Question

To fully appreciate how proteins function in a cell, it is helpful to have a threedimensional view of how proteins interact with other cellular components. Fortunately, this is possible using online protein databases and three- dimensional molecular viewing utilities such as JSmol, a free and user- friendly molecular viewer that is compatible with most browsers and operating systems. In this exercise, examine the interactions between the enzyme lysozyme and the Fab portion of the antilysozyme antibody. Use the PDB identifier 1FDL to explore the structure of the IgG1 Fab fragment-lysozyme complex (antibody- antigen complex). To answer the questions, use the information on the Structure Summary page at the Protein Data Bank (www.rcsb.org), and view the structure using JSmol or a similar viewer. a. Which chains in the three-dimensional model correspond to the antibody fragment, and which correspond to the antigen, lysozyme? b. What type of secondary structure predominates in this Fab fragment? c. How many amino acid residues are in the heavy and light chains of the Fab fragment? In lysozyme? Estimate the percentage of the lysozyme that interacts with the antigen- binding site of the antibody fragment. d. Identify the specific amino acid residues in lysozyme and in the variable regions of the Fab heavy and light chains that are situated at the antigen- antibody interface. Are the residues contiguous in the primary sequence of the polypeptide chains?

Short answer

Fab fragment chains: heavy (H) and light (L); lysozyme chain: A/B. Predominant secondary structure: beta sheets. Fab heavy/light residues: varies; lysozyme residues: varies. Interaction residues usually not contiguous.

Step-by-step solution

Access Protein Data Bank

Go to the Protein Data Bank website at www.rcsb.org. Enter the PDB identifier '1FDL' in the search bar to find the IgG1 Fab fragment-lysozyme complex. This identifier will pull up the specific structure summary page that contains necessary data on the protein complex.

Identify Chains

Open the 3D structure using the JSmol viewer. Look for labels on the chains to determine which belong to the Fab fragment (antibody) and which belong to the lysozyme (antigen). Typically, antibodies have two chains labeled light and heavy (e.g., H, L), and the lysozyme may be labeled differently (often as other letters like A or B).

Determine Secondary Structure

Navigate to the Structure Summary page and look under secondary structure information. You should see the predominant types of secondary structures such as alpha helices or beta sheets noted for the antibody Fab fragment.

Count Amino Acid Residues

Check the details tab or the sequence tab on the Structure Summary page to obtain the number of amino acid residues in the heavy and light chains of the Fab fragment, as well as those in the lysozyme. The chains are usually listed with their residue counts next to them.

Estimate Interaction Percentage

By examining the complex in the JSmol viewer, count the number of residues in lysozyme that directly interact with the antibody fragment. Compare this to the total number of residues in the lysozyme to estimate the percentage that is involved in antigen-antibody interaction.

Identify Interface Residues

In the JSmol viewer, visually identify and list specific amino acid residues at the interface of the lysozyme and the Fab fragment. Check if these residues are contiguous by comparing their sequence positions in the primary sequence of the polypeptide chains provided on the summary page or sequence viewer.

Key concepts

Protein Data Bank

The Protein Data Bank (PDB) is an essential online resource for the study of protein structures. It provides a wealth of information about proteins and other biological macromolecules that have been experimentally determined. To access specific protein structures, you can search for unique PDB identifiers. For example, the identifier '1FDL' corresponds to the IgG1 Fab fragment-lysozyme complex, which is an antibody-antigen complex.

The platform allows researchers to view three-dimensional structures, making it possible to understand how proteins function and interact within cells. Each entry in the PDB not only contains a three-dimensional model but also includes detailed data on the molecular components, sequence details, and annotations related to the structure.

• Explore molecular details and structure summaries.
• Find information on secondary structures, such as alpha helices and beta sheets.
• Access tools for visualization and analysis.

Utilizing the data available on the PDB can significantly enhance understanding of protein interactions and functions.

Molecular Viewing Utilities

Molecular viewing utilities such as JSmol offer interactive ways to examine protein structures. JSmol is a popular tool because it is a free, web-based application that runs on multiple platforms, requiring no software installation. It is specifically designed to work seamlessly across different browsers and operating systems, making it accessible to students and researchers alike.

These utilities allow users to rotate, zoom, and analyze protein structures in three dimensions. This capability is crucial for a deeper understanding of the spatial arrangement of amino acids and how proteins interact with other molecules.

• Visualize complex protein structures in 3D.
• Identify different chains in structures and their interactions.
• Assess structural details such as binding sites and interface residues.

By using molecular viewers, one can gain a clearer picture of how proteins operate in a biological context, which is vital for fields such as structural biology and drug design.

Antibody-Antigen Interaction

Antibody-antigen interactions are fundamental to the immune response, playing a crucial role in the recognition and neutralization of pathogens. This interaction is highly specific, with antibodies binding to antigens to form a complex. In the example of the PDB entry '1FDL', the Fab portion of an antibody binds to the lysozyme antigen.

Antibodies typically have two types of chains - light and heavy, and the antigen-binding site is usually located in the variable region of these chains. The binding of the antigen to the antibody is determined by the precise fit between the antigen’s epitope and the antibody’s paratope.

• Understand the complementary nature of antigen-antibody binding.
• Explore variable regions of antibodies for specificity.
• Study how binding interfaces form and stabilize.

This specific binding is instrumental in establishing the immune system's ability to target specific pathogens efficiently.

Amino Acid Residues

Amino acid residues are the building blocks of proteins, and their sequence determines a protein's structure and function. Proteins are composed of chains of amino acids linked by peptide bonds, and each amino acid in the protein is referred to as a residue.

In the context of proteins like the lysozyme and Fab fragments, understanding the number and types of residues is crucial. For instance, the PDB entry '1FDL' can provide details on how many residues are present in the heavy and light chains of the Fab fragment and the lysozyme. This information helps in analyzing protein structure and function.

• Count residues in different protein chains.
• Identify residues at interaction interfaces.
• Understand the role of different residues in protein stability.

By examining residues and their sequence, researchers can decipher the specific roles that these amino acid residues play in protein interactions, aiding in the advancement of biochemical research.