1. Macromolecular Structure: Introduction
Andy Howard Biology 555, Fall 2018
21 August 2018

2. Macromolecular Structure
This course is intended to familiarize you with the methods and the results associated with the structures of biological macromolecules.
We will look at several methods at varying levels of detail
We hope to leave you with an awareness of structural realities—this is not just a methods course
08/21/2018
Macromolecular Structure: Introduction

3. Macromolecular Structure: Introduction
Who are we?
I’m a protein crystallographer, so the extended period we spend talking about crystallography is from my own domain
Tom Irving is a physiologist and biophysicist, and is adept at building teams to do excellent science using SAXS and other techniques
Joseph Orgel is a fiber diffractionist and a world leader in connective tissue
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Macromolecular Structure: Introduction

4. Macromolecular Structure: Introduction
How this course fits in
To some degree this course is intended as the apex of the molecular biochemistry & biophysics graduate program
But it’s also a valuable elective for students in biochemistry and cell & molecular biology
It approaches biochemical issues without flinching at the rigor brought out through physics, particularly in terms of methods
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Macromolecular Structure: Introduction

5. How does this course help you?
If you’re a cell biologist, molecular biologist, or biochemist, you’re eventually going to need macromolecular structural information
This course will help you obtain that or at least read the literature with a critical eye
It will enable you to compare methods and choose tools that are appropriate to the problem you’re trying to address
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Macromolecular Structure: Introduction

6. Macromolecular Structure: Introduction
The Team
Andrew Howard: course manager and macromolecular crystallography
Tom Irving or Srinivas Chakravarthy: solution scattering
Likely Guest lectures: Grant Bunker (XAFS), Jeff Wereszczynski (simulations), Joseph Orgel (fiber crystallography)
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Macromolecular Structure: Introduction

7. Structure and function
The reason we care about macromolecular structure is that it clarifies function
If we know the structure of a macromolecule (protein or nucleic acid), we can:
Figure out how it does what it does if we already had an idea of its function
Determine its function if we don’t already know it
Once we recognize function, we can use it to deepen understanding or design drugs
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Macromolecular Structure: Introduction

8. Schedule: generalities
Full schedule is on the Blackboard site
We won’t make major adjustments in the schedule after the first week, although there will be minor shifts
As of this moment it’s pretty vague, though
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Macromolecular Structure: Introduction

9. Macromolecular Structure: Introduction
Schedule: specifics
Today: Fundamentals of protein structure
Thursday: Finish structure fundamentals, and then: biophysical mathematics
then: scattering and diffraction
see the Blackboard site for the rest
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Macromolecular Structure: Introduction

10. Macromolecular Structure: Introduction
Grading
This is a real graduate class, and we want the evaluation to be individualized
1/3 based on homework assignments that grow out of the lectures
1/3 based on a take-home final
1/3 based on three papers you’ll write
You may work together on homework but what you hand in must be your own
Final must be individual: cheating will not be tolerated
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Macromolecular Structure: Introduction

11. Macromolecular Structure: Introduction
Goals & Objectives
Recognize how the various methods work
Recognize which methods provide the particular kinds of information we seek
Know primary, secondary, tertiary, and quaternary structure elements in proteins and nucleic acids
Recognize the significance of mobility and dynamics in macromolecular structure and function
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Macromolecular Structure: Introduction

12. Macromolecular Structure: Introduction
What you need to know
Complex numbers, Fourier transforms, statistics
Protein structure elements
Central dogma
Role of solvent in macromolecules
Remember: macromolecules aren’t static
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Macromolecular Structure: Introduction

13. Lecture 1: General Principles of Macromolecular Structure
These lecture notes are a heavily modified form of what was originally a Tom Irving lecture
Macromolecules include proteins, RNA, DNA, and polysaccharides
What are some general rules governing macromolecular structure?
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Macromolecular Structure: Introduction

14. Macromolecular Structure: Introduction
What's a molecule?
Stoichiometry (chemical formula)
Bonds and symmetry
Not easily dissociated
Molecular identity depends on geometry, not just its chemical formula
Aldohexose sugars C6H12O6 : 16 = 24 possible stereoisomers
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Macromolecular Structure: Introduction

15. What’s a macromolecule?
A large molecule
Macromolecules are polymers of > ~50 residues
"Residue" = amino acid, nucleic acid base, sugar moiety i.e. monomers
Arbitrary distinction:
Fewer than residues is an oligomer
More than residues is a polymer
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Macromolecular Structure: Introduction

16. Size & complexity of biopolymers
Class
Example
Size
Molecular Weight
Subunit type
# of subunits
Oligomer
Actinomycin D
20Å sphere
Atoms /residues
102 / 10
Small proteins
Chymotrypsin
40Å sphere
amino acid residues
Nucleic acids
mRNA
100Å rod
nucleo-tides
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Macromolecular Structure: Introduction

17. Size & Complexity, concluded
Class
Example
Size
Molecular Weight
Subunit type
# of subunits
Large proteins
ATCase
70Å sphere
Subunits / chains
10-100
Small assemblies
Ribosome
200Å sphere
Large assemblies
Membranes, viruses
1000Å sphere
Com-ponents
Intact DNA
E.coli DNA
0.1cm rod
Genes
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Macromolecular Structure: Introduction

18. Hierarchy of Structural Levels
Primary structure
Linear sequence of monomers in macromolecule
Secondary structure
Local 3-D Structure
Defined primarily by main-chain H-bonds
Tertiary Structure
Global 3-D structure -”Fold”
Quaternary structure
Spatial arrangement of multiple polymeric chains.
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Macromolecular Structure: Introduction

19. Macromolecular Structure: Introduction
4 Levels
Secondary structures defined by main-chain hydrogen bonds and (possibly) disulfides
Tertiary and quaternary structures involve many H-bonds, van der Waals contacts
Image courtesy Wikimedia
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Macromolecular Structure: Introduction

20. Structure vs Structural Models
Cannot generally "see" a molecule
Biophysical techniques allow construction of "models" of molecular structure
Models may be very schematic
Block diagrams of various domains
Or detailed atomic "structures" from X-ray crystallography or 3-D NMR
A list of atomic coordinates
Should not be confused with "real thing"
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Macromolecular Structure: Introduction

21. Structural models, continued
So we need to be conscious of the deficiencies in our models
We also need to recognize that our visual representation of that model can be deficient
Often what we leave out of our visual representation is as important as what we include!
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Macromolecular Structure: Introduction

22. Macromolecular Structure: Introduction
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Macromolecular Structure: Introduction

23. Macromolecular Structure: Introduction
The "Folding Problem"
Primary structure contains all necessary information to determine tertiary structure
How does it get there?
How can we predict tertiary structure from primary structure?
Intense area of research
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Macromolecular Structure: Introduction

24. A subtle definitional issue
The folding problem as defined on the previous slide is the traditional one
An alternative is to emphasize the dynamics of protein folding:
How does the unique 3-D structure arise in the cell?
Probably it isn’t properly folded the moment it emerges from the ribosome
Presumably there are forces that direct the protein into its final conformation
So make sure your listeners know which definition you’re using!
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Macromolecular Structure: Introduction

25. Prominent secondary structures
 helix antiparallel  sheet polyproline helix
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Macromolecular Structure: Introduction