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Paper and Oral Presentation Guidelines

The Research Reports are an essential part of the course curriculum, and cover important topics in protein folding, misfolding, and their physiological roles.

Oral Presentation

The oral presentations will be 20 minutes each with each team member giving 10 minutes. A five minute question and discussion period will follow.

A 10-15 page paper requires 30-45 minutes for oral presentation. Therefore the live class presentation, though following your manuscript content, needs to be specifically constructed and tuned as an oral presentation. In particular you need to pull out a key question, critical experiment, its protocol, results, and interpretation.

Assume you are at a scientific meeting; use overheads to illustrate key points where convenient. Try to follow the format of:

first posing the question;
then describing the experiments designed to answer the question;
report the result;
finally analyze and interpret the results.

As in a professional presentation, the presentations should, if possible, be rehearsed and timed beforehand to another member of the class.

Timing

In order to present to the class, much of your reading, assimilation, and integration needs to be done before the day of presentation. However, the actual final written papers are due on the last day of class, session 24, regardless of when you presented. The exception is for the groups presenting on the last day of class, who will have two more days, to hand in written papers. You will need to have the abstracts available for the class on the day you are presenting.

Student presentations will start from session 19 onwards and continue through session 25.

Paper Guidelines

The format of the final papers should be a Minireview 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.

The text should begin with an introduction which gives the background and general context of the work. This is to be followed by a Critical Results and Discussion section which 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 a summary (<250 words) of the most important results and conclusions. At the end of the summary give the reference to a review article, a very recent research paper, and a paper you consider to be seminal. The abstracts will be copied and distributed to the class.

The length of the text proper should be 10-15 double spaced pages, with 15 pages the absolute limit. The references and figures are additional.

The references should include the titles of the papers.

The target audience is the other students in the class.

Student Presentation Topics

PROJECT #	TOPICS	DESCRIPTION
November Presentations: *Protein Folding in vitro* / Protein Structure and Sequences**
1	The Conformations of Aromatic Side Chains in Globular Proteins	Most aromatic rings are found in the interior of proteins. What kinds of interactions are aromatic rings involved in within protein interiors? There is evidence in some proteins that the rings can flip. How rapidly? How general is this motion?
2	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.
3	Two Stranded, Three Stranded, Four Stranded Coiled Coils	Coiled coils are not limited to pairs; depending on the details of the residues at the buried hydrophobic positions, the helices will form trimeric and higher associations. Recent studies reveal the fine points of the relationship between sequence and tertieary associations.
4	Electrostatic Interations in the Folding, Association and Registration of the Coiled Coils	Though the hydrophobic interactions are critical, charged side chains interactions also control the structure and association of coiled/coils in both tropomyosin, and leucine zippers. Recent papers report differing values for the contributions of these ion pairs to stability.
5	Do Beta Turns Form in Soluble Peptides?	Recent NMR studies of synthetic peptides suggest that beta turns may be more stable than expected and might be candidates for protein folding nuclei.
6	Helical Extension and Termination Signals in Globular Proteins	Analysis of sequences at the ends of helical regions reveal preferred residues. In both Barnase and T4 lysozyme substitutions have been generated which alter the termini of helices in the proteins.
Mid Session Topics - Late November
7	The Refolding Pathway For Apomyoglobin	Hydrogen exchange and NMR have been used to identify intermediates in the refolding of apomyoglobin. This allows interpretation of a variety of human hemoglobin mutants and other sequence data.
8	Circularly Permuted Polypeptide Chains	How important is the continuity and connectedness of amino acid sequences? In BPTI, the Greek key beta barrel proteins and some larger enzymes, the N- and C- termini have been joined together and new physical ends created, to examine the effects of sequence permutation on chain folding.
9	Mutational Studies with T4 Lysozyme	Among proteins of known atomic structure, extensive studies of the affects of mutations on the conformation and stability of the folded protein have been carried out with T4 lysozyme. These experiments have yielded both insight into the relationship of local sequence and overall fold, and some useful surprises.
10	Folding of Beta Sheet Proteins	Recent studies have begun to identify intermediates in the formation of small beta sheet proteins such as the interleukins and fatty acid binding proteins. These experiments utilize both hygrogen/deuterium exhange combined with spectroscopic procedures.
11	Coupling of Folding and Subunit Interaction in Luciferase	In many oligomeric proteins assembly proceeds not from native subunits but from folding intermediates of the subunits. One of the best understood cases is the heterdimeric luciferase from the bacteria that illuminate the eyes of deep sea fish.
12	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 mammalin opsin.
December Presentations: Cellular Apparatus for Protein Folding
13	The Conformations of Nascent Chains on 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?
14	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.
15	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 pro collagen? Prolyl isomerase, originally called cyclophilin is the target of the cyclosporin class of immunosuppressive drugs.
16	Folding and Assembly of Bacterial Porins	The porins are a class of membrane proteins making large pores which use large beta barrels rather than alpha helical proteins and whose 3-D structures have been solved.
17	Prokaryotic Proteins Involved in Disulfide Bond Formation	Genetic studies in bacteria have identified a family of proteins involved in reduction and oxidation of thiols, and presumed to be involved in the folding of some proteins.
18	The Role of Protein Disulfide Isomerase in the Endoplasmic Reticulum	How are disulfide bonds formed in newly synthesized polypeptide chains destined for export from eukaryotic cells?
19	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.
20	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.
21	Structure and Functions of the Eukaryotic Dedicated GroE S Chaperonins	A conserved class of 14 subunit oligomers, the GroE chapoeronins, is involved in insuring the correct folding of newly synthesized chains, at least at high temperature.
22	The Mechanism of GroE Function in Protein Folding and Asssembly	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?
23	Chaperonin Function in Bacterial Pilus Assembly	Bacteria use extra cellular flagelli 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.
24	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.
25	Function of the DNA K (HSP90) 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.
Later Presentations: Protein Misfolding and Disease
26	Lens Crystallins and Cataracts	The proteins of the lens, crystallins, have a variety of unusual properties, at least at high concentrations. The three-dimensional fold of the Gamma crystallin has been solved and the protein can be refolded in vitro. Some investigators believe incorrect association of these molecules leads to cataracts.
27	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: Studies on the in vitro association of the Alzheimer's peptide. Topic B: Formation of amyloid plaques in vivo.
28	Prion Diseases as Protein Association Phenomoma	The evidence is accumulating that prion diseases are due to proteins which change their conformation irreversibly during an association reaction, perhaps by mechanisms related to amyloid accumulation. Topic A: Indefication of the prion agent and its transmissability. Topic B: Structural characterization of the isolated prion protein.
29	Light Chain Amyloidosis	Cancer patients with a form of leukemia called multiple myeloma often accumulate amyloid deposits composed of the overproduced light chains. Some aspects of this aggregation reaction can be reproduced in vitro.
30	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.
31	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.
32	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.
33	Trans-thyretin and Amyloid Disease	A rare but well studied slass 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.
34	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. There is some evidence for the p16 ankyrin proteins that some of these mutations may represent protein folding defects.
35	Protein Aggregation in Huntington's Disease	The protein polyglutimate product associated with Huntington's disease has recently been identified. An aggregated form of it is found within the cell nucleus.