Difference between revisions of "20.109(S17):Identify chemical structures common among FKBP12 binders"

Introduction

Proteins and small molecules interact in a process referred to as molecular recognition. In molecular recognition, the non-covalent complexes that form are defined by two characteristics: specificity and affinity.

• Specificity distinguishes a specific binding partner from the milieu of potential binding partners in complex environments.
• Affinity dictates the likelihood of binding based on the concentration of a specific binding partner in a milieu of potential binding partners such that high affinity partners at low concentrations are not outcompeted by low affinity partners and high concentrations.

In cells, proteins are critical macromolecules that perform numerous roles related to structure, mechanics, metabolism, and signaling. In these roles, proteins do not work in a vacuum; rather the biological roles of proteins are dependent on direct physical interactions with other molecules. Though our focus in on small molecule binders, proteins also interact with other proteins, nucleic acids, oxygen, and metals. In all cases, the interactions are characterized by protein-ligand-solvent binding kinetics.

Though beyond the scope of this module, protein-ligand-solvent binding kinetics are defined as a thermodynamic system composed of solute (proteins and binders) and solvent (liquid that contains the proteins and binders). In that protein – small molecule complexes result in heat transfer, the driving forces that promote these interactions are due to energy exchanges that are characterized by Gibbs free energy (δG). δG measures the capacity of a thermodynamic system to do maximum or reversible work at constant temperature and pressure. When at equilibrium with constant temperature and pressue, protein – small molecule binding occurs when the change in δG is negative. The magnitude of δG provides insight into the stability of a protein – small molecule complex.

Protocols

Part 1: Visually evaluate chemical structures of positive hits

Part 2: Develop future works and implications section

Reagents

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