The Shape of Proteins

There are thousands of sets of signal proteins, like insulin and its receptor. These systems of paired protein-control molecules and their receptors have evolved over millions of years and provide the very precise orchestration of thousands of different chemical reactions that are required to keep our bodies alive and working. Although illness that develops because of a failure in these systems may seem like a terrible betrayal of how things should work, the fact that so many complex systems in so many 

Over many decades, scientists have worked to imderstand how each of these systems in each cell and in the whole organism 

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Although other secondary protein structures play roles in determining the shapes of proteins, the helix and pleated sheet occur most frequently. A discussion of less common secondary structures is beyond the scope of this text. 

Protein chains are not the sprawling, ill-defined structures that might be expected from a single polypeptide chain. Most proteins are compact molecules, and the relative positions of atoms in the molecule contribute significantly to its biological role. A particularly important contributor to the shape of proteins is provided by the peptide bond itself. Drawn in its simplest form, one might expect free rotation about single bonds, with a variety of conformations possible (see Section 3.3.1). However,... 

Sulfur has a striking ability to catenate, or form chains of atoms. Oxygen s ability to form chains is very limited, with H2Oz, 03, and the anions 02,022-, and 03 the only examples. Sulfur s ability is much more pronounced. It appears, for instance, in the existence of S8 rings, their fragments, and the long strands of plastic sulfur that form when sulfur is heated to about 200°C and suddenly cooled. The — S—S— links that connect different parts of the chains of amino acids in proteins are another example of catenation. These disulfide links contribute to the shapes of proteins, including the keratin of our hair thus, sulfur helps to keep us alive and, perhaps, curly haired. 

Amino acid side chains play a vital role in the shapes of proteins. They vary in their hydrophobicities and charges at physiological pH. Thus, when incorporated into proteins, hydrophobic amino acids that form part of membrane-bound proteins... 

Let us now examine the assumptions underljdng the Oncley treatment. First, thermodynamically V is defined as the increment of the volume of the solution per unit mass of the solute added and therefore is not identical with Fsp of the solute. These two quantities may be equal in magnitude if and only if the system is an ideal solution, that is, there is no solute-solvent interaction whatsoever present. To eliminate one unknown Fsp in Eq. (14) by introducing F we have at the same time added another uncertain term w into the equation. Thus this treatment offers at most a rough estimate of the shape of proteins for a chosen model, a prolate or an oblate ellipsoid. Furthermore the estimated p value corresponds only to the hydrated particle, which is slightly different from that of the unhydrated particle unless the bound water is so distributed throughout the protein molecule that it does not change its axial ratio because of hydration. 

This planar, trans peptide unit poses serious limitations on the shapes proteins can adopt. Understanding the shapes of proteins is very important—enzymes, for... 

Edsall, J. T. Rotary Brownian Movement. The Shape of Protein Molecules... 

J- L. Oncley and R. Simha Viscosity and the Shape of Protein Molecules. 

An important property of sulfur is its ability to form chains of atoms, catenation. The -S-S-links that connect different parts of the chains of amino acids in proteins are an important example. These disulfide links contribute to the shapes of proteins (see Chapter 19). 

Physical methods are often used to determine protein conformation. Describe how x-ray crystallography, cryoelec-tron microscopy, and NMR spectroscopy can be used to determine the shape of proteins. 

Looking at line spectra in discharge tubes to understand the model of the atom. Investigating the effect of the environment on the shape of proteins... 

With suitably sharp AFM tips, almost atomic resolution can be achieved, at least in principle, and it has been used to determine the shapes of protein and nucleic acid molecules adsorbed on surfaces. One major advantage is that the method does work under water, so that molecules can be studied under near physiological conditions. 

The solubility of the protein is minimal at the isoelectric point. Also, because protein shape is determined very much by intramolecular electrical attraction (see Section 3.8), the shapes of proteins can be dramatically altered by pH. Such abnormally shaped proteins are called denatured and no longer function for their intended purposes. 

Mehl, J. W., Oncley, J. L., Simha, R., Viscosity and the shape of protein molecules. 

It is valuable to understand the factors which affect the anisotropy decays. For a spherical molecule, the anisotropy is expected to decay with a single rotational correlation lime (0). Perhaps the most frequent interpretation of the correlation time is in terms of the overall rotational correlation lime of a protein. The measured values of 0 can compare with the value predicted for a hydrated sphere of equivalent molecular weight (Eq. [10.52]). However, numerous factors can result in muUiexponenUal anisotropy decays. Multiexponential anisotropy decays are expected for nonspherical fluorophores or proteins. In this case the correlation times are determined by the r es of rotation about the various molecular axes. Anisotropy decays can be used to estimate the shapes of proteins. 

Even the term intermolecular bonding needs to be applied carefully. Hydrogen bonding (usually considered to be a chemical bond, although sometimes that status has been questioned) can be intramolecular (being very important in determining the shape of proteins and nucleic acids, for example) or intermolecular. 

In our laboratory, SEC-viscometry has been used to estimate the aspect ratio of proteins (81). This ratio, which describes the shape of proteins, is calculated from the Scheraga-Mandelkem P function (82). To determine this function, the intrinsic viscosity of the protein must be known accurately. Through the use of SEC-viscometry, proteins can be separated from interfering conformers and associated species, and intrinsic viscosities can be determined accurately. 

The Dq values also depend on the amount of dissolved compounds (influencing their aggregation), pH value, and salinity of the aqueous solutions (affecting the shape of protein molecules). These effects and protein interactions with the CG membrane can result in broadening of the D value range. This range corresponds to a certain f(D) distribution that depends on individual protein types. 

Tetrahedral geometry plays a crucial role in describing the shapes of proteins and even their packed structure. On the other hand, the simplest chained structure carbon based is that of polyethylene, (-CH -). ... 

The interaction between the molecules in coffee that taste bitter and the taste receptors on the tongue is caused by intermolecular forces—attractive forces that exist between molecules. Living organisms depend on intermolecular forces not only for taste but also for many other physiological processes. For example, in Chapter 19, we will see how intermolecular forces help determine the shapes of protein molecules—the workhorse molecules in living organisms. Later in this chapter—in the Chemistry and Health box in Section 12.6—we learn how intermolecular forces are central to DNA, the inheritable molecules that serve as blueprints for life. 

Protein Structure The structure of proteins is critical to their function. The shapes of proteins largely determine how they interact with other molecular structures to do their job. That structure depends on the sequence of amino acids within the protein chain and how those amino acids interact with one another. 

Information regarding the shape of protein molecules may be obtained from measurements of viscosity, light scattering or streaming birefringence, aided by electron microscopy and X-ray diffraction analysis. This last technique is specially valuable since it can be used to provide not merely the overall shape of a protein molecule but also a detailed picture of its molecular architecture. 

Chapter 18, Biochemistry, looks at the chanicalstmctures and reactions of chemicals that occur in living systems. We focns on four types of biomolecules—carbohydrates, lipids, proteins, and nucleic acids— as well as their biochemical reactions. The shape of proteins is related to the activity and regnlation of enzyme activity. A discussion of the genetic code and protein synthesis completes the chapter. Combining Ideas from Chapters 17 and 18 follows as an interchapter problem set. 

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