PROTEIN STRUCTURE

Protein Structure & Techniques



Protein Structure

Introduction

Proteins are the most versatile macromolecules in living systems and serve crucial functions in essentially all biological processes. They function as catalysts, they transport and store other molecules such as oxygen, they provide mechanical support and immune protection, they generate movement, they transmit nerve impulses, and they control growth and differentiation. Indeed, much of this text will focus on understanding what proteins do and how they perform these functions. (Nenad Ban et al, 2000, pp905-920)

How can Knowledge of protein structure give insight into the function of the protein?

The primary structure of peptides and proteins refers to the linear number and order of the amino acids present. The convention for the designation of the order of amino acids is that the N-terminal end (i.e. the end bearing the residue with the free a-amino group) is to the left (and the number 1 amino acid) and the C-terminal end (i.e. the end with the residue containing a free a-carboxyl group) is to the right. (Figure 1).

Figure 1 Structure Dictates Function

Source: (Branden & Tooze 1999, pp45-51)

The ordered array of amino acids in a protein confer regular conformational forms upon that protein. These conformations constitute the secondary structures of a protein. In general proteins fold into two broad classes of structure termed, globular proteins or fibrous proteins. Globular proteins are compactly folded and coiled, whereas, fibrous proteins are more filamentous or elongated. It is the partial double-bond character of the peptide bond that defines the conformations a polypeptide chain may assume. Within a single protein different regions of the polypeptide chain may assume different conformations determined by the primary sequence of the amino acids.

Figure 2 A Complex Protein Assembly

Source: (Branden & Tooze 1999, pp45-51)

The a-helix is a common secondary structure encountered in proteins of the globular class. The formation of the a-helix is spontaneous and is stabilized by H-bonding between amide nitrogens and carbonyl carbons of peptide bonds spaced four residues apart. This orientation of H-bonding produces a helical coiling of the peptide backbone such that the R-groups lie on the exterior of the helix and perpendicular to its axis. (Figure 3).

Figure 3 Flexibility and Function

Source: (Branden & Tooze 1999, pp45-51)

Describe two techniques that can be used to gain information about protein structure?

Whereas an a-helix is composed of a single linear array of helically disposed amino acids, ß-sheets are composed of 2 or more different regions of stretches of at least 5-10 amino acids. The folding and alignment of stretches of the polypeptide backbone aside one another to form ß-sheets is stabilized by H-bonding between amide nitrogens and carbonyl carbons. However, the H-bonding residues are present in adjacently opposed stretches of the polypetide backbone as opposed to a linearly contiguous region of the backbone in the a-helix. ß-sheets are said to be pleated. This is due to positioning of the a-carbons of the peptide bond which alternates above and below the plane of the sheet. ß-sheets are either parallel or ...