Proteins three-dimensional shapes

The three dimensional shapes of many proteins are governed and stabilized by S—S bonds connecting what would ordinarily be remote segments of the molecule We 11 have more to say about these disulfide bridges m Chapter 27... 

Avery s studies shed light on the function of DNA. Chargaff s touched on structure in that knowing the distribution of A, T, G, and C in DNA is analogous to knowing the fflnino acid composition of a protein, but not its sequence or three-dimensional shape. 

When the polypeptide chains of protein molecules bend and fold in order to assume a more compact three-dimensional shape, a tertiary (3°) level of structure is generated (Figure 5.9). It is by virtue of their tertiary structure that proteins adopt a globular shape. A globular conformation gives the lowest surface-to-volume ratio, minimizing interaction of the protein with the surrounding environment. 

I The tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape. 

Figure 26.7 A representation of protein denaturation. A globular protein loses its specific three-dimensional shape and becomes randomly looped.

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

Each protein has a unique three-dimensional shape called its tertiary structure. The tertiary structure is the result of the bends and folds that a polypeptide chain adopts to achieve the most stable structure for the protein. As an analogy, consider the cord in Figure 13-39 that connects a computer to its keyboard. The cord can be pulled out so that it is long and straight this corresponds to its primary structure. The cord has a helical region in its center this is its secondary structure. In addition, the helix may be twisted and folded on top of itself This three-dimensional character of the cord is its tertiary structure. 

Hydrogen bonds and other intermolecular attractions are important in retaining the three-dimensional structure of certain proteins. When the pH is lowered or the temperature is raised, these attractions are disrupted, resulting in a change of the three-dimensional shape of the protein. 

There are three potential methods by which a protein s three-dimensional structure can be visualized X-ray diffraction, NMR and electron microscopy. The latter method reveals structural information at low resolution, giving little or no atomic detail. It is used mainly to obtain the gross three-dimensional shape of very large (multi-polypeptide) proteins, or of protein aggregates such as the outer viral caspid. X-ray diffraction and NMR are the techniques most widely used to obtain high-resolution protein structural information, and details of both the principles and practice of these techniques may be sourced from selected references provided at the end of this chapter. The experimentally determined three-dimensional structures of some polypeptides are presented in Figure 2.8. 

A number of different molecular mechanisms can underpin the loss of biological activity of any protein. These include both covalent and non-covalent modification of the protein molecule, as summarized in Table 6.5. Protein denaturation, for example, entails a partial or complete alteration of the protein s three-dimensional shape. This is underlined by the disruption of the intramolecular forces that stabilize a protein s native conformation, namely hydrogen bonding, ionic attractions and hydrophobic interactions (Chapter 2). Covalent modifications of protein structure that can adversely affect its biological activity are summarized below. 

The secondary structure of a protein is the three-dimensional shape of a polypeptide chain. 

In introductory biochemistry, one becomes familiar with amino acids (aa) and how they combine (polymerize) to become peptides and proteins. Proteins fold into three-dimensional shapes and become enzymes, the catalysts of... 

Proteins are polymers of L-amino acids containing numerous chiral centres, each possessing a characteristic three-dimensional shape, or conformation. Most globular proteins such as albumins undergo extensive folding of the chains into... 

Primary structure of a protein is simply amino acids sequence of the peptide chain. The secondary structure is a result of the different conformations that the chain can take. The tertiary structure refers to the three dimensional shape that results from twisting, bending and folding of protein helix. The quaternary structure refers to the way in which these amino acid chains of a complex protein are associated with each other (oligomer, dimers, trimers, etc.). 

Upon entering the cell, the steroid molecule initially binds to the steroid receptor protein (E domain) to form the steroid-hormone-receptor complex. This complex concomitantly binds to an additional eight or more other peptides (also via the E domain) these peptides are termed chaperone peptides and consist of macromolecules such as heat shock proteins (e.g., hsp70, hsp90). The chaperone peptides help to twist and turn the steroid receptor protein into an improved three-dimensional shape for final and optimal binding of the steroid molecule. Following binding of the chaperone peptides, the steroid-hormone-receptor complex becomes a mature steroid-hormone-receptor... 

The folding of proteins into their characteristic three-dimensional shape is governed primarily by noncovalent interactions. Hydrogen bonding governs the formation of a helices and [) sheets and bends, while hydrophobic effects tend to drive the association of nonpolar side chains. Hydrophobicity also helps to stabilize the overall compact native structure of a protein over its extended conformation in the denatured state, because of the release of water from the chain s hydration sheath as the protein... 

An important topic of current research is how the sequence of amino acids in a newly synthesized protein can direct the folding of the chain into a precise, biologically active shape. Can the amino acid sequence be used to predict the final three-dimensional shape of the protein The short answer to this question is, Not completely, not yet. Present computer-aided predictions are about 70% accurate with... 

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