BME-456-davidlin-2026-09-17-12-48-04
Title of Course: Protein Engineering
Prefix and Number: BME 456
Semester and Year: tbd
Number of Credit Hours: 3
Prerequisites: BME 321 with C or better
Course Details
Day and Time: tbd
Meeting Location: tbd
Instructor Contact Information
Instructor Name: tbd
Instructor Contact Information: tbd
Instructor Office Hours: tbd
TA Name: tbd
TA Contact Information: tbd
TA Office Hours: tbd
Course Description
Integrating molecular biology and engineering sciences to analyze, change, and design the structure and function of proteins.
Course Materials
Books: none
Other Materials: none
Fees: none
|
Course Learning Outcomes (students will be able to:) |
Activities Supporting the Learning Outcomes | Assessment of the Learning Outcomes |
|---|---|---|
|
Describe the fundamentals of protein structure. |
Lecture, project, quiz, test, homework |
Homework, Quiz, Test, Project presentation |
|
Understand structure-function relationship. |
Lecture, project, quiz, test, homework |
Homework, Quiz, Test |
|
Identify and select basic methods for protein structure analysis. |
Lecture, project, quiz, test, homework |
Homework, Quiz, Test |
|
Create protocols for structure analysis. |
Lecture, project, quiz, test, homework |
Homework, Quiz |
|
Design proteins with desirable properties. |
Lecture, project, quiz, test, homework |
Homework, Quiz, Test, Project presentation |
|
Analyze and change protein structures ‘in silico’. |
Lecture, project, quiz, test, homework |
Homework, Quiz, Test, Project presentation |
| Dates | Lesson Topic | Assignment | Assessment |
|---|---|---|---|
|
Week 1 |
Discussion of the syllabus, class organization, assignments Amino acids, their chemical and structural properties, classification Methods to determine and analyze protein sequences |
Quizzes | |
|
Week 2 |
Using programs to visualize protein structure (Chimera) Torsion angles Van der Waals interactions, salt bridges, hydrophobic interactions, hydrogen bonds |
Homework | Homework, quizzes |
|
Week 3 |
Secondary structure elements: a-helices, b-strands, b-turns and random coil Description and examples of tertiary and quaternary structure Intrinsically disordered proteins |
Quizzes | |
|
Week 4 |
Secondary structure prediction Protein modifications |
Homework, project | Homework, quizzes |
|
Week 5 |
Methods to study structure Engineering proteins with new properties (objectives and examples) |
Quizzes | |
|
Week 6 |
DNA-RNA-protein: Project assignments. DNA and RNA composition. Nucleotide pairing Codon tables and codon usage Vectors. Transformation Polymerase chain reaction (PCR) theory Restriction and ligation |
Exam | |
|
Week 7 |
Subcloning and mutagenesis 1: Primer design for subcloning |
Homework, project | Homework, quizzes |
|
Week 8 |
Subcloning and mutagenesis 2: Primer design for point mutagenesis (complementary) |
Quizzes | |
|
Week 9 |
Subcloning and mutagenesis 3: Primer design for point mutagenesis (overlapping) PCR (practical) |
Homework, project | Homework, quizzes |
|
Week 10 |
Using Chimera to change protein structure (in silico mutations) Designing polypeptides, saving as pdb files |
Exam | |
|
Week 11 |
Using AlphaFold to create structures Analysis of AlphaFold results |
Homework, project | Homework, quizzes |
|
Week 12 |
Structure analysis Preparing files for MDS Protocols to run minimization |
Quizzes | |
|
Week 13 |
Run minimization Protocols to run simulations Run simulations |
Homework, project | Homework, quizzes |
|
Week 14 |
MDS results analysis RMSD plots and video |
Project | |
|
Week 15 |
Project presentations. | Project | Project report and presentation |
Expectations for Student Effort
For each hour of lecture equivalent, students should expect to have a minimum of two hours of work outside of class.
Grading
| Type of Assignment (tests, papers, etc) | Points | Percent of Overall Grade |
|---|---|---|
| Homework | 30% | |
| Project | 30% | |
| Quizzes | 5% | |
| Exams | 35% |
| Grade | Percent | Grade | Percent |
|---|---|---|---|
| A |
>92 |
C | 73-76 |
| A- | 90-91 | C- | 70-72 |
| B+ | 87-89 | D+ | 67-69 |
| B | 83-86 | D | 60-66 |
| B- | 80-82 | F | <60 |
| C+ | 77-79 |
Percentage grades will be rounded to the nearest integer value.
Attendance and Make-Up Policy
Students should make all reasonable efforts to attend all class meetings. However, in the event a student is unable to attend a class, it is the responsibility of the student to inform the instructor as soon as possible, explain the reason for the absence (and provide documentation, if appropriate), and make up class work missed within a reasonable amount of time, if allowed. Missing class meetings may result in reducing the overall grade in the class.
Academic Integrity Statement
You are responsible for reading WSU's Academic Integrity Policy, which is based on Washington State law. If you cheat in your work in this class you will:
-Receive a grade of "zero" for the assignment
-Be reported to the Center for Community Standards
-Have the right to appeal my decision
-Not be able to drop the course of withdraw from the course until the appeals process is finished
If you have any questions about what you can and cannot do in this course, ask me.
If you want to ask for a change in my decision about academic integrity, use the form at the Center for Community Standards website. You must submit this request within 21 calendar days of the decision.