PART 3: EXPLORING PROTEIN STRUCTURE AND FUNCTION Proteins are essential parts of
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PART 3: EXPLORING PROTEIN STRUCTURE AND FUNCTION Proteins are essential parts of organisms and participate in every process within cells. Proteins act as enzymes that catalyze biochemical reactions. These enzymes can be free floating cata- lysts located in the cytosol or can be membrane bound in organelle or cell membranes. Proteins can serve a structural or mechanical function in the cell that provide a scaffold for maintaining the cell shape, vesicle transport, or even cellular movement. Even more proteins can act in cel- lular signaling, cell adhesion, the cell cycle, and morphological development. Below are two examples of very different types of proteins. Go to http://www.resb.org/pdb/101/motm archive.do to answer the questions below. To answer each set of questions go to the links below. Hemoglobin: http:/lpdb101.resb.org/motm/41 Potassium Channel: http://pdb101.rcsb.org/motm/38 A. Potassium Channel. l. Look at the potassium channel protein. How many subunits make up the final quater- nary shape of the potassium channel? 2. The Potassium channel has a selective pore which allows potassium ions into the cell but blocks sodium ions. How does the potassium channel differentiate between K and NA" ions? 3. Read the "A Poisonous Aside" section. It explains that scorpion venom (composed of charybdotoxin) binds tightly to the potassium channel, blocking the channel pore. The charybdotoxin protein surface is covered in positively-charged amino acids. A. If charybdotoxin binds tightly to the potassium channel, what does that say about the characteristics of the amino acids surrounding the potassium channel pore?Explanation / Answer
Answer 1) Potassium channel has a tetrameric structure where four identical protein subunits join to form the final quaternary structure. the four protein subunits interact to form a barrel like structure which functions as a gated channel.
Answer 2) Every potassium channel has a unique pore-loop structure on the top of the pore which enables selective permeability of potassium ion. The channel contains a highly conserved ‘signature’ amino acid sequence – TVGYG which is a prime component of the selectivity filter of potassium ion. When potassium ion passes through the filter, most of the waters forming the hydration shell of the ion are removed and replaced by atoms of the protein. To be more precise, the oxygen atoms of the protein act as a perfect replacement ofr the the water molecules surrounding the potassium. It is via this mechanism of dehydration that the four binding sites provide selectivity to potassium ions. Sodium ions are small in size. They are unable to interact with the oxygen atoms lining the pore of the protein. Thus, the selectivity filter selectively binds potassium ion whereas the binding of sodium ion becomes thermodynamically unfavourable and sodium ions cannot be efficiently transported across the membrane.
Answer 3) The amino acids surrounding the potassium channel pore are positively charged amino acids. The asparagine on charybdotoxin binds with aspartic acid of the potassium channel pore and blocks it.
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