Chapter 3 (part 2) – Protein Function

Test Your Knowledge (True/False) All proteins bind to other molecules. Explain. What sort chemical interactions create the “binding” between the ligand and its protein partner? Name at least two. (True/False) A ligand binding site can be kept dry from surrounding water molecules. Explain. Explain two different ways (structural) that proteins typically bind to other proteins. What is Km? What does having a low Km say about the binding between a protein and its ligand? What are some of the major functions of proteins in a cell? Name at least 3 “categories”.

Protein-Protein Binding Three major mechanisms: “surface string” interaction – “helix-helix” or “coiled coil” interaction – “surface-surface” interaction –

SH2 domain (example of surface string interaction) Central antiparallel  sheet surrounded by two alpha helices

Coiled coil regions of Rad50 molecules bind together to form a complex of molecules that help repair DNA Surface-to-surface interaction between trypsin and trypsin inhibitor protein

Protein Binding Sites –Sterically and chemically “fit” the ligand; Examples are antibodies and enzymes Water is typically excluded from the binding site, but is important to overall structure. Why? Protein-Ligand Interactions

Clustering of polar amino acid side chains can alter their reactivity and increase the attraction of the ligand for the binding site

cAMP bound to a binding site on a protein

Enzymes and bound ligand go through a number of intermediate forms of different geometry. They are all called transition states. The energy that it takes to get to the most unstable transition state is called the activation energy. Enzymes speed reactions by selectively stabilizing the transition state (ES) and actually have a much higher affinity for the ligand in its transition state than the stable form of the ligand.

Enzymes not only bind to the substrate, but the nature of the amino acids and their side chains within the binding site alter chemical bonds in the substrate. Many enzymes can perform both acid and base catalysis because of the different side chains in their binding site. This allows increased speed of catalysis.

Many Enzymes Require Tightly Bound Small Molecules to Function

Enzymes sometimes form complexes that also improve efficiency of reactions that may otherwise be diffusion-limited. Examples – pyruvate dehydrogenase, tryptophan synthase, aminoacyl t-RNA synthetase