You are here

Home » Current Project

Protein Modeling

Sample Portion Model

Advanced Project: Protein Structure and Folding

The 2023 WSSP offers the opportunity for up to two groups of students (1-2 students per group) from each school to participate in creating a physical model of a homolog of proteins identified during the screening of the cDNA library at their school during the academic year. This project is exclusively for advanced students who have completed the analysis of all their PCs and analyzed at least one unknown clone during the 2023 project. Participation is limited, with only two groups per school eligible. In the event of more than two group applications from the same school, selection will be based on the quality of their applications by the WSSP.

The next meeting will be from 4:00 to 6:00 PM on 4/23/24 in Waksman Room 1001.  You need to have sent Dr. Vershon the 6 models described on the Worksheet before the meeting.  Each group will need to prepare a 5 minute talk outlining the structure of their protein and how it relates to its function.    Power points should be sent to Dr Vershon by 12 noon on 4/23//24.  

Protein Modeling Resources

WSSP Protein Modeling Worksheet

Link to download Jmol

Jmol Command Sheet

WSSP Protein Modeling Meeting Handout (4/3/24)

Registration deadline for groups is 3/12/24.

The project commences in March 2024, with students required to attend two mandatory in-person meetings at the Waksman Institute from 4:00 to 7:00 PM on 4/3/24 and 4/23/24. These meetings will provide background information for the project and require students to present their findings. Both students in each group must attend both meetings.

Students will engage in reading original research articles on the structure and activity of their chosen protein and utilize molecular graphics programs to model it. Protein Modeling teams must adhere to assignment deadlines with no extensions or exceptions. Tentatively, models will be printed in May 2024, and students will present them at the WSSP poster session in June 2024. The WSSP will cover the printing costs for two models per school.

Proteins chosen for modeling must not be components of large complexes like those found in ribosomal or photosynthesis complexes. Ideally, proteins should exist in monomer or dimer (homo- or heterodimer) structures.

Applications should include the following information from each group of 1 or 2 students:

Please email this file to Dr. Vershon at vershon@waksman.rutgers.edu by 3/12/24.   Contact Dr. Vershon directly if you have qusestions about the program or your protein/structrue 

1.

A .doc or pdf file with the following information

 

a.

School name

 

b.

Names and emails of students participating in the project

 

c.

Protein Data Bank (PDB) file name (e.g. 1A3N.pdb)

 

d.

Name of the protein modeled (e.g. Hemoglobin) 

 

e

Primary citation associated with the pdb file (e.g. Tame, J.R., Vallone, B. (2000) The structures of deoxy human haemoglobin and the mutant Hb Tyralpha42His at 120 K. Acta Crystallogr.,Sect.D 56: 805-811)

 

f.

Name of the clone from the cDNA library you have annotated that corresponds to the protein you have modeled. (e.g. Clone 20XY23.22)

 

g.

A blast2 sequence alignment between the your protein and the protein that was used to determine the structure you are modeling (note: Landoltia protein sequences must be more than 40% similarity with the protein in the PDB structure.  Large protein complexes such as the photosynthesis apparatus and ribosomes are discrouaged)

2.

A one page description of the function of the protein you plan to model. What does the protein do in the cell or organism (e.g. glycolysis, protein translation, etc.)? Does it have a specific enzymatic activity (e.g. kinase, nuclease, etc)? What other proteins may it interact with? When is it likely expressed (e.g. in all cells all the time, just a subset of cells at specific times during development, etc)? This section must be at least one page long.