Extracting Pure Proteins from Cells

Purification of the Enzyme Xanthine Dehydrogenase from a Fungus 

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Many different proteins exist in a single cell. A detailed study of the properties of any one protein requires a homogeneous sample consisting of only one kind of molecule. The separation and isolation, or purification, of proteins constitutes an essential first step to further experimentation. In general, separation techniques focus on size, charge, and polarity—the sources of differences between molecules. Many techniques are performed to eliminate contaminants and to arrive at a pure sample of the protein of interest. As the purification steps are followed, we make a table of the recovery and purity of the protein to gauge our success. Table 5.1 shows a typical purification for an enzyme. The percent recovery column tracks how much of the protein of interest has been retained at each step. This number usually drops steadily during the purification, and we hope that by the time the protein is pure, sufficient product will be left for study and characterization. The specific activity column compares the purity of the protein at each step, and this value should go up if the purification is successful. 

Column chromatography is widely used to purify proteins. 

To begin the process of purification, proteins are released from cells with homogenization using a variety of physical techniques. 

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Most of the machinery of living cells is made of enzymes. Thousands of them have been extracted from cells and have been purified and crystallized. Many others are recognized only by their catalytic action and have not yet been isolated in pure form. Most enzymes are soluble globular proteins but an increasing number of RNA molecules are also being recognized as enzymes. Many structural proteins of the cell also act as catalysts. For example, the muscle proteins actin and myosin together catalyze the hydrolysis of ATP and link the hydrolysis to movement (Chapter 19). Catalysis is one of the most fundamental characteristics of life. 

Nucleoprotein complex can be extracted from cells with N NaCl solution. If the resulting viscous solution is shaken with chloroform containing a little cetyl alcohol, the protein forms a gel at the chloroform/water interface and the sodium salts of the nucleic acids remain in the aqueous phase. Chromatography and centrifuging can then be used to isolate pure specimens (Chapter 14.3). Samples of DNA can be dissolved in water to form very viscous solutions. On adding alcohol to these, a soggy cotton wool-type of precipitate is obtained, from which semi-crystalline threads of DNA can be picked out. 

Hence, at present, the main applications remain in the research environment. LB films are particularly useful for the reconstitution of natural cell membranes on planar substrates for various kinds of biologically oriented investigation. Although most reported work has used pure, synthetic lipids, the technique can equally well be used with natural cell membrane extracts containing proteins (J.J. Ramsden and V. Mirsky, unpublished observations). Langmuir monolayers have been used to create biomimetic structures (see, e.g., Nandi and VolLhardt s review of mono-layers made from chiral molecules ). 

Data from in vitro activity assays with these purified recombinant proteins can typically be interpreted much more easily than data obtained from experiments with crude or partially purified protein extracts, because (1) there will be no competing proteins with similar activity present in the assay, and (2) there will no enzymes present that convert the product generated by the enzyme of interest, and hence reduce the effective product concentration. A potential downside of the use of recombinant protein over crude extracts is the fact that critical co-factors that will ensure proper activity may not be present in the purified protein fraction. If that is the case, the researcher will have to empirically determine which co-factor and at what concentration needs to be included in the assay. Another consideration is that the native protein may have undergone post-translational processing, such as acetylation, glycosylation, myristoylation, etc. These modifications may not occur or may not occur properly when the protein is expressed in bacterial, fungal or insect cells. Assuming that these potential problems do not occur or can be dealt with, the availability of pure recombinant protein will enable the determination of substrate specificity, as well as kinetic experiments in which the rate of conversion is measured as a function of time and/or substrate concentration. 

The routine unit of enzyme activity has been the international unit (I.U.), namely xmoles P formed (or S consumed) per minute. The specific activity of an enzyme preparation is the number of xmoles P formed (or S consumed) per minute per milligram of protein (clearly this will be very low in a crude cell extract and have a maximal value for a pure preparation of the enzyme). If the molecular mass is known, the specific activity of a pure enzyme measured in saturating (Fmax conditions) can be used to calculate the turnover number (or molecular activity ) of an enzyme, namely the number of P molecules formed (or S molecules transformed) per molecule of enzyme per second (units sec- ). If we recall that the maximal velocity (Fmax) equals k+2 (sec " ) [ET], we can see that the molecular activity equals k+2 (sec -1), that is, fal (sec-1). The katal is the S.I. unit of enzyme activity (moles substrate transformed sec -I) from whence come the corresponding units for specific activity (katal kilogram-1) and molar activity (katal per mole of enzyme). 

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