Projects

Oral Presentation Guidelines

The goal of the oral presentation is for you to teach the class (including your instructors) about your topic. This will depend on the class size, but oral presentations are typically 30 minutes with a few interruptions for questions and clarification, followed by 5–10 minutes for questions and discussion period. Three days before your presentation send the instructor's assistant a one paragraph abstract to be shared with the class. Include a reference to a review article and a recent research paper or paper you consider to be seminal. Your instructors and fellow students will look these over before class so they can think about your topic in advance and formulate better questions for discussion.

Also before your presentation, preferably, 5 to 6 days, and at the very least 2 days before, you will practice your talks to one or more of the people scheduled to present that same day. You will write a brief description of your suggestions for improvement of the oral presentation of your team and this will be emailed to the instructor on the day of your group's presentations. It might be as brief as: "Jenny is an accomplished public speaker and gave a very well organized presentation. I suggested that she define her terms, and explain some concepts in the initial part of the talk." More likely it will include more specifics. For example:

"Josh has had little practice in public speaking. I suggested that he simplify his slides, and taught him how to use animation in Powerpoint to layer information more effectively. I suggested that he begin with a very general description of pathology, but he felt that would be too boring. He may be right. I also suggested that he provide a handout for medical terminology, for future reference. His slides on amyloid in the CNS and its correlation with disease were very difficult to see. I suggested he find better illustrations."

For your talk, use Powerpoints or other visual aids to illustrate key points. The general format:

  • first a broad overview of the problem and its importance,
  • pose the questions,
  • describe key experiments,
  • critically analyze and interpret the results,
  • present an eye to the future.

You can't cover everything that will appear in your final paper. The class presentation should be specifically constructed and tuned for an oral presentation. As in a professional presentation, your talk will be rehearsed and timed beforehand, with input from a peer reviewer in the class.

Final Paper Guidelines

The final papers are due the last week of classes. The format of the final papers should be a mini review of the selected topic. At the point you have completed the paper, you should be an expert on the subject, with the additional good feeling of having made your understanding available to your classmates and instructors during your oral presentation. The listed references are intended only to be starting points. You are responsible for finding the latest relevant results, using the tools built in to modern journal online resources. Just as with a scientific publication, the paper should be a single coherent integrated text.

The text should begin with an Introduction that gives the background and general context of the work, including the societal and biomedical importance. This is to be followed by a Critical Results and Discussion section that reviews the findings that you consider most relevant and important. Try to follow the format of first posing the question; then describing the experiment designed to answer the question; finally analyzing the resulting data. Reproduce a few figures to illustrate aspects of the subject. The paper should consist of a title page with an Abstract (<250 words) of the most important results and conclusions. The text proper should be 12–16 double spaced pages, with 16 pages the absolute limit. References and figures are additional. The references should include the full titles of the papers. The target audience is the other students in the class and your instructors.

One full week before the paper is due you will exchange drafts with the other members of your team.You will provide editorial suggestions—not just copy editing but substantive feedback on things that are unclear, things that are missing, things that are given too much space for their import, etc. Make a photocopy of your comments on your colleague's paper and hand them in with the final paper. They are an important part of your class participation.

Student Presentation Topics

The references listed are to get you started. They do not represent a complete or systematic sampling of the literature. Finding, reading and assimilating a subset of critical papers is your responsibility.

POSSIBLE TOPICS DESCRIPTIONS
Protein Folding and Chaperones
The Refolding Pathway for Apomyoglobin Hemoglobin is one of the paradigms for a protein whose conformation controls critical physiological processes, and whose malfunction leads to a variety of anemias. Hydrogen exchange and NMR have been used to identify intermediates in the refolding of apomyoglobin. This allows interpretation of a variety of human hemoglobin.
Trigger Factor and DNA K; The Conformations of Nascent Chains Emerging the Ribosome What is the conformation of the newly synthesized polypeptide chain as it exits the ribosome? Does the ribosome play a role in early stages of protein folding? What are the roles of Trigger Factor?
The Mechanism of GroE Function in Protein Folding and Assembly How does the chaperone actually function in ensuring productive protein folding? How does the Jack in the Box work, how is ATP hydrolysis coupled to chaperone function? What is the relationship of GroES binding and release to folding within the GroEL lumen? (Paul Sigler, Arthur Horwich, Helen Saibl; Ulrich Hartl, George Lorimer;)
Function of the DNA K (HSP70) Class of Chaperonins These appear to interact with newly synthesized chains at an earlier stage in folding than the GroE class, and function as a complex of DNA K, DNA J, and Grp E. They do not have a lumen, but appear to bind an unfolded peptide in an elongated cleft.
Function of the Lens Chaperone Alpha-crystallin This is a member of the small heat shock chapeorone family. It is present at high concentrations in the lens and is thought to protect lens crystallins from radiative or oxidative damage leading to cataract.
HSP90 A&B This chaperone is specialized for the maturation of metastable proteins that often play key roles in cell circuitry, such as transcription factors, kinas, phosphatases. It cooperates with a host of other co-chaperones. To recognize its targets, it is expressed at high levels in all eukaryotic cells and is induced by many types of stress. It is an exciting new target for cancer therapeutics. Useful websites: International Conference on the Hsp90 Chaperone Machine and Files from Professor Didier Picard's lab at the University of Geneva.
Organismal Biology, Evolution, and Medicine
HSP104 & ClpB These proteins belong to the AAA+ class of ATPases. They are large macromoleclar machines and use the energy of ATP to dissolve aggregated proteins. They play important roles in stress tolerance and in diverse processes such as the inheritance of prions in yeast.
The in Vitro Refolding of Collagen Short tripeptides with collagen-like sequences have recently been crystallized and their structure solved by X-ray diffraction. Using 2-D NMR it has been possible to follow the actual kinetics of the chain folding and association reaction and the effects of certain glycine substitutions.
Functions of Prolyl Hydroxylases in Collagen Chain Folding and Maturation Prolyl hydroxylase is responsible for the formation of hydroxyproline on newly synthesized chains and is thought to be involved in regulating triple helix formation. Underhydroxylation of prolines is the molecular defect in scurvy, vitamin C deficiency.
The Role of Prolyl Isomerase in Protein Folding What is the role of proline isomerization and proline isomerase in the folding of newly synthesized polypeptide chains within cells, including procollagen? Prolyl isomerase, originally called cyclophilin is the target of the cyclosporin class of immunosuppressive drugs. It turns out to function in many unexpected cellular processes.
Membrane Proteins and Transported Proteins
The SecB Chaperonins in Proteins Destined for Export A number of proteins destined for export (and perhaps folding) outside the cell must be maintained in a non-folded state after synthesis. Some of those are maintained in this state by the secB protein of E.coli, whose mechanism has been studied in considerable detail. (Linda Randall and coworkers).
Chaperonin Function in Bacterial Pilus Assembly Bacteria use extra cellular flagella and pili for swimming, attaching to other cells and transporting DNA. The folding and assembly of the proteins for these organelles utilize specialized chaperonins, some of which function in the bacterial periplasm. These function both in chain folding and in polymerization of the extracellular pilus organelle.
Folding and Insertion of Bacteriorhodopsin One of the very few membrane proteins whose three dimensional structure has been solved is the rhodopsin of the visual system. The best defined experiments on how these transmembrane helices associate within the membrane have been done with the bacterial and mammalian opsin. Rhodopsin mutation or damage is associated with a variety of human retinal pathologies.
Channels for Protein Import and Export Many newly synthesized proteins have to transit a membrane, for example, for import into mitochondria or for entry to the endoplasmic reticulum. In general, the polypeptide chains have to be maintained in an unfolded state. The proteins forming these channels have recently been identified in a number of organisms.
In Vivo Folding and Assembly of the Influenza Hemagglutinin The intracellular assembly and maturation of this trimeric viral coat protein is one of the better model systems in eukaryotic cells.
ERAD Endoplasmic reticulin associated degradation. For many years scientists searched for the protease within the ER that was responsible for getting rid of misfolded proteins, only to realize that it doesn't exist. Proteins in the ER are targeted for degradation and exported to the cytoplasm to be destroyed by the proteasome or sent to the lysosome (or vacuole) for degradation in that organelle. (see Prof. Lindquist for references)
Human Disease Associated with Protein Misfolding or Aggregation
Light Chain Amyloidosis Cancer patients with a form of leukemia called multiple myeloma often accumulate amyloid deposits composed of the overproduced light chains. Aspects of this aggregation reaction have been elucidated through in vitro experiments.
Superoxide Dismutase Defect in ALS (Lou Gehrig's Disease). Recent evidence indicates that amylotrophic lateral sclerosis is associated with a defect in the function of the widely distributed protein Superoxide Dismutase. The associated amino acid substitution may affect folding or stability rather than metabolic function.
The CFTR Defect in Cystic Fibrosis Cystic fibrosis is due to a defect in the chloride transporter protein in the respiratory tract. Recent evidence indicates that the most common inherited form is due to a protein folding defect. This is the most developed model of the role of protein folding defects in human disease.
Trans-thyretin and Amyloid Disease A rare but well-studied class of amyloid diseases are due to deposition of the carrier protein trans-thyretin which is a retinol carrier protein. Features of the in vitro unfolding/ refolding reaction correlate with the conditions that yield pathology.
The Anti-trypsin Defect in Familial Lung Disease Increased susceptibility to lung damage from smoking and dusts is associated with certain alleles of the anti-elastase that functions in the lung. Recent evidence reveals that their major familial form is due to a defect in the folding of the protein.
Mutations in Tumor Suppressor Proteins Loss of function of a number of cellular proteins, which control DNA replication and cell division, is associated with tumor formation. Particularly well-studied are p53 and p21. There is considerable evidence for the p16 ankyrin proteins that some of these mutations may represent protein folding defects.
Prions
Prions Prions are a diverse group of unrelated proteins that have very unusual folding properties. They can exist stably in profoundly different conformations, one of which (the prion conformation) can template other proteins of the same type to change into the prion conformation. This creates a protein conformational chain reaction that can cause terrible diseases, or serve as an epigenetic mechanism for the inheritance of new traits. (Prusiner, Lansbury).
Topic A: properties and transmissibility Mammalian PrP Cellular properties of the rodent prion agent and its transmissibility.
Topic B: structural characterization of mammalian prion protein Mammalian PrP Structural characterization of the isolated prion protein.
Topic C: characterization of prion protein in yeast Yeast Prions Characterization of the yeasts prion protein, genetics & cell biology. Sophisticated genetic analysis available in yeast has allowed a very penetrating analysis of the origin and pheotypes of the sup35 yeast prion protein.
Alzheimer's Disease
Amyloid Deposits in Alzheimers Disease Alzheimers patients have insoluble protein deposits in a number of their tissues. A major class are characterized by a distinctive cross beta rod structure.
Topic A: proteolytic cleavage Studies on the generation of the Alzheimer's peptide by proteolytic cleavage from its precursor.
Topic B: amyloid plaques and interactions Formation of amyloid plaques in vivo, including interactions with other factors such as the ApoE lipprotein, chaperonins, etc.
Topic C: therapeutic approaches

Therapeutic Approaches to Retarding or Alleviating Alzheimers (refs. to follow)

Therapeutic strategies for alleviating Alzheimers disease cover a vast landscape. They include, among others: attempts to reduce the production of ABeta by inhibiting a protease that cleaves APP, immunizing patients against ABeta, protecting mitochondrial function, providing nerve growth factors, and blocking amyloid assembly. Provide an overview, and then choose three strategies and report on them in detail. The rationale, evidence of success, reasons they might fail.
Parkinson's Disease
Parkinson's Disease and Alpha-synuclein Aggregation Parkinson's disease, due to damage to a very specific region of the brain, is associated with aggregation of a plentiful brain protein alpha-synuclein.
Topic A: alpha-synuclein aggregation and polymerization In vitro characterization of alpha-synuclein aggregation and polymerization:
Topic B: Etiology of Parkinson's Etiology of Parkinson's disease; MPTP, rotenone, paraquat as etiological agents; inherited mutations causing early onset PD.
Huntington's Disease
Protein Aggregation in Huntington's Disease The modified protein product associated with CCC expansions in Huntington's disease has recently been identified. The presence of polyglutamine insertions and expansions appears to be a more general source of cellular pathology. An aggregated form of Huntington's is found within the cell nucleus.
Topic A: polyglutamine aggregation In vitro characterization of polyglutamine aggregation.
Topic B: polyglutamine aggregation in experimental organisms Investigation of polyglutamine aggregation in experimental organisms; caenorhabditis elegans, Drosophila, or mice.