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Feature Articles : May 1, 2008 ( )
Tools for Protein Structure Characterization
Classic Biochemical Procedures Are Experiencing a Renaissance
A formidable array of techniques allows researchers to describe the properties of protein molecules. While nucleic acids are much more restricted in their structural variations, the universe of possible combinations for the 20 basic amino acids permits virtually unlimited variation in proteins. Powerful hardware including mass spec, x-ray crystallographic, and NMR machines have morphed dramatically into user-friendly companions while providing a wealth of descriptive data.
In some cases, this surfeit of information can confuse and retard analyses, wasting time and resources. For this reason, there is renewed interest in applying classic biochemical methods in novel ways to provide structural information concerning protein molecules of interest. Collectively, such innovative applications may provide decisive evidence regarding the utility of a protein for therapeutic use.
Many of these protein-characterization tools have been around since the early days of biochemistry. But, the refinement of automated and robotic instrumentation has greatly simplified their application, as has the introduction of many premade and disposable options.
“Light scattering is the only practical method that takes the ambiguities out of measurement of molecular weight and size,” said Geofrey Wyatt, president of Wyatt Technology. Wyatt developed the first multiangle laser-based commercial instruments 40 years ago, he claimed, and since that time has pioneered many light-scattering hardware and software advances.
Cleaving Antibody Genes
Antibody genes undergo shuffling and rearrangement in order to generate the diversity that is the hallmark of the immune response. This scrambling of antibody gene sequences is the result of lymphocytic events in which a family of enzymes clips out and sutures this information in order to produce new combinations of antibody-coding sequences.
Another unique approach to protein characterization does not rely on high- or low-tech instrumentation but rather defines protein structure and function through the effect of mutational changes on the target molecule. According to Cheryl Paes, Ph.D., research scientist at Integral Molecular, shotgun mutagenesis utilizes traditional mutation analysis, but in a high-throughput manner, to rapidly evaluate the effects of amino acid substitutions across the entire length of a protein.
Adequate Protein Supply
Galapagos uses many procedures to delve into protein structure and function, noted Patrick Mollat, Ph.D., protein sciences team leader. In order to pursue these goals, the company has developed a number of innovative protocols to generate proteins in sufficient purity and quantity for investigating protein interactions.
In analyzing protein structure and function, clearly there is no one-size-fits-all approach. Information collected through the use of shotgun mutagenesis provides insights into the 3-D configuration of proteins, bypassing the time-consuming and expensive process of crystallizing and x-ray mapping a target. Yet the approach may not provide the fine resolution gained through the use of traditional x-ray crystallography.
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