Protein Structure. W. M. Grogan, Ph.D. OBJECTIVES

Transcription

1 Protein Structure W. M. Grogan, Ph.D. OBJECTIVES 1. Describe the structure and characteristic properties of typical proteins. 2. List and describe the four levels of structure found in proteins. 3. Relate the primary amino acid sequence of a protein to its three dimensional structural motifs. RESOURCES Lehninger (5 th Ed.), Chapter 3 (continued), Chapter 4 OVERVIEW AND PERSPECTIVE Proteins are the principal agents through which the information carried in the genome is expressed in all life forms. The proteome of every higher organism contains many thousands of proteins, which provide the structural matrix, condition the environment and play essential dynamic roles in every process characteristic of biological life. With few exceptions, the enzymes which catalyze biochemical reactions are proteins. Proteins play essential roles in regulation, transport, immune response, hemostasis, digestion, motility and information storage. The diversity of these functions is reflected in the wide ranging properties of naturally occurring proteins (see Table 1). Yet, as we shall see, all proteins are constructed from various combinations of a limited number of recurring structural patterns or motifs. The structure of each protein, in turn, confers the properties required for its specific functions.

2 Table 1: Lehninger Table 3 2 I. Amino Acid Composition of Proteins Proteins have characteristic amino acid compositions (see Table 2). What could you infer about a protein from its amino acid composition alone?

3 Table 2: Lehninger Table 3 3 II. Other Chemical Groups Contained in Proteins Many proteins contain chemical groups other than amino acids (see Table 3). As you will see later, many of these groups make important contributions to the function of their proteins.

4 Table 3: Lehninger Table 3 4 III. The Structure of Proteins The observation that proteins can be crystallized provides evidence that they are distinct chemical entities with relatively stable three dimensional structures. The amino acid sequence of a protein determines its three dimensional structure, which in turn dictates its function, within the context of its location. The aggregate spatial arrangement of the various elements of a protein structure are referred to as its conformation. Proteins in solution are dynamic structures that can assume more than one conformation. As you will see later, changes in conformation often play an important role in protein function. It is useful to classify the structure of a protein at four different levels (see Figure 1). A. Primary Structure The linear sequence of the amino acids connected by covalent peptide bonds. Different proteins have different amino acid sequences. The amino acid sequence in turn determines higher levels of structure. B. Secondary Structure

5 A repeating pattern of structure defined by the spatial relationships between amino acid residues that are close to each other in the amino acid sequence. This level of structure is primarily stabilized by non covalent interactions (hydrogen bonding, hydrophobic, electrostatic), particularly hydrogen bonding. C. Tertiary Structure The structural pattern resulting from the three dimensional folding of elements that are distant from each other in the amino acid sequence. This structure may be stabilized by non covalent (hydrophobic, electrostatic, hydrogen bonding) or covalent (disulfide bonds) interactions between residues that are distant in the amino acid sequence. The contribution from hydrophobic interactions is particularly important in the core of a folded protein which is relatively inaccessible to water. D. Quaternary Structure The structural arrangement resulting from interactions among different polypeptides. This level of structure can be stabilized by either noncovalent or covalent (disulfide bonds) interactions. Figure 1: The four levels of protein structure defining the relationships among structural elements that are progressively further apart in the amino acid sequence. IV. General Principles that Govern the Formation of Protein Structures A. Proteins adopt preferred conformations that are based on the lowest energy structures available to them. The change in free energy between the native

6 protein and the unfolded protein is small (5 15 kcal/mol; 5 15% of the energy required to break a single covalent bond). Proteins can be unfolded (denatured) by disrupting the noncovalent interactions that maintain their structures (with heat, detergent or high salt) and refolded by removing the denaturing agent (see Figure 2). The refolded protein will often return to the same conformation as the native protein [What are the implications of this observation?]. Failure to do so is often indicative of some modification to the native protein or its environment after its initial folding. Figure 2: Folding of a protein from the disordered extended chain to the more highly ordered, lower energy conformation. B. Characteristics of the Preferred Conformation 1. Non polar (hydrophobic) amino acid residues are associated with each other inside the folded protein, minimizing their contact with water. Recall that we discussed the driving force for hydrophobic interactions in an earlier session. 2. Ionic and polar groups are located on the surface in contact with water. 3. Polar groups that are inside the folded protein are positioned to interact with other polar groups through electrostatic interactions or hydrogen bonding. 4. All atoms are positioned to avoid overlap between van der Walls radii. V. The most stable and consequently most common types of secondary structure are the α helix and the β sheet. Each represents a minimum energy structure which maximizes hydrogen bonds between the α amino and α carbonyl groups of nearby residues while minimizing steric hindrance and maximizing favorable electrostatic interactions between R groups. Thus, certain amino acids are better accommodated in one type of secondary structure than in other types, depending on the nature of their R groups.

7 Lehninger Figure 4 2. A. The α helix (see Figure 4) Lehninger Figure 4 4.

8 1. About 25% of the amino acid sequences of proteins are in this conformation (average), although this value varies greatly among proteins. 2. One turn = 3.6 residues. 3. Stabilized primarily by hydrogen bonding between the α amino hydrogen of the peptide bond and the carbonyl oxygen four residues distant in the direction of the amino terminus. 4. The tendency of a polypeptide sequence to form a stable α helix is greatly influenced by the constituent amino acids and the order in which they occur. a. The helix can be further stabilized by electrostatic interactions between oppositely charged R groups 3 4 residues removed or destabilized by identical charges on adjacent residues. b. The helix can also be destabilized by steric hindrance between bulky R groups located in close proximity in the amino acid sequence. c. The large number of aligned hydrogen bonds in the helix generates an electric dipole positively charged at the amino terminus and negatively charged at the carboxyl terminus. Consequently, negatively charged residues at the amino terminus and positively charged residues at the carboxyl terminus have a stabilizing effect, whereas the oppositely charged residues would have a destabilizing effect. d. The amino acids Pro and Gly have a particularly destabilizing effect on the helical structure. The rigid ring structure of Pro does not permit rotation around the carbon nitrogen bond and does not participate in hydrogen bonding. Gly contributes greater flexibility to a polypeptide chain and favors a different type of structure, as we shall see later.

9 Lehninger Figure 4 5 (4 th ed.) B. The β sheet structures (zigzag) (see Figure 6)

10 (4th ed., similar to Fig. 4 6 in 5th ed.) 1. This conformation is stabilized by hydrogen bonding between adjacent chains. The interacting chains are usually, but not always, closely located in the amino acid sequence. 2. The chains may be oriented in the same (parallel) or opposite directions (antiparallel) in terms of the amino and carboxyl terminal ends. 3. As in the case of the α helix, certain combinations of amino acids are best accommodated in the β structure due to restrictions on the ranges of rotation around the Cα N and Cα C bonds by steric hindrance. C. The Beta Turn Approximately a third of amino acids in a globular protein participate in turns or loops where the polypeptide chain makes a sudden reversal of direction. The turns or more extensive loops connect successive α helical and β sheet elements, permitting the polypeptide chain to fold into the compact structure that is characteristic of globular proteins. The most common of these, the β turn, is composed of four amino acid residues that effect a 180 degree turn.

11 Lehninger Figure Stabilized by formation of a hydrogen bond between the carbonyl oxygen of the first residue and the amino hydrogen of the fourth residue. The second or third residues don t hydrogen bond with peptide groups but may be stabilized by hydrogen bonding with water on the surface of the protein. 2. Gly and Pro are often found in turns; Gly, because of its unusual flexibility and Pro, because its imino nitrogen can form a peptide bond with the cis configuration, which facilitates a tight turn.