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], well 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 [ + = ] P [ ] P ][ L [ ] P ][ L [ + = a a K K a K 1 ] L [ ] L [ + = d K + = ] L [ ] L [ Binding: Graphical Analysis d K + = ] L [ ] L [ [L] [L] total d K + = ] L [ ] L [ 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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chapter5 RKW - Lecture Connections 5 | Function of Globular...

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