Visualizing the Structure and Function of Integral Membrane Proteins

1
Visualizing the Structure and Function of
Integral Membrane Proteins

• C. Watters1, D. Guertin2, D. Conache2, and D.
  Koparov2
• Department of Biology1 and Library
• and Informational Services2,
• Middlebury College
• 5 July 2005

2
Introduction Goals

• Create dynamic models of integral membrane
  proteins (IMP).
• Integrate functional and structural aspects of
  IMP simply but accurately.
• Render IMP behavior in a stochastic manner.

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The Na/K Pump A Case in Point
4
The Post-Albers Model of the Na/K Pump
5
Pump Structure and Function A Static Cartoon
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The Calcium PumpE1 State
E2 State

• (from PDB, after Toyoshima, et al., 2000 Xu, et
  al., 2002)

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Conservation of Pump Structures Na/K Pump
Ca2 Pump
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E1 Structure

• Helical membrane
• domains (M) open to
• cytoplasm Na sticky.

• Nucleotide- (N) and Phosphate- (P) binding
  domains separated from Activation (A) domain.

• ATP bound to N domain.

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E2 Structure

• Helical membrane domains open to exterior K
  sticky.

• ATP hydrolyzed ADP released P domain
  phosphorylated.

• P, N, A domains associated, forming active
  catalytic unit.

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Creating A Domain Structure

• Drawing splines and skinning the ATP-binding
  domain (N) using LightWave 3D.

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Assembled ATPase of the Na/K Pump

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Na/K Pump(a-subunit)
E1 E2
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Placing the Pump in a Membrane Perspective
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The Na/K Pump. THE MOVIES

• Pumping Ions 1
• PI 2. Ouabains Revenge the Pump Halted
• PI 3. Pump Redux, or Overwhelmed by the
  Gradients.
• PI 4. The Great Na - Na Exchange
• PI 5. The Great K - K Exchange

15
Limitations of Pump Models

• Crystallographic structures may not be accurate
  native structures.

• Organization of transmembrane helical domain is
  inaccurate. Helices not parallel no channel
  evident.
• Binding sites may not be arranged as depicted.
• Na- and K-binding sites may be different
  likely overlapping.
• Cooperative effects of N, P and A domains (
  catalysis) on transmembrane domain likely more
  complex than shown.

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Other Integral Membrane Proteins Tyrosine
Kinase and G-protein-linked Hormone Receptors
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Tyrosine Kinase ReceptorsInitial Events EGF
Binding to EGFR
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Tyrosine Kinase ReceptorsDownstream Transduction
Events
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Tyrosine Kinase ReceptorsKinase Inhibition by
4-Anilinolquinazoline
David put PDB 1M17 Here, to same Scale,
highlighting inhibitor.
EGFR - Kinase Domain
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Other Integral Membrane Proteins Signaling by
Tyrosine Kinase and G-protein-linked Hormone
Receptors
David provide link from each still to a QT movie.
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Acknowledgments

• Middlebury College
• Information and Library Services.
• Professional Development Fund provided by the
  Irene Heinz and John LaPorte Given Professorship
  in Premedical Sciences.

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The Na/K Pump. I. Forwards

• The Movie

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The Na/K Pump. II. Ouabain Inhibition

• The Movie

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The Na/K Pump. III. Backwards

• The Movie

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The Na/K Pump. IV. Exchanging Na for Na

• The Movie

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The Na/K Pump. V. Exchanging K for K

• The Movie