Protein Structure

Abstract

The great variety of structures and functions of proteins found in humans and other organisms conceals an underlying unity in chemical structure. All proteins share a common repetitive main chain, while differences in the sequences of side chains give proteins their differences in structure and function.

Keywords: secondary structure (α helix, β sheet); tertiary structure; protein folding; folding pattern; modular protein

Figure 1.

Proteins are constructed from a common and repetitive polypeptide main chain and an individual sequence of side chains. Si represents the side chain of the ith residue.

Figure 2.

Ramachandran plot, showing the contours of low energy for the conformation of a typical residue in a protein, as a function of two angles of internal rotation (ϕ and ψ) that determine the main chain conformation of a residue. The points correspond to the residues in crambin. Residues are found primarily in the allowed regions αR and β, except for glycine (marked by G), which has greater conformational freedom.

Figure 3.

(a) α Helix. (b) β Sheet. Single circles: carbon atoms; double circles: oxygen atoms; large triple circles: nitrogen atoms; small triple circles: hydrogen atoms; solid lines: primary chemical bonds; broken lines: hydrogen bonds. N and C indicate the N‐terminus and C‐terminus of the chains, showing their direction. (b) β sheet in which all strands are pointing in the same direction (a parallel β sheet); it is also possible to form sheets with strands pointing in opposite directions.

Figure 4.

Structure of human hemoglobin represented by threading the backbone atoms with a ribbon (based on Protein Data Bank entry 1bbb). The picture illustrates the different hierarchical levels of a structure: the amino acid sequence (primary structure) (1) governs the folding into secondary structure (here an α helix). (2) The α helices assemble together to form the tertiary structure or fold of the protein (3). The way in which different units (here a tetramer) assemble together determines the quaternary structure (4). The prosthetic group, the heme (shown in line representation in (3) and (4)), is noncovalently bound to hemoglobin.

Figure 5.

Extracellular modular proteins from the blood coagulation cascade. These contain different combinations of the same structural modules. EGF, F1, F2, γ and Kr identify the modules: epidermal growth factor, fibronectin type 1 and type 2, gla and kringle respectively. At the top, a representative example of each of these individual structures is illustrated, associated with an icon. Below, the structures of four different molecules in the blood coagulation cascade are shown in terms of their assembly as linear arrays of modules.

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References

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Further Reading

Bork P, Downing AK, Kieffer B and Campbell ID (1996) Structure and distribution of modules in extracellular proteins. Quarterly Reviews in Biophysics 29: 119–167.

Branden C‐I and Tooze J (1999) Introduction to Protein Structure, 2nd edn. New York, NY: Garland.

Lesk AM (2001) Introduction to Protein Architecture: The Structural Biology of Proteins. Oxford, UK: Oxford University Press.

Lesk AM (2002) Introduction to Bioinformatics. Oxford, UK: Oxford University Press.

Web Links

Protein Data Bank http://www.rcsb.org

SMART http://smart.embl‐heidelberg.de/

Structural Classification of Proteins http://scop.mrc‐lmb.cam.ac.uk/scop/

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How to Cite close
Pastore, Annalisa, and Lesk, Arthur M(Jan 2006) Protein Structure. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005714]