Protein purification via consecutive histidine-polyphosphate interaction.

While nickel-nitrilotriacetic acid (Ni-NTA) has greatly advanced recombinant protein purification, its limitations, including nonspecific binding and partial purification for certain proteins, highlight the necessity for additional purification such as size exclusion and ion exchange chromatography. However, specialized equipment such as FPLC is typically needed but not often available in many laboratories. Here, we show a novel method utilizing polyphosphate (polyP) for purifying proteins with histidine repeats via non-covalent interactions. Our study demonstrates that immobilized polyP efficiently binds to histidine-tagged proteins across a pH range of 5.5-7.5, maintaining binding efficacy even in the presence of reducing agent DTT and chelating agent EDTA. We carried out experiments of purifying various proteins from cell lysates and fractions post-Ni-NTA. Our results demonstrate that polyP resin is capable of further purification post-Ni-NTA without the need for specialized equipment and without compromising protein activity. This cost-effective and convenient method offers a viable approach as a complementary approach to Ni-NTA.

Combining the Benefits of Biotin-Streptavidin Aptamer Immobilization with the Versatility of Ni-NTA Regeneration Strategies for SPR.

The high affinity of the biotin-streptavidin interaction has made this non-covalent coupling an indispensable strategy for the immobilization and enrichment of biomolecular affinity reagents. However, the irreversible nature of the biotin-streptavidin bond renders surfaces functionalized using this strategy permanently modified and not amenable to regeneration strategies that could increase assay reusability and throughput. To increase the utility of biotinylated targets, we here introduce a method for reversibly immobilizing biotinylated thrombin-binding aptamers onto a Ni-nitrilotriacetic acid (Ni-NTA) sensor chip using 6xHis-tagged streptavidin as a regenerable capture ligand. This approach enabled the reproducible immobilization of aptamers and measurements of aptamer-protein interaction in a surface plasmon resonance assay. The immobilized aptamer surface was stable during five experiments over two days, despite the reversible attachment of 6xHis-streptavidin to the Ni-NTA surface. In addition, we demonstrate the reproducibility of this immobilization method and the affinity assays performed using it. Finally, we verify the specificity of the biotin tag-streptavidin interaction and assess the efficiency of a straightforward method to regenerate and reuse the surface. The method described here will allow researchers to leverage the versatility and stability of the biotin-streptavidin interaction while increasing throughput and improving assay efficiency.

Preparation and characterization of iron(III) nitrilotriacetate complex in aqueous solutions for quantitative protein binding experiments.

Various preparations of iron(III) nitrilotriacetate (FeNTA) solution reported in the literature lack a comprehensive method for accurate determination of FeNTA concentration and often result in unstable solutions. A detailed procedure for the preparation of FeNTA solution is presented that includes the standardization of both components of the chelate. The standardization of the components allowed the accurate determination of the molar absorption coefficients for the calculation of the FeNTA concentration in two different buffers at pH 5.6 and 7.4. The variation of pH in this range or ionic strength in the range from 0 M to 3 M (KCl) has little effect on the value of the molar absorption coefficient. The precise concentrations of all species involved in the equilibria between Fe and NTA were determined in the pH range 2-12 using the Jenkins-Traub algorithm to solve the 5th-order polynomial in Microsoft Excel. In view of the experimental observations and the calculated distribution of species, the stability of FeNTA solutions may be affected by the Fe : NTA ratio and the total concentrations, with dilute solutions and those with an excess of NTA over Fe showing higher stability.

Comparative assessment of two biodegradable chelants, S,S-ethylenediamine disuccinic acid and nitrilotriacetic acid, in facilitating Cd remediation by lesser swine cress (Coronopus didymus, Brassicaceae).

Chemically assisted phytoremediation is suggested as an effective approach to amplify the metal-remediating potential of hyperaccumulators. The current study assessed the efficiency of two biodegradable chelants (S,S-ethylenediamine disuccinic acid, EDDS; nitrilotriacetic acid, NTA) in enhancing the remediation of Cd by Coronopus didymus (Brassicaceae). C. didymus growing in Cd-contaminated soil (35-175 mg kg-1 soil) showed increased growth and biomass due to the hormesis effect, and chelant supplementation further increased growth, biomass, and Cd accumulation. A significant interaction with chelants and different Cd concentrations was observed, except for Cd content in roots and Cd content in leaves, which exhibited a non-significant interaction with chelant addition. The effect of the NTA amendment on the root dry biomass and shoot dry biomass was more pronounced than EDDS at all the Cd treatments. Upon addition of EDDS and NTA, bio-concentration factor values were enhanced by ~184-205 and ~ 199-208, respectively. The tolerance index of root and shoot increased over the control upon the addition of chelants, with NTA being better than EDDS. With chelant supplementation, bio-accumulation coefficient values were in the order Cd35 + NTA (~163%) > Cd105 + NTA (~137%) > Cd35 + EDDS (~89%) > Cd175 + NTA (~85%) > Cd105 + EDDS (~62%) > Cd175 + EDDS (~40%). The translocation factor correlated positively (r ≥ 0.8) with tolerance index and Cd accumulation in different plant parts. The study demonstrated that chelant supplementation enhanced Cd-remediation efficiency in C. didymus as depicted by improved plant growth and metal accumulation, and NTA was more effective than EDDS in reclaiming Cd.

A Simple and Versatile Strategy for Oriented Immobilization of His-Tagged Proteins on Magnetic Nanoparticles.

Oriented and covalent immobilization of proteins on magnetic nanoparticles (MNPs) is particularly challenging as it requires both the functionality of the protein and the colloidal stability of the MNPs to be preserved. Here, we describe a simple, straightforward, and efficient strategy for MNP functionalization with proteins using metal affinity binding. Our method involves a single-step process where MNPs are functionalized using a preformed, ready-to-use nitrilotriacetic acid-divalent metal cation (NTA-M2+) complex and polyethylene glycol (PEG) molecules. As a proof-of-concept, we demonstrate the oriented immobilization of a recombinant cadherin fragment engineered with a hexahistidine tag (6His-tag) onto the MNPs. Our developed methodology is simple and direct, enabling the oriented bioconjugation of His-tagged cadherins to MNPs while preserving protein functionality and the colloidal stability of the MNPs, and could be extended to other proteins expressing a polyhistidine tag. When compared to the traditional method where NTA is first conjugated to the MNPs and afterward free metal ions are added to form the complex, this novel strategy results in a higher functionalization efficiency while avoiding MNP aggregation. Additionally, our method allows for covalent bonding of the cadherin fragments to the MNP surface while preserving functionality, making it highly versatile. Finally, our strategy not only ensures the correct orientation of the protein fragments on the MNPs but also allows for the precise control of their density. This feature enables the selective targeting of E-cadherin-expressing cells only when MNPs are decorated with a high density of cadherin fragments.

Strategies for Mitigating Commercial Sensor Chip Variability with Experimental Design Controls.

Surface plasmon resonance (SPR) is a popular real-time technique for the measurement of binding affinity and kinetics, and bench-top instruments combine affordability and ease of use with other benefits of the technique. Biomolecular ligands labeled with the 6xHis tag can be immobilized onto sensing surfaces presenting the Ni2+-nitrilotriacetic acid (NTA) functional group. While Ni-NTA immobilization offers many advantages, including the ability to regenerate and reuse the sensors, its use can lead to signal variability between experimental replicates. We report here a study of factors contributing to this variability using the Nicoya OpenSPR as a model system and suggest ways to control for those factors, increasing the reproducibility and rigor of the data. Our model ligand/analyte pairs were two ovarian cancer biomarker proteins (MUC16 and HE4) and their corresponding monoclonal antibodies. We observed a broad range of non-specific binding across multiple NTA chips. Experiments run on the same chips had more consistent results in ligand immobilization and analyte binding than experiments run on different chips. Further assessment showed that different chips demonstrated different maximum immobilizations for the same concentration of injected protein. We also show a variety of relationships between ligand immobilization level and analyte response, which we attribute to steric crowding at high ligand concentrations. Using this calibration to inform experimental design, researchers can choose protein concentrations for immobilization corresponding to the linear range of analyte response. We are the first to demonstrate calibration and normalization as a strategy to increase reproducibility and data quality of these chips. Our study assesses a variety of factors affecting chip variability, addressing a gap in knowledge about commercially available sensor chips. Controlling for these factors in the process of experimental design will minimize variability in analyte signal when using these important sensing platforms.

Estimation of stability constants of Fe(III) with antibiotics and dissolved organic matter using a novel UV-vis spectroscopy method.

Determining conditional stability constant (Kcond) is paramount in assessing complex stability, particularly in Fe(III) complexes that are prevalent in actual surface water and wastewater matrices. In this study, existing methods of Kcond determination were evaluated and a novel UV-Vis spectroscopy method was proposed based on the evaluation of these approaches. Model ligands (ethylenediaminetetraacetic acid (EDTA), nitrilotriacetic acid (NTA), and oxalic acid (OA)), as well as common antibiotics (kanamycin (Kana) and tetracycline (TTC)), were employed to determine the Kcond of the Fe(III)-ligand complexes under neutral conditions (pH 6.5). The obtained fitting results revealed that the logKcond were in the order of Fe(III)-EDTA (7.08) > Fe(III)-NTA (4.67) > Fe(III)-OA (4.32) > Fe(III)-TTC (4.28) > Fe(III)-Kana (3.07). In addition to these single ligands, the methodology was extended to the Fe(III) complexation with humic acid (HA), a complex mixture of organic components, where the fitting result indicated a logKcond of 5.02 M-1. The method's application domain was analyzed by numerical analysis and combined with experimental results. The findings demonstrate that the proposed methodology possesses satisfactory measurement capability for Kcond ranging from 103 to 107 M-1, suggesting its broad applicability to the majority of complexes. This method can provide valuable insights into the impact of Fe(III) complexes within the water matrix.

Biosensors Based on the Binding Events of Nitrilotriacetic Acid-Metal Complexes.

Molecular immobilization and recognition are two key events for the development of biosensors. The general ways for the immobilization and recognition of biomolecules include covalent coupling reactions and non-covalent interactions of antigen-antibody, aptamer-target, glycan-lectin, avidin-biotin and boronic acid-diol. Tetradentate nitrilotriacetic acid (NTA) is one of the most common commercial ligands for chelating metal ions. The NTA-metal complexes show high and specific affinity toward hexahistidine tags. Such metal complexes have been widely utilized in protein separation and immobilization for diagnostic applications since most of commercialized proteins have been integrated with hexahistidine tags by synthetic or recombinant techniques. This review focused on the development of biosensors with NTA-metal complexes as the binding units, mainly including surface plasmon resonance, electrochemistry, fluorescence, colorimetry, surface-enhanced Raman scattering spectroscopy, chemiluminescence and so on.

Comparison of Usefulness of Four Chelating Agents (EDTA, NTA, ODA and IDA) for the Chromatographic Separation of Micro and Macro Amounts of Rare Earth Elements.

Literature on the use of four chelating agents namely: ethylenediaminetetraacetic acid, nitrilotriacetic acid, diglycolic acid and iminodiacetic acid for the chromatographic separation of micro and macro amounts of rare earth elements was critically reviewed and supplemented with some new unpublished data from our Laboratory. Advantages and disadvantages of ion exchange chromatography both in cation and anion mode as well as ion interaction chromatography techniques, which were used for rare earth elements separation, are discussed. The usefulness of some of the chromatographic systems for micro-macro separations was discussed and demonstrated. The importance of resilience of the separation method to column overloading in some analytical and larger scale separations was emphasized. The methods described in this article might suit well for recovering of individual lanthanides and yttrium from e-waste and other industrial wastes which were fast accumulating in recent years.

Ligand Immobilization Methods for Affinity Chromatography.

There is a plethora of chromatographic supports available in different shapes, sizes, functionalities, and chemical compositions, that could be employed for the numerous applications such as purification, scavenging, and target quantification. Therefore, it becomes critical to understand the chemical nature of these materials to select optimum conditions for ligand immobilization. In this chapter, we have explained some commonly employed ligand immobilization techniques to graft the ligand on the resin surfaces. For a quick reference, we have also included some functionalities of the resins that are commercially available.

Tyrosine-Based Dual-Functional Interface for Trapping and On-Site Photo-Induced Covalent Immobilization of Proteins.

Tyrosine, a simple and well-available natural amino acid, is featured by the small size of the compound that contains multiple reactive groups. This study developed an efficient bioconjugation strategy using tyrosine-based dual-functional interfaces. When tyrosine molecules are immobilized on the surface of a supporting material through amino groups, their carboxyl groups can function as an attracting trap due to their anionic nature at neutral pH and ability to chelate nickel(II) ions (Ni2+), allowing the capture and enrichment of cationic proteins and histidine (His)-tagged proteins on the surface. The trapped proteins can be further covalently immobilized on site through ruthenium-mediated photochemical cross-linking, which has been found to be highly efficient and can be completed within minutes. This strategy was successfully applied to two different material systems. We found that tyrosine-modified agarose beads had a binding capacity of the His-tagged enhanced green fluorescent protein comparable to that of commonly used nitrilotriacetic acid-based resins, and further covalent coupling via dityrosine cross-linking achieved a yield of 85% within 5 min, without compromising much on its fluorescence activity. On the surface of tyrosine-modified 316L stainless steel, lysozyme was captured through electrostatic interaction and further immobilized. The resultant surface exhibited remarkable antibacterial activity against both Staphylococcus aureus and Escherichia coli. Such a tyrosine-based capture-then-coupling method is featured by its simplicity, high coupling efficiency, and high utilization rate of target molecules, making it particularly suitable for the proteins that are highly priced or vulnerable to general immobilization chemistry.

Biodegradable chelant-metal complexes enhance cadmium phytoextraction efficiency of Solanum americanum.

Toxic contaminants (metals and metal-containing compounds) are accumulating in the environment at an astonishing rate and jeopardize human health. Remarkable industrial revolution and the spectacular economic growth are the prime causes for the release of such toxic contaminants in the environment. Cadmium (Cd) is ranked the 7th most toxic compound by the Agency for Toxic Substances and Disease Registry (USA), owing to its high carcinogenicity and non-biodegradability even at miniscule concentration. The present study assessed the efficiency of four biodegradable chelants [nitrilotriacetic acid (NTA), ethylenediamine disuccinate (EDDS), ethylene glycol tetraacetic acid (EGTA), and citric acid (CA)] and their dose (5 mM and 10 mM) in enhancing metal accumulation in Solanum americanum Mill. (grown under 24 mg Cd kg-1 soil) through morpho-physiological and metal extraction parameters. Significant variations were observed for most of the studied parameters in response to chelants and their doses. However, ratio of root and shoot length, and plant height stress tolerance index differed non-significantly. The potential of chelants to enhance Cd removal efficiency was in the order - EGTA (7.44%) > EDDS (6.05%) > NTA (4.12%) > CA (2.75%). EGTA and EDDS exhibited dose-dependent behavior for Cd extraction with 10 mM dose being more efficient than 5 mM dose. Structural equation model (SEM) depicted strong positive interaction of metal extraction parameters with chelants (Z-value = 11.61, p = 0.001). This study provides insights into the importance of selecting appropriate dose of biodegradable chelants for Cd extraction, as high chelant concentration might also result in phytotoxicity. In the future, phytoextraction potential of these chelants needs to be examined through field studies under natural environmental conditions.

The Interplay of Conjugation and Metal Coordination in Tuning the Electron Transfer Abilities of NTA-Graphene Based Interfaces.

An artificial leaf is a concept that not only replicates the processes taking place during natural photosynthesis but also provides a source of clean, renewable energy. One important part of such a device are molecules that stabilize the connection between the bioactive side and the electrode, as well as tune the electron transfer between them. In particular, nitrilotriacetic acid (NTA) derivatives used to form a self-assembly monolayer chemisorbed on a graphene monolayer can be seen as a prototypical interface that can be tuned to optimize the electron transfer. In the following work, interfaces with modifications of the metal nature, backbone saturation, and surface coverage density are presented by means of theoretical calculations. Effects of the type of the metal and the surface coverage density on the electronic properties are found to be key to tuning the electron transfer, while only a minor influence of backbone saturation is present. For all of the studied interfaces, the charge transfer flow goes from graphene to the SAM. We suggest that, in light of the strength of electron transfer, Co2+ should be considered as the preferred metal center for efficient charge transfer.

Using peptides to promote delivery and improve anti-tumour efficacy of liposomal drug.

Liposomal drugs exhibit advantages for cancer therapy, but efficacy is often limited by their rapid clearance from the blood by the reticuloendothelial system, and an inability to target and penetrate tumours. Interestingly, a 21-amino acid SIRP-α- (signal regulatory protein-α) interacting 'self' peptide is reported to inhibit uptake by phagocytes. Also, 'iRGD' a 9-amino acid cyclic peptide that binds αvß3 integrins and neuropilin-1 (NRP-1), promotes targeting and penetration of the drug into tumours. Here we explore the potential of nitrilotriacetic acid-ditetra-decylamine (NTA3-DTDA)-containing liposomes (NTA-liposomes) engrafted with His-tagged forms of 'self' peptide (pCD47) to prolong circulation time in blood after iv administration, and of iRGD peptide (piRGD) to enhance treatment efficacy of doxorubicin-containing liposomes (Caelyx). Our results show that pre-incubation of murine phagocytic DC2.4 and RAW246.7 cells with pCD47 inhibits the uptake of NTA-liposomes in vitro, but engraftment of pCD47 surprisingly reduces liposome lifetime in blood. Engraftment of piRGD promoted binding of NTA-liposomes to murine B16 melanoma and CT26 colorectal carcinoma cells in vitro. Importantly, iv administration of piRGD-engrafted Caelyx was found to significantly inhibit tumour growth and prolong survival in both B16 and CT26 murine tumour models. Our results show that engraftment of piRGD onto Caelyx is a convenient strategy to enhance treatment efficacy.

Pulse Dipolar EPR Reveals Double-Histidine Motif CuII-NTA Spin-Labeling Robustness against Competitor Ions.

Pulse-dipolar EPR is an appealing strategy for structural characterization of complex systems in solution that complements other biophysical techniques. Significantly, the emergence of genetically encoded self-assembling spin labels exploiting exogenously introduced double-histidine motifs in conjunction with CuII-chelates offers high precision distance determination in systems nonpermissive to thiol-directed spin labeling. However, the noncovalency of this interaction exposes potential vulnerabilities to competition from adventitious divalent metal ions, and pH sensitivity. Herein, a combination of room-temperature isothermal titration calorimetry (ITC) and cryogenic relaxation-induced dipolar modulation enhancement (RIDME) measurements are applied to the model protein Streptococcus sp. group G. protein G, B1 domain (GB1). Results demonstrate double-histidine motif spin labeling using CuII-nitrilotriacetic acid (CuII-NTA) is robust against the competitor ligand ZnII-NTA at >1000-fold molar excess, and high nM binding affinity is surprisingly retained under acidic and basic conditions even though room temperature affinity shows a stronger pH dependence. This indicates the strategy is well-suited for diverse biological applications, with the requirement of other metal ion cofactors or slightly acidic pH not necessarily being prohibitive.

Bioinspired Metal-Free Fluorescent Carbon Nanozyme with Dual Catalytic Activity to Confront Cellular Oxidative Damage.

Development of metal-free, recyclable enzyme mimics is challenging and requires key chemical modifications at the molecular level. Here, nitrilotriacetic acid-functionalized carbon nanospheres (LC-CNS@NTA) were prepared from the nitrogen-rich weed Lantana camara (LC) using a simple hydrothermal reaction condition. Transmission electron microscopy (TEM) studies revealed size of ∼160 ± 20 nm for LC-CNS@NTA whereas, the same showed fluorescence emission at ∼520 nm with a ∼63% quantum yield. Furthermore, LC-CNS@NTA showed strong peroxidase (Pxrd) activity toward a wide range of substrate viz., H2O2, 3,3',5,5'-tetramethylbenzidine, and o-phenylenediamine with Km and Vmax values of ∼257 µM and 1.06 µM/s, 282 µM and 1.47 µM/s, and 270.8 µM and 1.647 µM/s, respectively. Interestingly, this also showed catalase (CAT) activity against H2O2 with Km and Vmax values of ∼0.374 µM and 1.87 µM/s, respectively. It was observed that LC-CNS@NTA could effectively reduce the oxidative stress-induced cytotoxicity of HEK293 cells via retention of mitochondrial membrane potential, prevention of lipid peroxidation and DNA damage. It was further found that LC-CNS@NTA-treated cells showed reduced level of intracellular protein carbonylation and protein aggregation. The finding of the present study is expected to pave the path for designing engineered metal-free carbon nanozyme with dual enzyme mimic activity.

A general model to optimise CuII labelling efficiency of double-histidine motifs for pulse dipolar EPR applications.

Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to studies of biomolecules underpinning health and disease by providing highly accurate and precise geometric constraints. Combining double-histidine (dH) motifs with CuII spin labels shows promise for further increasing the precision of distance measurements, and for investigating subtle conformational changes. However, non-covalent coordination-based spin labelling is vulnerable to low binding affinity. Dissociation constants of dH motifs for CuII-nitrilotriacetic acid were previously investigated via relaxation induced dipolar modulation enhancement (RIDME), and demonstrated the feasibility of exploiting the dH motif for EPR applications at sub-µM protein concentrations. Herein, the feasibility of using modulation depth quantitation in CuII-CuII RIDME to simultaneously estimate a pair of non-identical independent KD values in such a tetra-histidine model protein is addressed. Furthermore, we develop a general speciation model to optimise CuII labelling efficiency, depending upon pairs of identical or disparate KD values and total CuII label concentration. We find the dissociation constant estimates are in excellent agreement with previously determined values, and empirical modulation depths support the proposed model.

Site-specific covalent labeling of His-tag fused proteins with N-acyl-N-alkyl sulfonamide reagent.

The ability to incorporate a desired functionality into proteins of interest in a site-specific manner can provide powerful tools for investigating biological systems and creating therapeutic conjugates. However, there are not any universal methods that can be applied to all proteins, and it is thus important to explore the chemical strategy for protein modification. In this paper, we developed a new reactive peptide tag/probe pair system for site-specific covalent protein labeling. This method relies on the recognition-driven reaction of a peptide tag and a molecular probe, which comprises the lysine-containing short histidine tag (KH6 or H6K) and a binuclear nickel (II)- nitrilotriacetic acid (Ni2+-NTA) complex probe containing a lysine-reactive N-acyl-N-alkyl sulfonamide (NASA) group. The selective interaction of the His-tag and Ni2+-NTA propeles a rapid nucleophilic reaction between a lysine residue of the tag and the electrophilic NASA group of the probe by the proximity effect, resulting in the tag-site-specific functionalization of proteins. We characterized the reactive profile and site-specificity of this method using model peptides and proteins in vitro, and demonstrated the general utility for production of a nanobody-chemical probe conjugate without compromising its binding ability.

An antibody-free dual-biomarker rapid enrichment workflow (AnDREW) improves the sensitivity of malaria rapid diagnostic tests.

Rapid diagnostic tests (RDTs) are critical to the success of malaria elimination campaigns. These tests are rapid, user-friendly, and field-deployable to resource-limited regions. However, RDTs demonstrate poor sensitivity because they can only tolerate a small (5 µL) volume of blood, which limits the amount of protein biomarker delivered to the test. We have developed the Antibody-free Dual-biomarker Rapid Enrichment Workflow (AnDREW) for purifying histidine-rich protein 2 (HRP2) and Plasmodium lactate dehydrogenase (PLDH) from large volume (150 µL) blood samples. We used Zn(II)NTA and aptamer-conjugated magnetic beads to capture HRP2 and PLDH, respectively. Both biomarkers were then eluted into RDT-compatible volumes using ethylene diamine tetraacetic acid (EDTA). We optimized both bead conjugates individually by enzyme-linked immunosorbent assays (ELISAs) and then combined the optimized capture and elution assays for both biomarkers to produce the AnDREW. The AnDREW-enhanced RDTs exhibited a 11-fold and 9-fold improvement in analytical sensitivity for detection of HRP2 and PLDH, respectively, when compared to unenhanced RDTs. Moreover, the limit of detection for PLDH was improved 11-fold for the AnDREW-enhanced RDTs (3.80 parasites/µL) compared to unenhanced RDTs (42.31 parasites/µL). Importantly, the AnDREW utilizes a pan-specific PLDH aptamer and improves upon existing methods by eluting both biomarkers without complexed antibodies.

Proteomics analysis of host cell proteins after immobilized metal affinity chromatography: Influence of ligand and metal ions.

Different degrees of protein purity have been observed in immobilized metal affinity chromatography ranging from extremely high purity to moderate and low purity. It has been hypothesized that the host cell protein composition and the metal ligands are factors governing the purity of a protein obtained after immobilized metal affinity chromatography (IMAC). Ni nitrilotriacetic acid (NTA) has become the first choice for facile His-tagged protein purification, but alternative ligands such as iminodiacetic acid (IDA) with other immobilized metal ions such as Zn, Cu and Co are valuable options when the expected purity or binding capacity is not reached. Especially Cu and Zn are very attractive, due to their reduced environmental and safety concerns compared to Ni. Co and Zn are more selective than Ni and Cu. This increased selectivity comes at the cost of weaker binding. In this work, the influence of ligand choice on protein purity after IMAC was evaluated by several methods, including peptide mapping. His-tagged GFP was used as model protein. We found that host cell protein (HCP) content varies drastically between ligands, as IDA eluates generally showing higher HCP concentrations than NTA. The relative content of the key amino acids His, Cys and Trp in the sequence of the co-eluted protein does not suffice to explain co-eluting propensity. The co-elution of HCPs is mostly influenced by metal binding clusters on the protein surface and not by total content or surface concentration of metal interacting amino acids. Prediction of co-elution is not dependent on these clusters alone, due to protein-protein interactions, indicted by a relative low metal binding cluster score but high co-elution propensity and in a lot of cases these proteins are often part of complex such as ribosome and chaperones. The different co-eluting proteins were presented by a heatmap with a dendrogram. Ward's linkage method was used to calculate the distance between groups of co-eluting proteins. Clustering of co-eluting HCPs was observed according to ligand and by metal ions, with Zn and Co forming one cluster and Ni and Cu another. The co-elution of host cell proteins can be explained by clusters of metal interacting amino acids on the protein surface and by protein-protein interactions. While Ni NTA still appears to be highly advantageous, it might not be the cure-all for all applications.