Protein units

Proteins are polymers made of amino acid units. The primary structure of a polypeptide is the sequence of amino acid residues secondary structure is the formation of helices and sheets tertiary structure is the folding into a compact unit quaternary structure is the packing of individual protein units together. 

Completely different mechanisms are involved in the self-assembly of the tobacco mosaic virus (TMV). This virus consists of single-strand RNA, which is surrounded by 2,130 identical protein units, each of which consists of 158 amino acid residues. A virus particle, which requires the tobacco plant as a host, has a rodlike structure with helical symmetry ( Stanley needles ). It is 300 nm long, with a diameter of 18nm. The protein and RNA fractions can be separated, and the viral... 

In summary, the formation of silk fibers involves superstructures such as, possibly, micelles and/or molecular rods (Akai, 1998 Jin and Kaplan, 2003 Knight and Vollrath, 2002) that are dependent on the packing and conformation of the individual protein units. The relationship, however, between the shapes of these superstructures and the various forms of protein conformation remains elusive (Valluzzi and Jin, 2004). Seeking to clarify this issue we will examine, in Section II.B, the role of shape and extended network formation modulating solubility, stability, and assembly. 

The specific activity of an enzyme preparation is expressed as the catalytic activity per milligram of protein (units mg-1 protein) and is a convenient... 

Let us consider the structure of the tobacco mosaic virus first. As shown schematically in Figure 5.1, it is composed of a single strand of ribonucleic acid, RNA, covered by a sheath formed from 2130 identical protein units. Thus the whole virus constitutes a rather simple supramolecular assembly. By changing... 

At the present time, there is no accepted chelating agent which can be used against common influenza viruses in humans. A virus has a core of either DNA or RNA and a protective coat of many identical protein units. All viruses are either rods or spheres, that is the protein coats are cylindrical shells having helical symmetry or spherical shells having icosahedral symmetry. Viruses reproduce inside living cells, where each viral nucleic acid directs the synthesis of about 1000 fresh viruses. These are then released and the host cell may die. 

Although the association between lipids and proteins is fundamental in understanding the physiological functions of membranes, information on such structures is very limited. Studies of a few systems of lipids and globular proteins indicate that the proteins tend to remain in their native form. The structures can be separated into two somewhat simplified types. Usually the lipid structure seems to dominate, and the protein molecules are incorporated into liquid crystalline structures of lipids. In other cases, the lipid molecules are distributed within the protein units,... 

Equation (4.7) shows that the number of available reflections depends only upon Vand A. For a modest-size protein unit cell of dimensions 40 x 60 x 80 A, 1.54-A radiation can produce 1.76 X 106 reflections, an overwhelming amount of data. Fortunately, because of cell and reciprocal-lattice symmetry,... 

Several diffraction criteria define a promising heavy-atom derivative. First, the derivative crystals must be isomorphic with native crystals. At the molecular level, this means that the heavy atom must not disturb crystal packing or the conformation of the protein. Unit-cell dimensions are quite sensitive to such disturbances, so heavy-atom derivatives whose unit-cell dimensions are the same as native crystals are probably isomorphous. The term isomorphous replacement comes from this criterion. 

Suppose we are able to locate a heavy atom in the unit cell of derivative crystals. Recall that Eq. (5.15) gives us the means to calculate the structure factors Fhkl for a known structure. This calculation gives us not just the amplitudes but the complete structure factors, including each of their phases. So we can compute the amplitudes and phases of our simple structure, the heavy atom in the protein unit cell. Now consider a single reflection hkl as it appears in the native and derivative data. Let the structure factor of the native reflection be Fp. Let the structure factor of the corresponding derivative reflection be FHp. Finally, let FH be the structure factor for the heavy atom itself, which we can compute if we can locate the heavy atom. 

Enzyme activity is commonly expressed by the initial rate (l/0) of the reaction being catalyzed. The units of V0 are pmol min-1, which can also be represented by the enzyme unit (U) or the katal (kat), where 1 pmol min-1 = 1 U = 16.67 nanokat. The term activity (or total activity) refers to the total units of enzyme in a sample, whereas specific activity is the number of units per milligram of protein (units mg-1). 

In hemoglobin, O2 binding to Fe2+ does not oxidize it to Fe3+, as it is protected by protein units around the heme group. A nonaqueous environment is required for reversible O2 binding. 

The bacterial enzyme chorismate mutase-prephenate dehydrogenase is peculiar because it is a single protein unit with two catalytic activities. It catalyzes the sequential reactions of mutation of chorismate to prephenate and then the reaction that leads to the formation of phenylalanine and tyrosine, through oxidation of prephenate. The first of these reactions is interesting because it is one of the few strictly single-substrate enzymatic reactions it entails... 

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