry and ITC measurements show that the unique Asp-only peptide SAAP3 (DDDDDDD) and its analogs SAAP2 (GDDDDDD) and SAAP6 (GADDDDD) have a similar micromolar affinity for Zn(II), which binds to the N-terminal amine and Asp carboxylates in a net entropically-driven process. All three peptides also bind Cu(II) with a net entropically-driven process but with higher affinity than they bind Zn(II) and coordination that involves the N-terminal amine and deprotonated amides as the pH increases. The parent SAAP3 binds Cu(II) with the highest affinity; however, as shown with potentiometry and absorption, CD and EPR spectroscopy, Asp residues in the first and/or second positions distinguish Cu(II) binding to SAAP3 and SAAP2 from their binding to SAAP6, decreasing the Cu(II) Lewis acidity and suppressing its square planar amide coordination by two pH units. We also show that these metal ions do not stabilize a membrane disrupting ability nor do they induce the antimicrobial activity of these peptides against a panel of human pathogens.

Mass Spectrometry and Structural Biology Techniques in the Studies on the Coronavirus-Receptor Interaction

Mass spectrometry and some other biophysical methods, have made substantial contributions to the studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human proteins interactions. The most interesting feature of SARS-CoV-2 seems to be the structure of its spike (S) protein and its interaction with the human cell receptor. Mass spectrometry of spike S protein revealed how the glycoforms are distributed across the S protein surface. X-ray crystallography and cryo-electron microscopy made huge impact on the studies on the S protein and ACE2 receptor protein interaction, by elucidating the three-dimensional structures of these proteins and their conformational changes. The findings of the most recent studies in the scope of SARS-CoV-2-Human protein-protein interactions are described here.

A novel approach for obtaining α,β-diaminophosphonates bearing structurally diverse side chains and their interactions with transition metal ions studied by ITC

Aminophosphonates are an important group of building blocks in medicinal and pharmaceutical chemistry. Novel representatives of this class of compounds containing nontypical side chains are still needed. The aza-Michael-type addition of amines to phosphonodehydroalanine derivatives provides a simple and effective approach for synthesizing N′-substituted α,β-diaminoethylphosphonates and thus affords general access to aminophosphonates bearing structurally diverse side chains. Thermodynamic analysis of the chosen aminophosphonates at physiological pH proves that they serve as potent chelators for copper(ii) ions and moderate chelators for nickel(ii) ions.

A convenient and general reaction is presented for the preparation of diaminophosphonates further evaluated as chelators of metal ions.

His18 promotes reactive oxidative stress production in copper-ion mediated human islet amyloid polypeptide aggregation

Copper ions play a critical role in human islet amyloid polypeptide (hIAPP) aggregation, which has been found in more than 90% of patients with type-2 diabetes (T2D). The role of Cu(ii) in the cell cytotoxicity with hIAPP has been explored in two aspects: inhibiting the formation of fibrillar structures and stimulating the generation of reactive oxygen species (ROS). In this work, we carried out spectroscopic studies of Cu(ii) interacting with several hIAPP fragments and their variants as well. Electron paramagnetic resonance (EPR) measurements and Amplex Red analysis showed that the amount of H₂O₂ generated in hIAPP(11-28) solution co-incubated with Cu(ii) was remarkably more than hIAPP(1-11) and hIAPP(28-37). Furthermore, the H₂O₂ level was seriously reduced when His18 of hIAPP(11-28) was replaced by Arg(R) or Ser(S), indicating that His18 is the key residue of Cu(ii) binding to hIAPP(11-28) to promote H₂O₂ generation. This is likely because the donation of electrons from the peptide to Cu(ii) ions would result in the formation of the redox-active complexes, which could stimulate the formation of H₂O₂. Overall, this study provides further insight into the molecular mechanism of Cu(ii) induced ROS generation.

His18 promotes H₂O₂ production in copper-ion mediated hIAPP aggregation.