BIOMATERIALS:

STRUCTURAL BIOLOGY & DESIGN

CBEMS 119/219
Rowland Hall RH 108, Tu/Th 11:00am-12:20pm

Instructor:
Hung Nguyen, Ph.D.
Email: hdn@uci.edu, Tel: 824-6589
Office: 616E Engineering Tower
Office hours: Th 2:00-3:00pm or by appointment

Syllabus

This course is an introduction to designing biomaterials through assembly by covering basic
concepts in structural biology from physical perspectives. Besides providing a fundamental
background in biochemistry, it also surveys a wide variety of applications using computational
methods to the current biomaterials research fields. The course does not train students to be
expert users of specific computational methods, but train students to appreciate the basic ideas of
computational tools and how these tools are used in the analysis of design processes.

The goal of this course is to equip students from different backgrounds with the following skills
necessary to understand and possibly design molecular simulations to examine self-assembly in
biological systems: (1) formulation of both atomistically detailed and simplified molecular models,
(2) basic algorithms for computing thermodynamic and kinetic behavior, (3) modern analysis
techniques and visualization packages, and (4) physical intuition for developing and interpreting
new simulation experiments.

Student involvement in the classroom is an integral component for this course. Successful
completion of the course will benefit students in the following crucial areas that are often
overlooked in other classes on campus: (a) development of skills to summarize and critique
formal research reports; (b) development of abilities to prepare and present a scholarly subject
professionally in front of a large audience.

Prerequisite: willing to think quantitatively in biology, i.e. comfortable with college mathematics,
physics, and chemistry.

Grading Policy for undergraduate students:

Team presentation, 35%, is a formal presentation of an assigned journal article.
Presentation is set to last for 15 minutes (about 15 slides) and 5 minutes of questions.
Follow your summary outlines (below) to prepare your presentations. Starting on the fifth
week of class, the first half of each meeting consists of lecture while the second half consists
of either one or two presentations; each is given by two students of the same team. Since
the class is divided into three groups, each group presents once a week on either Tuesday
or Thursday. For each presentation, the instructor will select two students and a volunteer
in the audience to ask questions.

Class participation, 10%
 Literature critique, 20%, is a weekly summary of an article assigned for your groups
presentation. The students who are presenting that week are exempt from this assignment.
The summary should highlight the following:

Use 500 words in five paragraphs to answer the following five questions: (1) What is the
motivation of this research? (2) What specific questions did the authors try to answer? (3)
How did the authors address each of those questions? Briefly describe key experiments (or
simulations) and results. (4) What are the conclusions? Are the conclusions sufficiently
supported by the observations and results? (5) What are the limitations of this study? How
could the authors improve this study?

Also, prepare two questions that you can potentially ask the presenters.

Quizzes, 35%, in-class and online, based on textbook reading, lectures, student
presentations and weekly review article.

Grading Policy for graduate students:

Team presentation on a research article and class participation, 30%
Team presentation on a review article, 20%
Literature critique, 20%
Quizzes, 30%

Grades will not be curved. Class attendance is mandatory but you can miss at most two lectures.

Textbook: The Molecules of Life: Physical and Chemical Principles by John Kuriyan, Boyana
Konforti and David Wemmer, Garland Science

Supplementary References: Molecular Modelling by Leach; Covered chapters: 1, 4-9, 10, and 11.
Students are encouraged to explore online for alternative reading materials.

Literature: Historical literature papers are either reviewed in the lecture or assigned each week
for critique and individual presentation starting the fifth week.

Outline: review of chemistry and biochemistry (proteins, DNA/RNA, glycan and lipid),
biomolecular graphics, thermodynamics, molecular mechanics, molecular dynamics, Monte Carlo,
molecular interactions, solvation and electrostatics, free energy. Also, review of currently active
research areas such as folding (protein, DNA/RNA), structure prediction/design, self-assembly
(aggregation/misfolding), ion transport, drug design.

These topics will be covered along with the discussions of selected papers:
Topic Chapter
Introduction to Nucleic Acids and Proteins 1.5-1.22
Interactions between molecules 1.1-1.4, 6.12-6.24
Protein Structure 4.1-4.30
Simulation Methods
Statistical Thermodynamics 7.1-7.25, 8.1-8.14, 9.1-9.10
Free-energy changes in Protein Folding 10.19-10.29, 18.1-18.12
 Nucleic Acid Structure 2.1-2.26, 18.23-18.28
Glycans and Lipids 3.1-3.23, 4.31-4.44