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.