lecture 1: bio-molecules and intermolecular interactions · lecture 1: bio-molecules and...
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Lecture 1: Bio-molecules and intermolecular interactions
Bio-molecules: DNA, proteins, lipids
Short range Interactions: hydrogen bonding, ionic
interaction, crosslinking
Large scale phenomena: protein aggregation, phase transitions, large scale patterns, etc.
J. X. Tang, Brown University 1
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Biology in action: neutrophil chasing bacteria
Movie taken in film by David Rogers, Tufts University, 1970s J. X. Tang, Brown University
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Listerial motility and reconstituted mimics
J. Theriot Lab Website, Stanford Univ.
Weisner and Carlier, J. Cell Biol., 2004
Borisy Lab Website, Northwestern Univ.
J. X. Tang, Brown University
Polymers-An ultra brief introduction • Linear polymers
– Polyethylene CH3-CH2-CH2-…-CH2-CH2-CH3, formed by conservative addition (CH2=CH2 + CH2=CH2 -> CH3-CH2-CH=CH2)
– Polyethylene glycol (PEG) HO-CH2-CH2-O-CH2-CH2-O-… -O-CH2-CH2-O-CH2-CH2-OH, formed by condensation (HO-CH2-CH2-OH+ HO-CH2-CH2-OH -> HO-CH2-CH2-O-CH2-CH2-OH+H2O)
• Crosslinked polymers – Isomers in crude oil – Rubber (vulcanization, 1839, Goodyear) – Polyacrylamide
J. X. Tang, Brown University 4
Biopolymers: proteins, polynucleotides & polysaccharides
• Poly-amino acids (proteins)
• Poly-nucleotides (DNA, RNA)
• Poly-sugars (glycopolymers, or polysaccharides)
J. X. Tang, Brown University 5
Peptides to protein-an overview • Categorizing 20 amino acids (Cell-A molecular
approach, by COOPER, pp49) – hydrophobic or nonpolar – neutral but polar – acidic (anionic) – basic (cationic)
• Peptide bond:
J. X. Tang, Brown University 6
Levels of protein structure – Primary structure – Secondary structure – Tertiary structure – Quaternary structure
J. X. Tang, Brown University 7
Nucleic acids • DNA (deoxyribonucleic acid) & RNA
(ribonucleic acid) are both polymers of nucleic acids)
• Nucleotide = nucleoside + phosphate • Nucleoside = nitrogenous base (purine or
pyrimidine) + pentose sugar • Polycondensation (3’ and 5’)
J. X. Tang, Brown University 8
DNA on genetics • Codon • Base pairing • Supercoiling and recognition • A, B, & Z-forms • DNA mechanics-bending and twisting
stiffness, extensibility • Replication folk • Topoisomerases and helicases
J. X. Tang, Brown University 9
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Cytoskeleton and its major components
J. X. Tang, Brown University
Actin in Cells
• Alberts et al., Molecular Biology of the Cell
Role of actin in cell motility
• Protrusion • Attachment • Retraction • Repeat Protrusion Albert et al, Molecular Biology of the Cell
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Microtubule network is essential for cell functions
http://www.probes.com/servlets/photo?fileid=g001163
http://www.itg.uiuc.edu/exhibits/gallery/pages/image-66.htm
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Dynamic assembly of microtubules
Protofilament
Tubulin Dimer
α Tubulin β Tubulin
GTP Cap
(-)end
(+)end
Microtubule Microtubule (MT) diameter: 24 nm length: many mmJ. X. Tang, Brown University
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Specific Topic Electrostatics and depletion effect on actin
bundle formation and large actin granules
Stress fibers filapodia J. X. Tang, Brown University
Atomic structure of F-actin
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Holmes et al. Nature, 1990
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Physical Parameters of F-actin
• Length 0-30 µm • Diameter 8 nm • Persistence length
17 µm • 370 G-actin/µm • MW=42,000
dalton/G-actin
J. X. Tang, Brown University
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Polymerization of Actin
• G-F transition • Condensation model
(F. Oosawa, 1960s) • Binding energy ~14 kBT • Critical concentration <1 µM, or 0.04 mg/ml
• ATP hydrolysis
J. X. Tang, Brown University
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Polyelectrolyte nature of F-actin • Counterion layer
• Counterion condensation (Oosawa-Manning Theory)
• Delocalized binding • Significance of
polyvalency • Attractive interaction • Competition effects • … Tang & Janmey, JBC, 1996, 271, 8556 Tang et al, Biophys J., 2002 Wen & Tang, Phys Rev Lett, 2006
J. X. Tang, Brown University
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Ion-mediated formation of actin bundles
Tang et al., 1996, Ber. Bunsen-ges. Phys Chem., 100, 796
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Entropy driven lateral aggregation
• Osmotic effect • Steric exclusion • Depletion force • Macromolecular
crowding
Tang et al., 1997, Biochem., 36, 12600 Hosek & Tang, 2004, PRE, 65, 051907
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Transition between isotropic & nematic phases
L. Onsager, 1949, Ann. NY Acad. Sci., 51, 627
J. X. Tang, Brown University
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Isotropic-nematic transition of F-actin
Selected publications on actin I-N transition:
• Suzuki, Maeda, Ito, Biophys. J. 1991 • Furukawa, Kundra & Fechheimer, Biochem, 1993 • Coppin & Leavis, Biophys J, 1992 • Kas et al., Biophys J., 1996 …
A. isotropic phase B. nematic phase
Fluorescence images of labeled actin filaments embedded in the network of unlabelled filaments
J. X. Tang, Brown University
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nx and ny (index of refraction) x-axis is the slow axis
Dn=nx-ny>0 (birefringence) Dd=Dnxd (retardance)
Optical birefringence-an essential measurement of molecular alignment
The “pol-scope” technology • insertion of adjustable compensators (LC materials) • imaging transmitted light intensity of 4 settings • instant calculation of birefringence at microscopic scales
Ref: Oldenbourg and Mei, J. Microscopy, 1995
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The I-N Phase Transition of F-actin determined by the optical birefringence measurements
Isotropic
Nematic
Viamontes, Narayanan, Sandy & Tang, Phys. Rev. E, 73, 061901 (2006)
J. X. Tang, Brown University
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F-actin I-N Transition-from Continuous to First Order
Isotropic Transition Region Nematic
Average Filament Length = 11 µm
Average Filament Length = 1 µm
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Discontinuous in Concentration and Alignment
Viamontes, Oakes & Tang, Phys. Rev. Lett., 97, 118103 (2006)
J. X. Tang, Brown University
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Growth kinetics I: Nucleation and Growth
Nucleation and Growth
Growth, fusion & growth Growth Kinetics J. X. Tang, Brown University
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Growth kinetics II: Spinodal decomposition
Key findings: Characteristic size 20 µm X 10 µm Slow growth in late stage ~t1/3
Metastability
Spinodal Decomposition
J. X. Tang, Brown University
Oakes, P., W., Viamontes, J., & Tang, J. X., Phys Rev E., 2007, 75:061902.
Lecture Summary
• Brief intro on biomolecules & biopolymers • Various interactions and forces • Self-assembly of actin and tubulin filaments • Patterns and structures formed by actin
filaments and various interactions involved.
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Key References • 1. Tang, J.X. and P.A. Janmey, Polyelectrolyte Nature of F-actin and
Mechanism of Actin Bundle Formation. Journal of Biological Chemistry, 1996. 271: p. 8556-8563.
• 2. Viamontes, J., P.W. Oakes, and J.X. Tang, Isotropic to nematic liquid crystalline phase transition of F-actin varies from continuous to first order. Phys Rev Lett, 2006. 97(11): p. 118103.
• 3. Oakes, P., W., Viamontes, J., and Tang, J. X., Growth of tactoidal droplets during the first order isotropic to nematic phase transition of F-actin, Phys Rev E., 2007, 75:061902.
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