Types of protein structure

N ow that some of the major types of protein structures have been described it is appropriate to turn to the question of how protein structure relates to protein function. To explore this question, two protein systems, hemoglobin and the actin-myosin complex, are examined in detail. 

Figure 3.2 Above are the four types of protein structures. All proteins have a primary, secondary, and tertiary structure. Some have a quaternary structure as well.

Lundstrom, A. and Egelrud, T., Cell shedding from plantar skin in vitro evidence that two different types of protein structures are degraded by a chymotrypsin-like enzyme, Arch. Dermatol. Res., 282, 234, 1990. 

Let s summarize the various types of protein structure and their relationship to one another (Figure 19.12). 

In general, there are two types of protein structures (1) fibrous, elongated proteins which are not soluble in water and provide structural support and (2) globular spherical proteins which are water soluble and have specific functions in the immune system and metabolism. 

By the time Pauling became engaged in this research it had been established from rudimentary X-ray diffraction patterns that there might be two principal types of protein structure. Keratin fibers, such as hair, horn, porcupine quill, and... 

Many biomolecules are large proteins and each type of protein structure consists of a precise sequence of amino acids that allows it to fold up into a particular three-dimensional shape or conformation. The lowest... 

During the formation of the polypeptide polymeric chain, one water molecule is lost per amino acid. This is why the constituents of the proteins are called amino acid residues. There are four different types of protein structures recognized in the field. These are described in the subsequent text. 

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

Figure 2.10 Examples of schematic diagrams of the type pioneered by Jane Richardson. Diagram (a) illustrates the structure of myoglobin in the same orientation as the computer-drawn diagrams of Figures 2.9b-d. Diagram (b), which is adapted from J. Richardson, illustrates the structure of the enzyme triosephosphate isomerase, determined to 2.5 A resolution in the laboratory of David Phillips, Oxford University. Such diagrams can easily be obtained from databases of protein structures, such as PDB, SCOP or CATH, available on the World Wide Web.

The interiors of protein molecules contain mainly hydrophobic side chains. The main chain in the interior is arranged in secondary structures to neutralize its polar atoms through hydrogen bonds. There are two main types of secondary structure, a helices and p sheets. Beta sheets can have their strands parallel, antiparallel, or mixed. 

What can be done by predictive methods if the sequence search fails to reveal any homology with a protein of known tertiary structure Is it possible to model a tertiary structure from the amino acid sequence alone There are no methods available today to do this and obtain a model detailed enough to be of any use, for example, in drug design and protein engineering. This is, however, a very active area of research and quite promising results are being obtained in some cases it is possible to predict correctly the type of protein, a, p, or a/p, and even to derive approximations to the correct fold. 

Oi Hel ix (Section 27.19) One type of protein secondary structure. It is a right-handed helix characterized by hydrogen bonds between NH and C=0 groups. It contains approximately 3.6 amino acids per turn. 

Cellulase enzyme complexes consist of three major types of proteins that synergistically catalyze the breakdown of a cellulosic substrate. Because the enzymes are strictly substrate-specific in their action, any change in the structure or accessibility of the substrate can have a considerable influence on the course of the hydrolysis reaction. A pretreatment method based on exposing cellulosic substrate to phosphoric acid solution [9] and addition of the nonionic... 

In 1990, work was started to characterize the human genome which had been shown to consist of about 3 billion base pairs. The final result was announced in the year 2000. All of the chromosomes have been characterized. The human genome has been shown to contain some 30,000 genes (which are sections of the chromosome which code for specific proteins). Each cell produces the t T)e of proteins needed for it to function. The function of mRNA is to transfer information from the DNA. so as is to fix the limits of the protein needed. The vast majority of the proteins found in living organisms are composed of only 20 different kinds of amino acids, repeated many times and strung together in a particular order. Each type of protein has its own unique sequence of amino acids. This sequence, known as its primary structure, actually... 

Although heme is absent in Clostridia, it was early recognized that anaerobic bacteria may contain substantial levels of iron (44). To date the best characterized iron compounds from this source are the iron-sulfur proteins termed ferredoxins and rubredoxins. Molecular structures of representatives of both types of protein have been worked out by Jensen and his colleagues by X-ray diffraction analysis (see below). 

Table 13.3. A guide to genes and proteins. All life forms are made up of material that includes proteins, which are involved in nearly every aspect of structure and function. In humans there are around 40,000 different types of proteins (there may be thousands or millions of each type). The same protein can differ slightly between individuals although it does the same job.

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