Recombinant Archaeoglobus fulgidus UPF0132 membrane protein AF_0736 (AF_0736)

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Product Specs

Form
Lyophilized powder
Note: We will prioritize shipping the format we have in stock. However, if you have specific format requirements, please indicate them in your order. We will fulfill your request whenever possible.
Lead Time
Delivery time may vary depending on the purchase method and location. Please consult your local distributor for specific delivery estimates.
Note: All our proteins are shipped with standard blue ice packs by default. If you require dry ice shipping, please inform us in advance as additional fees will apply.
Notes
Repeated freezing and thawing is not recommended. Store working aliquots at 4°C for up to one week.
Reconstitution
We recommend centrifuging the vial briefly before opening to ensure the contents settle at the bottom. Reconstitute the protein in deionized sterile water to a concentration of 0.1-1.0 mg/mL. We recommend adding 5-50% glycerol (final concentration) and aliquoting for long-term storage at -20°C/-80°C. Our default final glycerol concentration is 50%. Customers can use this as a reference.
Shelf Life
Shelf life is influenced by factors such as storage conditions, buffer composition, storage temperature, and the protein's inherent stability.
Generally, the shelf life of liquid forms is 6 months at -20°C/-80°C. The shelf life of lyophilized forms is 12 months at -20°C/-80°C.
Storage Condition
Upon receipt, store at -20°C/-80°C. Aliquoting is necessary for multiple uses. Avoid repeated freeze-thaw cycles.
Tag Info
Tag type will be determined during the manufacturing process.
The tag type will be determined during the production process. If you have a specific tag type in mind, please inform us, and we will prioritize developing it according to your specifications.
Synonyms
AF_0736; UPF0132 membrane protein AF_0736
Buffer Before Lyophilization
Tris/PBS-based buffer, 6% Trehalose.
Datasheet
Please contact us to get it.
Expression Region
1-95
Protein Length
full length protein
Species
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Target Names
AF_0736
Target Protein Sequence
MCYTLGFVTGVLFLLFDRSPFVRFHAVQSTLTFSTITALVILLPVLPGGALLSRVVMAFS IILWAFCIVKASRGEAFKLPIFGDIAEEQLSLNYT
Uniprot No.

Target Background

Database Links

KEGG: afu:AF_0736

STRING: 224325.AF0736

Protein Families
UPF0132 family
Subcellular Location
Cell membrane; Multi-pass membrane protein.

Q&A

What is Archaeoglobus fulgidus UPF0132 membrane protein AF_0736?

Archaeoglobus fulgidus UPF0132 membrane protein AF_0736 is a small integral membrane protein encoded in the genome of the hyperthermophilic archaeon Archaeoglobus fulgidus, which optimally grows at 83°C under strictly anaerobic conditions. The protein belongs to the UPF0132 family of proteins with unknown function. The full-length protein consists of 95 amino acids and is typically studied as a recombinant protein with a histidine tag for purification purposes .

While the exact biological function of AF_0736 remains to be fully characterized, it represents an important research target for understanding membrane protein biology in extremophiles. As a membrane protein from a hyperthermophilic organism, AF_0736 may play roles in maintaining membrane integrity under extreme temperature conditions or participating in specialized metabolic pathways unique to Archaeoglobus fulgidus.

How is recombinant AF_0736 typically expressed and purified for research purposes?

The expression and purification of recombinant AF_0736 typically follows a methodology similar to that used for other archaeal membrane proteins. The protein is commonly expressed in E. coli expression systems using vectors that incorporate a histidine tag to facilitate purification . The standard workflow involves:

  • Gene Cloning and Vector Construction: The AF_0736 gene is amplified from Archaeoglobus fulgidus genomic DNA and inserted into an expression vector that includes a histidine tag sequence.

  • Expression in E. coli: The recombinant vector is transformed into an appropriate E. coli strain optimized for membrane protein expression. Expression conditions must be carefully controlled to prevent inclusion body formation.

  • Cell Lysis and Membrane Fraction Isolation: Following expression, cells are lysed and membrane fractions are isolated through differential centrifugation.

  • Detergent Solubilization: Membrane proteins require detergent solubilization to extract them from the lipid bilayer. Selection of appropriate detergents is critical for maintaining protein structure and function.

  • Affinity Chromatography: The histidine-tagged protein is purified using nickel or cobalt affinity chromatography.

  • Quality Assessment: Purity is confirmed using SDS-PAGE, and structural integrity can be assessed through circular dichroism or other biophysical techniques.

A typical recombinant form is designated as "Recombinant Full Length Archaeoglobus Fulgidus Upf0132 Membrane Protein Af_0736 (Af_0736) Protein, His-Tagged" produced in E. coli with the complete 95-amino acid sequence .

What experimental approaches are recommended for characterizing the function of AF_0736?

Characterizing the function of a membrane protein with unknown function like AF_0736 requires a multidisciplinary approach:

  • Comparative Genomic Analysis: Identifying homologs in other organisms can provide functional insights through evolutionary conservation patterns. For example, comparing AF_0736 to other membrane proteins in Archaeoglobus fulgidus and related species may identify conserved domains or motifs.

  • Protein-Protein Interaction Studies: Co-immunoprecipitation experiments using antibodies against the His-tagged recombinant AF_0736 can identify potential binding partners. This approach has been successfully used to characterize other proteins in A. fulgidus, such as the immunodepletion studies used to identify the role of the Afung protein in uracil-DNA glycosylase activity .

  • Localization Studies: Immunogold electron microscopy can determine the precise subcellular localization of AF_0736 within the A. fulgidus membrane system.

  • Functional Reconstitution: Purified AF_0736 can be reconstituted into liposomes to assess potential transport or catalytic activities. Methods similar to those used for studying the membrane-bound enzyme complexes in A. fulgidus could be adapted .

  • Spectroscopic Analysis: UV/Vis and EPR spectroscopy methods can identify potential cofactors or prosthetic groups, as was done for the heme/iron-sulfur protein complex in A. fulgidus .

  • Structural Biology Approaches: X-ray crystallography or cryo-electron microscopy can reveal structural features that might suggest function.

  • Gene Knockout/Knockdown Studies: Genetic manipulation to reduce or eliminate AF_0736 expression can reveal phenotypes associated with its function.

The experimental design should incorporate appropriate controls and collect both qualitative and quantitative data. Qualitative data should be organized into tables categorizing observations by factors such as localization patterns, binding partners, and phenotypic changes .

What are the challenges in working with recombinant hyperthermophilic proteins like AF_0736?

Working with recombinant proteins from hyperthermophilic organisms like Archaeoglobus fulgidus presents several significant challenges:

  • Protein Folding and Stability in Mesophilic Expression Systems:

    • When expressed in E. coli (growth optimum ~37°C), thermophilic proteins may not fold correctly since they evolved for stability at much higher temperatures (83°C for A. fulgidus) .

    • Hyperthermophilic membrane proteins often require specialized chaperones that are absent in E. coli.

  • Membrane Integration Issues:

    • Differences in membrane composition between E. coli and A. fulgidus can affect proper insertion and folding.

    • Archaeal lipids differ significantly from bacterial lipids, potentially affecting protein conformation and function.

  • Purification Challenges:

    • Detergent selection is critical for maintaining structural integrity during extraction and purification.

    • Standard purification buffers may not mimic the high-temperature, high-salt conditions preferred by hyperthermophilic proteins.

  • Activity Assessment:

    • Enzymes from hyperthermophiles often show minimal activity at standard laboratory temperatures.

    • Functional assays may need to be conducted at elevated temperatures to observe physiologically relevant activity.

    • Equipment limitations for high-temperature assays can complicate analysis.

  • Stability of Cofactors and Substrates:

    • At temperatures optimal for protein activity (>80°C), many cofactors and substrates may degrade rapidly.

    • Alternative energy sources like ADP rather than ATP may be more relevant at high temperatures due to their greater heat stability .

  • Anaerobic Requirements:

    • A. fulgidus is a strict anaerobe, meaning oxygen exposure during protein handling may alter protein structure or function.

    • Maintaining anaerobic conditions throughout purification and analysis presents logistical challenges.

Addressing these challenges requires specialized equipment, modified protocols, and careful experimental design that considers the unique properties of hyperthermophilic proteins.

What methodologies are most effective for analyzing protein-protein interactions involving AF_0736?

Analyzing protein-protein interactions for membrane proteins like AF_0736 requires specialized approaches that accommodate their hydrophobic nature. The following methodologies are particularly effective:

  • Crosslinking Mass Spectrometry (XL-MS):

    • Chemical crosslinkers can capture transient interactions in their native membrane environment.

    • Subsequent mass spectrometry analysis identifies interaction partners and potential binding interfaces.

    • For thermophilic proteins like AF_0736, temperature-resistant crosslinkers should be employed.

  • Proximity-based Labeling:

    • Techniques like BioID or APEX2 fusion proteins can identify neighboring proteins in the native cellular context.

    • These approaches are particularly valuable for membrane proteins where traditional pull-downs may disrupt weak interactions.

  • Co-purification Studies with Quantitative Assessment:

    • Quantitative proteomics comparing purifications under different conditions can distinguish specific from non-specific interactions.

    • Similar approaches have been used successfully with other A. fulgidus proteins .

  • Membrane Yeast Two-Hybrid (MYTH) System:

    • Modified yeast two-hybrid systems specifically designed for membrane proteins.

    • Requires adaptation for thermophilic proteins, potentially using thermotolerant yeast strains.

  • Surface Plasmon Resonance (SPR) with Nanodiscs:

    • Incorporation of purified AF_0736 into nanodiscs allows for maintenance of native-like membrane environment.

    • SPR can then quantitatively measure binding kinetics with potential interacting partners.

  • Native Electrophoresis Techniques:

    • Blue-native PAGE can preserve protein complexes during separation.

    • Subsequent mass spectrometry identifies components of stable complexes.

  • Computational Prediction with Experimental Validation:

    • Bioinformatic approaches to predict interactions based on structural modeling.

    • Predictions should be validated using one or more experimental techniques above.

Successful interaction studies require careful documentation of both qualitative observations and quantitative measurements. Data should be presented in tables that include details such as binding affinities, stoichiometry, and conditions that affect interaction strength.

How can researchers investigate the potential role of AF_0736 in cellular pathways of Archaeoglobus fulgidus?

Investigating the role of AF_0736 in cellular pathways requires a systems biology approach that integrates multiple lines of evidence:

  • Transcriptomic Analysis Under Various Conditions:

    • RNA-seq experiments comparing expression profiles under different growth conditions (temperature, nutrient availability, stress conditions).

    • Co-expression analysis to identify genes with similar expression patterns to AF_0736.

    • This approach can reveal potential functional relationships similar to how other A. fulgidus proteins have been characterized in putative transcription units .

  • Metabolomic Profiling:

    • Comparative metabolomics between wild-type and AF_0736 knockout/knockdown strains.

    • Identification of metabolites that accumulate or decrease when AF_0736 function is compromised.

  • Protein Localization Studies:

    • Immunogold electron microscopy to determine if AF_0736 localizes to specific membrane regions associated with particular cellular functions.

    • Co-localization with proteins of known function may suggest pathway involvement.

  • Genetic Interaction Mapping:

    • Synthetic lethal screens to identify genes whose function becomes essential in the absence of AF_0736.

    • This approach can reveal functional redundancy or pathway connections.

  • Comparative Analysis with Related Organisms:

    • Identification of AF_0736 homologs in related species and correlation with specific metabolic capabilities.

    • Phylogenetic profiling to associate protein presence with specific ecological niches or metabolic capabilities.

  • Biochemical Pathway Reconstitution:

    • In vitro reconstitution of suspected pathways with and without AF_0736.

    • Assessment of flux through these pathways under various conditions.

    • This approach has been successfully used for other A. fulgidus membrane proteins involved in electron transport chains .

  • Phenotypic Characterization of Mutants:

    • Growth rate analysis under various conditions.

    • Membrane integrity assessment.

    • Electron microscopy to detect ultrastructural changes.

Data collection should focus on both qualitative observations (membrane morphology changes, growth characteristics) and quantitative measurements (metabolite concentrations, gene expression levels, growth rates). Results should be organized into clearly labeled tables with appropriate statistical analysis to identify significant changes associated with AF_0736 function.

What considerations are important for designing site-directed mutagenesis experiments with AF_0736?

Designing effective site-directed mutagenesis experiments for AF_0736 requires careful planning and consideration of several key factors:

  • Target Selection Based on Sequence Conservation:

    • Conduct multiple sequence alignments of AF_0736 with homologs across archaea and bacteria.

    • Prioritize highly conserved residues, which often indicate functional importance.

    • Consider residues conserved specifically in hyperthermophiles versus mesophiles for thermostability studies.

  • Structural Considerations:

    • If structural data is unavailable, use computational prediction methods to generate structural models.

    • Target residues in predicted functional domains, membrane-spanning regions, or potential interaction interfaces.

    • Consider the following structural elements for mutation:

      • Charged residues in transmembrane domains (often functionally important)

      • Conserved motifs characteristic of specific transporter or channel families

      • Potential ligand-binding residues

  • Mutation Type Selection:

    • Conservative mutations (maintaining similar physicochemical properties) to probe subtle functional effects.

    • Non-conservative mutations to significantly alter charge, size, or hydrophobicity for pronounced effects.

    • Alanine scanning of specific regions to identify critical residues.

    • Cysteine substitutions for accessibility studies using cysteine-reactive probes.

  • Expression System Adaptations:

    • Consider codon optimization for the expression host when designing mutagenic primers.

    • Include appropriate controls for expression level differences between mutants.

    • Be prepared to adjust expression conditions for mutants that may affect protein stability.

  • Functional Assay Design:

    • Develop assays capable of detecting both complete loss of function and subtle functional changes.

    • Include temperature-dependent assays to assess effects on thermostability.

    • Consider multiple readouts (binding, activity, oligomerization, localization).

  • Thermostability Considerations:

    • For a hyperthermophilic protein like AF_0736, mutations may have different effects at physiological (83°C) versus experimental temperatures.

    • Include thermostability assays such as differential scanning calorimetry or thermal shift assays.

    • Consider the interplay between function and stability in interpreting results.

  • Data Collection and Analysis Plan:

    • Use systematic approaches similar to those employed for other A. fulgidus proteins .

    • Collect both qualitative and quantitative data for comprehensive phenotypic characterization .

    • Plan statistical analysis to determine significance of observed changes.

A well-designed mutagenesis study should include a comprehensive table documenting the mutations created, their rationale, and multiple phenotypic characteristics for each mutant. This provides a foundation for understanding structure-function relationships in this poorly characterized membrane protein.

What are the best approaches for studying the membrane topology of AF_0736?

Determining the membrane topology of AF_0736 is crucial for understanding its function and can be approached through multiple complementary methods:

  • Computational Prediction as a Starting Point:

    • Begin with computational topology prediction using multiple algorithms (TMHMM, MEMSAT, TOPCONS).

    • Generate a consensus prediction identifying likely transmembrane domains, cytoplasmic, and extracellular/periplasmic regions.

    • This provides hypotheses to test experimentally.

  • Substituted Cysteine Accessibility Method (SCAM):

    • Generate cysteine-free version of AF_0736 (replace native cysteines with serine or alanine).

    • Introduce single cysteines at positions throughout the protein sequence.

    • Treat intact cells or membrane vesicles with membrane-impermeable and membrane-permeable sulfhydryl reagents.

    • Differential labeling indicates cytoplasmic versus extracellular/periplasmic exposure.

    • This approach has been successfully adapted for thermophilic proteins by conducting reactions at elevated temperatures.

  • Fusion Protein Reporters:

    • Create fusions with reporter proteins like alkaline phosphatase (PhoA) and green fluorescent protein (GFP).

    • PhoA is active when located in the periplasm/extracellular space but inactive in the cytoplasm.

    • GFP typically folds correctly only in the cytoplasm.

    • Systematically create fusions at different positions and measure reporter activity.

    • Note: Thermostable variants of reporter proteins may be required for proper folding.

  • Protease Protection Assays:

    • Prepare membrane vesicles in both orientations (right-side-out and inside-out).

    • Treat with proteases under controlled conditions.

    • Identify protected fragments using antibodies against different protein regions or mass spectrometry.

    • Comparison between vesicle orientations reveals topology.

  • Glycosylation Mapping:

    • Introduce consensus N-glycosylation sites at various positions.

    • Express in a system capable of glycosylation.

    • Glycosylation occurs only on extracellular/periplasmic domains.

    • Detect glycosylation through mobility shifts or glycan-specific staining.

  • Antibody Accessibility:

    • Generate antibodies against different regions of AF_0736.

    • Test accessibility in intact cells versus permeabilized cells.

    • Regions accessible only after permeabilization are cytoplasmic.

  • Data Integration and Model Refinement:

    • Create a topology table summarizing results from all methods for each region.

    • Resolve discrepancies through additional targeted experiments.

    • Refine the final topology model based on all available data.

The topology data should be presented in a comprehensive table that indicates the predicted location of each protein segment (cytoplasmic, transmembrane, or extracellular/periplasmic) along with the experimental evidence supporting each assignment.

How can researchers address the challenges of structural characterization for membrane proteins like AF_0736?

Structural characterization of membrane proteins like AF_0736 presents significant challenges that require specialized approaches:

  • Optimization of Expression and Purification:

    • Screen multiple expression systems (E. coli, yeast, insect cells, cell-free systems).

    • Test various fusion tags beyond the standard His-tag to improve expression and solubility .

    • Evaluate a comprehensive panel of detergents for extraction and purification.

    • Consider fusion with crystallization chaperones like T4 lysozyme or BRIL.

    • For hyperthermophilic proteins like AF_0736, thermostable expression hosts may improve folding.

  • Membrane Mimetic Selection:

    • Systematically test detergents, lipid nanodiscs, amphipols, and lipidic cubic phases.

    • For archaeal membrane proteins, consider archaeal lipid mixtures to better mimic native environment.

    • Evaluate protein stability in each system using techniques like thermofluor assays.

  • Crystallization Strategies:

    • Implement sparse matrix screening with commercial membrane protein-specific crystallization kits.

    • Utilize lipidic cubic phase (LCP) crystallization, particularly effective for membrane proteins.

    • Consider in situ diffraction to avoid crystal manipulation damage.

    • For thermophilic proteins, attempts at crystallization at elevated temperatures may be beneficial.

  • Cryo-EM Approaches:

    • Single-particle cryo-EM is increasingly successful for membrane proteins.

    • Size limitations (AF_0736 is small at 95 amino acids ) can be addressed by:

      • Antibody fragment complexation to increase size

      • Fusion with larger protein partners

      • Analysis as oligomeric assemblies if applicable

  • NMR Spectroscopy Options:

    • Solution NMR for smaller membrane proteins in detergent micelles.

    • Solid-state NMR for proteins in native-like lipid bilayers.

    • Selective isotopic labeling to focus on specific regions.

  • Integration with Computational Methods:

    • Molecular dynamics simulations to model protein-lipid interactions.

    • Homology modeling based on structurally characterized homologs.

    • Validation of computational models with limited experimental constraints.

  • Hybrid Approaches:

    • Combine low-resolution techniques (SAXS, SANS, cryo-EM) with high-resolution techniques (X-ray, NMR).

    • Integrate crosslinking and mass spectrometry data to provide distance constraints.

    • Use EPR spectroscopy to determine distances between labeled residues.

The structural characterization workflow should be systematic and iterative, with results from initial attempts informing refinement of approaches. Complementary techniques provide validation and can resolve ambiguities in the structural models. Given the hyperthermophilic nature of AF_0736, structural studies at elevated temperatures may reveal functionally relevant conformational states not observed under standard conditions.

What experimental approaches can determine if AF_0736 functions as a transporter or channel?

Determining whether AF_0736 functions as a transporter or channel requires a systematic functional characterization approach:

  • Sequence-Based Analysis:

    • Compare AF_0736 sequence with characterized transporters and channels.

    • Identify conserved motifs associated with specific transporter classes.

    • Look for sequence signatures like ATP-binding motifs, ion coordination sites, or substrate-binding domains.

  • Liposome Reconstitution Assays:

    • Purify AF_0736 and reconstitute into liposomes with defined lipid composition.

    • For transporter assessment:

      • Load liposomes with potential substrates

      • Measure time-dependent efflux/uptake

      • Test ATP-dependence or ion gradient-dependence

    • For channel assessment:

      • Measure passive diffusion rates of various molecules

      • Test voltage-dependence using ionophores to establish potential

    • Methods similar to those used for other A. fulgidus membrane proteins can be adapted .

  • Electrophysiological Characterization:

    • Reconstitute AF_0736 in planar lipid bilayers.

    • Perform patch-clamp recordings to detect channel activity.

    • Measure conductance, selectivity, gating properties, and voltage-dependence.

    • For hyperthermophilic proteins, elevated temperature recordings may be necessary.

  • Transport Assays in Cell Systems:

    • Express AF_0736 in model cell systems deficient in specific transporters.

    • Measure uptake of radiolabeled or fluorescently labeled potential substrates.

    • Perform competition assays to determine substrate specificity.

  • Fluorescence-Based Flux Assays:

    • Reconstitute AF_0736 in liposomes containing fluorescent indicators.

    • Monitor real-time changes in fluorescence in response to substrate gradients.

    • Commonly used for:

      • pH changes (BCECF, pyranine)

      • Membrane potential (DiSC3(5), Oxonol V)

      • Ion concentrations (Calcium Green, SBFI for Na+)

  • Structure-Guided Functional Analysis:

    • If structural data becomes available, identify potential substrate-binding sites or translocation pathways.

    • Design mutations to disrupt these features and assess functional consequences.

    • Compare with similar structural motifs in characterized transporters/channels.

  • Thermodynamic and Kinetic Characterization:

    • Determine concentration and temperature dependence of transport/channel activities.

    • Calculate activation energies and compare with known transporters/channels.

    • For thermophilic proteins like those from A. fulgidus, temperature-dependent studies are particularly informative .

Data should be collected in a systematic manner and presented in well-organized tables showing transport rates, substrate selectivity profiles, inhibitor sensitivities, and thermodynamic parameters. Both qualitative observations and quantitative measurements should be documented to provide a comprehensive functional profile .

How can researchers investigate the thermostability mechanisms of AF_0736 as a hyperthermophilic membrane protein?

Investigating the thermostability mechanisms of AF_0736 as a hyperthermophilic membrane protein requires specialized approaches that address both protein intrinsic properties and membrane environment factors:

  • Comparative Sequence Analysis:

    • Align AF_0736 with mesophilic homologs to identify thermostability-associated substitutions.

    • Analyze amino acid composition differences, focusing on:

      • Increased charged residue content (especially internal ion pairs)

      • Higher proportion of hydrophobic amino acids in the core

      • Reduction in thermolabile residues (Asn, Gln, Cys, Met)

      • Proline content in loops and turns

  • Thermal Denaturation Studies:

    • Conduct differential scanning calorimetry (DSC) to determine melting temperatures.

    • Perform circular dichroism (CD) spectroscopy with temperature ramping to monitor secondary structure loss.

    • Use intrinsic tryptophan fluorescence to track tertiary structure changes.

    • Compare stability in different detergent and lipid environments.

  • Investigation of Stabilizing Interactions:

    • Use site-directed mutagenesis to disrupt potential stabilizing features:

      • Salt bridges and ion pairs

      • Hydrogen bonding networks

      • Disulfide bonds (if present)

      • Hydrophobic packing

    • Measure thermostability changes resulting from each mutation.

  • Membrane Environment Engineering:

    • Reconstitute AF_0736 in liposomes with varying lipid compositions:

      • Archaeal lipids (which naturally contain ether linkages rather than ester linkages)

      • Varying acyl chain lengths and degrees of saturation

      • Different head group compositions

    • Measure protein stability and activity across temperature ranges in each lipid environment.

  • Structural Dynamics Analysis:

    • Perform hydrogen-deuterium exchange mass spectrometry at different temperatures.

    • Use molecular dynamics simulations to identify regions with different flexibility at various temperatures.

    • Compare conformational flexibility between AF_0736 and mesophilic homologs.

  • Functional Assays Across Temperature Ranges:

    • Determine the temperature optima for function (transport, binding, etc.).

    • Compare activity profiles from sub-optimal to extreme temperatures.

    • Investigate whether activity and stability optimums coincide or diverge.

    • Consider alternative energy sources like ADP which may be more relevant at high temperatures due to greater heat stability .

  • Oligomeric State Assessment:

    • Determine if temperature affects oligomerization using size exclusion chromatography, analytical ultracentrifugation, or native gel electrophoresis.

    • Investigate whether oligomerization contributes to thermostability.

Data should be collected systematically across multiple experimental conditions and temperatures. Results should be presented in clearly formatted tables showing thermodynamic parameters, melting temperatures, and activity measurements with appropriate statistical analysis. Comparison data between AF_0736 and mesophilic homologs should highlight specific adaptations that contribute to the protein's exceptional thermostability.

What are the considerations for developing antibodies against AF_0736 for research applications?

Developing effective antibodies against AF_0736 for research applications requires careful planning and consideration of several factors specific to hyperthermophilic membrane proteins:

  • Antigen Design Strategy:

    • Full-length protein approach:

      • Expression and purification of recombinant His-tagged AF_0736

      • Purification under native conditions in appropriate detergents

      • Advantage: Antibodies may recognize native conformational epitopes

      • Challenge: Membrane proteins often have limited soluble exposed regions

    • Synthetic peptide approach:

      • Design peptides corresponding to predicted extramembrane loops or termini

      • Utilize computational topology predictions to identify accessible regions

      • Advantage: Simpler production, can target specific regions

      • Challenge: May not recognize native conformation

    • Recombinant fragment approach:

      • Express soluble domains as fusion proteins

      • Advantage: Easier production than full-length membrane proteins

      • Challenge: AF_0736 is small (95 amino acids) with potentially limited soluble domains

  • Immunization Considerations:

    • Select adjuvants compatible with membrane protein antigens

    • Consider multiple host species (rabbit, mouse, goat) to maximize epitope recognition options

    • Implement longer immunization schedules for potentially weakly immunogenic membrane proteins

    • Monitor antibody titers throughout immunization process

  • Screening and Validation Strategies:

    • Develop a comprehensive validation plan including:

      • ELISA against immunizing antigen

      • Western blotting against recombinant and native AF_0736

      • Immunoprecipitation efficiency testing

      • Immunofluorescence or immunogold electron microscopy

      • Testing for cross-reactivity with homologous proteins

      • Validation in immunodepletion experiments similar to those used for Afung protein

  • Specialized Considerations for Hyperthermophilic Proteins:

    • Epitopes accessible at physiological temperatures may differ from those at A. fulgidus growth temperatures

    • Test antibody binding at various temperatures including elevated temperatures

    • Consider native vs. denatured detection requirements

  • Production Formats:

    • Polyclonal antibodies: Broader epitope recognition but batch variability

    • Monoclonal antibodies: Consistent specificity but narrower epitope recognition

    • Recombinant antibodies: Customizable formats with renewable supply

  • Application-Specific Modifications:

    • Direct labeling options (fluorophores, enzymes, gold particles)

    • Fragment preparation (Fab, F(ab')2) for specific applications

    • Considerations for use in thermophilic conditions

  • Quality Control Parameters:

    • Establish specificity, sensitivity, and reproducibility metrics

    • Determine working concentrations for each application

    • Validate lot-to-lot consistency for long-term studies

A systematic antibody development program should document all testing results in clear tables showing specificity, sensitivity, and application performance data. This documentation provides critical validation information for research applications and enables troubleshooting if performance issues arise.

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