Visualizing the Structure and Function of Integral Membrane Proteins C. Watters 1, D. Guertin 2, D....

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.