Write a paper about the structure and function of their selected protein of biomedical or
health relevance. The guideline and selected protein is attached below. 4 attachmentsSlide 1 of 4
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105 SUMMARY OF JMOL SCRIPT COMMANDS A select command specifies a set of atoms, and then the following directions apply only to the selected set. A restrict command specifies a set of atoms, and then only the atoms specified are displayed. A delete command irreversibly removes the selected set; they can be restored only be reopening the file in a new Jmol session. Select and restrict commands are described at the web page www.umass.edu/microbio/rasmol/seleccmd.htm. The Select commands in the programs Chime and Rasmol are the same ones used in Jmol. You can select everything elements types of atoms all e.g. carbon, sulfur, iron n = NH nitrogen, o = CO oxygen, c = CO carbon, ca = alpha carbon, cb = beta carbon, etc. specific atoms atomno= (Both the atom type and atom number are displayed when you click on an atom.) residue numbers e.g. 5, 278-283 types of amino acids e.g. ala, ile hetero groups we had the example nag in lysozyme, with the abbreviations defined on the structure info page polypeptide chains e.g. :A, :B alpha (meaning alpha carbons) amino or protein (protein only, not solvent or hetero groups) backbone sidechain cyclic (aromatic amino acids and proline) acyclic aliphatic aromatic hydrophobic or nonpolar polar charged neutral basic (or positive) acidic (or negative) cystine (cysteines linked by a disulfide bond) surface 106 buried helix sheet turn (after doing a DSSP structure calculation) hetero (non amino acid) water ions (e.g. phosphate or sulfate) solvent (water or ions) ligands (hetero and not solvent) within (x.x,species) within x.x Ångstrom units of the designated species e. g. select within (5.0,hem) within 5.0 Å of the heme select within (4.0,:A) within 4.0 Å of chain A) To select a named chemical component type select followed by the identifier, e.g. select hem (Exercise 11). If the name of the chemical identifier begins with a number within it, you must put it in brackets, e.g. select [3pg] (Exercise 5, FE1). You can also create “Boolean expressions” combining more than one term. not solvent :A and lys lys and 23 neutral and not hydrophobic :B and 43-50 3 or 7 or 11 (can also be written 3,7,11) (3,7,11) and :A 1-40 and hydrophobic lys and nz and :B (sidechain nitrogens of lysines in chain b) If you need to select the same set of atoms over and over again, you can create a name for that set of atoms, for example: define myatoms helix and backbone and (3,13,53,186,187,204) and polar select myatoms; spacefill Once atoms are selected you can color them whatever color you like. Examples: color red color structure (different colors for different secondary structures) color cpk color group (cool colors at the N-terminus going to warm colors at the Cterminus) color chain (each polypeptide chain a different color) 107 You can also select the color of the background by typing background . You can change the display mode of the selected atoms by typing spacefill only, wireframe only, backbone only, ribbons only , strands only or cartoon only or by typing simply spacefill, wireframe, backbone, etc. and turning the previous display off (e.g. spacefill off). You can also determine the width of the bonds or the diameter of the spheres by specifying a number. For example, wireframe 80, spacefill 200, cartoon 500, etc. You can do a DSSP structure calculation by typing calculate structure. After this is done, coloring by structure will separately code turns and pi helices, in addition to alpha helices, 310 helices and beta sheets. You can turn hbonds and ssbonds on and off (hbonds calculate (or hbonds on once they have been calculated), hbonds off, ssbonds on, ssbonds off). set hbonds backbone and set hbonds sidechain determine whether H-bonds connect alpha carbons or amide and carbonyl groups. set ssbonds backbone and set ssbonds sidechain determine whether disulfide bonds connect alpha carbon atoms or cysteine sulfur atoms ssbonds 20 or hbonds 50 controls the thickness of the bonds. You can manipulate the molecule with the mouse (a summary of mouse commands is given in Exercise 1), but you can also do this with a typed command, such as: zoom 100 (a number between 10 and 1000) translate x 20 (a number between –100 and 100) and translate y –10 move the molecule in the x and y directions rotate x 90 rotates the molecule 90 degrees about the x axis (rotate y and rotate z commands can also be used) show info shows the information for the molecule show sequence displays the amino acid sequence show selected lists the atoms that are currently selected show structure displays information about the secondary structure of the protein undo reverses the last command; redo reverses the undo command SOME ADVANCED COMMANDS To measure the distance between two atoms, type set picking distance. Double-click successively on each of the atoms. The identity of the atoms and the distance between 108 them will be displayed in the Command window and on the structure. When you are finished, type set picking on. To measure the angle between three atoms, type set picking angle. Double-click on the first atom, click on the second (central) atom, and double-click on the third atom. When you are finished, type set picking on. Typing slab on; slab 50 will slice the molecule through the middle and display the surface. You can vary the depth at which the slice is taken from 0 to 100. For instructions on use of a command, click on the Help button on the scripts console and scroll down to that command. For more information on Jmol commands, you can consult the Jmol scripting documentation at http://jmol.sourceforge.net/docs, the Jmol scripting documentation at http://chemapps.stolaf.edu/jmol/docs/, or the RasMol manual at www.bernsteinplus-sons.com/software/rasmol/doc/rasmol.html. There is also a Jmol wiki at http://wiki.jmol.org, that has links to lots of sites with information about how to use Jmol. COPYING AND PASTING To copy and paste text within the Script Console use the keystrokes Control-C and Control-V. Note that these keystrokes are used on Macs as well as PCs, even though the usual keystrokes for Copy and Paste on a Mac are Command-C and Command-V. 109 PRINTING AND SAVING AN IMAGE There are a few different ways of printing Jmol images. 1. Direct printing: Choose Print from the Jmol File menu. The disadvantage of this method is that the image is not saved and is lost as soon as you quit Jmol. 2. Copying the image and pasting it into another application: Choose Copy Image from the Edit menu. Then open another application (like Microsoft Word) and choose Paste. (Alternatively you can save the file and insert it later – see paragraph 3.) 3. Exporting a file and saving it as a graphics file: From the File menu choose Export/Export Image, assign a filename, and save as a .jpg file. The image can then be opened in a graphics program and printed. Alternatively, the image can be inserted into a Microsoft Word or PowerPoint document by using the Insert/Picture/From File… command from the Insert menu. Finally the image can be attached to an e-mail or uploaded to a web site that accepts student assignments. 4. Screen capture: On a PC hold down the Shift key and press the Print Screen button (to the right of the function keys) to copy a screen image onto the clipboard which can then be pasted into an application like MS Word, or saved as a file that can be attached to an e-mail or uploaded to a web site. In Mac System X, launch the application Grab (from Applications/Utilities) and click on Capture/Screen. Note: Generally you will want to use a white background for a printed image, because printing an image with a black or colored background uses LOTS of ink. 110 SAVING SCRIPTS Want to save a state of the protein (including both view formats and labels) to open it later in Jmol and manipulate it further? From the Jmol File menu, choose Export/Write State. A Save window will open. Give the file a name and save it as an .spt (script) file. Make sure that you save it to your Jmol folder (the folder that contains the jmol.jar file). How can you restore that state of the protein? Let’s assume that you named the file myview.spt. Launch Jmol and type script myview.spt. If you are in the middle of a complicated project and don’t have time to finish, save your work as a script file, and pick up later where you left off. You should be able to copy the script file to a flash drive and open it on a different computer. First copy the file into the folder on the computer that contains the Jmol executable jar file. Then launch Jmol, select the Open command from the File menu, and open the script file. This way you can generate the saved state of your protein on the other computer. This is handy if you are working on a computer that is not connected to a printer, or if you don’t have a color printer at home and want to print out an image on a color printer somewhere else. CREATING LABELS In order to label an amino acid residue, select an atom where you want the label to be, and note the atom number. For example, if clicking on the atom brings up the line:[PHE]137:G CE2 #1043 –34.397 28.993 20.914, then the atom number is 1043, and you would type select atomno=1043. To turn on the label, type label %n %r (%n means 3-letter residue name and %r means residue number – to see other options, click the Help button and go to label.) The default color for the label is white. To get different colors use the command color label . To turn the label off, type label off. If you want to change the text of the label, just type label . The font size of the lettering can be controlled with the command set fontsize (e.g. set fontsize 30). 111 ADDING HYDROGENS TO A STRUCTURE Here’s one final trick that may come in handy. PDB files generally do not contain coordinates for hydrogen atoms. Sometimes it’s useful to be able to visualize hydrogen atoms, for example when looking at a closeup of the active site of an enzyme. Jmol is capable of adding hydrogens to a structure. In order to do this the following command must be typed before you open a structure file: set pdbAddHydrogens. The Script Console will respond with pdb AddHydrogens = true. As an example, you can try taking another look at the active site of chymotrypsin. Type the above command and then download and open the file 1YPF. Now restrict (57,102,195). Since the structure contains two chymotrypsin molecules, type restrict :C,:E to display only one of the two. Set the style scheme to Sticks. You will now have a view of the charge relay system that includes the hydrogens. The program has added hydrogen atoms to the N-H nitrogens, the histidine imidazole and the serine hydroxyl. Note that Jmol adds hydrogens to both of the imidazole nitrogens of histidines to produce the protonated form of histidine that exists at acidic pH. (At higher pH, only one or the other of the imidazole nitrogens is protonated.) A hydrogen has been added to the serine side chain oxygen in a conformation in which the new hydrogen is trans to the alpha carbon of the serine. This is not necessarily the actual conformation, as there is free rotation about the C-O bond. Nevertheless, you can see how the three residues form a hydrogen-bonded network that facilitates the charge relay that is important in catalysis. Now load the file 6GCH. Type restrict (57,102,193,195). Set the style scheme to Sticks. You will now have a view of the substrate, the charge relay system and the oxyanion hole that includes the hydrogens. Select the inhibitor (select apf) and put it in Spacefill. In this structure the oxygen of the serine hydroxyl has reacted with the carbonyl oxygen of the inhibitor APF, forming a covalent bond. Consequently, the hydrogen previously attached to that oxygen is not present. You can still see the protonated histidine. In addition you can now clearly see the role of the NH groups of residues 193 and 195 in forming H-bonds to the carbonyl oxygen of the inhibitor. This illustrates how the oxyanion hole is involved in binding the substrate and the transition state. If you now want to load a different structure file in the normal way, without adding hydrogens, first type the command set pdbAddHydrogens false. 112 WORKING WITH NMR STRUCTURE FILES Nearly all of the structures we have examined were determined by X-ray crystallography. Another technique used by biochemists to determine the threedimensional structure of macromolecules is NMR (nuclear magnetic resonance). The information contained in an NMR structure file is different from that contained in a file derived from X-ray crystallography, and there are some important things to know if you are to use these files correctly. The basic concepts underlying the determination of a protein structure from NMR data are simple. The signals corresponding to individual amide hydrogens in a protein can be identified and information can be obtained about which amino acid residues are close in space, as well as some information about the values of the various dihedral angles in the protein. This information forms a set of constraints for a molecular dynamics analysis. A computer starts out with a model of the protein in a completely random conformation. The computer then subjects the protein model to random fluctuations in conformation and calculates the energy of the structure after each fluctuation. When the protein settles into a conformation that satisfies the distance constraints from the NMR data and also appears to be at a minimum potential energy, the computer produces a threedimensional structure. This is repeated 20 to 30 times. Since each molecular dynamics run starts from a slightly different random conformation, a slightly different structure is produced each time. We end up with an ensemble of structures. This information can be deposited in the PDB in three forms. One type of file simply contains all the NMR structures. Another type of file contains something called the minimized average structure, which is produced by obtaining an average position for each atom and then adjusting the structure to minimize the potential energy (e.g. by avoiding unfavorable steric interactions). A third type of file is a representative structure, usually the single structure that is closest to the average. (Many biochemists think that a representative structure is more likely to be an accurate representation of the protein than an average structure, and newer NMR structure files are often representative structures.) As an example, examine the structure of 1FO7. This is an ensemble of 30 NMR structure models for a fragment of the bovine prion protein. When you open the file in Jmol, it automatically displays model number 1. You can view other models by typing model 2 or model 3, etc. To see all the models displayed, type model all. Note that in some regions the different models are almost perfectly superimposed, while in some of the nonhelical regions the superimposition is not as good. 1FKC is the minimized average structure of the same protein. However, go to the EMBL-EBI site www.ebi.ac.uk/pdbe-apps/nmr/main.html, and click on Olderado. On the next page, 113 enter 1FO7 in the window and click on View Report. The window that opens next, under NMR Resources, tells us that structure 14 is the most representative structure. In the opinion of many if not most biochemists, model 14 is the best one to work with. You can view this structure in Jmol by typing model 14. Note that PDB file 1FKC is the minimized average structure of the same protein. Another thing to keep in mind is that an NMR structure, unlike an X-ray structure, contains all the hydrogen atoms. For a display that looks more like what you are used to, go to the Display menu of the Jmol window and uncheck the box Hydrogens (see the portion of Exercise 4 dealing with the helix-turn-helix motif). If you want to restore the hydrogens, simply uncheck the box. To irreversibly remove the hydrogens, you can type delete hydrogen. 114 JSMOL, A WEB BROWSER BASED VERSION OF JMOL The lessons in this manual use the standalone version of Jmol. They can also be done with JSmol, a version of Jmol that runs in a browser window. When you download Jmol as described in the first section of this manual, the downloaded folder contains JSmol as well as Jmol. One way to access JSmol is through the site chemapps.stolaf.edu/jmol/jsmol/simple.htm. Click on Load PDB by ID. Enter the PDB ID in the window that open, and click OK. An image of the molecule (asymmetric unit) will appear. If you want to display the biological assembly, check the box next to biomolecule 1 before clicking on Load PDB by ID. (See Exercise 10 for an explanation of asymmetric units and biological assemblies.) You can type script commands into the window next to the console button. 115 JMOL WEB PAGES There are many web pages that have prescripted animated lessons that use Jmol. For example, go to http://bioinformatics.org/jmol-tutorials/jtat/hemoglobin/contents/contents.htm. You can go through this lesson by clicking on the links and buttons in the text. Also, for any image you can bring up the Jmol pop-up menu by right-clicking (Control-clicking), and you can change the representation of the molecule using the menu commands. There are also many Jmol lessons available on the internet. There are several excellent places to find these web sites. The site molviZ.org provides links to excellent Jmol lessons on protein structure, hemoglobin, antibodies, and lipid bilayers. The Online Macromolecular Museum (https://earth.callutheran.edu/Academic_Programs/Departments/BioDev/omm/exhi bits.htm) has some excellent tutorials on basic protein and nucleic acid structure, as well as tutorials on enzymes involved in replication and transcription and many other biochemical processes. There are also links from the CSULB Biochemistry Links web page (www.csulb.edu/~cohlberg/biochemlinks.html) under Molecular Modeling/Images. The Jmol wiki (http://wiki.jmol.org) also has a link to Websites Using J(S)mol. 116 Term Paper Assignment Summary of the Assignment: Pick any protein other than the ones that were the subjects of the lessons in this manual, and write a short paper on the protein illustrated with figures which you prepared by using Jmol. The paper should have as a major focus the relationship between the structure of the protein and its function. The main body of the paper should be 1-1/2 to 3 pages long (double-spaced, 12 point font, 1 inch margins). In addition you should have a list of references, plus at least three Jmol figures, each with a title and a brief legend, which illustrate the points in your text. This is a suggested format for the assignment. Your own instructor may choose to modify these instructions or those that follow. How can I pick a protein? Try looking ahead in your text to see what interesting proteins we’ll be studying (for example, some of the enzymes of carbohydrate metabolism). Maybe you’ve heard about some interesting proteins in a cell biology course (a polymerase, a viral protein, a growth factor, etc.). Look them up in the PDB and see if their structures are known. Or look in your cell biology textbook. Or consult the journals BioEssays or Trends in Biochemical Sciences, both of which have short review articles. Or follow the link to Molecule of the Month from the PDB web site. Or browse the PDB-101 site (http://pdb101.rcsb.org/). How can I locate the right PDB file for my protein? Review Exercise 7, “Searching for PDB Files.” After doing an intial search, don’t just choose the first file in the list. Try to obtain a file that contains the entire structure, not just a fragment or a single domain. Use the instructions in Exercise 7 to locate a file that contains bound ligands that are relevant to the function of the protein. After you have chosen a protein and verified that a structure is available, submit your choice to your instructor. There are thousands of known protein structures, so it should be possible for everyone to write about a different protein. If two people want to do the same protein, your instructor may try to suggest alternatives. What should I write about? You can choose various things to write about. You can say something about the general secondary structure organization. If you have a multidomain protein, you can talk about the different domains and their different functions. If it’s an enzyme, you can talk about how the amino acid sidechains at the active site participate in the binding and catalysis. If it’s not an enzyme but a protein that binds something else, you can talk about the amino acid sidechains involved in the binding reaction. If the protein undergoes a conformational change, you can say something about the nature of the change at a molecular level. You don’t have to cover everything that’s known about the structure and function of the protein in this short paper, as long as you include material on at least some aspect of the structural basis of the protein’s 117 function at an atomic level. Consider this as something with a level of detail somewhere between an illustrated show-and-tell exercise and a more traditional term paper. How should I organize the paper? Different types of organization are possible. You will probably want to start with an explanation of what the protein is, what it does, and its significance in the cell or the body. Then you might describe the overall structure of the protein, finally zeroing in on a particular aspect of the protein which you will illustrate with your Jmol figures. Your discussion should refer to the figures as you go along. e.g. “As you can see in Figure 2, lysine 85 (shown in red) forms a salt bridge with….” Every figure in your paper should be referenced at some point in your text. Where can I get more information about the protein? Consult the PDB page for a citation of the original publication describing the protein structure. If your protein is an enzyme, try the BRENDA database (look under the Metabolism heading in CSULB www.brenda-enzymes.org) or go to Pubmed (pubmed.gov). Put your protein name in the search field. When the search results come back, look at the Reviews tab. This will list only review articles on your protein and will prevent you from getting long lists of primary research articles. Read the PDB page and the header for the pdb file – both have important information. If you haven’t already gone through Exercise 8, “What’s in a File?” do it now. It has valuable instructions on how to get information about your protein from these documents. Examine the diagram in the Molecular Description box of the PDB page. It often contains valuable information about the primary structure of the protein and its posttranscriptional processing, the location of modified amino acids, the secondary structure and the locations of active site residues. (See the section of Exercise 1 on the immunoglobulin binding domain.) Is the structure file derived from X-ray crystallography or NMR, or is it a theoretical model? If it’s an NMR structure, you MUST read the appendix “Working With NMR Structure Files.” What should be in the figure titles and legends? The title of the figure should be a short phrase or sentence indicating what is shown or what the main point of the figure is. The legend, which goes into this in greater detail, could be as short as one sentence or longer if necessary. It should point out the features that are being illustrated and explain any color schemes or labels whose meaning is not obvious. At least one figure should identify the accession number of the protein. If you did anything unusual with Jmol or with another computer program to help prepare the figure, this should also be 118 explained in the legend. The legend may be printed on the same page as the figure that it refers to, or you may have your legends printed on separate pages. How should I cite my sources? If you use only one source, it’s adequate to list it in your reference list. If you use multiple sources, you should identify which material came from which reference. The easiest way to do this is to number your references and then put a number in parentheses in the text at the end of a sentence to indicate the source of the information in the preceding sentences. How should I list the references? Please use the following formats. (Don’t change these formats; we want you to demonstrate that you are capable of following directions.) journal article — Mucklefutz, Q., and Gesundheit, A. C. (1997) “The secret of life as revealed in the molecular structure of cookie dough,” J. Biol. Chem. 458, 134-142 book – Darwin, C. (1999) “Evolution for Dummies: A Guide for the Kansas Board of Education,” Neanderthal Press, Wichita, pages 115-164 article from a book — Winken, R., Blinken, L. M., and Nod, U. U. (1992) “Structure of lactate dehydrogenase from the roadrunner Beepbeep californicus,” in Simon, P., and Garfunkel, A. (editors) “Collected Essays in Comparative Biochemistry”, Wiley Coyote Press, Phoenix, 1998, pages 59-87 web site — www.crazyguys.csulb.edu/toocool/proteins, “Famous Proteins We Have Known” (give the web address and the title of the web page) Can I copy material word-for-word from a reference? NO. Copying word-for-word (or copying entire passages almost word-for-word with only slight paraphrasing) is plagiarism. Please put your ideas in your own words. If you must quote from a paper, put the quote in quotation marks. If you simply quote verbatim from a reference, we have no way of knowing whether you have any real understanding of the stuff you’ve copied. If you don’t think that you’re capable of putting things in your own words, see your instructor for help in getting started. If we suspect that you’ve plagiarized, we will take time to look at your original references and will penalize you heavily if we find that you have copied the original language. This is my first biochemistry course and I haven’t taken any cell biology. I’m not very good with computers. I really don’t know what to do and I’m frankly very intimidated by this assignment. What can I do to keep from totally freaking? Hey, chill out! First of all, if you need help with any aspect of this assignment, please come and see your instructor. If you’ve done some looking but just can’t figure out what protein to choose, the instructor can make some suggestions. If you’ve chosen a protein but don’t know where to find the information you need, the instructor can point you in the right direction. If you found a discussion of your protein that you can’t understand, bring it in and look at it together with your instructor. If you’ve done your research but can’t figure out what to focus on, let your instructor help you. If you’ve gone through the 119 Jmol exercises but can’t figure out how to manipulate the images the way you want to, you may be able to sit down at the computer with your instructor and figure it out together. (Of course this means that you can’t start the paper two days before it is due.) Second, we don’t expect everyone to hand in a masterpiece. We understand that this will be difficult for some of you, but if you demonstrate that you put in a reasonable effort and were able to make some nice pictures and explain some things reasonably well, you’ll get a good grade. You’ll have to earn your A, but there should be a lot of B’s on this assignment, and no one will get a D or F who puts forth any reasonable effort. You can write as little as two pages, so you are not expected to do the amount of work for this project that you’d do for most term papers. Common mistakes that students make when doing this assignment that prevent them from getting a favorable grade: — Some PDB files represent an individual domain of a protein rather than the entire protein. Read the PDB page to make sure you know what it represents. — In some X-ray structures there are missing amino acid residues that are not resolved in the X-ray data and are therefore omitted from the structure. You need to be aware of this to understand what you are looking at. This information is contained in the header of the PDB file. — If your structure has bound ligands, be sure to include them in your figures and comment on their significance. — In many cases you have a choice of a structure with bound ligands and a structure with the protein alone. Choose one with bound ligands and comment on them. Don’t take the first structure that pops up on the page of search results. — Find out whether the asymmetric unit and the biological assembly are the same. If they are different, use the biological assembly for your report (See Exercise 10 for instructions). — If your structure has lots of water molecules, eliminate them from your figures. — If a file is based on an NMR structure, see if an X-ray structure exists. A file based on an X-ray structure will be easier to work with. If only an NMR structure is available, you MUST follow the instructions in “Working with NMR Files” in the Appendix and select a single model for your analysis, and you must explain how you selected the model to work with. 120 — The text of your discussion should focus on the structure of your protein as illustrated by your figures. Don’t just generate some figures and then simply discuss the biological function of the molecule without referring to the figures. — Use the label commands (see “Creating Labels” in the Appendix) rather than adding handwritten labels. Authenticating your paper: In order to authenticate your paper, do the following: 1. Form an image in the Jmol main window similar to one of your figures. 2. In the script console window, type your name and the date. 3. Capture an image of the screen and include a printout with your paper. On a PC hold down the Shift key and press the Print Screen key (the key just to the right of the function keys) to copy a screen image onto the clipboard which can then be pasted into an application like MS Word. In Mac OS X, launch the application Grab (from Applications/Utilities) and click on Capture/Screen. Name: Khanh Cao ID: 027517072 / Hoa Nguyen ID: 026841072/ Ann Vu ID: 025282931 Date: 05.07.2021 Human Serum Albumin Abstract: The protein is called the human serum albumin. Its PDB identifier is 2XW0. This protein can only be found in the blood of humans. It has two binding sites that drugs molecules can bind. The amount of this protein in the blood can reduce when there is an inhibiting factor that causes protein loss through the kidney or that which increases the volume of plasma, therefore, diluting the blood. The method used to obtain this structure is xray diffraction. This falls under resolution 2.40 Å. (Ryan et al., 2010). Introduction Human serum albumin can be simply defined as the serum albumin present in the blood of human beings. Of all the components in the human blood, the human serum albumin is the greatest accessible protein found in the plasma. This type of serum albumin is vital because it binds a variety of drugs and other small molecules. Research has shown that it constitutes approximately fifty percent of serum protein (Hickman et al., 2004). This type of protein is considered to be monomeric, and it is soluble in water. The human serum albumin is produced in a functioning liver in the human body. Albumin in the blood is used to keep fluid from seeping out of the blood vessels. Structure and Function: Human serum albumin is a relatively small globular protein that has a molecular weight of 66.5kDa and contains 16,961 nucleotides in length. As figure 1, these amino acids have been arranged into three repeating homology domains that are identified as sites I, II and III. Each of these domains has Figure 1: Three domains of Human Serum Albumin been split into two separate domains that are identified as A and B. There will be a link between IB and IIA which is formed by the interdomain helices (Fasano et al., 2005). The mutations of this gene can affect the protein structure and make the protein anomalous. The carbohydrates are not part of the protein structure. This is determined from the putative site to the initial poly addition site. The human albumin gene is separated into 15 exons placed into three domains assumed to have developed by triplication. Figure 2: Secondary structure of Human serum albumin from one of the primordial domains Albumin transports various ions in the circulatory system, they include calcium, copper, and zinc. Albumin has a function as a toxic waste which is a product of the heme broken down then transports to the liver, where it is set for hepatic excretion. Albumin also has antioxidant functions because it is able to Figure 3: Two chain of Human Serum Albumin protect substances such as fatty acids and lipoproteins from peroxidative damages. It is able to bind with copper, therefore reducing its reactions and the production of radicals. Albumin has also been known to be the source of thiols. These are scavengers that seek reactive oxygen and nitrogen species. Biomedical and Health Relevance Research has shown that the changes in human behavior and lifestyles have resulted in a rise in the prevalence of diabetes over the last century. Glycation has significant implications for albumin actions as it can impact the functions of cells. Human serum albumin is one of the serum proteins in the human blood that is abundant and has physiological functions that can be modulated by redox modifications (Tabata et al., 2021). Hypoalbuminemia is the main indicator that there has been a progression in the development of many human diseases that can include diabetes, cancer, liver, and rheumatic diseases. References: Hickman, Dean et al. “Estimation of serum-free 50-percent inhibitory concentrations for human immunodeficiency virus protease inhibitors lopinavir and ritonavir.” Antimicrobial agents and chemotherapy vol. 48,8 (2004): 2911-7. doi:10.1128/AAC.48.8.2911-2917.2004 Tabata, Fuka et al. “Serum Albumin Redox States: More Than Oxidative Stress Biomarker.” Antioxidants (Basel, Switzerland) vol. 10,4 503. 24 Mar. 2021, doi:10.3390/antiox10040503 Fasano, Mauro et al. “The extraordinary ligand binding properties of human serum albumin.” IUBMB life vol. 57,12 (2005): 787-96. doi:10.1080/15216540500404093 Ryan, A.J., Curry, S. (2010) “Human serum albumin complexed with dansyl-Lphenylalanine.” RCSB PDB: 2XW0. Authentication of the paper:
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