NTU Course
Overview

Protein Structure and Dynamics

Offered in 114-1

  • Serial Number

    33417

  • Course Number

    Chem5127

  • Course Identifier

    223 U1170

  • No Class

  • 3 Credits

  • Elective

    DEPARTMENT OF CHEMISTRY / DIVISION OF CHEMICAL BIOLOGY / DIVISION OF CHEMISTRY

      Elective

    • DEPARTMENT OF CHEMISTRY

    • DIVISION OF CHEMICAL BIOLOGY

    • DIVISION OF CHEMISTRY

  • MANUEL MAESTRE-REYNA
  • Wed 8, 9, 10

  • 化217

  • Type 2

  • 60 Student Quota

    NTU 60

  • No Specialization Program

  • English
  • NTU COOL
  • Core Capabilities and Curriculum Planning
  • Notes

    The course is conducted in English。

  • Limits on Course Adding / Dropping

    • Restriction: juniors and beyond and Restriction: within this department (including students taking minor and dual degree program)

  • NTU Enrollment Status

    Enrolled
    0/60
    Other Depts
    0/0
    Remaining
    0
    Registered
    0
  • Course Description
    In this course, students will get an introduction to the principles of 3D structures of proteins, which underlie all protein function, as well as the techniques used to obtain and analyze protein structures. There will be a strong emphasis on protein dynamics as well, i.e. how protein structural flexibility permits enzymatic/receptor/structural activity. Finally, there will be a strong hands-on experience for all students, with in-silico analysis of protein structure, motion and activity.
  • Course Objective
    Students who successfully pass this course will have an overview of the field of protein biophysics and structure, with a strong emphasis on practical analysis and structural evaluation.
  • Course Requirement
    Students shouldbring a virtualbox-compatible computing device (windows, mac x386, and linux work, not sure about mac ARM, iOS or Android), with virtualbox installed (https://www.virtualbox.org/wiki/Downloads). I will provide a virtual machine with all required software for students to work during the practical part of the course.
  • Expected weekly study hours before and/or after class
    For every hour of class, I expect students to have to review the materials for another hour.
  • Office Hour
    Thu15:00 - 17:00
  • Designated Reading
    No overall designated reading, but for every class a list of references will be provided.
  • References
  • Grading
    30%

    Midterm

    midterm exam will evaluate the progress of the students through the class

    30%

    Final

    A final exam will evaluate the progress of the students through the class. Here ALL topics of the class will be asked, not only the second half.

    30%

    Projects

    During class, students will be asked to solve exercises regarding protein structure in motion. They will also be asked to evaluate structure quality, process data from different sources, etc. Students will then be asked to present their results to the rest of the class, for which they will be evaluated. Importantly, they will not be evaluated on the correctness of their analysis, but on creativity and the capacity to come up with reasonable results based on the provided data

    10%

    Participation

    Beyond projects, students will also be asked to participate regularly during class. Importantly, participation will NEVER decrease a student's overall grade, but will only improve it. Thus, enthusiastic students can look forwards to a bump in their grades, while shy students can be assured that their performance will not be affected by lack of participation.

    1. NTU has not set an upper limit on the percentage of A+ grades.
    2. NTU uses a letter grade system for assessment. The grade percentage ranges and the single-subject grade conversion table in the NATIONAL TAIWAN UNIVERSITY Regulations Governing Academic Grading are for reference only. Instructors may adjust the percentage ranges according to the grade definitions. For more information, see the Assessment for Learning Section。
  • Adjustment methods for students
  • Make-up Class Information
  • Course Schedule
    2025/09/03Week 1Introduction, installation of virtual machines, playing with structures
    2025/09/10Week 2The hierarchy of protein structure I: Overview and the nature of amino-acids
    2025/09/17Week 3The hierarchy of protein structure II: Secondary and Tertiary structure
    2025/09/24Week 4Protein folding: Anfinsen boxes and folding dynamics
    2025/10/1Week 5Water I
    2025/10/8Week 6Water II and the hierarchy of protein structure III: Quaternary structure
    2025/10/15Week 7The molecular and thermodynamic basis of cooperativity
    2025/10/22Week 8Midterm
    2025/10/29Week 9In silico protein structure: Molecular Dynamics & Alphafold
    2025/11/05Week 10Introduction to protein structural techniques: CryoEM and NMR
    2025/11/12Week 11X-ray crystallography I: Theory of diffraction
    2025/11/19Week 12X-ray crystallography II: Data Acquisition and Structure Refinement
    2025/11/26Week 13Introduction to time-resolved crystallography: a new era in protein dynamics
    2025/12/03Week 14Time-resolved analysis of protein structure: 3D movies of proteins at work
    2025/12/10Week 15Time-resolved analysis of protein structure: the intersection between quantum chemistry and protein folding
    2025/12/17Week 16Final