08/25/10 -- Contradicting the widely held view that detergents cause irreparable harm to proteomics experiments, Protein Discovery today introduced the UPX Universal Protein Extraction Kit for unbiased, high-yield detergent extraction of proteins from cells and tissues. Unlike other commercially available products for protein extraction, the UPX kit extracts both soluble and insoluble proteins at high efficiency, enabling subsequent analysis of membrane proteins and other hydrophobic proteins. These elements of the "deep proteome" are refractory to extraction and solubilization by conventional methods, and Protein Discovery's UPX Universal Protein Extraction Kit opens a rich vein of exploratory research opportunity to investigators seeking either to analyze specific insoluble proteins, or to obtain a more encompassing understanding of the proteome.     Link

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New Roche deal could net Aileron $1.1B

Aileron Therapeutics Inc., a Cambridge biotech focused on protein-based treatments, has entered into a development deal with Roche that could bring as much as $1.1 billion to Aileron.

The Swiss pharmaceutical giant Roche will be working with Aileron to develop a class of drugs called Stapled Peptide Therapeutics, based on Aileron’s peptide stabilization technology. To start the collaboration, Roche will give Aileron $25 million in up front fees to gain access to the technology.

The deal calls for Roche and Aileron to work on drug candidates to target five undisclosed diseases or conditions. Those five do fall into Roche’s overall key areas of oncology, virology, inflammation, metabolism and central nervous system disorders, according to officials. To reach the $1.1 billion level, Aileron will have to meet a series of milestones in discovery, development, regulation and commercialization. But the $1.1 billion isn’t the final cap on the deal – Aileron is also eligible for royalties on any future sales that come out of the partnership.     Link

Citizen science: People power

The whole thing began by accident, says David Baker, a biochemist at the University of Washington in Seattle. It was 2005, and he and his colleagues had just unveiled Rosetta@home — one of those distributed-computing projects in which volunteers download a small piece of software and let their home computers do some extracurricular work when the machines would otherwise be idle. The downloaded program was devoted to the notoriously difficult problem of protein folding: determining how a linear chain of amino acids curls up into a three-dimensional shape that minimizes the internal stresses and strains — presumably the protein's natural shape. If the users wanted, they could watch on a screen saver as their computer methodically tugged and twisted the protein in search of a more favourable configuration.   Link

Pity the poor protein biologist. DNA sequence gurus have GenBank, structural biologists, PDB. But those looking to data-mine the spectral peaks and valleys of today’s burgeoning proteomics literature are out of luck. Or are they?

Several freely available databases are dedicated to the storage, annotation, and analysis of mass spectrometric proteomics data. Yet because they are both poorly advertised and sparsely populated, mining them to feed the sorts of meta-analyses that have become staples of gene sequence and gene expression studies largely has not been possible.   Link

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