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Analytical Ultracentrifugation (AUC) Services for Protein Aggregation & Interaction Analysis

First-Principles Biophysical Characterization — No Labels, No Standards, No Surfaces, No Dilution Required

AUC services provide first-principles characterization of protein aggregation, size, and molecular interactions directly in formulation buffer — no labels, no standards, no surfaces. SV-AUC resolves monomers through subvisible aggregates at undiluted >100 mg/mL samples via interference optics — making it the regulatory gold standard for aggregate quantification and AAV empty/full capsid ratio. SE-AUC measures KD and stoichiometry for reversible interactions at true thermodynamic equilibrium in free solution.

Unlike SEC — which dilutes samples and strips reversible aggregates — SV-AUC measures aggregation undiluted, in the native formulation. Multi-wavelength detection (260/280 nm) simultaneously quantifies empty, partial, and full AAV capsids with baseline resolution — the method recommended by FDA guidance for IND-enabling characterization. SE-AUC provides label-free KD and stoichiometry for complexes that cannot be immobilized or crystallized — from mM to pM affinity, at true equilibrium.

Core Capabilities:

  • SV-AUC Aggregation Analysis — resolves monomers through subvisible aggregates (0.1–50 S) in undiluted formulation; interference optics for >100 mg/mL samples
  • AAV Empty/Full/Partial Capsid Ratio — multi-wavelength SV-AUC (260/280 nm) quantifies empty, partial, and full capsids — the regulatory gold standard for IND-enabling characterization
  • SE-AUC Interaction Analysis — label-free KD, stoichiometry, and B22 for reversible protein–protein, protein–nucleic acid, and protein–small molecule interactions at true equilibrium

Discuss Your AUC Project

What Is Analytical Ultracentrifugation?

AUC measures macromolecular movement under centrifugal force in free solution — determining mass, size, shape, and interactions from first principles without calibration standards. SV-AUC drives molecules toward the cell bottom at 40,000–60,000 RPM; the moving boundary — tracked by UV, interference, or fluorescence optics — yields a continuous c(s) distribution that resolves monomers through aggregates. SE-AUC establishes a reversible sedimentation–diffusion equilibrium at lower speed; the steady-state gradient directly yields molecular weight, stoichiometry, and KD from thermodynamic fundamentals — no kinetic fitting, no surface artifacts.

AUC is the reference method against which other aggregation techniques are validated. Unlike SEC-MALS — where dilution and column interaction can dissociate aggregates — SV-AUC reports the true mass fraction of each species directly in formulation buffer. For AAV, SV-AUC is the FDA-recommended method for empty/full capsid ratio. For interactions, SE-AUC measures affinity at true thermodynamic equilibrium in free solution — no surfaces, no labels, no kinetic assumptions.

What Questions Does AUC Answer?

  • Is my 150 mg/mL mAb formulation truly aggregate-free? — SV-AUC with interference optics measures aggregation directly in undiluted formulation — no dilution, no column interaction, no artifacts.
  • What is the empty/full/partial capsid ratio of my AAV batch? — Multi-wavelength SV-AUC resolves empty (~65S), partial (~80–90S), and full (~100S) AAV capsids — the only method that provides baseline resolution without reference standards.
  • What is the KD and stoichiometry of this reversible protein–protein interaction? — SE-AUC measures binding affinity at true thermodynamic equilibrium in free solution — no SPR chip, no ITC cell, no labels.
  • Does SEC overestimate my sample purity? — SV-AUC frequently detects aggregates that SEC misses due to column dilution and filtration — the gold standard for orthogonal purity verification.
  • How do mutations or formulation conditions affect self-association? — Concentration-dependent SV-AUC quantifies B22 and kD — predicting high-concentration behavior from dilute-solution measurements.

If your protein characterization or interaction data must withstand regulatory scrutiny — or if SEC, DLS, and SPR have given you conflicting or incomplete results — AUC provides the definitive, first-principles measurement.

Why AUC for Protein Characterization & Interaction Analysis?

First-Principles Measurement — No Standards, No Labels, No Surfaces

AUC calculates mass, size, and stoichiometry from fundamental physical constants — not calibration curves. No fluorescent labels, no SPR chips, no SEC columns — the sample is measured directly in free solution. For regulatory submissions where orthogonal methods must agree, AUC provides the independent, first-principles reference that SEC, DLS, and SEC-MALS are validated against.

True Aggregation State — No Dilution, No Column Interaction

SV-AUC measures aggregation directly in formulation buffer — the sample is loaded as-is, undiluted. For >100 mg/mL mAb formulations, interference optics bypass the concentration limits of UV detection. SEC dilution can dissociate reversible aggregates, making a formulation appear cleaner than it is — SV-AUC reveals the aggregation state that actually exists in the vial or pre-filled syringe.

AAV Empty/Full Resolution — The Regulatory Gold Standard

Multi-wavelength SV-AUC (260/280 nm) is the only method that simultaneously quantifies empty, partial, and full AAV capsids with baseline resolution. a 2024 multi-lab validation (Hirohata et al., Human Gene Therapy) demonstrated RSD for major species and validated the method for IND-enabling characterization. For AAV-specific protocols, our dedicated AUC for AAV Characterization service.

Reversible Interaction KD and Stoichiometry at True Equilibrium

SE-AUC measures KD directly from the equilibrium concentration gradient in free solution — no surface, no kinetic fitting. The sample reaches true thermodynamic equilibrium under centrifugal force; the steady-state gradient is governed solely by mass and solution properties. No SPR chip, no mass transport limitation. SE-AUC detects interactions from mM to pM KD and resolves 1:1, 2:1, and higher-order stoichiometries that single-technique SPR or ITC cannot distinguish.

Technical Services
Capabilities Method Comparison Workflow Platform Sample Requirements Deliverables FAQ Get a Proposal

AUC Analysis Services

AUC analysis services spanning aggregation, AAV capsid characterization, high-concentration formulation, interaction KD/stoichiometry, and density-based profiling.

01

SV-AUC Aggregation & Purity Analysis

  • c(s) distribution resolves monomers through subvisible aggregates (0.1–50 S) at formulation-relevant concentrations
  • Quantifies % monomer, % oligomer (dimer/trimer/tetramer), and % HMW aggregate — mass fractions, not intensity-weighted estimates
  • UV (280/214 nm), Rayleigh interference, and fluorescence detection for concentration ranges spanning 0.01–150 mg/mL
  • Directly supports formulation development, forced degradation studies, batch-to-batch comparability, and biosimilar analytical similarity assessment
02

AAV Empty/Full/Partial Capsid Analysis

  • Multi-wavelength SV-AUC (260/280 nm) simultaneously quantifies empty (~65S), partial (~80–90S), and full (~100S) AAV capsids — regulatory gold standard per FDA guidance
  • Serotype-independent — validated for AAV1–AAV9 and engineered variants; minimum 400 µL at ≥5 × 10¹¹ vg/mL
  • 2024 multi-lab validation (Hirohata et al., Human Gene Therapy): intermediate precision RSD
  • IND-enabling characterization, process development support, and QC release testing — orthogonal to AUC for AAV page for capsid-focused protocols
03

High-Concentration Formulation & Excipient Screening

  • Rayleigh interference optics measure aggregation in undiluted formulations at >100 mg/mL — directly in the formulation buffer, as-is
  • Quantifies self-association and non-ideality at high concentration — detects weak, reversible self-association that causes viscosity and opalescence at clinical doses
  • B22 and kD from concentration-dependent SV-AUC — predicting high-concentration stability from measurements at 1–10 mg/mL
  • Supports subcutaneous formulation development (>100 mg/mL), excipient screening, and manufacturing process comparability
04

SE-AUC Interaction KD & Stoichiometry

  • Measures KD and stoichiometry at true thermodynamic equilibrium in free solution — no SPR chip, no ITC cell, no labels
  • Resolves 1:1, 2:1, 3:1, and higher-order stoichiometries — distinguishes weak self-association from specific complex formation
  • Detects interactions from mM to pM KD — complementary to SPR (kinetics) and ITC (thermodynamics), resolving cases where surface or thermal artifacts produce conflicting results
  • Ideal for reversible protein–protein, protein–nucleic acid, and protein–small molecule complexes that cannot be immobilized or crystallized
05

DGE-AUC — Capsid Density Heterogeneity

  • Density gradient equilibrium AUC complements SV-AUC by resolving AAV capsids by particle density — not sedimentation rate
  • Distinguishes capsids with identical S-values but different DNA content — detecting subtle packaging heterogeneity that SV-AUC alone may miss
  • 2024 Analytical Chemistry validation: DGE-AUC + SV-AUC together provide the most complete capsid characterization available
  • Recommended when SV-AUC shows unresolved shoulders or broad peaks that may indicate density heterogeneity within the full or empty capsid population

AUC vs. Other Biophysical Characterization Methods

AUC is the reference method. Use it when you need first-principles data without labels, standards, surfaces, or dilution — or when SEC, DLS, and SPR give conflicting results.

Feature SV-AUC SEC-MALS DLS DSC
What It MeasuresMass fraction of each species (monomer, oligomer, aggregate) by sedimentation rateAbsolute MW + size after SEC separationHydrodynamic radius (intensity-weighted)Thermal unfolding (Tm, ΔH)
% Aggregate — QuantitativeYes — mass fraction, not intensity-weightedYes — after column separationNo — intensity-weighted, 0.1% aggregate dominates signalNo — detects unfolding, not aggregates
Dilution During MeasurementNone — measured in formulation buffer as-is10–50× dilution during SECNoneNone
High-Concentration (>100 mg/mL)Yes — interference opticsNo — overloads SEC columnLimited — multiple scattering artifactsYes
AAV Empty/Full RatioYes — gold standard, multi-λChallenging — similar hydrodynamic volumeNo — cannot resolve ~25 nm particlesNo
Requires Standards / CalibrationNo — first-principlesYes — column calibrationNo — but assumes spherical particlesNo
Sample per Run7–12 samples (multi-cell rotor)1 sample per SEC run1 sample (cuvette) or 96/384-well plate1 sample per cell
Turnaround3–8 hours per rotor (7–12 samples)15–30 min per sample~1 hour per thermal ramp
Best ForAggregate quantification (regulatory gold standard), AAV empty/full ratio, high-concentration formulation, orthogonal purity, label-free interaction KDAbsolute MW, oligomer MW, rapid purity checkRapid formulation and aggregation screening, PDI, thermal stabilityThermal stability ranking, domain unfolding, formulation excipient screening

SV-AUC Workflow: From Sample to c(s) Distribution

SV-AUC Workflow Diagram
1

Sample preparation & buffer matching

  • Sample buffer-exchanged or dialyzed against reference buffer; reference buffer used as optical blank and for cell meniscus matching
  • Concentration: 0.1–1.0 mg/mL (UV), 0.5–150 mg/mL (interference); volume: 400 µL per cell
  • 0.22 µm filtration or centrifugation to remove dust; sample loaded into 2-sector centerpiece with reference buffer in reference sector
2

Rotor loading & temperature equilibration

  • 7–12 samples loaded into 4-hole or 8-hole An-50 Ti or An-60 Ti rotor; cells balanced to within 0.5 g
  • Rotor brought to vacuum (<5 microns) and temperature equilibrated at 20°C (or user-specified, 4–40°C range) for 1–2 hours before acceleration
  • Temperature stability ±0.1°C throughout the run — critical for sedimentation coefficient accuracy
3

Sedimentation velocity data acquisition

  • Rotor accelerated to 40,000–60,000 RPM depending on analyte size; sedimentation monitored in real time
  • UV absorbance scans (190–800 nm) at 2–5 min intervals; Rayleigh interference images acquired simultaneously for high-concentration samples
  • 50–200 scans per cell over 4–12 hours — sufficient for complete sedimentation of the smallest species of interest
4

c(s) distribution analysis

  • Raw sedimentation boundaries fitted to the Lamm equation using SedFit or UltraScan software
  • Continuous c(s) distribution generated — each peak represents a sedimenting species with its sedimentation coefficient (S) and relative abundance
  • For AAV: peaks at ~65S (empty), ~80–90S (partial), and ~100S (full) with absorbance ratio A260/A280 confirming DNA content
5

Species identification & MW determination

  • S-value converted to molecular weight via Svedberg equation using partial specific volume and buffer density/viscosity
  • Multi-signal SV-AUC (UV + interference + fluorescence) deconvolutes co-sedimenting species with different spectral properties
  • For SE-AUC: equilibrium gradient fitted to single-species or self-association models; KD and stoichiometry extracted from concentration-dependence
6

Report delivery & interpretation

  • c(s) distribution plot with peak integration: % monomer, % oligomers, % HMW aggregate
  • For AAV: % empty, % partial, % full capsids with A260/A280 ratio confirmation
  • For SE-AUC: KD value with 95% confidence interval, stoichiometry, and model selection statistics
  • Full experimental report with methods, raw data, fitted parameters, and expert interpretation

AUC Instrumentation & Quality Standards

Beckman Coulter ProteomeLab XL-I Analytical Ultracentrifuge

All AUC experiments are performed on the Beckman Coulter ProteomeLab XL-I platform — the industry-standard analytical ultracentrifuge, equipped with dual UV/visible absorbance and Rayleigh interference optics for simultaneous detection across a broad concentration range.

  • UV/Visible Absorbance Optics: 190–800 nm wavelength range; multi-wavelength acquisition for spectral deconvolution (e.g., 260/280 nm for AAV protein/DNA quantification)
  • Rayleigh Interference Optics: Refractive index-based detection for high-concentration samples (>100 mg/mL) and samples lacking chromophores — no concentration-dependent non-linearity
  • Fluorescence Optics (Optional): Laser-induced fluorescence detection for tracer-level concentrations (nM–pM), ideal for weak interactions and low-abundance aggregates
  • An-50 Ti and An-60 Ti Rotors: 4-hole and 8-hole configurations; 7–12 samples per run with reference cells; speed range 3,000–60,000 RPM
  • Temperature Control: 4–40°C, ±0.1°C stability — critical for accurate sedimentation coefficient determination and SE-AUC equilibrium measurements
  • Software: SedFit, SedPhat, UltraScan for c(s) analysis, MW determination, and multi-signal deconvolution

Data Quality Standards

Metric Target Purpose
c(s) Fit RMSDConfirms the Lamm equation model adequately describes sedimentation data; higher RMSD triggers model refinement
Meniscus PositionConsistent across cells ±0.01 cm; verified visuallyMeniscus mismatch is the single largest source of systematic error in SV-AUC
Temperature Stability±0.1°C throughout runTemperature gradients drive convection; >0.2°C drift invalidates sedimentation coefficient accuracy
Buffer BaselineReference sector absorbance Buffer mismatch between sample and reference sectors generates systematic baseline offsets
Multi-Wavelength A260/A280A260/A280 ratio within ±0.05 of expected for pure DNA or proteinValidates species identification for AAV: empty capsids (protein-only, A260/A280 ~0.6), full capsids (DNA + protein, A260/A280 ~1.3)
Beckman Coulter ProteomeLab XL-I Analytical Ultracentrifuge

Beckman Coulter ProteomeLab XL-I

Sample Requirements for Analytical Ultracentrifugation

Parameter Specification
Sample TypesPurified proteins (mAbs, bispecifics, Fc-fusions, enzymes), AAV vectors, LNPs, liposomes, protein–nucleic acid complexes, virus-like particles, nanoparticles
Concentration (UV Detection)0.1–1.0 mg/mL (optimal 0.5 mg/mL for A280 detection); adjustable by wavelength selection (280 nm, 230 nm, 214 nm)
Concentration (Interference Optics)0.5–150 mg/mL — the only method that measures aggregation directly in undiluted high-concentration formulations
Sample Volume400–450 µL per cell; recommended to provide 500 µL per condition (allows for rinsing and loading)
Reference Buffer≥2 mL of exact formulation buffer or dialysate — must match sample buffer precisely; dialyze sample against reference buffer for ≥12 hours before experiment
AAV Samples≥5 × 10¹¹ vg/mL; 400 µL minimum; compatible with standard AAV formulation buffers (PBS + 0.001% Pluronic F-68, or similar)
ShippingPurified proteins: ship on dry ice; AAV: ship on dry ice; pre-dialyzed samples ready-to-load preferred — contact us for dialysis coordination if needed

Buffer matching is the single most critical sample preparation step for AUC. Even minor differences in salt concentration, pH, or excipient composition between sample and reference buffer generate systematic baseline offsets that compromise data quality. We strongly recommend dialyzing your sample against the reference buffer for ≥12 hours with at least one buffer exchange — and saving the dialysate as the reference buffer. Our team can perform dialysis upon sample receipt if preferred.

Deliverables for AUC Studies

c(s) Distributions, Aggregation Quantification, and Interaction Parameters

Every AUC project includes raw data, fitted c(s) distributions, species quantification, and a full experimental report.

SV-AUC c(s) Distribution

c(s) Distribution & Species Quantification

Continuous sedimentation coefficient distribution with integrated peak areas: % monomer, % dimer, % trimer, and % HMW aggregates. For AAV: % empty (~65S), % partial (~80–90S), and % full (~100S) capsids with A260/A280 confirmation.

Raw Sedimentation Boundaries

Raw Data & Fitted Boundaries

Complete set of raw sedimentation boundaries (absorbance or interference) with Lamm equation fits overlaid. Fit residuals and RMSD values for each cell. Multi-wavelength data for AAV: 260 nm and 280 nm scans with spectral deconvolution.

SE-AUC Equilibrium Gradient and KD

SE-AUC Equilibrium Analysis

Equilibrium concentration gradients fitted to single-species or self-association models. KD and stoichiometry values with 95% confidence intervals. Model selection statistics (F-test or AIC) for comparing alternative stoichiometries.

Frequently Asked Questions About Analytical Ultracentrifugation

Why does SV-AUC detect aggregates that SEC-MALS misses?

Three reasons: (1) SEC dilutes the sample 10–50×, which can dissociate reversible aggregates — SV-AUC measures directly in formulation buffer at native concentration. (2) SEC column frits and guard columns filter out larger aggregates before they reach the detector. (3) SEC separates by hydrodynamic volume — aggregates and monomers of similar elution time may co-elute without baseline resolution. SV-AUC separates by sedimentation coefficient — a mass- and shape-dependent property — providing baseline resolution of monomers, dimers, trimers, and larger aggregates. This is why regulatory agencies consider SV-AUC the gold standard for aggregation analysis and why it is frequently used to validate SEC-based purity methods.

How does SV-AUC quantify AAV empty, partial, and full capsids?

Empty AAV capsids (~3.7 MDa, no DNA) sediment at ~65S. Full capsids (~5.1 MDa, with 4.7 kb ssDNA genome) sediment at ~100S. Partially filled capsids sediment at intermediate S-values (~80–90S). Multi-wavelength detection at 260 nm (DNA absorbance maximum) and 280 nm (protein absorbance) confirms species identity by A260/A280 ratio: empty capsids (~0.6, protein-only), full capsids (~1.3, DNA + protein). The three populations are baseline-resolved in the c(s) distribution, and peak integration directly quantifies the percentage of each. This method is serotype-independent, matrix-free, and requires no reference standards — making it the method recommended by FDA guidance for IND-enabling AAV characterization.

Can AUC measure my sample at >100 mg/mL — without diluting it?

Yes — using Rayleigh interference optics. Interference detects refractive index differences between sample and reference sectors, which are proportional to protein concentration. Unlike UV absorbance, interference optics have no upper concentration limit for non-linearity — they work directly at >100 mg/mL in undiluted formulation. This is critical for subcutaneous mAb formulations, where the clinical dose concentration (often 100–150 mg/mL) must be characterized for aggregation state — and dilution would dissociate reversible aggregates that actually exist in the pre-filled syringe or autoinjector. UV absorbance optics saturate at these concentrations; interference optics do not.

How does SE-AUC measure KD — and how is it different from SPR or ITC?

SE-AUC measures KD at true thermodynamic equilibrium: the sample is centrifuged at a lower speed until sedimentation and diffusion reach a steady state. The resulting concentration gradient is governed solely by the molecular mass, partial specific volume, and solution density — no kinetic fitting, no surface, no heat of binding. This differs from SPR (measures kon/koff on a surface, extrapolates KD) and ITC (measures heat of binding, requires high concentrations for weak interactions). SE-AUC is particularly valuable when: (1) SPR immobilization perturbs binding, (2) ITC requires more sample than is available, or (3) the interaction is too weak for SPR (mM KD) or too tight for reliable SPR off-rate measurement (pM KD).

What is the throughput — and how many samples can I run at once?

A single AUC rotor accommodates 7 samples (4-hole rotor) or 12 samples (8-hole rotor) plus reference cells — all run simultaneously under identical conditions. A standard SV-AUC run takes 4–8 hours depending on rotor speed and analyte size. This means 7–12 samples can be analyzed in a single working day — comparable throughput to SEC-MALS when accounting for column equilibration between runs. For high-throughput screening applications (e.g., formulation excipient screening, 20+ conditions), we recommend DLS as a first-pass screen, with SV-AUC deployed on the 5–10 most promising conditions for definitive aggregate quantification.

What is the difference between SV-AUC and DGE-AUC for AAV?

SV-AUC separates AAV capsids by sedimentation rate — reflecting both mass and shape. Empty, partial, and full capsids have distinct sedimentation coefficients (~65S, ~85S, ~100S). DGE-AUC (density gradient equilibrium AUC) separates capsids by buoyant density in a CsCl or iodixanol gradient. Capsids with identical sedimentation coefficients but different DNA content (e.g., a capsid with a truncated genome vs. a full-length genome) may have different densities and are resolved by DGE-AUC. The two methods are complementary: SV-AUC for routine empty/full quantification; DGE-AUC when SV-AUC shows unexplained peak broadening or when capsid density heterogeneity is suspected. A 2024 Analytical Chemistry study established the combined SV-AUC + DGE-AUC workflow as the most complete AAV capsid characterization strategy.

Key Literature on Analytical Ultracentrifugation

Schuck, P. (2016). Sedimentation Velocity Analytical Ultracentrifugation: Discrete Species and Size-Distributions of Macromolecules and Particles. CRC Press. DOI: 10.1201/9781315331767
— The definitive textbook on SV-AUC by the developer of SedFit — covers c(s) analysis, experimental design, and interpretation for proteins, AAV, and nanoparticles.

Hirohata, K. et al. (2024). Methodological Validation of Sedimentation Velocity Analytical Ultracentrifugation Method for Adeno-Associated Virus. Human Gene Therapy. 35(11-12):432-443. DOI: 10.1089/hum.2023.169
— Multi-lab collaborative validation of SV-AUC for AAV empty/full capsid quantification — validated for specificity, accuracy, precision (RSD

Hirohata, K. et al. (2024). Applications and Limitations of Equilibrium Density Gradient Analytical Ultracentrifugation for AAV Vectors. Analytical Chemistry. 96(2):850-858. DOI: 10.1021/acs.analchem.3c01955
— Establishes DGE-AUC as a complementary method to SV-AUC for AAV capsid density heterogeneity — resolving capsids with identical S-values but different DNA content.

Zhao, H. et al. (2015). Overview of current methods in sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation. Current Protocols in Biophysics. 71:7.12.1-7.12.34. DOI: 10.1002/0471250953.bi0712s50
— Practical protocols for SV-AUC and SE-AUC — covers sample preparation, data acquisition, c(s) analysis with SedFit, and SE-AUC model fitting.

Resource

Analytical Ultracentrifugation: Techniques, Principles, and Applications in Biochemistry and Polymer Science

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