Recombinant Phenylalanine--tRNA ligase alpha subunit (pheS)

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Description

Neurological Disorders

  • ALS/FTD: C9orf72 antisense RNA repeats inhibit pheS activity, reducing charged tRNAPhe^{\text{Phe}} levels by 40–60% and impairing synthesis of phenylalanine-rich proteins .

  • Mitochondrial disorders: Mutations in FARS2 (encoding mitochondrial PheRS) cause Alpers syndrome, with p.D391V destabilizing Phe binding (KMK_M increase >2-fold) .

Antimicrobial Development

  • PheRS is a target for antibiotic design due to structural divergence from human orthologs. For example, Staphylococcus aureus PheRS exhibits unique insertions in the ACB domain .

Evolutionary and Taxonomic Distribution

PheRS phylogeny reveals horizontal gene transfer events and adaptation to genomic contexts:

  • Bacteria: Tetrameric α2β2 architecture (e.g., E. coli, Bacillus) .

  • Mitochondria: Monomeric chimeric forms combining α- and β-subunit domains .

  • Archaea/Protozoa: Divergent ACB domains with pathogen-specific insertions (e.g., Plasmodium AspRS) .

Challenges and Future Directions

  • Drug resistance: Pathogen-specific PheRS mutations (e.g., Mycobacterium tuberculosis) necessitate dynamic structure-activity studies .

  • Gene therapy: Delivery of engineered pheS variants could ameliorate tRNA charging deficits in mitochondrial diseases .

Product Specs

Form
Lyophilized powder. We will ship the available format, but you can request a specific format when ordering.
Lead Time
Delivery times vary. Contact your local distributor for details. Proteins are shipped with blue ice packs. Request dry ice in advance (extra fees apply).
Notes
Avoid repeated freeze-thaw cycles. Store working aliquots at 4°C for up to one week.
Reconstitution
Briefly centrifuge the vial before opening. Reconstitute in sterile deionized water to 0.1-1.0 mg/mL. Add 5-50% glycerol (final concentration) and aliquot for long-term storage at -20°C/-80°C. Our default final glycerol concentration is 50%.
Shelf Life
Shelf life depends on storage conditions, buffer, temperature, and protein stability. Liquid form: 6 months at -20°C/-80°C. Lyophilized form: 12 months at -20°C/-80°C.
Storage Condition
Store at -20°C/-80°C upon receipt. Aliquot for multiple uses. Avoid repeated freeze-thaw cycles.
Tag Info
Tag type is determined during manufacturing. If you require a specific tag, please let us know and we will prioritize its development.
Buffer Before Lyophilization
Tris/PBS-based buffer, 6% Trehalose.
Datasheet
Please contact us to get it.
Expression Region
1-341
Protein Length
full length protein
Purity
>85% (SDS-PAGE)
Target Names
pheS
Target Protein Sequence
MLSPEALTTA VDAAQQAIAL ADTLDVLARV KTEHLGDRSP LALARQALAV LPKEQRAEAG KRVNAARNAA QRSYDERLAT LRAERDAAVL VAEGIDVTLP STRVPAGARH PIIMLAEHVA DTFIAMGWEL AEGPEVETEQ FNFDALNFPA DHPARGEQDT FYIAPEDSRQ LLRTHTSPVQ IRTLLARELP VYIISIGRTF RTDELDATHT PIFHQVEGLA VDRGLSMAHL RGTLDAFARA EFGPSARTRI RPHFFPFTEP SAEVDVWFAN KIGGAAWVEW GGCGMVHPNV LRATGIDPDL YSGFAFGMGL ERTLQFRNGI PDMRDMVEGD VRFSLPFGVG A
Uniprot No.

Q&A

What is Phenylalanine-tRNA Ligase Alpha Subunit (pheS) and what is its biological function?

Phenylalanine-tRNA Ligase Alpha Subunit (pheS), also known as FARSA, is a crucial component of the Phenylalanine-tRNA synthetase (FARS) complex. This enzyme plays a fundamental role in protein synthesis by catalyzing the aminoacylation of tRNA^Phe with phenylalanine, enabling the incorporation of phenylalanine into nascent polypeptide chains during translation.

The FARS complex consists of two main subunits: the alpha subunit (FARSA/pheS) and the beta subunit (FARSB). The alpha subunit contains the catalytic domain responsible for the aminoacylation reaction, while the beta subunit contributes to tRNA binding and structural stability of the complex. Together, they ensure accurate charging of tRNA^Phe, which is essential for maintaining translational fidelity .

Recent research has revealed that FARSA is also a significant interactor with CCCCGG antisense repeat RNA in the cytosol, establishing its relevance to neurodegenerative conditions including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) .

How does pheS relate to neurological disorders?

The relationship between pheS and neurological disorders has emerged as an important area of research. The hexanucleotide GGGGCC repeat mutation in the C9orf72 gene represents the primary genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). According to recent findings, FARSA functions as the main interactor of the CCCCGG antisense repeat RNA in the cytosol .

This interaction has significant functional consequences. The aminoacylation of tRNA^Phe by FARS becomes inhibited in the presence of antisense RNA, resulting in decreased levels of charged tRNA^Phe. Remarkably, this inhibition leads to a global reduction of phenylalanine incorporation in the proteome and decreased expression of phenylalanine-rich proteins, as observed in both cellular models and patient tissues .

These findings suggest that compromised aminoacylation of tRNA^Phe could lead to impairments in protein synthesis, potentially contributing to C9orf72 mutation-associated pathology. This mechanistic insight provides a novel perspective on how repeat expansions in neurodegenerative diseases might disrupt fundamental cellular processes.

What are the common methods for measuring pheS activity?

Researchers typically employ several methodologies to assess pheS activity:

  • Aminoacylation Assays: These assays measure the rate at which pheS charges tRNA^Phe with phenylalanine. This is commonly done using radiolabeled phenylalanine (^14C or ^3H) and monitoring the incorporation into tRNA over time.

  • ATP-PPi Exchange Assays: This approach measures the activation of amino acids, the first step in the aminoacylation reaction, by quantifying the exchange between ATP and pyrophosphate.

  • Charged tRNA Quantification: Methods such as acid gel electrophoresis can separate charged from uncharged tRNAs, allowing for the quantitative assessment of aminoacylation levels.

  • Global Proteome Analysis: Mass spectrometry-based approaches can be used to evaluate phenylalanine incorporation into the proteome, as demonstrated in studies examining the effects of FARSA inhibition by antisense RNA repeats .

When conducting these assays, it's essential to include appropriate controls and standardize conditions across experiments to ensure reliable and reproducible results.

What are the most effective expression systems for recombinant pheS production?

The choice of expression system for recombinant pheS production depends on your specific research requirements. Based on established protocols and research findings, several effective systems can be considered:

Bacterial Expression Systems (E. coli):

  • Most commonly used due to rapid growth, high yields, and cost-effectiveness

  • BL21(DE3) strains with pET vectors provide robust expression

  • Fusion tags (His6, GST, MBP) can enhance solubility and facilitate purification

  • Best suited for structural studies and biochemical assays requiring large quantities

Yeast Expression Systems:

  • Pichia pastoris and Saccharomyces cerevisiae can provide proper folding and post-translational modifications

  • Particularly useful when eukaryotic processing is important

  • The approach used with Rhodosporidium toruloides for PAL production provides a potential framework for pheS expression

Mammalian Expression Systems:

  • HEK293 or CHO cells provide the most native-like processing

  • Recommended when studying interactions with mammalian partners

  • Essential for functional studies in the context of neurodegenerative disease models

When selecting an expression system, consider the compatibility with downstream applications and the need for post-translational modifications. For most biochemical and structural studies, bacterial expression systems provide sufficient quality and quantity.

What purification strategy yields the highest purity and activity of recombinant pheS?

An optimized purification strategy for recombinant pheS typically involves multiple chromatographic steps to achieve high purity while maintaining enzymatic activity:

  • Initial Capture:

    • Affinity chromatography using nickel-NTA (for His-tagged proteins) or glutathione sepharose (for GST-tagged proteins)

    • This step rapidly isolates pheS from the majority of contaminating proteins

  • Intermediate Purification:

    • Ion exchange chromatography (typically anion exchange using Q-sepharose)

    • Separates pheS from proteins with different charge properties

  • Polishing Step:

    • Size exclusion chromatography to remove aggregates and achieve final purity

    • Also useful for buffer exchange into storage buffer

Critical Considerations:

  • Maintain all buffers at 4°C and include protease inhibitors to prevent degradation

  • Include reducing agents (DTT or β-mercaptoethanol) to maintain cysteine residues

  • Consider including tRNA and/or phenylalanine in buffers to stabilize the active site

  • Test activity after each purification step to monitor retention of function

A typical purification yield table might look like:

Purification StepTotal Protein (mg)pheS Activity (Units)Specific Activity (Units/mg)Purification FactorYield (%)
Crude Extract85042,500501100
Affinity Chromatography9533,250350778
Ion Exchange4229,4007001469
Size Exclusion2825,2009001859

This multi-step approach typically yields pheS with >95% purity and preserved enzymatic activity suitable for detailed biochemical and structural studies.

How should I design single-subject experimental designs (SSEDs) for studying pheS function in disease models?

When designing single-subject experimental designs (SSEDs) for investigating pheS function in disease models, consider the following methodological framework:

  • Select an Appropriate SSED Type:

    • Multiple baseline designs are valuable when studying the effects of pheS manipulation across different behaviors or physiological parameters

    • Withdrawal designs (A-B-A) can demonstrate reversibility of pheS intervention effects

    • Alternating treatment designs help compare different pheS-targeting approaches

  • Establish Rigorous Phase Requirements:

    • Include at least 5 data points per phase to meet standard requirements for experimental rigor

    • 3-4 data points per phase may be acceptable with reservations

    • Fewer than 3 data points per phase does not meet acceptable standards

  • Ensure Proper Control of Variables:

    • The independent variable (e.g., pheS manipulation) must be actively controlled by the researcher

    • The dependent variable must be measured systematically over time

    • Include measurement by multiple assessors with interassessor agreement on at least 20% of data points in each phase

  • Analyze Results Appropriately:

    • Conduct visual analysis to assess changes in level, trend, and variability between phases

    • Look for evidence of experimental effects, such as consistent separation between data paths or reversal of trends

    • Be aware of potential demonstrations of non-effect

When implementing SSEDs for pheS studies, particularly in neurodegenerative disease models, it's crucial to establish stable baselines before intervention and to replicate effects at least three times to demonstrate experimental control.

What controls are essential when studying the interaction between pheS and disease-associated RNA repeats?

When investigating interactions between pheS (FARSA) and disease-associated RNA repeats, such as those found in C9orf72-related neurodegeneration, the following controls are essential:

  • RNA Sequence Controls:

    • Non-repetitive RNA sequences of similar length

    • Scrambled versions of the repeat sequence

    • RNA repeats with different nucleotide compositions

    • These controls help establish specificity of the pheS-repeat RNA interaction

  • Protein Controls:

    • Mutant versions of pheS with altered RNA-binding domains

    • Other aminoacyl-tRNA synthetases to assess specificity

    • Unrelated RNA-binding proteins as negative controls

    • These help determine whether the interaction is specific to pheS

  • Functional Assays Controls:

    • Measurement of aminoacylation with and without repeat RNA

    • Dose-dependent experiments with varying RNA repeat concentrations

    • Competition assays with non-labeled RNA repeats

    • These validate the functional impact of the interaction

  • Cellular Model Controls:

    • Cell lines not expressing repeat expansions

    • Cells with FARSA/pheS knockdown or knockout

    • Rescue experiments with wild-type pheS expression

    • These establish the cellular relevance of observed interactions

In studies examining the interaction between pheS and CCCCGG antisense repeat RNA, it was observed that aminoacylation of tRNA^Phe by FARS is inhibited by antisense RNA, leading to decreased levels of charged tRNA^Phe. This was associated with global reduction of phenylalanine incorporation in the proteome and decreased expression of phenylalanine-rich proteins in cellular models and patient tissues . Such findings underscore the importance of comprehensive controls to validate both the interaction and its downstream consequences.

How can recombinant pheS be used to study mechanisms of neurodegeneration in C9orf72-related ALS/FTD?

Recombinant pheS (FARSA) serves as a powerful tool for investigating the mechanisms of neurodegeneration in C9orf72-related ALS/FTD through several advanced research applications:

  • Biochemical Characterization of RNA-Protein Interactions:

    • In vitro binding assays using purified recombinant pheS and synthetic CCCCGG repeat RNA

    • Determination of binding affinities, stoichiometry, and kinetics

    • Mapping of interaction domains through mutagenesis studies

    • These approaches have identified pheS as the main interactor of CCCCGG antisense repeat RNA in the cytosol

  • Structural Biology Approaches:

    • X-ray crystallography or cryo-EM structures of pheS-RNA complexes

    • NMR studies to identify dynamic interaction interfaces

    • These methods can reveal molecular details of how repeat RNA binding inhibits pheS function

  • Functional Consequences Assessment:

    • Aminoacylation assays comparing activity with and without repeat RNA

    • Global proteomics to quantify changes in phenylalanine incorporation

    • Ribosome profiling to identify translational defects

    • Research has shown that inhibition of tRNA^Phe aminoacylation leads to global reduction of phenylalanine incorporation in the proteome

  • Therapeutic Target Validation:

    • High-throughput screening for compounds that disrupt pheS-repeat RNA interactions

    • Testing peptides or nucleic acids that compete with pathological interactions

    • Development of modified pheS variants resistant to inhibition by repeat RNA

  • Mouse Model Development:

    • Creating transgenic models expressing both C9orf72 repeat expansions and modified pheS

    • Using recombinant pheS for enzyme replacement strategies

    • Testing approaches similar to those used with PAL in phenylketonuria models

These approaches collectively provide a comprehensive framework for understanding how CCCCGG repeat expansions in C9orf72 lead to neurodegenerative pathology through their interaction with pheS, potentially opening new avenues for therapeutic intervention.

What are the challenges and solutions in maintaining activity of recombinant pheS during experimental procedures?

Maintaining the activity of recombinant pheS throughout experimental procedures presents several challenges that require specific solutions:

Challenges and Solutions Table:

ChallengeMechanismSolution
Oxidative inactivationOxidation of catalytic cysteine residues- Add reducing agents (2-5 mM DTT or β-mercaptoethanol)
- Perform experiments under nitrogen atmosphere
- Include antioxidants in buffers
Thermal denaturationUnfolding at elevated temperatures- Maintain samples at 4°C whenever possible
- Add stabilizing agents (10-20% glycerol)
- Include molecular chaperones during expression
Proteolytic degradationCleavage by contaminating proteases- Add protease inhibitor cocktails
- Reduce handling time
- Maintain strict cold chain
Loss of metal cofactorsDissociation of structural/catalytic metals- Include Zn²⁺ or Mg²⁺ in buffers (1-2 mM)
- Avoid strong chelating agents like EDTA
AggregationExposure of hydrophobic surfaces- Add non-ionic detergents (0.01-0.05% Tween-20)
- Include stabilizing excipients (arginine, trehalose)
- Optimize protein concentration
Subunit dissociationSeparation of alpha and beta subunits- Co-express both subunits
- Use chemical crosslinking
- Include both subunits in reaction mixtures

Activity Preservation Strategies:

  • Substrate Stabilization: Including low concentrations of substrates (phenylalanine, ATP, tRNA) in storage buffers can protect the active site.

  • Storage Conditions: Optimal preservation is achieved by flash-freezing small aliquots in liquid nitrogen and storing at -80°C rather than repeated freeze-thaw cycles.

  • Formulation Optimization: For functional assays examining the effect of repeat RNAs on pheS activity, buffer composition significantly impacts reliability. Screening different buffer systems can identify conditions that maintain activity while allowing RNA-protein interactions.

  • Activity Monitoring Protocol: Implementing routine activity checks before experiments using a standardized aminoacylation assay helps ensure experiment-to-experiment consistency.

Methodologically, researchers studying the interaction between pheS and C9orf72 repeat expansions must carefully balance conditions that preserve enzyme activity while allowing pathological RNA-protein interactions to occur, as these interactions are central to understanding disease mechanisms .

How should researchers analyze data from experiments on pheS inhibition by repeat expansions?

When analyzing data from experiments investigating pheS inhibition by repeat expansions, researchers should implement a comprehensive analytical approach that combines multiple methodologies:

  • Dose-Response Analysis:

    • Plot aminoacylation activity against increasing concentrations of repeat RNA

    • Calculate IC50 values to quantify inhibitory potency

    • Use nonlinear regression to fit appropriate inhibition models (competitive, non-competitive, or mixed)

    • Compare inhibition parameters across different repeat lengths or sequences

  • Kinetic Parameter Determination:

    • Measure initial velocities at varying substrate concentrations with and without repeat RNA

    • Generate Lineweaver-Burk or Eadie-Hofstee plots to determine changes in Km and Vmax

    • Calculate kinetic parameters to distinguish between modes of inhibition

    • This approach can reveal whether repeat RNA affects substrate binding or catalytic efficiency

  • Visual Analysis for Time-Series Data:

    • Examine changes in level, trend, and variability across experimental phases

    • Look for consistent separation between data paths that indicates treatment effects

    • Analyze the immediacy of effects following intervention

    • These visual analysis techniques follow established SSED methodology principles

  • Proteomics Data Processing:

    • Normalize phenylalanine incorporation data relative to appropriate controls

    • Categorize affected proteins based on phenylalanine content

    • Conduct pathway analysis to identify biological processes most affected

    • Compare findings with patient tissue samples to validate disease relevance

  • Statistical Analysis Considerations:

    • For SSED data, consider non-parametric approaches or randomization tests

    • For group designs, use appropriate statistical tests (t-tests, ANOVA, etc.)

    • Calculate effect sizes to quantify the magnitude of observed effects

    • Adjust for multiple comparisons when analyzing large proteomics datasets

When interpreting results, it's essential to consider biological significance alongside statistical significance, particularly when examining the downstream consequences of pheS inhibition on cellular function and protein synthesis.

What are the best practices for reconciling contradictory findings in pheS research?

Reconciling contradictory findings in pheS research requires a systematic approach to evaluate methodological differences, biological variables, and interpretation frameworks:

  • Methodological Assessment:

    Begin by thoroughly examining experimental designs between contradictory studies:

    • Protein Production Differences: Variations in expression systems, purification methods, and protein constructs can significantly affect pheS activity and interaction properties.

    • Assay Conditions: Compare buffer compositions, temperature, pH, salt concentrations, and presence of stabilizing agents that might influence results.

    • RNA Preparation: Assess whether synthetic or in vitro transcribed RNAs were used, and whether they underwent proper folding steps.

    • Experimental Design Quality: Evaluate whether studies meet the established standards for experimental design, with appropriate controls and replication .

  • Biological Variable Analysis:

    Consider sources of biological variation that might explain disparate findings:

    • Cell Type Specificity: Results may differ between neuronal and non-neuronal cells, or between different neuronal subtypes.

    • Species Differences: Compare studies using human versus rodent or other model organism systems.

    • Disease Models: Different C9orf72 models may exhibit varying levels of repeat expression or different cellular phenotypes.

    • Patient Heterogeneity: Clinical samples may represent different disease stages or genetic backgrounds.

  • Data Integration Strategies:

    Implement approaches to synthesize contradictory findings:

    • Meta-analysis: When multiple studies address similar questions, quantitatively combine their results to identify consistent patterns.

    • Bayesian Analysis: Incorporate prior knowledge and uncertainty when interpreting new data.

    • Computational Modeling: Develop models that can accommodate seemingly contradictory results within a unified framework.

    • Multi-omics Integration: Combine data from different molecular levels (transcriptomics, proteomics, etc.) to obtain a more comprehensive view.

  • Validation Experiments:

    Design experiments specifically to address contradictions:

    • Side-by-side Comparisons: Replicate contradictory protocols in parallel under identical conditions.

    • Parameter Scanning: Systematically vary experimental conditions to identify factors driving different outcomes.

    • Independent Methodologies: Confirm findings using orthogonal techniques that measure the same phenomenon differently.

    • Collaborative Verification: Engage multiple laboratories to independently test critical findings.

  • Interpretation Framework:

    Consider how different theoretical frameworks might accommodate seemingly contradictory results:

    • Spectra of Effects: Instead of binary outcomes, consider results along a continuum of effect sizes.

    • Context Dependence: Acknowledge that pheS function may be highly context-dependent.

    • Multiple Mechanisms: Different experimental conditions may reveal distinct aspects of pheS biology.

By systematically applying these best practices, researchers can move beyond simply identifying contradictions to developing more nuanced and comprehensive understandings of pheS biology in health and disease.

How might CRISPR-based approaches advance research on pheS and disease mechanisms?

CRISPR-based technologies offer transformative opportunities to advance pheS research and deepen our understanding of its role in disease mechanisms:

  • Precise Genomic Editing:

    • Introduction of patient-specific mutations in FARSA/pheS

    • Creation of isogenic cell lines differing only in pheS sequence

    • Development of humanized mouse models with patient-derived pheS variants

    • These approaches enable direct assessment of how specific genetic variations affect pheS function

  • Endogenous Tagging and Visualization:

    • Knock-in of fluorescent tags to monitor pheS localization in real-time

    • Insertion of affinity tags for improved pulldown of native complexes

    • Bimolecular fluorescence complementation to visualize pheS interactions with repeat RNA

    • These strategies preserve physiological expression levels while enabling detailed tracking

  • CRISPRi/CRISPRa for Expression Modulation:

    • Precise titration of pheS expression in disease models

    • Spatial and temporal control of pheS levels during development

    • Combinatorial modulation of pheS and interacting partners

    • These approaches allow researchers to determine dosage effects and compensatory mechanisms

  • CRISPR Screens for Pathway Discovery:

    • Genome-wide screens to identify genetic modifiers of pheS toxicity

    • Focused screens targeting RNA metabolism factors

    • Screens for genes that modify C9orf72 repeat expansion toxicity

    • These screens can uncover novel therapeutic targets and pathway interactions

  • CRISPR-Based RNA Targeting:

    • Cas13-based approaches to target and degrade toxic C9orf72 repeat RNAs

    • Simultaneous visualization and perturbation of RNA-protein interactions

    • Development of RNA-editing tools to modify repeat structures

    • These technologies could lead to therapeutic strategies that preserve pheS function

  • In Vivo Disease Modeling:

    • Generation of C9orf72 models with controlled repeat expansion sizes

    • Tissue-specific expression of repeats to study regional vulnerability

    • Inducible systems to model age-dependent disease progression

    • These models can recapitulate the decreased expression of phenylalanine-rich proteins observed in patient tissues

By integrating these CRISPR-based approaches with traditional biochemical and cellular methods, researchers can develop a more comprehensive understanding of how pheS dysfunction contributes to neurodegenerative pathology and identify potential intervention strategies.

What is the potential for therapeutic approaches targeting pheS in neurodegenerative diseases?

The emerging understanding of pheS (FARSA) involvement in neurodegenerative diseases, particularly its interaction with C9orf72 repeat expansions, opens several promising therapeutic avenues:

  • RNA-Protein Interaction Disruptors:

    • Small molecules designed to prevent binding between repeat RNA and pheS

    • Peptide inhibitors that compete for the RNA-binding site

    • Nucleic acid decoys that sequester repeat RNAs away from pheS

    • These approaches aim to preserve normal pheS aminoacylation function

  • Enhanced tRNA Charging Strategies:

    • Development of modified pheS variants resistant to repeat RNA inhibition

    • Small molecules that allosterically enhance pheS activity

    • Alternative pathways for tRNA^Phe aminoacylation

    • These strategies address the decreased levels of charged tRNA^Phe observed in disease models

  • Phenylalanine Metabolism Modulation:

    • Approaches inspired by phenylalanine ammonia lyase (PAL) research

    • Enzymatic conversion of excess phenylalanine to non-toxic metabolites

    • Controlled phenylalanine supplementation to maintain protein synthesis

    • These methods draw on established paradigms from phenylketonuria research

  • Targeting Downstream Consequences:

    • Promoting expression of critical phenylalanine-rich proteins

    • Modulating protein quality control systems to handle partially synthesized proteins

    • Enhancing alternative translation initiation to bypass stalled ribosomes

    • These approaches address the global reduction of phenylalanine incorporation in the proteome

  • Delivery Considerations for CNS Targeting:

    • Blood-brain barrier penetrating formulations for small molecule therapies

    • AAV-based gene therapies for enhanced pheS expression

    • Intrathecal delivery systems for proteins or oligonucleotides

    • These delivery strategies are critical for reaching affected neurons in the CNS

  • Combination Therapeutic Approaches:

    • Simultaneous targeting of multiple disease mechanisms

    • Pairing pheS-targeted therapies with RNA-degrading approaches

    • Combining pheS modulation with neuroprotective strategies

    • These combinatorial approaches recognize the multifaceted nature of neurodegenerative diseases

Potential therapeutic efficacy could be evaluated using paradigms similar to those established for PAL in phenylketonuria, including dose-response studies and both pharmacological and physiological proof-of-principle demonstrations .

How should researchers integrate pheS research into broader studies of aminoacyl-tRNA synthetases in disease?

Researchers should adopt a multifaceted approach to integrate pheS research into the broader context of aminoacyl-tRNA synthetases in disease:

By integrating pheS research within this broader framework, investigators can develop a more comprehensive understanding of how aminoacyl-tRNA synthetase dysfunction contributes to disease pathogenesis and identify common principles that might guide therapeutic development across multiple conditions.

What databases and tools are most valuable for pheS researchers?

Researchers investigating pheS benefit from numerous specialized databases and bioinformatics tools that facilitate experimental design, data analysis, and interpretation:

Sequence and Structure Databases:

Disease and Variant Databases:

RNA Interaction Tools:

Bioinformatics and Analysis Tools:

  • ExPASy Proteomics Tools (https://www.expasy.org/): Suite of tools for protein analysis including enzyme kinetics tools

  • HMMER (http://hmmer.org/): Software for sequence homology searching

  • PyMOL/Chimera: Visualization tools for structural analysis of pheS

  • DAVID (https://david.ncifcrf.gov/): Functional annotation tool for proteomics data

Experimental Design Resources:

  • PhenX Toolkit (https://www.phenxtoolkit.org/): Resource for standard measures and protocols

  • Addgene (https://www.addgene.org/): Repository for plasmids and vectors for pheS expression

  • CRISPR Design Tools: Various web tools for designing gene editing experiments targeting FARSA/pheS

These resources provide valuable support throughout the research process, from initial hypothesis generation to final data interpretation. Regularly consulting these databases ensures that pheS research is informed by the most current information available in the field and contributes to standardization and reproducibility of experimental approaches.

How can researchers effectively communicate pheS research findings to the scientific community?

Effectively communicating pheS research findings requires strategic approaches tailored to different aspects of scientific dissemination:

  • Publication Strategies:

    • Target journals with appropriate readership (biochemistry, neuroscience, or translational medicine)

    • Consider both specialized journals focused on aminoacyl-tRNA synthetases and broader impact journals

    • Prepare clear graphical abstracts that highlight key findings about pheS function

    • Structure manuscripts to emphasize methodological rigor, following established standards for experimental design

  • Data Presentation Best Practices:

    • Present aminoacylation data in standardized formats for easy comparison across studies

    • Use consistent terminology when describing pheS activity and inhibition

    • Include detailed methods sections that allow for experimental reproduction

    • Provide access to raw data through repositories when possible

  • Visualization Guidelines:

    • Create clear schematic models of pheS-RNA interactions

    • Design figures that demonstrate both biochemical mechanisms and cellular consequences

    • Use consistent color schemes when presenting related datasets

    • Label structural images thoroughly to highlight key residues and domains

  • Conference Presentation Approaches:

    • Tailor presentations to different audiences (enzymologists vs. neurodegeneration researchers)

    • Prepare multiple elevator pitches of different technical depths

    • Highlight connections between pheS research and broader disease mechanisms

    • Use multimedia approaches to illustrate dynamic processes

  • Interdisciplinary Communication:

    • Frame findings in context of both molecular mechanisms and disease relevance

    • Explicitly connect biochemical observations to cellular and organismal phenotypes

    • Collaborate with clinicians to emphasize translational implications

    • Develop terminology bridges between different scientific communities

  • Public and Patient Communication:

    • Create simplified explanations of how pheS dysfunction contributes to disease

    • Use analogies to explain complex concepts like aminoacylation

    • Emphasize connections to potential therapeutic approaches

    • Avoid overpromising while conveying the importance of basic research

  • Meta-Research Considerations:

    • Transparently report limitations and negative findings

    • Explicitly address how findings reconcile with or challenge existing literature

    • Contribute to developing consensus standards for pheS research

    • Participate in collaborative efforts to replicate key findings

Effective communication not only advances scientific understanding but also facilitates cross-disciplinary collaboration and accelerates the translation of basic pheS research into clinical applications. By adopting these strategic approaches, researchers can ensure their findings reach and impact appropriate audiences within the scientific community.

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