Lecture 1: Bio-molecules and intermolecular interactions · Lecture 1: Bio-molecules and...

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

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Biopolymers: proteins, polynucleotides & polysaccharides

•  Poly-amino acids (proteins)

•  Poly-nucleotides (DNA, RNA)

•  Poly-sugars (glycopolymers, or polysaccharides)

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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:

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Levels of protein structure – Primary structure – Secondary structure – Tertiary structure – Quaternary structure

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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’)

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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

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Cytoskeleton and its major components

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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

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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

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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

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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

J. X. Tang, Brown University

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Transition between isotropic & nematic phases

L. Onsager, 1949, Ann. NY Acad. Sci., 51, 627

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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

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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)

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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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