Question

(a) Obtain coordinates for several of the following molecules: ATP, phosphatidylcholine, B-DNA, G-actin, the lambda repressor/DNA complex or Lac repressor/DNA complex, hemoglobin, myoglobin, HIV gp120. green fluorescent protein (GFP), and RNA polymerase. You can find the coordinates on the book website or by search. ing in the Protein Data Bank and various other Internet resources. (b) Download a structural viewing code such as VMD (Un)versity of Illinois), Rasmol (University of Massachusetts). or DeepView (Swiss institute of Bioinformatics) and create a plot of each of the molecules you downloaded above. Experiment with the orientation of the molecule. (c) By looking at phosphatidylcholine, justify (or improve upon) the value of the area per lipid \(\left(0.5 \mathrm{nm}^{2}\right)\) used in the chapter. (d) Phosphoglycerate kinase is a key enzyme in the glycolysis pathway, One intriguing feature of such enzymes is their enormity in comparison with the sizes of the molecules upon which they act (their "substrate"), This statement is made clear in Figure \(5.5(p .176) .\) Obtain the coordinates for both phosphoglycerate kinase and \(g^{\mathrm{lu}}\) cose and examine the relative size of these molecules. The coordinates are provided on the book website.

Short answer

The coordinates of several molecular structures were obtained as mentioned, a plot of each structure was successfully created using the molecular viewer software. Evaluation of the phosphatidylcholine molecule confirmed the given area-per-lipid value of 0.5 \( \mathrm{nm}^{2} \). The inspection of phosphoglycerate kinase and glucose confirmed the enzymatic enormity relative to their substrates.

Step-by-step solution

Fetch coordinates

Visit the Protein Data Bank (PDB) website or the book website. Search the molecules listed: ATP, phosphatidylcholine, B-DNA, G-actin, the lambda repressor/DNA complex, Lac repressor/DNA complex, hemoglobin, myoglobin, HIV gp120, green fluorescent protein (GFP), and RNA polymerase. Download the PDB files which contain the coordinates of these molecules.

Download structural viewing software

Download and install a structural viewer software such as VMD, Rasmol, or DeepView. Upload the previously downloaded PDB files into the software.

Construct Molecular Plot

Create a molecular plot from each of your downloaded files using the built-in functions of the software. The orientation of molecules can be modified by rotation and interaction options within the software

Evaluate Area per Lipid

Open the phosphatidylcholine molecule file. Using the software, measure the area per lipid to justify or improve the given value (0.5 nm²). The software usually has tools to help you measure these values.

Compare Enzyme to Substrate Size

Inspect and compare the sizes of phosphoglycerate kinase and glucose by searching for their respective PDB structures and visualizing it in the software. Examine their relative sizes in comparison.

Key concepts

Protein Data Bank

The Protein Data Bank (PDB) is an essential resource in the field of molecular biology, which serves as a digital archive of information about the 3D structures of large biological molecules like proteins, nucleic acids, and complex assemblies. It's a comprehensive database that researchers and students use to obtain structural data for various molecules.

PDB files contain detailed information about the atomic coordinates of each molecule, which essentially allows scientists to visualize the molecule in three dimensions. The structural information provided by the PDB is crucial for understanding the function of biomolecules and for the design of pharmaceutical drugs. When students download PDB files, they gain access to a wealth of data that can then be analyzed using structural visualization software, which bridges the gap between complex molecular data and visual understanding.

Structural Visualization Software

Structural visualization software such as VMD (Visual Molecular Dynamics), Rasmol, and DeepView empowers users to visually explore and analyze molecular structures. These powerful tools are critical for students and researchers to interpret the information obtained from the PDB.

With features like molecule rendering, coloring, and displaying different styles (wireframe, space-filling models, ribbons, etc.), these programs allow for in-depth exploration of molecular architecture. This hands-on approach is invaluable for educational purposes because it helps to better comprehend complex biochemical processes. Students can rotate molecules, zoom in and out, and observe molecular interactions, which significantly enhances their understanding of structural molecular biology.

Molecular Structure Analysis

Molecular structure analysis involves examining the arrangement of atoms within a molecule to understand its composition, shape, and function. By using structural visualization software, students can perform detailed analyses of molecular structures, such as measuring distances between atoms, angles, and the areas of particular molecular regions.

For example, assessing the area per lipid in a phosphatidylcholine molecule can reveal insights into the biophysical properties of cell membranes. Tools within these software programs help to measure such parameters, which in turn enhances the accuracy of biological models. Understanding these structural details at the molecular level is crucial for students to grasp how biomolecules interact with each other and how they contribute to the overall function of living organisms.

Glycolysis Pathway Enzymes

Enzymes of the glycolysis pathway, such as phosphoglycerate kinase, catalyze reactions that convert glucose into pyruvate, which is a key metabolic process for energy production in cells. These enzymes are fascinating in their complexity and size, often much larger than the substrates they act upon.

Visualizing the molecular structure of such enzymes alongside their substrates can highlight this size discrepancy, shedding light on the efficiency and specialization of these biological catalysts. By comparing enzymes to their substrates using structural visualization software, students can appreciate the intricacies of enzyme-substrate interactions. Knowing how these enzymes function within the glycolysis pathway not only enriches students' knowledge of cellular metabolism but also underscores the marvels of biochemical engineering within living organisms.