crystallography and storytelling with dataunit cell: smallest repetitive volume which contains the...
TRANSCRIPT
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CRYSTALLOGRAPHY AND STORYTELLING WITH DATA
President, Association of Women in Science, Bethesda Chapter
STEM Consultant
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MY STORY
Passion for Science
BS Biology Major
MS Biotechnology & Project in Bioinformatics fascination with computational biology
PhD in Biochemistry + Protein Crystallography
MBA - Science Management
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CRUX OF MY STORY
Passion for Science
Excelling at what I do
What Next?
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SKILLS COVERED IN THIS PPT
Biochemistry
Molecular biology
Crystallography
Computer Simulations
Creativity in science
Data tools
Storytelling (Communication)
Problem solving
Collaboration
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WHAT IS PROTEIN X- RAY CRYSTALLOGRAPHY?
X-ray crystallography is essentially a form of very high resolution microscopy. It enables us to visualize protein structures at the atomic level and enhances our understanding of protein function. Specifically we can study how proteins interact with other molecules, how they undergo conformational changes, and how they perform catalysis in the case of enzymes. Armed with this information we can design novel drugs that target a particular protein, or rationally engineer an enzyme for a specific industrial process.
Steps :
Protein purification
Crystallization
Data collection
Data analysis
Structure solution
Story telling!
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THE METHOD
Protein Crystals X-rays
diffraction Refined structure
FT FT-1
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TYPES OF MACROMOLECULES 1. Proteins
2. DNA
3. RNA
4. Complexes: protein-protein, protein-DNA/RNA
Lipids, peptides, sugars, etc are categorized as
non macromolecules
Today’s discussion is more focused on protein
molecules
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FOUR LEVELS OF PROTEIN STRUCTURE
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Diffraction from a single molecule is weak, hence we need crystals that
have ordered three-dimensional array of molecules.
A small protein crystal contains a billion molecules.
Need to get great quality single crystals: Multiple trials & persistence !
Protein Crystals
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CRYSTAL SYSTEMS – SOME DEFINITIONAL INFORMATION
7 crystal systems of varying
symmetry are known
These systems are built by
changing the lattice
parameters:
a, b, and c are the edge
lengths
, , and are interaxial
angles
Unit cell: smallest repetitive volume which contains the complete
lattice pattern of a crystal.
a
b
c
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Crystal systems
System Interaxial Axes
Angles
Triclinic ≠ ≠ ≠ 90° a ≠ b ≠ c
Monoclinic = = 90° ≠ a ≠ b ≠ c
Orthorhombic = = = 90° a ≠ b ≠ c
Tetragonal = = = 90° a = b ≠ c
Cubic = = = 90° a = b = c
Hexagonal = = 90°, = 120° a = b ≠ c
Trigonal = = 90°, = 120° a = b ≠ c
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PEPTIDE BOND LENGTHS
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X-RAY DIFFRACTION
Spacing should be comparable to the wavelength of diffracted radiation.
To resolve interatomic distances should be less that the distances.
Spacing is the distance between parallel planes of atoms.
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Diffraction Data
Sequence
Initial Phases
Quality Control
Refinement
Validation
Phase Combination
Model Building
The steps to solve the macromolecular crystal structure
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X-RAY DIFFRACTOMETER
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CRYSTAL MOUNTING AND CRYO-CRYSTALLOGRAPHY
X-ray sources: synchrotron X-rays, 106 times stronger.
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CRYSTAL MOUNTING AND CRYO-CRYSTALLOGRAPHY
Data Collection
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DIMENSIONS X-ray detector
Beam width: ~0.20 mm
Crystal thickness: 0.10-1.00 mm
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10K+ REFLECTIONS
•Moving the X-rays and the detector gives a new set of
planes.
•Changing the angle of reflection changes the spacing
(resolution).
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GENERAL AMINO ACID STRUCTURE
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Diffraction image from a RAXIS-IV image plate
Frame Oscillation = 1o
Exposure time = 20 min
Maximum resolution = 2.5 Å
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Protein bonds & angles
• Torsion angle (dihedral angle)
– Measures orientation of four linked atoms in a molecule: A, B, C, D
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THE RAMACHANDRAN PLOT
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DATA ANALYSIS SOFTWARE (TRANSFERRABLE SKILLCCP4 suite
Graphic softwares (Coot, Quanta)
Python
Excel
R
SPSS
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DATA COLLECTION STRATEGY AND DATA PROCESSING
• How many images to collect?
• Exposure time
• Expected statistics
• Design the right strategy to collect data
and get good results!
• Data processing : index, integrate,
merge and calculate structure factor
amplitudes.
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Electron Density Map
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TELLING YOUR STORY
Amino-acid alignment at the active site of dGluR
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Active site
residues in
Drosophila
Glutamate
Receptors
Tell a great story
with results !
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Bioinformatics
Interdisciplinary science :
Mathematics, Biology, chemistry.
Physics, engineering etc.
Career paths:
• Health informatics
• Data scientists
• Financial consultants
• Fintech careers
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MY STORY PART 2: MBA AND LEADERSHIP
Skills:
Project Management
Finance
Team working skills
Received Leadership
Award !!
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PR0GRAM MANAGEMENT
Managing multiple projects in one portfolio
Organization management
Planning
Time management
Strategy
Finances
Communication
Collaboration
Team work
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On this Sunday from
3-5 pm
Collaboration with Astrazeneca/MedImmune,
Booz Allen Hamilton and BioHealth
Innovations
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Advocacy at the Capitol hill for science funding ! We got the funding
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STEM
Outreach at
Universities
Area Colleges
Pharma
companies
Collaborations!
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Mentoring workshop 2018 – 24 mentors and almost 100 participants!
Dr. Judy Stavley was there too!
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STEM EDUCATION & OUTREACH
Our mission is to promote student achievement and career
exploration in math and science while increasing student
exposure to the science, technology, engineering and
mathematics communities.
Experimental Design Program teaches students how to
design and conduct experiments for math and science fairs
utilizing research, laboratory and scientific literacy skills
gained through individual and group mentoring and
learning opportunities
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WHY I DO WHAT I DO?
Love for Science
Passion for mentoring
Supporting the creative development in STEM professionals
Serve as a leader
Team player
Science communication
STEM outreach
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Crystal growth
Diffraction theory
Symmetry
Experimental methods
Interpretation of data
Software