Student Guide. Concluding module. Visualizing proteins

Transcription

1 Student Guide Concluding module Visualizing proteins

2 Developed by bioinformaticsatschool.eu (part of NBIC) Text Hienke Sminia Illustrations Bioinformaticsatschool.eu Yasara.org All the included material is protected by the Creative Commons Naamsvermelding-Niet-commercieel-Gelijk delen 3.0 Nederland license ( CC BY-NC-SA 2009 Netherlands Bioinformatics Centre For any questions or comments, please contact the Travelling DNA Labs

3 Student Guide Proteins This lesson is about protein structure. The lesson consists of four exercises: 1. How is a protein made? 2. Practicing with Yasara 3. Studying hemoglobin 4. Choose a protein of your own Each exercise consists of a short theoretical text and some questions. Exercise 1 How is a protein made? A protein is made of amino acids. Humans are capable of making proteins from 20 amino acids. These amino acids are displayed below. Discover the new world of genomics 3

4 Question 1.1 a. What does the chemical formula of an amino acid look like? You may indicate the side chain with a capital letter R. b. Circle the carboxyl group and the amine group in your answer to question a. Discover the new world of genomics 4

5 Protein structure The structure of a protein can be assigned in four levels: Primary structure This is a chain of amino acids Secondary structure Atoms or groups of atoms in amino acids can attract other atoms or atom groups. The specificity of this attraction often results in the same kinds of structures: α-helices and β- sheets. α-helices are often found going through a membrane. β-sheets are often hydrophobic on the one side and hydrophilic on the other. Tertiary structure By even more interactions between atoms, the whole amino acid chain (including its secondary structures) can fold back on itself, or create other sorts of bends and nicks. This way, the protein will get its eventual shape. Quaternary structure Some proteins work with other proteins to be able to exert their function. To do so, several proteins (several copies of the same or different ones) will form a complex. Discover the new world of genomics 5

6 Question 1.2 There are several types of atomic interactions. The hydrogen bond is a good example of such an interaction. a. Between which atoms can a hydrogen bonds be established? b. What is the reason that this is not a true covalent bond, but just an atomic interaction? Other atomic interactions are the disulfide bond (between two sulfur atoms), the hydrophobic interactions (between two large carbon groups) and the ionogenic interaction. The ionogenic interaction is the nicest interaction found in proteins. It takes place between two ions: a positively and a negatively charged ion. Its mechanism can be compared to that of a magnet: plus and minus attract each other. Different interactions between atoms: Hydrogen bond Hydrophobic interaction Disulfide bond Ionogenic interaction Discover the new world of genomics 6

7 Shape and function The shape and function of a protein are very closely related. The shape is designed to make the protein function optimally. Generally, a protein can have one of these functions: Transport: transporting other proteins or small molecules, for example throughout the blood or through a cell membrane Chemical reactions: breaking down or converting big molecules or proteins into smaller pieces Communication: receiving signaling proteins and passing on signals to other proteins. The signaling proteins themselves also fall in this category Structure: giving structure to specific parts of the cell Regulation: regulating several systems, for example, by modifying other proteins or stimulating or inhibiting the production of other proteins. Antibodies fall into this category. Question 1.3 The different functions of proteins correlate with their structures. Can you indicate for the figures below what function these proteins are likely to have? Explain your choice for every protein. a. b. C. c. In exercise 3, you will find out what a hemoglobin protein looks like. And in exercise 4, you may think of an own protein to study. Always remember that what you see is not just coincidence. Discover the new world of genomics 7

8 Exercise 2 practicing with Yasara Yasara is a 3D visualisation software which allows you to look at proteins in 3D. Bioinformaticians use such software often to predict protein structures and to unravel its function. Opening Yasara The software can be downloaded for free from the website: Fill in your name, organization and address on the website. For organization, simply provide the name of your school. You will then receive an with the download link on the account you provided. This way, Yasara-view can be downloaded for free on your computer. (The provided address will not be used for commercial purposes) After completing installation, Yasara can be opened using the Yasara.exe file. On the website you will find several files to download. Download the file introduction.sce. Then, load this file in Yasara using File > Load > Yasara scene. In the browser, choose the file introduction.sce which you just downloaded. You will now see a small practising protein. This protein consists of 8 amino acids. The balls represent the different atoms and the short white and yellow sticks are single or double covalent bonds, respectively. The long blue, orange and green sticks are atomic interactions. Discover the new world of genomics 8

9 Configuration Yasara If you keep your cursor in the lower part of the Yasara screen, the amino acid bar appears. Here, you can find all the amino acids in this protein. With the button in the left top corner (which looks like a blue thumbtack) you can make the bar permanently visible. If you click an amino acid in the bar, the Cα-atom of that amino acid will start blinking. If you hold down the Ctrl key while clicking, the view will adjust to show where this amino acid is located. Use the mouse to move the protein, by pressing these mouse buttons: Left: Rotate Middle: Move Right: Zoom Question 2.1 a. Which ball color represents which atom? Light blue:.. Dark blue:.. Red: Green: b. Which atom is not displayed in Yasara?.... c. Which atomic interaction is represented by the orange sticks?..... The difference between a hydrogen bond and an ionogenic interaction is not clearly visible. If you recall that an ionogenic interaction is many times stronger than a hydrogen bond, what then is the answer to these questions: d. Which stick color represents a hydrogen bond? And which color represents an ionogenic interaction? Hydrogen bond:.... Ionogenic interaction:... Check your answers using the function Edit > Add > Hydrogens to All. e. What is an alternative name for an ionogenic interaction?.. Question 2.2 (bonus) The protein is surrounded by a cloud-like shape. What does this cloud indicate? Discover the new world of genomics 9

10 Exercise 3 Hemoglobin Hemoglobin is a protein found in blood. Red blood cells produce this protein and fill themselves with it: a red blood cell contains approximately 640 million hemoglobin proteins! Hemoglobin is responsible for the capability of blood to transport oxygen. Question 3.1 In what way can hemoglobin transport oxygen? On the website you can download hemoglobin.pdb. Load this file in Yasara using File > Load > PDB file. In the browser, choose the file hemoglobin.pdb which you just downloaded. Using the F1-F7 keys, you can change the display of the protein. Using F8, you can hide or show the side chains of the amino acids. Question 3.2 a. Which display mode displays secondary structures best? Heme groups are visible on different places throughout the protein. b. How many heme groups does hemoglobin have? Discover the new world of genomics 10

11 Every heme group is captured in a separate protein: globin. All globin proteins together have formed a complex: a quaternary structure. c. Of how many globins does hemoglobin consist?... The globins are not all the same. You can easily distinguish them by their amounts of amino acids. d. Of how many amino acids does every globin consist? (tip: look in the amino acid bar) How many different types of globin does hemoglobin have?.. Every heme group in a globin is constructed from the same building blocks: a carbon ring with a pink ball inside. e. Which atom is represented by this pink ball? (tip: zoom in on the ball, making you pass through it)... Oxygen transport Oxygen can bind to a heme group in an alkaline (basic) environment, such as in the lungs. The oxygen is released in an acidic environment, such as near tissues which need oxygen. Question 3.3 a. With what does oxygen interact in the hemoglobin?. b. How much oxygen can one hemoglobin molecule bind?. Discover the new world of genomics 11

12 Exercise 4 Choose a protein of your own On the internet, you can find all sorts of proteins 3D structure in the Protein Data Bank (PDB), which you can then view in Yasara. Many of these proteins are raw proteins, which are difficult to understand. Scientists are able to comprehend these raw proteins, so they often use the PDB database. On the website you will find several proteins that have been selected and processed for you to understand them. Download a protein of your choice and answer the questions below. For answering these questions, you may use the internet. Most of the proteins in this list are also on Wikipedia, but you can also search for information via the molecule of the month section of the PDB website ( 1. Acetylcholine receptor 2. Amylase 3. Calcium ATPase 4. Collagen 5. Insulin 6. Potassium channel 7. Myoglobin 8. Pepsin 9. Serum albumin 10. Testosterone carrier 11. Thyroxine 12. You may also search for another protein in the PDB. This can be done online via or you can send an to hienke.sminia@nbic.nl to get help finding a suitable protein. Question 4.1 Protein Which protein did you choose?. Question Structure a. Does the protein have a quaternary structure? If so, of how many tertiary structures does the protein consist? b. Of how many amino acids does the protein consist? If the complex consists of several small proteins, give the amount of amino acids of the largest protein. c. Which secondary structures does the protein have?. Question 4.3 Function a. Which function do you know of this protein? Discover the new world of genomics 12

13 b. Does the protein bind to a molecule or to another protein? If so, can you find the binding site? (The binding site is often in a cavity in the protein) c. Where is the protein found in the body of the organism? For example, is it in the cell wall? Or does it float around in the cytoplasm? How can you tell by the shape of the protein? d. What kind of protein is it? (transport, chemical reaction, communication, structure or regulation) How can you tell? Question 4.4 Various Can you find any remarkable features on this protein? Can you explain them? Suggestion: to be sure that you now fully understand the protein, you can describe your findings to a classmate. If your class mate thinks your description is completely clear, you know this protein enough! For more information about bioinformatics, visit: Discover the new world of genomics 13