Biochemistry and Molecular Biology
Penn State Science
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BMMB 531: Biomolecular Structure

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BMMB 531: Biomolecular Structure                                Spring 2017

Course Objective                   To understand the methods used to determine macromolecular structure at atomic resolution and to understand how the three-dimensional structures of bio-molecules relate to their function.

Location and Time                    010 Life Sciences Bldg, Wed & Fri 4:40 - 5:30 p.m.

Lecturers                                 
Dr.
Hemant Yennawar email:  hpy1@psu.edu
8 Althouse Laboratory                     814-865-8383

Dr. Song Tan email:  sxt30@psu.edu
468A North Frear Laboratory          814-865-3351

Secretary                           
Lorraine Grattan                           email:  lul4@psu.edu
107 Althouse Laboratory                814-863-4655

Office Hours                             Drs. Yennawar and Tan are usually available from 9 a.m. to 5 p.m. in their offices.  Feel free to stop by, preferably with an appointment.

Required Texts                       Crystallography Made Crystal Clear
by Gale Rhodes, 3rd edition, 2006, Academic Press

Introduction to Protein Structure
by Carl Branden and John Tooze, 2nd edition, 1999, Garland Publishing

Web Site (ANGEL)                http://cms.psu.edu

Evaluation                              The course grade will be based primarily on performance on the two written tests and student presentations. The test on Mar 1st will cover the first half of the course, while the one on Apr 28th will cover only the second half of the course.

Group study                            Working in groups on problem sets is not only permitted, but also encouraged.

Make-up Examinations       Make-up exams will be given without penalty only when documentation of hospitalization, death in the family, or other emergency is provided.
If you have an emergency that necessitates your leaving campus immediately, you should contact the Assistance and Information Center in the HUB (814-863-2020). Counselors at the Center will get the relevant information and, with your permission, pass it along to academic departments in which you are taking courses.

Calculators                              Non-programmable scientific calculators may be used during examinations and quizzes.  Graphing calculators, handheld computers and laptops may not be used.

Course Modification             The syllabus is only a guideline. Although we plan to follow this syllabus closely, we may make changes in either the schedule or evaluation procedure.

The Eberly College of Science Code of Mutual Respect and Cooperation (www.science.psu.edu/climate/Code-of-Mutual-Respect final.pdf) embodies the values that we hope our faculty, staff, and students possess and will endorse to make The Eberly College of Science a place where every individual feels respected and valued, as well as challenged and rewarded.

The Eberly College of Science is committed to the academic success of students enrolled in the College's courses and undergraduate programs. When in need of help, students can utilize various College and University wide resources for learning assistance:  http://www.science.psu.edu/advising/success

Penn State welcomes students with disabilities into the University's educational programs. If you have a disability-related need for reasonable academic adjustments in this course, contact the Office for Disability Services (ODS) at 814-863-1807 (V/TTY). For further information regarding ODS, please visit the Office for Disability Services Web site at http://equity.psu.edu/ods/. In order to receive consideration for course accommodations, you must contact ODS and provide documentation (see the documentation guidelines at http://equity.psu.edu/ods/guidelines/documentation-guidelines). If the documentation supports the need for academic adjustments, ODS will provide a letter identifying appropriate academic adjustments. Please share this letter and discuss the adjustments with your instructor as early in the course as possible. You must contact ODS and request academic adjustment letters at the beginning of each semester.”

Reading
1/11 X-rays, safety issues, production, different sources of X-rays Rhodes:  Chapter 4
1/13 Crystals, unit cells, orthogonal and fractional coordinates, symmetry Rhodes:  Chapter 3
1/18 Symmetry elements, non crystallographic symmetry (NCS)
1/20 Crystal mounting, data collection, Bragg's law, Miller indices
1/25 Ewald construction, unique data, space group determination
1/27 Data processing/corrections, periodic functions Rhodes:  Chapters 2, 5
2/1 Diffraction Rhodes:  Chapter 5
2/3 Matthew's coefficient, Molecular replacement Rhodes:  Chapter 6
2/8 Structure refinement Rhodes:  Chapter 7
2/10 Multiple isomorphous refinement (MIR) Rhodes:  Chapter 6
2/15 Multiwavelength Anomalous Dispersion (MAD) Rhodes:  Chapter 6
2/17 Computer Programs Rhodes:  Chapter 11
2/22 Review session  (reading published papers and how to judge crystal structures)
2/24 Tour of X-ray facility (some hands-on activity)
3/1 Exam 1
3/3 Atomic Forces & Amino Acids structure and function Branden&Tooze:  Chapter 1
3/8 Spring Break
3/10 Spring Break
3/15 Secondary structure, domains and motifs Branden&Tooze:  Chapter 2
3/17 Protein structure, Protein sizes Branden&Tooze:  Chapter 3
3/22 Protein folding and flexibility Branden&Tooze:  Chapter 6
3/24 Enzymes and substrates:  Serine proteinases Branden&Tooze:  Chapter 11
3/29 Signal Transduction:  Ras and Ga Branden&Tooze:  Chapter 13:251-261
3/31 Signal Transduction:  Gb and trimeric G complex Branden&Tooze:  Chapter 13:261-280
4/5 Immune System:  Fab and IgG Branden&Tooze:  Chapter 15:299-312
4/7 Immune System:  MHC complexes Branden&Tooze:  Chapter 15:312-321
4/12 Protein/DNA interactions: DNA structure, Helix-turn helix motif Branden&Tooze:  Chapters 7, 8
4/14 Protein/DNA interactions: TBP, TFIIA, Zinc fingers, Leucine zippers Branden&Tooze:  Chapters 9, 10
4/19 Protein/DNA interactions: nucleosome core particle Nature 389:251-260, 1997
4/21 Student Presentations
4/26 Protein structure prediction and engineering Branden&Tooze:  Chapter 17
4/28 Exam 2

 

Academic Integrity Policy In an examination setting, unless the instructor gives explicit prior instructions to the contrary, violations of academic integrity shall consist of any attempt to receive assistance from written or printed aids, from any person or papers or electronic devices, or of any attempt to give assistance, whether the student doing so has completed his or her own work or not. Other violations include, but are not limited to, any attempt to gain an unfair advantage in regard to an examination, such as tampering with a graded exam or claiming another's work to be one's own. Failure to comply will lead to sanctions against the student in accordance with the Policy on Academic Dishonesty in the Eberly College of Science at http://www.science.psu.edu/academic/Integrity/Policy.htm.

Course objectives for BMMB531:  Biomolecular Structure

Objective 1 Structural Methods        Students will understand the various concepts in X-ray crystallography, including what are X-rays, and crystals, how the two interact to yield X-ray diffraction data which in turn leads to solving the crystal structure to atomic detail.

Learning Outcomes

Students will know:

1.     what are X-rays, how they are produced in different ways –locally and at synchrotrons, and how to use them safely

2.     different techniques to grow crystals of macro-molecules like proteins, what is crystal quality and how to improve it

3.    anatomy of crystals i.e. unit cell or building blocks and the symmetry elements in the crystal –and how to obtain this

information

4.    what is X-ray diffraction, Bragg’s law and how to collect diffraction data on a crystal

5.    what is Friedel’s law, concept of reciprocal lattice, and Ewald construction to understand diffraction in reciprocal

space

6.    Miller indices and resolution of X-ray data as a function of crystal quality, X-ray data processing

7.    how to estimate number of molecules in the asymmetric unit of the crystal or Matthew’s coefficient

8.    solving the crystal structure with help of a related known structure and obtaining initial electron-density maps.

9.    refining the crystal structure to an acceptable level, and how to eliminate bias in the structure

10.    other techniques e.g. MIR and MAD to solve crystal structure when a related structure is not available (as in step 8

above)  and the need to collect X-ray data at synchrotron

11.   various computer programs used for calculations and graphics to visualize the crystal structure

12.   various terminology used in crystallography and thereby be able to read and critically evaluate published reports

13.   –students will also get to experience some hands-on activity in the laboratory with exposure to X-ray

instrumentation, crystallization robot etc.

Objective 2 Structure & Function     Students will understand key concepts in biomolecular structure including the forces responsible for protein and DNA structures, common biomolecular structural motifs and how biological macromolecules interact with each other.

Learning Outcomes

Students will be able to:

1.     use molecular graphics software such as PyMOL to visualize any biological macromolecule

2.     obtain molecular coordinates from the Protein Data Bank (PDB) for a biological macromolecule

3.     identify the atomic forces involved in biomolecular structure

4.     identify and describe the 20 amino acids

5.     identify and explain protein secondary structure, and its relationship to protein tertiary structure

6.     explain the difference between domains and motifs

7.     identify and discuss common protein domains and motifs

8.     estimate protein sizes given protein molecular weights

9.     explain how protein structure relates to enzyme function using serine proteases as an example

10.  identify and describe Ras and Ga signal transduction molecules

11.  identify and describe trimeric G protein signal transduction molecules, including the interactions between G protein component molecules

12.  explain how the structure of signal transduction molecules relate to their biological function

12.  identify and describe the immunoglobulin fold

13.  explain the structure and function of IgG molecules in terms of the constituent immunoglobulin folds

14.  explain the structure and function of MHC (major histocompatibility complex) immunoglobulin molecules

15.  identify and describe the 4 DNA and RNA bases

16.  explain DNA secondary structure, including dimensions for DNA double helices

17.  identify geometric parameters used to describe DNA structure

18.  describe different DNA binding motifs and how their structure relate to their biological function

19.  understand terminology used to describe elements of chromatin

20.  describe and explain the histone fold motif and how this motif relates to the structure of the nucleosome core particle

21.  provide a 5-10 min presentation using molecular graphics to illustrate a biological macromolecule

22.  understand basics of protein structure prediction and protein engineering

23.  read, understand and critically evaluate any macromolecular structure paper