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BioTechniques, Vol. 56, No. 5, May 2014, pp. 212–215
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Can small molecule studies decipher protein folding landscapes and perhaps identify the next wonder drug? Nathan Blow looks at how chemical biology is changing our view of protein folding.

Misfolded proteins can cause problems. They damage cells and tissues, and in some instances, cause diseases such as Alzheimer's, Parkinson's, and type II diabetes. In fact, they can be so disruptive that cells have developed sophisticated quality control mechanisms to target and dispose of their misfolded proteins. But how much misfolded protein is too much in a particular cell, and how do misfolded proteins actually affect cell health?

If you think about it, answering these seemingly simple questions presents significant technical challenges. Both folded and misfolded versions of any particular protein are composed of the same basic amino acid sequence, so you are essentially looking to separate the two based on differences in the final, folded structures. This means that some form of structural analysis is likely required to identify and measure the quantity of misfolded protein in a particular sample. Or could there be another way?—What if it were possible to tag one version of the protein versus the other using specific chemicals?

Recently, researchers at The Scripps Research Institute in La Jolla, California did just that by taking advantage of a little small molecule chemistry. The team, led by senior author Jeffrey Kelly, who is the Lita Annenberg Hazen Professor of Chemistry and Chairman of the Department of Molecular and Experimental Medicine at Scripps, designed fluorescent-tagged small molecule “folding probes” that could be used to visualize the interplay between the fully folded and unfolded forms of any protein (1).

Straddling the line between chemistry and biology, small molecule studies and screens, alongside technical advances such as Kelly's, are now driving research into the impact of misfolded proteins on cells, attracting new scientists to the field and creating unique possibilities for understanding the role protein folding plays in basic biology and human disease.

Littering the landscape with small molecules

Protein folding is a complex business. Making the transition from a linear sequence of amino acids to a fully folded, three-dimensionally active protein requires some favorable thermodynamics, the correct physiological environment, and in some instances, a little help from other biological molecules.

As anyone who has taken a biochemistry lab course can tell you, cellular environment plays a large role in protein folding dynamics. In fact, a number of basic biochemistry techniques and applications work by altering the chemical environment surrounding a protein—at times employing harsh pH changes and chemicals to efficiently denature (unfold) native proteins for purification or analysis. But when scientists are interested in understanding or even refolding misfolded proteins, they need to reverse this strategy and look for ways to change the chemical environment to create more favorable conditions for proper folding. In 2012, Ashok Deniz and his colleagues at The Scripps Research Institute in La Jolla, California published an article in the journal Proceedings of theNational Academy of Sciences focusing on so-called chemical chaperones: small, low molecular weight compounds that do the job of stabilizing a protein as it folds into the proper form (2). Deniz was interested in the folding and misfolding balancing act that takes place with alpha-synuclein, a protein implicated in Parkinson's disease. By employing a single molecule FRET approach in the study, Deniz and his team were able to test that counterbalance using a protecting osmolyte called trimethylanime-N-oxide (TMAO), which promoted folding, and a denaturing osmolyte, urea, which promoted unfolding of the protein (this chemical is often used in those biochemistry labs). This was one of the first studies showing how chemical chaperones affect fold cycling for alpha-synuclein.

Interestingly, there was a clear neutral ratio between the protective and denaturing chemicals for alpha-synuclein that seemed to hold regardless of the absolute osmolyte concentration—illustrating the exacting balance between the folded and unfolded states of the protein. Deniz's study suggested an important direction for future protein folding studies—investigating the ability of low-molecular weight compounds to influence the chemical environment surrounding a protein and thus impact how a particular protein folds in the cell.

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