\(\mathrm{C} / \mathrm{EBP} \beta\) is a \(b Z I P\) transcription factor in neuronal differentiation, learning and memory process, and other neuronal and glial functions. The structure of the \(b Z I P\) domain of \(C / E B P \beta\) bound to DNA is shown in pdb file \(1 \mathrm{GU} 4 .\) Explore this structure to discover the leucine zipper dimerization domain and the DNA-binding basic regions. On the left side of the www.pdb.org \(1 \mathrm{GU} 4\) page under "Display Files," click "pdb file" to see the atom-by-atom coordinates in the three-dimensional structure (scroll down past "Remarks" to find this information). Toward the end of this series, find the amino acid sequence of the \(\mathrm{C} / \mathrm{EBP} \beta\) domain used in this study. Within this amino acid sequence, find the leucine residues of the leucine zipper and the basic residues in the DNA-binding basic region.

Step by step solution

01

Access the website

Type in 'www.pdb.org' in an internet browser to access the Protein Data Bank (PDB). On the homepage, enter '1GU4' in the search bar, which is the PDB ID for the C/EBP beta protein, and click on 'Go'.

02

Locate the file

On the search results page, look for 1GU4 - C/EBP BETA ON DNA. Click on it to open the detailed information. On the left side of the resulting page, under 'Display Files', click on 'pdb file'.

03

Find the structure

Scroll down past the 'Remarks' section until you find the atom-by-atom coordinates of the three-dimensional structure of the protein. This is how this protein molecule is built and organized.

04

Locate the amino acid sequence

Continue scrolling down until you find the amino acid sequence for the C/EBP beta protein, located toward the end of the pdb file. This sequence represents the order of amino acids in the C/EBP beta protein.

05

Identify the particular regions

Within this amino acid sequence, look for the leucine residues (represented by 'Leu' or 'L' in the sequence) which make up the leucine zipper. Then, find basic residues which participate in the DNA-binding basic region. These residues will be represented by their respective abbreviations (Arg - R, Lys - K, His - H).

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Key Concepts

These are the key concepts you need to understand to accurately answer the question.

Leucine Zipper Dimerization Domain

The leucine zipper dimerization domain is a crucial feature in many transcription factors, including C/EBP beta. This particular domain is characterized by a repeating pattern of leucine residues at every seventh position in an alpha-helix structure. This repetitive pattern allows two alpha-helices to fasten together, like the interlocking teeth of a zipper, hence the name 'leucine zipper'.

When these leucine side chains interlock, they enable the dimerization of two protein subunits, which is fundamental for the protein's ability to bind to DNA. This physical interaction between the subunits is not only pivotal for DNA binding but also stabilizes the protein structure, influencing the transcription of specific genes. Identification of leucine residues in C/EBP beta's amino acid sequence is the first step in understanding how this protein functions at a molecular level.

DNA-binding Basic Region

Adjacent to the leucine zipper domain is the DNA-binding basic region in C/EBP beta, which plays a key role in recognizing and binding to specific DNA sequences. This region is rich in positively charged basic amino acids—such as arginine (Arg or R), lysine (Lys or K), and histidine (His or H)—which facilitate the attraction to the negatively charged phosphate backbone of the DNA.

The proper alignment and spacing of these amino acids are essential for the protein to latch onto the correct DNA sequence. This region's interaction with DNA allows C/EBP beta to regulate gene expression, impacting numerous biological processes, such as neuronal differentiation and function. The identification of the basic region within the protein's structure is revealing for students who aim to comprehend the intricate details of gene regulation and protein-DNA interactions.

Protein Data Bank (PDB)

The Protein Data Bank (PDB) is an indispensable resource for students and researchers studying molecular biology. It is an online database that provides detailed information about the 3D structures of proteins, nucleic acids, and complex assemblies. The PDB allows users to visualize protein structures, such as C/EBP beta, and examine how these structures relate to the protein's function.

When exploring the PDB, users can input the unique identification code, such as '1GU4' for C/EBP beta, to access a protein's structure. From there, one can download the pdb file that contains the atom-by-atom coordinates, which are instrumental in understanding the orientation and interaction of amino acids within the protein. Familiarity with navigating the PDB is essential for anyone delving into structural biology or bioinformatics.

Amino Acid Sequence

An amino acid sequence is the order in which amino acids are linked together to form a protein. Each amino acid is represented by a specific abbreviation in the sequence, such as 'L' for leucine or 'R' for arginine. The sequence dictates the protein's three-dimensional structure, which in turn determines its function.

Understanding the amino acid sequence of a protein like C/EBP beta provides insight into the protein's characteristics and how it interacts with other molecules. In the context of the given exercise, identifying the sequence aids students in locating functionally important regions, such as the leucine zipper and the DNA-binding domain. By studying the sequence, one can predict the protein’s behavior, stability, and interaction with other molecules, like DNA, ultimately leading to a deeper understanding of its role within a living organism.