Lecture 6 Summary

The conformational space of a polypeptide chain can be represented as an ordered set of points on a Ramachandran plot. Locally repeating patterns of main-chain dihedral angles give rise to what we call secondary structure - principally involving α-helix and β-strand conformations - correspond to clusters of points on a Ramachandran plot.

Motifs and supersecondary structure

Small motifs, like the βαβ unit introduced earlier, can combine to form larger elements of structure. The figure at left shows two ways in which βαβ units can combine to form a four-stranded parallel beta sheet. Motifs, supersecondary structure, and domains are terms used to describe structural levels that bridge from simple, repetitive secondary structures to more complex and unique tertiary structures.

α/β structures

The parallel β-sheets that result from the stringing together of βα units take on two typical tertiary structure patterns. If the sheet curves around to form a closed cylinder, a structure called an alpha/beta (α/β) barrel forms. This is sometimes called a TIM barrel, after the enzyme triose phosphate isomerase (TIM) in which this tertiary structure was first observed. In the barrel, eight beta strands form the core of the protein, while α-helices all lie on the outside.

Protein structure determination: X-ray crystallography and multidimensional NMR. X-ray crystallography provides a high-resolution view of the structures of molecules. As applied to proteins, it typically reveals the locations of all non-hydrogen atoms that are well-localized in a tertiary structure to a resolution range of 3 - 1 Å.

Membrane proteins

Membrane proteins can be very tightly associated with the lipid bilayer, others more loosely. The former are termed integral membrane proteins, while the latter are termed peripheral membrane proteins. Most integral membrane proteins are deeply embedded in the lipid bilayer, typically extending completely through it. Bacteriorhodopsin is a "light harvesting" integral membrane protein with seven α-helices that span the hydrophobic interior of the membrane. Porins are a class of channel-forming proteins with a β-barrel membrane-spanning architecture. Protein-lipid linkages are also used to promote the membrane association of some proteins. Attachment of nonpolar chains of fatty acids or isoprenoids via the reactive cysteine side chain, and C-terminal glycosyl phosphatidyloinositol (GPI) "anchors" serve in this capacity.

Common features of protein tertiary structure

We can summarize much of what has been learned about protein structure in the form of some generalizations that describe features common to most if not all proteins.

• Proteins have well-packed, non-polar interiors, whereas polar and charged groups are accessible to the outside. Where polar groups occur in the interior (e.g. main chain carbonyls and amides), they tend to be paired.
• The interior of proteins are close-packed, i.e. there are no large cavities.
• The protein chains do not generally form "knots" (although see Ref. 4 below).
• In comparing proteins, it is found that sequence (1° structure) similarity usually implies structural similarity. Note that there are numerous instances in which two proteins with little or no detectable sequence similarity nonetheless adopt very similar structures.
• Overall, there is very little strain in protein structures. In cases where local strain exists, the energetic cost is covered by numerous favorable interactions within the rest of the structure.

Quaternary (4°) structure

The top of the protein structure hierarchy is the description of how polypeptide chains with defined tertiary structures associate (noncovalently) to form stable complexes called multimers. The classic example illustrating the difference between tertiary and quaternary structure is the comparison between myoglobin (Mb) and hemoglobin (Hb).

Learning objectives

• Define the terms primary, secondary, tertiary, and quaternary structure.
• Learn how to use a structure viewing program (such as PyMOL or Swiss PDB Viewer).
• Describe motifs and supersecondary structure
• Represent motifs with topology diagrams.
• Describe and explain general features of protein tertiary structure.
• For each of the following techniques, describe the principles upon which it is based, the type of information obtained through its use, and any significant limitations:
  • X-ray crystallography
  • multidimensional NMR

Page updated 8-17-09

References:

1. Branden, Carl & Tooze, John Introduction to Protein Structure (1st ed. 1991, Garland Publishing)
2. Lesk, AM. Introduction to Protein Architecture (2001, Oxford University Press).
3. Creighton, TE. Proteins: Structure and Molecular Properties (2nd ed, 1993. Freeman)
4. Taylor,WR, Lin, K. "Protein knots: A tangled problem" (2003) Nature 421: 25.
5. Web resource: Orientations of Proteins in Membranes (OPM) database @ University of Michigan.