Research Paper Overview

Physics 323/623: Computational Biophysics Lab

Instructors: Drs. Jacquelyn S. Fetrow and Freddie R. Salsbury, Jr.

Research-based learning: The best way to learn to use computational biophysics methods is to apply those methods in a research-based format, an approach that we will follow in this course.  We will teach methods and theory, but you will apply the methods and theory to a problem for which we do not yet know the “right answer;” however, it is a problem in which we are interested. 

            This semester, we have chosen the protein peroxiredoxin (Prx) for analysis.  Each of you will be assigned a different Prx structure.  This structure will be the one that you use and analyze during each of the laboratory exercises.  Your grade will be partially dependent on your knowledge of your structure, your observations and analysis of the results you obtain for your structure, and your critical comparison of your data to the results produced by other students on their own Prx structures.

Research paper, the product of research-based learning:  You will be required to write a research paper on the structure and analysis of your Prx structure and comparison to the structures and results that other students obtained for their structure.  Paper drafts will be turned in during the course of the semester.  The final product will be a complete research paper on the work you have done on your Prx structure. 

            Your grade will be based on the writing and organization of the paper; your explanation and critical analysis of your structure and experimental results; your critical comparison to the results of other students in the class; and your response to comments from previous drafts.

            Do not forget that figures are essential to any research paper.  Well-designed and focused figures will be awarded extra points. Some figures that you may wish to use for your research paper will be created during the laboratory exercises. Feel free to use your own graphs, even if you already turned them in as part of another lab exercise. Give some consideration to making the figure specific for the paper.  Non-essential figures, or figures that do not have a specific point or purpose, will detract from the paper and from the grade you receive.

            Plagiarism is cheating!  It is expected that you will completely reference all statements and ideas in the paper that are not your own.  When you reference another scientist’s work, you should still put the idea into your own words.  If you use a sentence from another author word-for-word, you must indicate such by using quotation marks.  Plagiarism in the research paper will result in 0 points for the research paper. 

Paper submission:  You will be required to turn in your paper (and drafts) by 5 pm on the due date.  The paper (and drafts) should be submitted electronically to both instructors. Please be sure to include your last name as part of the filename. Also, please submit a hard copy to Professor Fetrow by the due date and time.  You are responsible for determining that the hard copy is of professional quality and that the electronic and hard copy versions are identical. 

Outline:  This is a suggested list of chapters for the research paper and possible topics to cover in each chapter.  You do not need to follow this outline exactly, nor limit yourself to the suggested topics, but we expect that your paper will be well organized and logically presented. 

Title page.

Table of contents.

Chapter 1.  Peroxiredoxin sequence, structure and function

· Overview of peroxiredoxin biochemical and cellular function

· Peroxiredoxin sequences and sequence comparison

· Overview of known peroxiredoxin structures

· Detailed “tour” of your assigned peroxiredoxin sequence and structure

· Comparison between your peroxiredoxin and the sequences and structures of other peroxiredoxins

            Chapter 2.  In vacuo and explicit solvent simulations of peroxiredoxin

· Rationale for performing simulations

· Molecular dynamics methods (this does not need to be a general overview of MD methods, but a description of the methods that you used explicitly, so that another researcher could repeat your results)

· Analysis of the quality of the simulations (Do the simulations look “good”? Are they consistent with any experimental evidence?)

· Critical analysis of the simulation of your structure

· Comparison of in vacuo and solvent simulations on your structure; implications for biochemical or cellular function

· Comparison of your simulation results with those of other students on other peroxiredoxin structures

            Chapter 3.  Electrostatic calculations of peroxiredoxins

· Rationale for performing electrostatic calculations

· Electrostatic calculation methods (this does not need to be a general overview of electrostatic methods, but a description of the methods that you used explicitly, so that another researcher could repeat your results)

· Analysis of the quality of the calculations (Do they look “good”? Are they consistent with any experimental evidence?)

· Critical analysis of the calculations on your structure; implications for biochemical or cellular function

· Comparison of your simulation results with those of other students on other peroxiredoxin structures

Chapter 4.  Interpretation of molecular dynamics and electrostatic calculations in the context of peroxiredoxin function

· Put the results of the MD and electrostatic calculations together—do the results together tell you anything interesting?

· What implications do your results have for peroxiredoxin function? 

            Chapter 5.  Summary and suggestions for future work. 

· What questions are still unanswered about peroxiredoxins?  Can you identify any hypotheses that are suggested by your results?

· Suggest computational or laboratory experiments that would answer your questions or test your hypothesis.

            References.