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 College5 July 2005
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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
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The Post-Albers Model of the Na+/K+ Pump
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Pump Structure and Function: A Static Cartoon
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The Calcium Pump
E1 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
Nucleotide- (N) and Phosphate- (P) binding domains separated from Activation (A) domain.
Helical membrane domains (M) open to cytoplasm; “Na+ sticky”.
ATP bound to N domain.
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E2 Structure
P, N, A domains associated, forming active catalytic unit.
Helical membrane domains open to exterior; “K+ sticky”.
ATP hydrolyzed: ADP released; P domain phosphorylated.
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Creating A Domain StructureDrawing 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(subunit)
E1 E2
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Placing the Pump in a Membrane Perspective
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The Na+/K+ Pump.
THE MOVIESTHE MOVIESPumping Ions 1PI 2. Ouabain’s Revenge: the Pump HaltedPI 3. Pump Redux, or Overwhelmed by the
Gradients.
PI 4. The Great Na+ - Na+ Exchange PI 5. The Great K+ - K+ Exchange
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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 1M17Here, to sameScale, 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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