Molecular Profiling With SeraFILE™: Prospecting for Conformational Variants
Swapan Roy and Matthew Kuruc
ProFACT Proteomics, Inc., Monmouth Junction, NJ
Presented at Cambridge Healthtech ADAPT Conference, Washington DC, Sept, 2009
Abstract
SeraFILE™ – a proprietary, surface-based separations reagent set and associated exploratory protocols - addresses the disconnect between proteomics and functional mechanisms. Clients and collaborators now employ it as a targeted proteomics approach: for low-abundance enrichment, enzymatic activity-state profiling and functional proteomic prospecting. Preliminary data has established that SeraFILE™ can differentiate conformational variants, suggesting even the characterization of sub-unit equilibrium. These are critical data for drug development and not otherwise available with other proteomics methods, e.g., Mass Spec.
SeraFILE™ encompasses innovations in surface chemistry and associated process methods that obviate the need for bioengineering, greatly reducing cost and increasing throughput. SeraFILE™ separations and protocols are seamless with existing proteomic assay and detection infrastructure. Unique sub-proteomes are generated efficiently and in parallel, while maintaining the functional characteristics that define the conformational variability associated with crude soluble proteins.
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New Proteomic Subfractionation Surfaces - Innovative Technology For The Improved Resolution of Serum Proteins
Swapan Roy. Ph.D., John Krupey. Ph.D., Matthew Kuruc, Devjit Roy
ProFACT Protomics, Inc.
Commercialization Center for Innovative Technologies
675 Route One
North Brunswick NJ 08902
Tel: 732-246-1190
Fax: 732-246-3118
Abstract
ProFACT™ is a new sorting, or subfractionation methodology designed for comparative proteome analysis. Electrophoretic profiles of serum subfractions demonstrate improved resolution and quantification. Carryover from the three highest abundance serum proteins, albumin, IgG and Transferrin is minimal. The process starts with a separation platform utilizing a new combination of surface microenvironments substituted with low molecular weight substrates that feature drug-binding motifs. With the ProFACT™ surface library, undenatured, bioactive proteins can be subfractionated into differential pools.
Separations are universal as they do not require pre-qualified binding knowledge, a key limitation of affinity-type techniques. The surfaces utilized are disposable and versatile to meet sample size and scale requirements. A simple bind, wash and elute protocol is completed in 30 to 60 minutes.
As elutions are mild and consistent, a direct handoff can be made to subsequent interrogation. The interrogation strategy is adaptable to meet investigative inquiry using conventional reporter/probe bioassays, high performance resolution or optical techniques. Subsequent patterns may have diagnostic potential as biomarkers, or be useful for research-driven needs as a means to reduce the initial complexity of the crude sample down to a manageable number of subfractions that show differences, the “hits”. These hits can then be further analyzed by HPLC, Capillary Electrophoresis, 1 and 2D Electrophoresis, and Mass Spectrometry to more definitively identify and characterize discoveries.
As structural modifications of proteins can alter their binding affinities to the surface library, differences in structural features are revealed upon quantitative interpretation of ProFACT™ subfraction profiles. Future investigations will focus on comparing normal and disease state sera.
