Myoglobin tertiary

KNOT REPRESENTATIONS AND JONES POLYNOMIALS V(t) OF MYOGLOBIN TERTIARY STRUCTURE... 

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

The properties of individual hemoglobins are consequences of their quaternary as well as of their secondary and tertiary structures. The quaternary structure of hemoglobin confers striking additional properties, absent from monomeric myoglobin, which adapts it to its unique biologic roles. The allosteric (Gk alios other, steros space ) properties of hemoglobin provide, in addition, a model for understanding other allosteric proteins (see Chapter 11). 

Myoglobin the p Subunits of Hemoglobin Share Almost Identical Secondary and Tertiary Structures... 

The term quaternary structure is employed to describe the overall shape of groups of chains of proteins, or other molecular arrangements. For instance, hemoglobin is composed of four distinct but different myoglobin units, each with its own tertiary structure that comes together giving the hemoglobin structure. Silk, spiderwebs, and wool, already described briefly, possess their special properties because of the quaternary structure of their particular structural proteins. 

When a protein contains more than about 200 amino acid groups, it often assumes two or more somewhat spherical tertiary structural units. These units are often referred to as domains. Thus, hemoglobin is a combination of four myoglobin units with each of the four units influenced by the other three, and where each unit contains a site to interact with oxygen. 

FIGURE 16.2 Generalized myoglobin structure showing some amino acid units as open circles to illustrate the folded tertiary structure. 

Many examples of recurring domain or motif structures are available, and these reveal that protein tertiary structure is more reliably conserved than primary sequence. The comparison of protein structures can thus provide much information about evolution. Proteins with significant primary sequence similarity, and/or with demonstrably similar structure and function, are said to be in the same protein family. A strong evolutionary relationship is usually evident within a protein family. For example, the globin family has many different proteins with both structural and sequence similarity to myoglobin (as seen in the proteins used as examples in Box 4-4 and again in the next chapter). Two or more families with little primary sequence similarity sometimes make use of the same major structural... 

Globular proteins have more complicated tertiary structures, often containing several types of secondary structure in the same polypeptide chain. The first globular protein structure to be determined, using x-ray diffraction methods, was that of myoglobin. 

Myoglobin is a single polypeptide of 153 amino acid residues with one molecule of heme. It is typical of the family of proteins called globins, all of which have similar primary and tertiary structures. The polypeptide is made up of eight a-helical segments connected by bends (Fig. 5-3). About 78% of the amino acid residues in the protein are found in these a helices. 

FIGURE 24.9 Secondary and tertiary structure of myoglobin, a globular protein found in the muscles of sea mammals. Myoglobin has eight helical sections. 

J. R. Gunn, A. Monge, R. A. Friesner, and C. H. Marshall, /. Phys. Chem., 98,702 (1994). Hierarchical Algorithm for Computer Modeling of Protein Tertiary Structure Folding of Myoglobin to 6.2 A Resolution. 

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