Biochemistry 4420A: Molecular Biology of ProteinsFall Term, 2019

Course ObjectiveBiochemistry is a discipline that is focussed on achieving a molecular-level understanding of how macromolecules function in biological systems. Proteins are often represented in textbooks and scientific literature as various simple shapes. For example, the MAP kinase signalling pathway can be illustrated as follows:

Cartoon diagrams with squares, circles, or triangles representing proteins can illustrate the connections between molecules in a pathway; however these diagrams offer little information about what is actually happening at an atomic and molecular level. For example, it is not clear why certain mutations in the receptor tyrosine kinase (RTK) can cause it to signal in an unregulated and inappropriate manner. Other questions concern the nature of the interactions that result in "activation" of signalling molecules. For example, in the diagram above, how does the interaction between the RTK and RAS allow RAS to activate RAF?

For a biochemist, diagrams such as the one above are unsatisfying because they do not explain why or how these processes take place at the molecular level. Characterization of events at the molecular level allows one to understand why certain ligands or mutations have particular effects. Knowledge of the molecular structure, chemistry and driving forces facilitates drug design and discovery, and opens the door for molecular engineering.

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Given the very large number of protein-mediated interactions, processes, and pathways in living systems, it is daunting to consider actually being able to understand them all at a detailed molecular level. The good news is that we have sufficient knowledge of how proteins work that their functions can be framed and understood using general principles. The aim of this course is to uncover and discuss the general principles that govern protein structure, folding, and stability; their interactions with other molecules; their ability to catalyze complex chemical reactions; and their biogenesis and degradation.

Activation of ParkinParkin is an E3 ubiquitin ligase that ubiquitinates outer mitochondrial proteins. Parkin adopts an auto-inhibited state that can be converted to an activated form by phosphorylation of the ubiquitin-like (Ubl) domain and binding of the E2-ubiquitin complex, UbcH7-Ub. This activation is shown in cartoon format at the top of the figure. The crystal structure of auto-inhibited Parkin is shown below: the effects of phosphorylation and binding of UbcH7-Ub have been investigated using hydrogen-deuterium exchange and NMR spectroscopy. The figure is adapted from Condos et al. (2018) Synergistic recruitment of UbcH7-Ub and phoshporylated Ubl domain triggers parkin activation. EMBO J 37:e10001.

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Schedule and Lecture OutlineRoom & Time: Medical Sciences DSB 2016 on Tuesdays and Thursdays, 9:30 AM

 Date Topic InstructorSeptember 5 Course Introduction Shilton

Section 1 Protein Folding, Stability, and Interactions

September 10 Protein Folding & Misfolding I Choy

September 12 Protein Folding & Misfolding II Choy

September 17 Folding Pathways and Kinetics Choy

September 19 Protein Stability Choy

September 24 Intrinsically disordered proteins Choy

September 26 Protein-Protein Interactions Choy

 Section 2 Protein Dynamics and Allostery

October 1  Ligand Binding and Conformational Change Shilton

October 3 Driving Forces: Enthalpy and Entropy in Binding Shilton

October 8 The Conformational Ensemble Shilton

October 11 Energy and the Boltzmann Distribution Shilton

October 15 Introduction to Dynamics: Timescales and Energy Barriers Shilton

October 17 Hemoglobin: Introduction to Cooperativity Shilton

October 22 Allostery and Cooperativity in Hemoglobin Shilton

October 24 Transmembrane Signalling by Receptor Tyrosine Kinases Shilton

October 29 Binding of Imatinib to the Src and Abl Kinases Shilton

October 31 Evolutionary and Molecular Origins of Imatinib Specificity Shilton

November 5,7 Fall Reading Week

November 12 Dynamics in Enzyme Catalysis I Shilton

November 14 Dynamics in Enzyme Catalysis II Shilton

 Section 3

November 19 The Discovery of Ubiquitin Shaw

November 21 Functions of Ubiquitination and Related Modifications Shaw

November 26 The N-End Rule Shaw

November 28 The Ubiquitin Conjugation System - Part 1 Shaw

December 3 The Ubiquitin Conjugation System - Part 2 Shaw

December 5 UbiquitinationandNeurologicalDiseases Shaw

TBA FinalExam

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Instructors

Regular office hours are not scheduled. For questions or discussion, students should contact the instructors or teaching assistant to arrange an appointment. The teaching assistant will schedule office hours in the weeks prior to assignment due dates.

Course Work and EvaluationThe course covers the chemistry and molecular biology of proteins. The first section delivered by Dr. Choy is focused on protein structure and stability, and the chemistry of protein folding and protein-protein interactions. Included in this section are discussions of proteins that are intrinsically disordered, and diseases associated with protein mis-folding. The second section, delivered by Dr. Shilton, will explore the nature of protein dynamics and the role of dynamics in binding, catalysis, and allostery. The third section by Dr. Shaw will cover post-translational modifications, in particular ubiquitination, and their roles in protein function and neurological disease. There will be two assignments that provide an opportunity to work through problems and literature related to the course material. The third assignment will be a group-based production of a short video that will illustrate, in a simple, compelling, and entertaining (hopefully!) manner, a key concept from the course. The final exam will cover the material from the entire course.

Late AssignmentsA 5% penalty per day will be applied in the case of late assignments. Once the solutions to the assignment have been posted, the assignment will no longer be accepted for grading.

If a student misses an assignment deadline as a result of a self-reported absence, the revised deadline for that student will be 48 hours after the end of their self-reported absence.

Instructor Location & Hours E-mail Web Site

Dr. Brian Shilton (Course Coordinator) Medical Sciences Rm 332 Dr. Brian Shilton Shilton

Dr. James Choy Medical Sciences Rm 302 Dr. James Choy Choy

Dr. Gary Shaw Medical Sciences Rm 306 Dr Gary Shaw Shaw

David Wright(Teaching Assistant) Medical Sciences Rm 362 David Wright

Task Particulars and Start Date Date Due  Percent

Assignment #1 Video Assignment - September 12 November 28 20

Assignment #2 1st Half of Course - October 8 October 22 20

Assignment #3 2nd Half of Course - November 21 December 5 20

Final Exam Whole Course TBA 40

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Course MaterialsThere is no single text that provides adequate coverage of the course material, however much of the material is nicely covered in the following chapters of two recent books:

The Molecules of Life (John Kuryan, Boyana Konforti, David Wemmer)Chapter 4 Protein Structure 4.1 - 4.44Chapter 10 Chemical Potential and the Drive to Equilibrium 10.19 - 10.29Chapter 12 Molecular recognition 12.1 - 12.11Chapter 13 Specificity of macromolecular recognition 13.10 - 13.21Chapter 14 AllosteryChapter 18 Folding 18.1-18.12, 18.17-18.22

How Proteins Work (Mike Williamson)Chapter 4 Protein Interactions in vivo 4.3 and 4.5 Chapter 6 Protein Flexibility and Dynamics

Proteins: Concepts in Biochemistry (Paulo Almeida)Chapter 1 Statistical Thermodynamics of Biological MacromoleculesChapter 6 Binding, Allostery, and Cooperativity.

These texts will be on reserve at the Taylor Library and can be purchased as electronic or hard-copy versions from the Garland Publishing web site (http://www.garlandscience.com/) . A less costly alternative than purchasing the whole books would be to rent the electronic versions, or purchase individual chapters for $9 each. To purchase individual chapters, search for the book under “Products” and you’ll find a list of options when you follow the title link.

Additional reading material will be specified by the instructors and put on reserve in the library if not available through the internet. Alternatively, material will be made available through the 4420A Owl site.

The following books on protein structure and function will be put on reserve:1. The Molecules of Life by John Kuriyan (2013)2. How Proteins Work by Mike Williamson (2012).3. Proteins: Concepts in Biochemistry by Paulo Almeida (2016)4. Proteins: Structures and Molecular Properties, by Thomas E Creighton (1993).5. Structure and Mechanism in Protein Science: a guide to enzyme catalysis and protein folding, by Alan

Fersht (1999). 6. Protein Structure and Function by Gregory Petsko and Dagmar Ringe (2004).

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Additional Information and Statements

RequisitesPrerequisite(s): Biochemistry 3381ASenate regulation regarding the student’s responsibility regarding requisitesUnless you have either the requisites for this course or written special permission from your Dean to enrol in it, you may be removed from this course and it will be deleted from your record. This decision may not be appealed. You will receive no adjustment to your fees in the event that you are dropped from a course for failing to have the necessary prerequisites.

EvaluationA detailed and comprehensive set of regulations concerning the scheduling of tests, assignments, etc. is available at: http://www.uwo.ca/univsec/academic_policies/examinations.html

Policy on the Rounding and Bumping of Marks Across the Basic Medical Sciences Undergraduate Education programs and within the Department of Biochemistry we strive to maintain high standards that reflect the effort that both students and faculty put into the teaching and learning experience during this course. All students will be treated equally and evaluated based only on their actual achievement. Final grades on this course will be rounded to the nearest integer (e.g., a 74.4 becomes a 74 and 74.5 becomes a 75). Marks WILL NOT be bumped to the next grade or GPA level (e.g., a 79 will NOT be rounded up to an 80). The mark attained is the mark you achieved and the mark assigned; requests for mark “bumping” will be denied.

Student ConductWestern’s Code of Student Conduct (see https://www.uwo.ca/univsec/pdf/board/code.pdf) prohibits assault, harassment, intimidation, threats, or coercion, as well as discrimination based on grounds including race, ethnic origin, sex, sexual orientation, gender identity, and disability. Students in this course are expected to speak and act in ways that maintain an environment in which all people feel safe and respected.

Cell Phone and Electronic Device PolicyThe Schulich School of Medicine & Dentistry is committed to ensuring that testing and evaluation are undertaken fairly across all our departments and programs. For all tests and exams, it is the policy of the School and the Department of Biochemistry that any electronic devices, i.e., cell phones, tablets, cameras, or iPod are strictly prohibited. These devices MUST be left either at home or with the student’s bag/jacket at the front of the room and MUST NOT be at the test/exam desk or in the individual’s pocket. Any student found with one of these prohibited devices will receive a grade of zero on the test or exam. Non-programmable calculators are only allowed when indicated by the instructor. The Department of Biochemistry is not responsible for stolen/lost or broken devices.

Academic OffensesScholastic offences are taken seriously and students are directed to read the appropriate policy, specifically, the definition of what constitutes a Scholastic Offence, at the following website: http://www.uwo.ca/univsec/pdf/academic_policies/appeals/scholastic_discipline_undergrad.pdf.

All required assignments may be subject to submission for textual similarity review to the commercial plagiarism detection software under license to the University for the detection of plagiarism. All assignments submitted for such checking will be included as source documents in the reference database for the purpose of detecting plagiarism of papers subsequently submitted to the system. Use of the

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service is subject to the licensing agreement, currently between The University of Western Ontario and Turnitin.com (http://www.turnitin.com).

Plagiarism is defined as misappropriation of another person's language, thoughts, ideas, or expressions and the presentation of these as one's original work. Plagiarism is a serious academic offence. To avoid plagiarism:1. Always write using your own thoughts and language - do not paraphrase or copy text from the

published literature or your peers. Having the published literature close at hand when answering questions or writing an essay can lead to inadvertent inclusion of paraphrased or verbatim text from the published source. To avoid this problem, assignments should be completed using your own short notes or outline.

2. Communication and discussion with peers is encouraged, but a submitted assignment must consist only of your own work.

3. If it is necessary to use text verbatim from a published source, ensure that it is clearly identified using quotations and/or indentations, and properly referenced.

4. Use your own original artwork and/or figures. In rare cases when it may be necessary to use published figures or artwork, then permission from the publisher is required, along with proper referencing.

Copyright MaterialsCourse material produced by faculty is copyrighted and to reproduce this material for any purposes other than your own educational use contravenes Canadian Copyright Laws. This includes the lectures themselves, which may be recorded but may not be posted.

Absence from Course CommitmentsAcademic Consideration for Student AbsencesIf you are unable to meet a course requirement due to illness or other serious circumstances, you must seek approval for the absence as soon as possible. Approval can be granted either through a self-reporting of absence or via the Academic Counselling Office of the Faculty of Science located in NCB 280, and can be contacted at scibmsac@uwo.ca .

NEW!! For further information, please consult the university’s policy on academic consideration for student absences as there are updates to the academic consideration procedures. https://www.uwo.ca/univsec/pdf/academic_policies/appeals/Academic_Consideration_for_absences.pdf

The policy on Accommodation for Religious Holidays can be found here:http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_religious.pdf

A. Absence for medical and non-medical reasons:Students must familiarize themselves with the Policy on Accommodation for Medical Illness for Undergraduate Students, located at: http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_medical.pdf

A Western Student Medical Certificate (SMC) is required when a student is seeking academic accommodation. This documentation should be obtained at the time of the initial consultation with the physician/nurse practitioner or walk-in clinic. http://www.uwo.ca/univsec/pdf/academic_policies/appeals/medicalform.pdf

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Medical/Compassionate Relief Program PolicyIt is current policy that students who are unable to write a test or examination or other form of course evaluation are required to obtain a medical certificate that is taken to the Academic Counselling Office, NCB 280 (for Science and Basic Medical Science students) or to your appropriate Home Faculty Counselling Office. In the case of an unexpected absence on compassionate grounds, documentation is also requested. Such documentation must be submitted by the student directly to the Academic Counselling office and not to the instructor. An academic counsellor in that office will review and either approve or deny the accommodation request. It will be the Academic Counselling office that will determine if accommodation is warranted. This policy applies to all forms of assessment, including evaluations that are less than 10%.

Statement from the Academic Counselling Office, Faculty of Science (for Science and BMSc students):If you are unable to meet a course requirement due to illness or other serious circumstances, you must provide valid medical or other supporting documentation to the Academic Counselling Office as soon as possible and contact your instructor immediately. It is the student's responsibility to make alternative arrangements with their instructor once the accommodation has been approved by the Academic Counselling Office and the instructor has been informed.

C. Special Examinationshttp://www.uwo.ca/univsec/pdf/academic_policies/exam/definitions.pdf

A Special Examination is any examination other than the regular final examination, and it may be offered only with the permission of the Dean/Academic Counselling Office of the Faculty in which the student is registered, in consultation with the instructor and Department Chair. Permission to write a Special Examination may be given on the basis of compassionate or medical grounds with appropriate supporting documents. You may also be eligible to write the Special Examination if you are in a “Multiple Exam Situation”. See: http://www.registrar.uwo.ca/examinations/exam_schedule.html

A Special Examination must be written at the University or an Affiliated University College no later than 30 days after the end of the examination period involved. To accommodate unusual circumstances, a date later than this may be arranged at the time permission is first given by the Dean/Academic Counselling Office of the Faculty. The Dean/Academic Counselling Office will consult with the instructor and Department Chair and, if a later date is arranged, will communicate this to the Office of the Registrar.

If a student fails to write a scheduled Special Examination, permission to write another Special Examination will be granted only with the permission of the Dean/Academic Counselling Office in exceptional circumstances and with appropriate supporting documents. In such a case, the date of this Special Examination normally will be the scheduled date for the final exam the next time the course is offered.

When a grade of Special (SPC) or Incomplete (INC) appears on a student's record, the notations will be removed and replaced by a substantive grade as soon as the grade is available.

Support Services:

Academic Counselling (Science and Basic Medical Sciences): http://www.uwo.ca/sci/counselling

Accessibility: Please contact the course instructor if you require material in an alternate format or if you require any other arrangements to make this course more accessible to you. You may also wish to contact Services for Students with Disabilities (SSD) at 661-2111 x 82147 for any specific question

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regarding an accommodation. The policy on Accommodation for Students with Disabilities can be found here: https://www.uwo.ca/univsec/pdf/academic_policies/appeals/Academic%20Accommodation_disabilities.pdf

Student Development Centre (SDC): Learning-skills counsellors at SDC are ready to help you improve your learning skills. They offer presentations on strategies for improving time management, multiple-choice exam preparation/writing, textbook reading, and more. Individual support is offered throughout the Fall/Winter terms in the drop-in Learning Help Centre, and year-round through individual counselling. http://www.sdc.uwo.ca

Mental Health: Students who are in emotional/mental distress should refer to Mental Health@Western for a complete list of options about how to obtain help. http://www.health.uwo.ca/mental_health

Student Health Services: https://www.uwo.ca/health/shs/index.htmlAdditional student-run support services are offered by the USC, http://westernusc.ca/services

OWLOWL has a help site at https://owlhelp.uwo.ca/ that has information on using OWL as well as contact information for ITS support.

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