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Biological Chemistry I

by: Patrick Schmeler

Biological Chemistry I CHEM 4410

Marketplace > University of Virginia > Chemistry > CHEM 4410 > Biological Chemistry I
Patrick Schmeler
GPA 3.55

Charles Grisham

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Charles Grisham
Class Notes
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This 28 page Class Notes was uploaded by Patrick Schmeler on Monday September 21, 2015. The Class Notes belongs to CHEM 4410 at University of Virginia taught by Charles Grisham in Fall. Since its upload, it has received 65 views. For similar materials see /class/209792/chem-4410-university-of-virginia in Chemistry at University of Virginia.


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Date Created: 09/21/15
PSAFE PROJECT WEEK 3 SEPTEMBER 5 2010 CLARIFICATION ON PROJECT 2 Describe Biological Function and Significance Compare your POI assigned protein s function to a protein of similar primary structure Protein BLAST Compare your POI s function to a protein of similar tertiary structure Dali Server Justify these comparisons Figure out MW and pi of POI Must have 3 journal article references and l Dali Server reference Must contain Appendices which should show your Protein BLAST results Dali Server Results and EXPASY Results and the amino acid sequence of your protein VV V VVV V CITATIONS gt Here is an example citation 0 Crystal structure of an aspartate aminotransferase TMi 255 from Thermotoga maritime at i 90 A resolution Schwarzenbacher R Jaroszweski L von Delft F Abdubek P Ambing E Biorac T Brinen LS CanavesJM CambeIIJ Chiu HJ Proteins 55759 763 2004 0 Use the above format AA 0 Cite within paper Example Bacteriorhodopsin is an integral membrane protein The 1 refers to Reference 1 in your separate reference section 0 Cite appendices The 2 score Appendix A of 32 indicates ACCESSING PUBM E ARTICLES gt To get full text for ajournal UVA does not have a subscription to request an InterLibrary loan wwwlibvirqiniaedueo gt To access journals offgrounds download a proxy server wwwibvirqiniaedutoosoffqroundshtm amp FAQS Protein BLAST gt I have Protein BLAST results however none of them have structural coordinates deposited in the PDB What do I do 0 Indicate this in your report Still research one of the protein s biological function gt I have Protein BLAST results However all of the E values are exactly zero What do I do 0 Do not use any of your Protein BLAST data Include this in your report Instead use your DALI results gt The Protein BLAST results are 40 pages Do I have to print all 40 pages a No Only print the page with the protein you are comparing your protein to Copy and paste into Microsoft Word FAQS CONTINUE gt How many proteins should I compare my protein to o This depends If you have no Protein BLAST results and do have DALI results compare two DALI of the DALI results to your protein a Ideally you should compare your protein to one protein that appears in BOTH your Protein BLAST and DaIi Server results You may do two if you want 0 However make sure you go into enough depth about your protein s function FAQS CONTINUE gt My protein is an enzyme Should I include the reaction my protein catalyzes 0 YES Do it in ChemDraw gt Should I include figures 0 This is optional but it may be helpful for you to include some images you generate in ICM Browser Pro DO NOT COPY AND PASTE FIGURES FROM JOURNAL ARTICLES YOU MAY ONLY USE SELF GENERATED FIGURES gt Should I include the organism my protein is from 0 YES What is the point of this project gt To demonstrate that protein structure determines function MOST OF THE TIME gt Slight variations in protein structure can completely change a protein s function gt You will use the information obtained during this project to make a slide in which you superimpose the structure of your POI with the structure of the protein you are using for your comparisons Make note of differences in structure amp Example Bacteriorhodopsin from Haobacterum sainarum PDB Dl fbb A Z score of 343 and rmsd07A indicate that the mutant bacteriorhodopsin PDB Ditn5 has similar three dimensional structure to the POI K 41 of ifbb is mutated to P 4i in itn5 Now we will look at the superimposed structures of these two proteins in ICM Browser Pro Literature indicates that the mutant bacteriorhodopsin is not functional amp v V V V PSAFE PROJECT WEEK OF SEPTEMBER 20 2010 COMMENTS ABOUT FIRST PROJECT 0 CITATIONS SHOULD BE IN THE FORMAT DESCRIBED IN WEEK 3 PSAFE PROJECT SLIDES 0 REFERENCES SHOULD BE NUMBERED AND ON A SEPAMTE PAGE 0 On the next paper points will be taken off if references are not in this format The actual Citation style should be from Week 3 PSAFE slides xJ REFERENCES Buttlaire D 1980 32 Puri cation and properties of f0rmyltetrahydrofolate syntlletase IMefhods in Engvnologv 66 585599 Holm L Kaariaiuen S Rosenstrom P Schenkel A 2008 Searchng protein structure databases with DaliLite v3 Bioinformatics 24 278027811 Radfar R et a 2000 The crystal structure ome formyltetrahydrofolate syntlletase 39om lMooreHa rhermoaeetica Biachemis jy 39 39203 926 MORE COMMENTS 0 IN TEXT CITATIONS 0 Should either utilize subscripts or superscripts or reference the speci c citation by number in parentheses EX cation binding site 1 0 This method will be easiest for you because this is what you will have to do in your molecular document 0 Points will be taken off on your first paper if this format is not followed ADDITIONAL COMMENTS 0 In your papers do not use your protein s PDB ID to refer to your protein 0 ie Do not say 1de is a transmembrane protein You must state the NAME of the protein PDB ID is not the name 0 Do cite your PDB ID in parentheses when you talk about your protein s crystal structure 0 ie Bacteriorhodopsin pdb id1fbb is a transmembrane protein CHEM DRAW For the next project if you have an enzyme utilizing ChemDraw is mandatory HOW TO ACCESS CHEM DRAW FROM CHEM411 StartAll programs ChemBioOf cezom ChemBioDrawUltra12 0 OH r 1 NH 2 fx 1 4 L H i N e W h N N H I n l H H NH2 1 2 MAXIMUM 15 POINTS 0 Create five images in ICM Browser Pro of your protein 0 Watch the Tutorials and read the Possible Slides document on Collab for ideas 0 These figures should have captions and be appropriately labeled for full credit 0 Attach this to the back of your Protein Structure Paper I CHECKLIST Due October 7th 0 This paper should detail important structural information about your protein including but not limited to your protein s physiological form subunit structure secondary structure and functionall important residues for example those found within an enzyme s active site If speci ic ionic interactions or hydrogen bonds are known for your protein these should be noted If your protein is an enzyme and if the binding sites of substrates products metal ions etc are known these should be clearly identified If your rotein contains prosthetic groups substrates roducts metal ions etc these s ould be described If your protein s structure has een solved in several dima mu 1 m n I u um ii Ii39ll w these different conformations should be explained If the different conformations involve alterations at an active site or other similar localized changes these should be discussed If your protein is the target of one or m ore drugs and i the structure of the protein drug complex is known these structures should be carefully described Your paper should ultimately illustrate the relationship between your protein s structure and its function 0 You should also fill out TYPE and print the Structural Feature Checklist Staple this on top of your paper FROM PSAFE PROJEC T DESCRIPTYON Format Times New Roman Size 12 font Double spaced Up to 3 pages of content References will be a 4th page You should have a MINIMUM of 7 references These may include your references from the Bioinformatics paper No title page The first three lines should look like this Last name F1151 name computing ID PDB JED Name of Protein Genus spec 1235 PROTEIN S PHYSIOLOGICAL FORM 0 Some of your proteins will physiologically exist in different oligomeric states 0 By looking through the literature you should determine what these are and include the protein s oligomeric state in your paper 0 NOTE Your protein may have been crystallized in this structure or may have been crystallized in a monomeric form Use literature to determine oligomeric state not the appearance of your protein in ICM Pro Subunit Structure 0 Some of your protein s contain many subunits 0 The structure and function of these subunits should be clearly described 0 EX the photosynthetic reaction center PDB ID1PCR includes three subunits light medium and heavy which perform different functions and have different structures Secondary Structure 0 The secondary structure of your protein should be carefully described Indicate the presence of alpha helices beta sheets ad random coils Functionally Important Residues 0 May include residues at a ligand binding site 0 If your protein is an enzyme these may be residues at enzyme active site 0 The purpose of these residues even if it is hypothesized should be noted 0 If your protein has cation anion binding sites these should be described 0 If your protein participates in specific hydrogen bonds these should be explained Binding Sites 0 All binding sites for your protein should be described 0 EX Metal ion binding sites Cofactor binding sites Substrate binding sites Drug binding sites Product binding sites And more Functions of Ligands 0 The purpose of associated ligands should be explained in your papers 39 For example in the case of bacteriorhodopsin ligand retinal is a chromophore Upon photoillumination retinal isomerizes and a subsequent conformational change in bacteriorhodopsin occurs Different Conformations 0 Different conformations of your protein should be identified and explained 0 For instance bacteriorhodopsin has both an open and a closed conformation closed 0pm DRUG TARGETS 0 If your protein is the target of a drug and there is a crystal structure of your protein attached to the drug this complex should be thoroughly described 0 You will find this information by conducting literature searches Other Information to Include 0 You may include differences similarities between the structure of your protein and your comparison protein 0 Particularly interesting information to include would be differences or similarities in binding sites 0 It will also be interesting to note differences in structure that contribute to function of these proteins Protein Structure Checklist 0 Found on Collab 0 Fill out this structural checklist as you research remembering to note the reference which you find information from 0 The structural checklist is designed to make writing your paper easier 0 The structural checklist MUST be typed and stapled to the back of your paper after references


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