Kinetics of Protein-Protein Interactions

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Kinetics of Protein-ProteinInteractions

• November 2002

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Content

• Preview Basic kinetics
• Protein-protein Kinetics Basic view
• Electrostatic steering study review

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1.Preview Basic kinetics
Reaction Rate (V) Change of concentration over
time

• Basic Reaction
• A C

Rate slows as concentration of A decreases
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Reaction Rate constant

• A B C
• V K A B

Rate is dependant on preliminary concentration
of reactants
Rate (at first stage of reaction)
Kinetic Constant
Would expect NO2NO2

• It appears things are not that
• simple
• Mechanism
• Different Ks

K1
(K1 Slow) F2 NO2
NO2F F Fast Equilibrium NO2 F
NO2F
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Factors Influencing K

• Arrhenius

Activation Energy Limiting Barrier

• Constant
• Size
• Orientation
• Solvent
• electrostatics

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2.Protein-Protein Kinetics Basic View
A
B
A
B

• Kd Kdissociation / Kassociation
  (dissociationoff, associationon)
• ?G -RTln(Kd)

• Physiological conditions
• Possible concentration of a unique Protein in a
  cell 10-6 10-8 M
• Protein diameter 50 100 A (Protein surface
  8,000 A)
• Free Walk collision with interacting designated
  protein 1000A 2000A

A
B
A
B
1000 2000A
A
B
A
B
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A more elaborate representation
Transition-State
Diffusion Possible Steering
Intermediate
Desolvation, VDW, Electrostatics
?
?
?
v
v
v
Random Diffusion
Electrostatic Steering
Encounter Complex
Final Complex
Transition
Intermediate
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Reaching the Encounter Complex

• Random diffusion according to the
  Smolochowski-Einstein equation - 109 - 1010
  1/MS
• With geometrical constraints - 105
  106 1/MS
• Adding electrostatic steering could enhance rate
  to 109 1/MS

Attraction
Steering

• Energetic factors

Electrostatic
?S
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An example of electrostatic steering
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Barnase-Barstar Electrostatic potential Landscape
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3.Evaluation of steering effect (Camacho, Vajda)
Complex separation (5A) XY rotation

• A. Chymotrypsin with turkey ovomucoid third
  domain (1CHO)
• B. human leukocyte elastase with turkey ovomucoid
  third domain (1PPF), ionic strength
• 0.15 M and protein dielectric 4
• C. kallikrein A and pancreatic trypsin inhibitor
  (2KAI), ionic strength 0.15 M and protein
  dielectric 4
• D. barnase and barstar (1BGS)
• E. subtilisin and chymotrypsin inhibitor (2SNI)
• F. subtilisin and eglin-c (1CSE), ionic strength
  0.15 M and protein dielectric 4
• G. trypsin and bovine pancreatic trypsin
  inhibitor (2PTC).

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Evaluation of steering effect (Wade)

• ccpcc - cytochrome c peroxidasecytochrome c
• achefas - acetylcholinesterase fasciculin-2
• Bnbs - Barnase-Barstar
• hyhel5hel - HyHEL-5 antibody hen egg white
  lysozyme
• hyhel10hel - HyHEL-10 antibodyhen egg white
  lysozyme

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Evaluation of steering effect (Wade)
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Evaluation of steering effect (Wade)
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Structure Tem1 ß Lactamase
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Structure Tem1 ß Lactamase
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Structure BLIP-??
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Bound Blip-?? TEM1
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Bound Blip-?? TEM1
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Mutations on BLIP outside the active site
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Results
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Results
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Possible Transition state orientation

• Still water molecules awaiting extraction
• Possibly a core of atoms in proximity with final
  orientation

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Encounter complex modeling
Barnase - Barstar

• Bound Model

• Camacho/wade Electrostatic minima

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Encounter complex modeling
Barnase - Barstar

• Bound Model

• Janin 50 surface area rotational limit

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Encounter complex modeling
Barnase - Barstar

• Bound Model

• Vijayakumar solvent separation (2 angles
  3dg limit)