thua ie d - Amazon S3 · 2017-01-26 · 2 Key References • Mechanics of Motor Proteins & the...

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Transcript of thua ie d - Amazon S3 · 2017-01-26 · 2 Key References • Mechanics of Motor Proteins & the...

Page 1: thua ie d - Amazon S3 · 2017-01-26 · 2 Key References • Mechanics of Motor Proteins & the Cytoskeleton, J. Howard • Biophysical Chemistry, C. Cantor and P. Schimmel • Mechanical
Page 2: thua ie d - Amazon S3 · 2017-01-26 · 2 Key References • Mechanics of Motor Proteins & the Cytoskeleton, J. Howard • Biophysical Chemistry, C. Cantor and P. Schimmel • Mechanical
Page 3: thua ie d - Amazon S3 · 2017-01-26 · 2 Key References • Mechanics of Motor Proteins & the Cytoskeleton, J. Howard • Biophysical Chemistry, C. Cantor and P. Schimmel • Mechanical
Page 4: thua ie d - Amazon S3 · 2017-01-26 · 2 Key References • Mechanics of Motor Proteins & the Cytoskeleton, J. Howard • Biophysical Chemistry, C. Cantor and P. Schimmel • Mechanical
Page 5: thua ie d - Amazon S3 · 2017-01-26 · 2 Key References • Mechanics of Motor Proteins & the Cytoskeleton, J. Howard • Biophysical Chemistry, C. Cantor and P. Schimmel • Mechanical
Page 6: thua ie d - Amazon S3 · 2017-01-26 · 2 Key References • Mechanics of Motor Proteins & the Cytoskeleton, J. Howard • Biophysical Chemistry, C. Cantor and P. Schimmel • Mechanical
Page 7: thua ie d - Amazon S3 · 2017-01-26 · 2 Key References • Mechanics of Motor Proteins & the Cytoskeleton, J. Howard • Biophysical Chemistry, C. Cantor and P. Schimmel • Mechanical
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GEM4 Summer School 2006Cell and Molecular Mechanics in BioMedicineAugust 7–18, 2006, MIT, Cambridge, MA, USA

“Reactions”,Energy Landscapes

& KineticsPat Doyle

[email protected] Engineering Dept.

MIT

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Key References

• Mechanics of Motor Proteins & the Cytoskeleton,J. Howard

• Biophysical Chemistry, C. Cantor and P. Schimmel

• Mechanical Processes in Biochemistry, Bustamante etal., Ann. Rev. Biochem., 73, 705-748, 2004

• Brownian Motion in a Field of Force and the DiffusionModel of Chemical Reactions, H.A. Kramers, Physica, 4,284-304, 1940

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“Reactions”

Fisher, Marszalek & Fernandez, Nature 2000

Binding of TAT box-binding protein

Titin unfolding

RNA unfolding

Receptor-ligand

DNA-protein

Bustamante et al. 1997

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Diffusion Limited Reactions

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5Geometry matters…

Some details….

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First Passage Time

Need to input U(x) to solve…..

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Relaxation time of a damped spring

Exponential Effect of Barrier Height

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Details of Derivation…

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Things that Affect Energy Landscapes

• Force (pulling/pushing, rate)• Enzymes (catalysts)• Salt, pH• “additives” (protein drug stabilization)• ….

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17Strick, Allemand, Bensimon, Croquette, Ann. Rev. Biophys. 2000

Two State Example: Protein Unfolding

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Force Changes the Energy Landscape

Bustamante et al., Ann. Rev. Biochem. 2004