chapter5 RKW

chapter5 RKW - Lecture Connections 5 | Function of Globular...

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Unformatted text preview: Lecture Connections 5 | Function of Globular Proteins © 2009 W. H. Freeman and Company CHAPTER 5 Function of Globular Proteins – Reversible binding of ligands – Structure of myoglobin and hemoglobin – Origin of cooperativity in hemoglobin – Structure and function of antibodies – Molecular mechanism of muscle movements Key topics in protein function : Functions of Globular Proteins • Storage of ions and molecules – myoglobin, ferritin • Transport of ions and molecules – hemoglobin, serotonin transporter • Defense against pathogens – antibodies, cytokines • Muscle contraction – actin, myosin • Biological catalysis – chymotrypsin, lysozyme Protein Binding Ligands • In this chapter we focus on proteins that bind ligands. • Next chapter we focus on Enzymes. Protein that bind substrate and convert it into Product. Interaction with Other Molecules • Reversible, transient process of chemical equilibrium: A + B → AB • A molecule that binds is called a ligand (typically a small molecule) • A region in the protein where the ligand binds is called the binding site • Ligand binds via non-covalent forces, which enables the interactions to be transient ← Binding: Quantitative Description • Consider a process in which a ligand (L) binds reversibly to a site in the protein (P) • The kinetics of such a process is described by: the association rate constant k a the dissociation rate constant k d • After some time, the process will reach the equilibrium where the association and dissociation rates are equal • The equilibrium composition is characterized by the the equilibrium constant K a + k a k d PL P L d a a k k K = ⋅ = ] L [ ] P [ ] PL [ ] PL [ ] L [ ] P [ d a k k = ⋅ Binding: Analysis in Terms of the Bound Fraction • In practice, we can often determine the fraction of occupied binding sites • Substituting [PL] with K a [L][P], we’ll eliminate [PL] • Eliminating [P] and rearranging gives the result in terms of equilibrium association constant: • In terms of the more commonly used equilibrium dissociation constant : ] P [ PL] [ ] PL [ + = θ ] P [ ] P ][ L [ ] P ][ L [ + = a a K K θ a K 1 ] L [ ] L [ + = θ d K + = ] L [ ] L [ θ Binding: Graphical Analysis d K + = ] L [ ] L [ θ [L] ≈ [L] total d K + = ] L [ ] L [ θ Kd Summary • Kd is where half of the binding sites are filled. • The lower value of Kd corresponds to greater binding affinity. Binding: Thermodynamic Connections • Interaction strength can be expressed as: – association (binding) constant K a , units M-1 – dissociation constant K d , units M, K d = 1/K a – interaction (binding) free energy ∆ G o , units: kJ/mol Definitions: ∆ G o = ∆ H o - T ∆ S o : enthalpy and entropy – K a = [PL]/[P][L]...
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This note was uploaded on 03/08/2012 for the course CHEM 481 taught by Professor Wood during the Fall '10 term at BYU.

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chapter5 RKW - Lecture Connections 5 | Function of Globular...

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