Elucidating protein structure

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It bases on Thermodynamic hypothesis predicts that the native conformation of a protein corresponds to a global free energy minimum of the protein/solvent system.

Homology modeling is a class of methods for constructing an atomic-resolution model of a protein from its amino acid sequence.

An advantage of the method of single-particle reconstruction, in comparison to protein crystallography, is that it does not require the protein to be crystallized, since in many cases may be difficult and may require a lot of effort.

However, in electron crystallography, which is primarily used for membrane proteins, we do need crystals, so called two-dimensional crystals of a protein.

Because x-ray crystallography and NMR require large amounts (on the order of milligrams) of a purified protein (often unattainable with complications in current purification techniques) to analyze the protein’s structure, recombinant techniques are usually employed whereby a host organism is manipulated to express the protein to be studied.

Usually, protein refolding methods must then be used because the protein does not fold properly and abnormalities, known as inclusion bodies, in the protein’s structure develop.

People often say: Crystallization is an art and not a science.

A visualization can be created by this method which takes place at or below liquid nitrogen temperatures.

It is a fairly new technique that can create visualizations at an extremely high resolution.

However, for accurate modeling we need high percentage identity between the amino acid sequence of the given protein and its homologue for which the tertiary structure is known (the template).

Additional methods used in obtaining partial (local) structural information include mass spectrometry, analytical ultracentrifugation, various fluorescent spectroscopic methods, etc.

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