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Structural Basis for Ligand-Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425, 431 [email protected]
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Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Dec 18, 2015

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Page 1: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Structural Basis for Ligand-Receptor Recognition and

Dimerization

Moosa MohammadiDept. of PharmacologyMedical Science Building, 4th Floor, Rooms 425, [email protected]

Page 2: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

In multicellular organisms, the decision a cell has to make whether to divide, to differentiate or to die is controlled by ligands (growth factors, hormones) that circulate outside of the cell. These ligands in order to transmit their signals must interact with cell surface receptors that possess

enzymatic activity known as protein kinase activity.

Nucleous

Plasmamembrane Barrier

Ligands

Covalently linkedAssociatedkinase

kinase

Page 3: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Single Transmembrane-Spanning Receptors

Extracellular

Intracellular

Ligand

Receptor

Page 4: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Mechanisms of Signal Transduction

Extracellular

Intracellular

Conformational Change

GDPGTP

Page 5: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,
Page 6: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Receptor Dimerization

Extracellular

IntracellularY

YY

YY

Y

Page 7: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

ATP

PP

P P

ATP

1. Inactive receptor monomers 2.Trans-autophosphorylation

3. Active phosphorylated receptor dimer

Page 8: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Early experiments suggesting that receptors undergo

dimerization

•Truncated receptors lacking the cytoplasmic domain inhibit signaling.

•Transmembrane helices are interchangeable betweendifferent receptors.

•Antibodies against the cytoplasmic domain activate the kinase domain.

Page 9: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,
Page 10: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Antibody-mediated activation

Extracellular

Intracellular

Receptor

Page 11: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Extracellular

Intracellular

Receptor

Fab

Page 12: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,
Page 13: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Receptor Ras

Raf

MAPKK

MAPKSos

Grb2

Growth factor

Shc

Jun Fos

NUCLEUS

Page 14: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Phenotypes of patients with Apert syndromewhich results from point mutation in FGF receptor

Page 15: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

•Growth Hormone (GH) Receptor

•Erythropoietin (EPO) Receptor

•Bone Morphogenic Protein (BMP) Receptor

•Vascular Endothelial Growth (VEGF) Receptor

•Nerve Growth Factor (NGF) Receptor

•Fibroblast Growth factor (FGF) Receptor

Ligand-Receptor Systems

Page 16: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

• Large family of single-pass transmembrane receptors.

• Receptors bind polypeptide ligands: mediators of cell growth, differentiation and immune responses.

• Cytoplasmic domain does not contain intrinsic protein tyrosine kinase activity - associated with Jak tyrosine kinases.

Cytokine Receptors

Page 17: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Cytokine Receptors

Page 18: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

• GH stimulates the growth and metabolism of muscle, bone and cartilage cells.

• GH is a member of the 4-helix bundle family.

• The active form of GH is a monomer. Stoichiometry of binding is 1:2 GH-GHR.

Activation Through Binding of a Monomeric Ligand – Growth Hormone

Page 19: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Ribbon Diagram of Growth Hormone

Page 20: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

A

CD

B

Four-Helix-Bundle Structure

Page 21: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Four-Helix-Bundle is Stabilized by Hydrophobic Contacts Between the Four Helices

Page 22: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Ribbon Diagram of Extracellular Domain of Growth Hormone Receptor

Page 23: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Fibronectin Type III Domain is a Close Cousin of Immunoglobulin Superfamily Domains

Page 24: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,
Page 25: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,
Page 26: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,
Page 27: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Ribbon Diagram of the 1:2 Complex between GH and GHR

Page 28: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

GH-GHR Complex

GH-GHR contact I: 1230 Å2

GHR-GHR contact: 500 Å2

GH-GHR contact II: 900 Å2

Page 29: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Details of GH-GHR Interactions

Page 30: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Ribbon Diagram of the 1:1 Complex Between GH and Prolactin Receptor

Page 31: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Hormone-Receptor Interactions Involving the Linker Region of the Receptor

Page 32: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Hormone-Receptor Interactions Involving the F-G Loop in the C-terminal Fibronectin Domain

Page 33: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Activation Through Binding of a Monomeric Ligand – Erythropoietin (EPO)

• EPO is a haematopoietic cytokine required for differentiation and proliferation of precursor cells into red blood cells.

• Like GH, EPO is monomeric and belongs to the 4-helix bundle family.

• EPO binds to its receptor (EPOR) with a stoichiometry of 1:2 EPO-EPOR.

Page 34: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Epo:EpoR Complex - Dependence on Receptor Orientation

Page 35: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

RasMol Presentation of the Dimeric EPO-EPOR Structure

Page 36: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Growth Hormone Paradigm

Page 37: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

• Bone morphogenic proteins (BMPs) belong to the Transforming Growth Factor (TGF superfamily of ligands which includes TGF activins/Inhibins and GDFs.

• BMPs regulate bone and cartilage formation in adults and are also involved in central steps in early embryonic development.

•BMPs are dimeric ligands and have the characteristic “Cystine Knot “ motif found in other members of TGFfamily.

• The receptors for TGFfamily of ligands are transmembrane receptors with intrinsic serine/threonine kinase activity.

Activation of a Receptor Serine/Threonine Kinase – Bone Morphogenic Protein (BMP) Receptor

Page 38: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

TGF Receptors

Extracellular

Intracellular

Ser/Thr kinase

Cys-rich

Page 39: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Activation via Dimeric Ligand: BMP-BMPR Structure

Page 40: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

RasMol Presentation of the Dimeric BMP-BMPR Structure

Page 41: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

• Large family of single-pass transmembrane receptors.

• Receptors are predominantly for growth factors but also for insulin.

• Cytoplasmic domain contains intrinsic protein tyrosine kinase activity.

Receptor Tyrosine Kinases

Page 42: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Receptor Tyrosine Kinase Family

Page 43: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

• VEGF is a mitogen that is highly specific for endothelial cells.

• VEGF is a potent angiogenic factor involved in the development of the vascular system and also in tumor angiogenesis.

• VEGF is a covalent (disulfide-linked) dimer.

Activation Through Binding of a Dimeric Ligand – Vascular Endothelial Growth Factor

Page 44: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

VEGFR Family

Ig-like

Page 45: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

VEGF-Flt1 Dimer

Page 46: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

VEGF-Flt1 Dimer

Flt1-D2

Flt1-D2

VEGF

VEGF

Page 47: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

VEGF Interacting Residues

Ig domain 2

Page 48: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

RasMol Presentation of the Dimeric VEGF-FLT1 Structure

Page 49: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Model for Flt1 Dimerization

Page 50: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

• NGF is a member of a family of neurotrophins which also includes brain-derived neurotrophic factor (BDNF), NT-3, NT-4/5 and NT-6.

• NGF mediates neuronal differentiation and survival.

• These neurotrophins are non-covalent dimers, members of the cystine knot family.

Activation Through Binding of a Dimeric Ligand – Neurotrophic Growth Factor

Page 51: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Trk (NGF Receptor) Family

Cys-richLeu-rich

Ig-like

Page 52: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

NGF-Trk Dimer

Domain 5 Domain 5

Page 53: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Common and Specific Interaction Sites

Common interface

Specificity interface

Page 54: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Common and Specific Interaction Sites

Specificity interface

Common interface

Page 55: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Alignment of Neurotrophic Factors and Trk-D5

Common siteSpecificity site

Ligands

Receptors

Page 56: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

RasMol Presentation of the Dimeric NGF-TRK Structure

Page 57: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Dimeric Ligands with “Cystine Knot” Motif

(BMP-2)

Page 58: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Receptor Dimerization by Dimeric Ligands with “Cystine Knot” Motif

Page 59: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Growth Hormone Paradigm

Page 60: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Crystal Structure of Flt3 Ligand;Dimer of two 4-helix Bundels

Page 61: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

RasMol Presentation of FLT3 Ligand;Dimer of two 4-helix Bundles

Page 62: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,
Page 63: Structural Basis for Ligand- Receptor Recognition and Dimerization Moosa Mohammadi Dept. of Pharmacology Medical Science Building, 4th Floor, Rooms 425,

Dimerization by Flt3L Versus VEGF

Flt3L-Flt3 (model) VEGF-Flt1 (partial model)