Protein Database and Protein Visualization Lecture

Lesson Plan

Program         Molecular Genetics and Genetic Engineering

Course            MBMG 515 Protein Technologies and Applications

Lecture topic Protein Database and Protein Visualization

Lecturer         Asst.Prof. Dr.Duangrudee Tanramluk

Date/Time      Monday 4 December 2023 (9.00  – 11.30 hrs)

Room              Third Floor Computer Room

Learning Objectives:

At the end of this lecture, students should be able to

  1. describe about protein structural database characteristics and applications
  2. query sequence and structure data retrieval using structural database query forms
  3. become familiarized with protein structure molecular visualization tools

Lesson contents in brief:

Structural database characteristics, structure data retrieval, Gene Ontology, structure visualization, creating molecular graphics and animations

References:

  1. Lesk, A.M. (2008) Introduction to Bioinformatics. Oxford University Press.
  2. Bourne, P.E. and Weissig, H., eds (2003) Structural Bioinformatics. John Wiley & Sons.

Learning organization:

  1. Lecture
  2. Hands on practice
  3. Questions and answers

Learning materials provided:

  1. Powerpoint slides
  2. Handout

Class Materials

  • Interactive Slides
  • Handout: Protein Database and Protein Visualization
  • Please download & install Discovery Studio Visualizer Client (Windows) , PyMOL & PhotoScape before attending the class

Assignments

1.Take a photo of physical model of the four helix bundle cytochrome b562, PDBID: 256b. Browse Protein structures in http://www.CATHdb.info/ and if possible make your physical model and take picture with your name written underneath.

2.(a) How many hemoglobin structures that cause sickle cell anemia (hemoglobin S) are deposited in the PDB?   (b)What is the part of the protein (buried/surface) that this amino acid mutation occurs? (c) Discuss why normal hemoglobin (Glu 7, Asp73) is less likely to form fibers than Hemoglobin C-Harlem (D73N, Chain B + E7V, Chain H).

3.(a)How many CDK kinases with resolution < 1.5Å are deposited in the PDB? (b)Send me a picture of the CDK-ligand interaction, tell which PDB code you have got it from. –done in class

4.Learn to create a poster of the structure from Nishimasu H, et al.’s CRISPR-Cas9 paper (Source: http://www.sciencedirect.com/science/article/pii/S0092867414001561)

5. Make protein structure animations and send the file to me.

Student Assessment:  

Assessment
#2, #4, #5 above with the file name (StudentName_XXX.YYY)

Practical on hemoglobin & CDK (.docx), Protein animation (.gif)

Please post the folder (containing 3 files per each student) to Google Class by December 20, 2023.

Returned Homeworks

Physical Models

CRISPR-Cas9 poster