CRYSTALLOGRAPHY AND STORYTELLING WITH DATA. President, Association of Women in Science, Bethesda Chapter STEM Consultant
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1 CRYSTALLOGRAPHY AND STORYTELLING WITH DATA President, Association of Women in Science, Bethesda Chapter STEM Consultant
2 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
3 CRUX OF MY STORY Passion for Science Excelling at what I do What Next?
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5 SKILLS COVERED IN THIS PPT Biochemistry Molecular biology Crystallography Computer Simulations Creativity in science Data tools Storytelling (Communication) Problem solving Collaboration
6 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!
7 THE METHOD FT FT -1 Protein Crystals X-rays diffraction Refined structure
8 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
9 FOUR LEVELS OF PROTEIN STRUCTURE
10 Protein Crystals 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!
11 CRYSTAL SYSTEMS SOME DEFINITIONAL INFORMATION Unit cell: smallest repetitive volume which contains the complete lattice pattern of a crystal. a c b 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
12 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
13 PEPTIDE BOND LENGTHS
14 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.
15 The steps to solve the macromolecular crystal structure Diffraction Data Sequence Initial Phases Quality Control Phase Combination Model Building Refinement Validation
16 X-RAY DIFFRACTOMETER
17 CRYSTAL MOUNTING AND CRYO-CRYSTALLOGRAPHY X-ray sources: synchrotron X-rays, 10 6 times stronger.
18 CRYSTAL MOUNTING AND CRYO-CRYSTALLOGRAPHY Data Collection
19 DIMENSIONS X-ray detector Beam width: ~0.20 mm Crystal thickness: mm
20 10K+ REFLECTIONS Moving the X-rays and the detector gives a new set of planes. Changing the angle of reflection changes the spacing (resolution).
21 GENERAL AMINO ACID STRUCTURE
22 Maximum resolution = 2.5 Å Exposure time = 20 min Frame Oscillation = 1 o Diffraction image from a RAXIS-IV image plate
23 Protein bonds & angles Torsion angle (dihedral angle) Measures orientation of four linked atoms in a molecule: A, B, C, D
24 THE RAMACHANDRAN PLOT
25 DATA ANALYSIS SOFTWARE (TRANSFERRABLE SKILL CCP4 suite Graphic softwares (Coot, Quanta) Python Excel R SPSS
26 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.
27 Electron Density Map
28 TELLING YOUR STORY Amino-acid alignment at the active site of dglur
29 Tell a great story with results! Active site residues in Drosophila Glutamate Receptors
30 Bioinformatics Interdisciplinary science : Mathematics, Biology, chemistry. Physics, engineering etc. Career paths: Health informatics Data scientists Financial consultants Fintech careers
31 MY STORY PART 2: MBA AND LEADERSHIP Skills: Project Management Finance Team working skills Received Leadership Award!!
32 PR0GRAM MANAGEMENT Managing multiple projects in one portfolio Organization management Planning Time management Strategy Finances Communication Collaboration Team work
33 On this Sunday from 3-5 pm Collaboration with Astrazeneca/MedImmune, Booz Allen Hamilton and BioHealth Innovations
34 Advocacy at the Capitol hill for science funding! We got the funding
35 STEM Outreach at Universities Area Colleges Pharma companies Collaborations!
36 Mentoring workshop mentors and almost 100 participants! Dr. Judy Stavley was there too!
37 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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39 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
40 Poorva Dharkar
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43 Crystal growth Diffraction theory Symmetry Experimental methods Interpretation of data Software
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