INDEX     BCH2021S COURSE     bch2021 assignments     PROTEOMICS BCH2021S WWW assignments

Outline We are developing these pages into an Introduction to Proteomics and Bioinformatics teaching resource on the WWW, your course assignments will become part of this resource. This is intended to build something of lasting value from your work and that of others. Here are the rules, details and topics. Please e-mail boris.steipe@utoronto.ca with any questions you may have ! There will be a total of three assignments to author or contribute to a Web page. Assignments will be given to each registered student at the end of each course section. No prior knowledge of Web authoring is required. Templates will be supplied and an introductory lecture offered. As an example, a Web page on a specific topic may comprise a brief introduction, links to Internet resources and the current literature, images of protein structures or animated examples, step-by-step tutorials, problems, and worked-out answers. Depending on the topic, the assignment may comprise all or part of a page. The Web pages will be graded and each graded assignment will count towards 12% of the final grade (total of 36% for the 3 assignments). There are three types of assignments: concepts, molecules and resources. Each student should submit one assignment of each of the three types. As a rule of thumb, concentrated work for about a day should probably suffice to cover your subject to the detail we expect. Concepts Concept assignments provide an overview of our current understanding. They review textbook knowledge and current literature from the perspective of how the proteome is generated and functions. Remember to cite literature properly. Since the text will be posted on the Web, you need to supply the PubMed IDs with each reference. Other Web links will be appreciated. Try to get an overview of the topic from a current review, then point out key issues, examples and future challenges. I recommmend (but do not require) that you discuss your concepts/molecules/resources assignments relating to the same topic with your colleagues to make sure you complement each other in the best possible way. Molecules Molecules assignments illustrate the molecular components of the proteome (proteins, mostly) and demonstrate the molecular mechanisms that underly the molecular biology we discuss. These assignments are to be submitted as RASMOL scripts, as discussed in our RASMOL tutorial, together with explanatory text. You should scan the available literature, download and analyse the appropriate structures from the PDB and provide overviews, and detailed explanations with appropriate colors and labels. Resources Resource assignments can be step-by-step tutorials on the use of bioinformatics Web-sites, or a collection of exam-type problems and worked out solutions, or annotated bibliographies. Note that we need the URLs for your resources, even if you chose not to submit your assignment as HTML.

Formats All assignments have to be submitted electronically by e-mail to boris.steipe@utoronto.ca. I suggest (but do not require) that you use the HTML templates I will provide linked to this page and submit your assignments in HTML. These templates will be discussed in a brief HTML authoring tutorial. Images have to be submitted in GIF or JPEG format if they are linked into HTML documents, TIFF is also acceptable for images that are not linked. Use GIF to render vectorgraphics (drawings) and JPEG for pixel graphics (halftone images).

Authorship & Copyright You should work on your assignments alone, except where teamwork is explicitly called for. If you accept substantial help from someone, that help should be acknowledged. If you incorporate text fragments directly, the source has to be properly referenced. If you fail to acknowledge your sources for cited text, you are committing plagiarism and will receive a failing grade for the assignment. If you incorporate copyrighted material, e.g. images from text-books or journals, you should obtain the permission of the copyright holder. All material should ultimately end up on the Web, either in it's original form, or edited. It will contribute to a free, academic teaching resource. I have designed a Copyright and General Public License Statement to this effect, it is linked here and on each page from the © symbol in the footer. By submitting your assignment, you implicitly agree that the material will be subject to this Copyright and General Public License. If you do not agree, you must state this clearly on your assignment, the assignment will then not be posted on the Web. Whether or not you agree to have your work contribute to this teaching resource will have no influence on your grade.

Dates Assignments received after the due date will only be accepted in case of documented unforseeable circumstances outside your control that have prevented you from completing your assignment in time. Assignments received after May 1. cannot be accepted. Introductory tutorials Tuesday, Jan 22, 17:00: Introduction to RASMOL - use and scripting. Room: TBA Tuesday, Jan 29, 17:00: Introduction to HTML authoring for the course. Room: TBA Section 1: Proteomics Principles Assignments given out: January 30. Assignments due: February 17 (extended !). Section 2: Proteomics Methods Assignments given out: March 6. Assignments due: March 20. Section 3: Bioinformatics Methods Assignments given out: April 3. Assignments due: April 24.

Topics You are welcome to suggest your own topics ! The list of is still under construction and all topics are subject to revision. Section 1: Proteomics Principles Concepts Topic Name Description From genome to proteome   Overview of how the proteome is dynamically modified by transcriptional control, control of translation, splicing, posttranslational modification, transport and sequestration, assembly into molecular complexes and finally degradation. This is a linking page into the more in-depth discussions below. Control of transcription Benjamin Jung Current concepts of transcriptional control by transcription factors Control of transcription Quang Vinh Nguyen Current concepts of transcriptional control through chromatin remodelling Control of splicing XueSen Dong Current concepts of control of splicing and alternate splicing Posttranslational modifications Roni Gordon Current concepts of how protein function is rapidly and dynamically modulated through posttranslational modifications. Special focus on how posttranslational modifications precede altered transcription levels. Large molecular complexes Sherrie Kelly What have we learned from atomic detail knowledge of the ribosome ? Unstructured proteins Negah Fatemi Current concepts and examples, the fly-casting mechanism... Current Degradation Concepts MaryLisa Castelli The N-end rule and PEST sequences, control of ubiquitination, the proteasome, SUMO Interaction networks Doron Betel What are we learning from the yeast genome-wide interaction studies ? Molecules Topic Name Description Control of transcription Jennifer Marles A RASMOL tutorial on structural principles of the TATA box binding protein Structure Jeffrey Lee A RASMOL tutorial on beta-strands and sheets Modification Ravi Ramjeesingh A RASMOL tutorial on catalytic mechanism of kinases and phosphatases Modification ShinYop Kim A RasMol tutorial on switching in Ras: conformational chnages and catalytic mechanism Association Peter Hwang A RASMOL tutorial on protein interfaces in integral membrane proteins Association Arianna Rath A RASMOL tutorial on protein interface properties Association ShaoYang Ku A RASMOL tutorial on protein-protein recognition in SH2, SH3 and other domains Receptors and signalling Linh My Van A RasMol tutorial of conformational changes in G-alpha Receptors and signalling Paul Park A RasMol tour of the G-beta/gamma complex Receptors and signalling JianFei Qi A RasMol tour of the heterotrimeric G protein complex Resources Topic Name Description Transcription May Tsai "Further Reading" - annotated bibliography of recent important developments in understanding transcriptional control Translation Chrissie O'Brien "Further Reading" - annotated bibliography of recent important developments in understanding the control of splicing and of translation Translation Trent Yang 10 exam-style questions with worked-out answers and references to the control of splicing and translation Folding Manu Sharma "Further Reading" - annotated bibliography of recent important developments in understanding folding landscapes and the relationship of structure and transition state. Folding Sean Reichheld "Further Reading" - annotated bibliography of recent important developments in 3D-structure prediction; Compilation of WWW resources for folding prediction. Modification Sten Thomson "Further Reading" - annotated bibliography of recent important developments in understanding regulation of function through post-translational modifications. Special emphasis on cytosolic glycosylation and on acetylation, to balance phosphorylation. Modification Patty Tam Review of and step-by-step tutorial for use of PROSITE Database to find patterns for posttranslational modification, of signal peptide predictions, GPI anchor site predictions etc. Association and degradation Jamie Snider "Further Reading" - annotated bibliography of recent important developments of protein degradation: the N-end rule and PEST sequences, control of ubiquitination, the proteasome, SUMO. Protein interaction databases James Shaw Review of and step-by-step tutorial for use and interpretation of DIP, BIND and MIPS interaction Databases Signalling Roberta Siu "Further Reading" - annotated bibliography of recent important developments in understanding enzyme linked receptors Section 2: Proteomics Methods Concepts Topic Name Description 2D IEF Sten Thomson Current concepts of high-throughput proteome analysis with 2D-IEF problems. Special focus on automation and key examples of recent successful application of the method. co IP Trent Yang Current concepts of co-immunoprecipitation for protein interaction analysis. Special focus on methodological requirements and key examples of recent successful application of the method. LC MS-MS Manu Sharma Current concepts of peptide sequencing with MS-MS methods. Key examples of recent successful application of the method. Phage Display Jamie Snider Method and important variations (e.g. SIP). Key examples of recent successful application of the method for proteomics experiments. Protein Chips James Shaw Current concepts of constructing protein chips, technical issues and methodological considerations. Key examples of recent successful application of protein chips. TAP tags Roberta Siu Current concepts of TAP tag methods for interaction analysis. Key examples of recent successful applications. 2 Hybrid methods May Tsai Current concepts of 2 hybrid methods for interaction analysis. Key examples of recent successful applications. GFP tags Patty Tam Current concepts of GFP tags for the analysis of expression levels or localization. Key examples of recent successful applications. Syntethic Lethal Screens Chrissie O'Brien Current concepts of the analysis of functional (not physical) interactions for interaction analysis. Key examples of recent successful applications. Inteins and Protein Splicing Sean Reichheld Current concepts of the use of inteins for interaction analysis. Key examples of recent successful applications. Molecules Topic Name Description Intein Ben Jung A Rasmol tutorial of intein structure and function. GFP Quang Vinh Nguyen A Rasmol tutorial of GFP fluorophore formation, key fluorophore residues and overall structure. Calmodulin Doron Betel A Rasmol tutorial of conformationla changes and peptide binding of calmodulin HSP 60 family Negah Fatemi A Rasmol tutorial of structure/function relationships in GroEL. HSP 70 family Sherrie Kelly A Rasmol tutorial of structure/function relationships in DnaK and Hsc70. PPI Roni Gordon A Rasmol tutorial of cis-proline residues in proteins and structure/function relationships in the peptidyl-prolyl cis-trans isomerase Phage display MaryLisa Castelli A Rasmol tutorial on the structural basis of phage display (fusions to Gene 3 protein). Hormone receptors XueSen Dong A Rasmol tutorial on the progesterone receptor: hormone binding, conformational changes, DNA binding and site discrimination. Resources Topic Name Description Tags Paul Park A comparison table of protein tags (e.g. 6 x His, GST, MBP, CBD, CBP, FLAG, Myc, HA, T7, RNAse S-peptide, Strep-tag) listing: sequence, properties, affinity, advantages, references etc. 2D IEF Ravi Ramjeesingh "Further reading" - an annotated bibliography of 2D IEF methods for proteomics and relevant Web resources. 2 Hybrid Jennifer Marles "Further reading" - an annotated bibliography of genome-wide 2 hybrid methods and related Web resources. Phage display Peter Hwang "Further reading" - an annotated bibliography of current phage display methods as applied to proteomics and related Web resources. MS Jeff Lee "Further reading" - an annotated bibliography of mass-spectrometry methods for proteomics and related Web resources. Assisted folding Arianna Rath "Further reading" - an annotated bibliography on chaperones and related Web resources. GFP JianFei Qi "Further reading" - an annotated bibliography of recent applications of GFP and other AFPs for proteomics. Functional proteomics ShaoYang Ku "Further reading" - an annotated bibliography of experiments targeted to characterize protein function (e.g. kinases) on a proteome wide scale. Protein chips Linh My Van "Further reading" - an annotated bibliography of recent developments in the manufacture and use of protein chips. Genetics ShinYop Kim "Further reading" - an annotated bibliography of recent developments of synthetic lethal screens and other genetic approaches to define functional interactions of proteins. Section 3: Bioinformatics Methods Concepts Topic Name Description Micro Arrays Linh My Van and Ravi Ramjeesingh Hierarchical clustering of microarray expression data and correlation analysis (E.g. Stuart Kim's group). Key examples of recent successful application of gene expression profiling technology. Proteomics Paul Park Current concepts in structural proteomics Bioinformatics ShaoYang Ku Algorithms for protein structure comparison - DALI, VAST, SSAP (others ?) outline of algorithms and key results Bioinformatics JianFei Qi Signal peptide prediction and trans-membrane helix prediction: Description of neural network approach, availability and key results Bioinformatics Jennifer Marles Sequence similarity and the meaning of homology (in terms of structural and functional similarity) Bioinformatics ShinYop Kim Secondary structure prediction - Current approaches, outline of algorithms, successful applications Bioinformatics Jeffrey Lee 3D-structure prediction - Current approaches, outline of algorithms, successful applications (for "real" problems, not just CASP) Bioinformatics Peter Hwang Homology Modelling - Current approaches, outline of algorithms, successful applications (for "real" problems, not just CASP) Bioinformatics Arianna Rath Consensus based approaches for protein engineering (eg: IG-domains, Phytases, P53, SH3, WW domains ...) Molecules Topic Name Description Structure May Tsai A RASMOL tutorial on alpha-helices: principles, N- and C-cap, examples Assisted folding Jamie Snider Dsb A - A Rasmol tutorial of structure/function relationships in the protein-disulfide isomerase (oxidase) DsbA Assisted folding Sten Thomson Periplasmic assembly factors - A Rasmol tutorial of PapD and FimC structure and function and related assembly factors. Assisted folding Roberta Siu Cold-shock proteins - A Rasmol tutorial on structure/function relationships in cold-shock proteins. 2-Hybrid system Chrissie O'Brien A Rasmol tutorial on the structural basis of the two hybrid system. Homology at work Trent Yang Manu Sharma Sean Reichheld James Shaw Patty Tam Pick sets of homologuous sequences (with known structure) posessing approx. 80%, 50%, 30% and less than 20% identity, compare structural differences and consequences for function. Discuss what you could have / could not have predicted from knowing the homologuous structure (Using FSSP, it is easy to find suitable primary datasets). Resources Topic Name Description Protocols Negah Fatemi Laboratory protocols for limited proteolysis Databases Roni Gordon Human Genome (NCBI, Ensembl ...), OMIM and related resources: Concept, contents, queries and key references of results that have been obtained with the use of the database. Databases XueSen Dong E. coli genome and related resources: Concept, contents, queries and key references of results that have been obtained with the use of the database. Databases Sherrie Kelly Mouse Genome: Concept, contents, queries and key references of results that have been obtained with the use of the database. Databases Doron Betel Genbank and curated sequence databases (e.g. Swissprot and PIR): Concepts, differences, contents, queries and key references of results that have been obtained with the use of the database. Databases Benjamin Jung Review of and step-by-step tutorial for use of TRANSFAC Database incl. key references of results that have been obtained with the use of the database. Databases MaryLisa Castelli Protein domains: ProDom, PFAM, SMART, CDD, RPS Blast ... : Concept, differences, contents, queries and key references of results that have been obtained with the use of the database. Databases Quang Vinh Nguyen The BIND Database: Concept, contents, queries and key references of results that have been obtained with the use of the database.

INDEX BCH2021S COURSE bch2021s assignments PROTEOMICS

B. Steipe and Program in Proteomics and Bioinformatics, University of Toronto boris.steipe@utoronto.ca Last revision: Jan. 2002 ©