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Interaction of Molecules

Module by: Lydia E. Kavraki. E-mail the author

Summary: This module provides a brief introduction to the classes of protein interactions that mediate biological processes, with examples.


Life is based on molecular interactions. Underlying every biological process is a multitude of proteins, nucleic acids, carbohydrates, hormones, lipids, and cofactors, binding to and modifying each other, forming complex frameworks and assemblies, and catalyzing reactions.

Classes of Molecular Interactions

Protein-Nucleic Acid Interactions

Proteins that bind to DNA and RNA mediate a number of processes, including regulation of gene expression, gene transcription, DNA replication, and mRNA intron splicing.

Example 1: A DNA-binding protein: TATA box-binding protein (TBP)

Figure 1: Schematic picture of TBP (blue) bound to a promoter DNA sequence (red) (PDB structure ID 1tgh)
Figure 1 (1tgh-cartoon.jpg)

TBP is responsible for initiating gene transcription on the chromosome. It specifically recognizes the promoter DNA sequence TATAAA. The promoter sequence lies about 25 base pairs upstream of a gene, and marks the location where an RNA polymerase complex must bind to transcribe that gene. Upon binding, TBP induces a kink in the DNA strands and forces open the minor groove of the DNA double helix, where most of its contacts with the DNA occur. Other transcription factors, as well as the RNA polymerase II complex, assemble around it. The TBP-DNA complex is slightly assymetrical, ensuring that transcription occurs on the correct strand of DNA.

Protein-Ligand Interactions

The function of many proteins is to bind some target molecule or set of target molecules and perform some action. Enzymes bind to substrate molecules and then catalyze chemical reaction that would otherwise occur too slowly to be biologically useful. Some proteins involved in cellular signaling bind a signal molecule and undergo a conformational change leading to further signaling or changes in cellular processes.

Example 2: An enzyme and inhibitor: HIV-I protease

Figure 2: A stereo view of HIV-I protease (blue) bound to MVT-101 (red), an inhibitor (PDB structure ID 4hvp)
Figure 2 (hiv1p-stereo.jpg)

The human immunodeficiency virus (HIV) is widely known as the cause of acquired immune deficiency syndrome (AIDS). One peculiarity of HIV and other retroviruses is that one of their genes encodes a polyprotein. In most organisms, each gene typically corresponds to a single protein. A gene is transcribed to mRNA and then translated into a functional protein. The HIV genome contains a single gene that codes for three proteins. These proteins are synthesized attached end-to-end, and are not functional until they are cut apart. HIV protease is the enzyme that makes these cuts. Because it constitutes a potential single point of failure in the HIV life cycle, it is a very attractive target for drug design. Inhibitors function by binding to the active site of the protease, preventing it from carrying out its function. In order to be a good drug candidate, an inhibitor must bind very specifically to its target enzyme and only to its target enzyme. Binding to non-viral proteins can lead to unpleasant side effects and even outright toxicity. Protease inhibitors are one of three major classes of anti-HIV drugs.

Protein-Protein Interactions

Many proteins function by forming active complexes with each other. The RNA polymerase II complex is an example of such an assembly. Protein-protein interactions are also involved in antibody-antigen binding, large scale organismal motion, and cell adhesion.

Example 3: A molecular motor: Myosin and actin

Figure 3: A theoretical representation of myosin (blue, green) bound to an actin filament (red) (PDB structure ID 1alm)
Figure 3 (myosin.jpg)

Myosin and actin provide a mechanism for the transduction of coordinated, microscopic movement into motion on an organismal scale. The club-like head (blue) of myosin binds to an actin filament. Fueled by ATP hydrolysis, it detaches and changes shape, binds to a different subunit of the actin, and then changes conformation again, pulling itself along the actin filament. Directed intracellular transport occurs by this mechanism. If the myosin tail (green) is tethered to other myosin tails, it forms a relatively immobile immobile filament, and instead of moving itself, the myosin causes the actin filament to slide. This is the molecular basis of muscular contraction. Muscles consist of interleaved fibers of actin and myosin. Roughly 10^15 molecules of myosin are involved in the simple action of flexing the elbow.

Example 4: Humoral immunity: Antibody-antigen recognition

Figure 4: Half of a human immunoglobulin, or antibody (IgG1) (PDB structure ID 1mco)
Figure 4 (antibody.jpg)

An antibody consists of a two heavy chains (blue, above) and two light chains (green). Each light chain is bound to the one end of one of the heavy chains, and the two heavy chains are joined together at their other ends. The image above is of a single heavy chain bound to its light chain. The binding surface is at the center-right of the image, and spans both chains. Each antibody binds to a specific target molecule. Antibodies effectively act as tags to label foreign molecules and cells for removal or destruction by immune system cells. They also pull foreign molecules out of solution in the blood, limiting their mobility and ability to cause damage. Antibodies are secreted by B-cells, and the parts of the gene that code for the binding surface undergo extremely high mutation rates in the reproduction of these cells within a single organism. This ensures that the organism is capable of mounting a response to a wide range of pathogens.

Because of the wide range of antibody specificity, and the high affinity of a given antibody for its target, many laboratory assays and techniques make use of them, including immunofluorescence (with applications to flow cytometry), radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), and Western blots.

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