User:Wally Novak/Sandbox Hicks

Proliferating Cell Nuclear Antigen (PCNA) is a cyclic trimer involved with a number of cellular processes. In general, PCNA works as a sliding ring-shaped clamp that anchors replisome proteins to double stranded DNA to prevent dissociation. In processive elongation of the leading and lagging strands of DNA, PCNA assembly is coupled with ATP hydrolysis by Replication Factor C (RFC) onto a primed DNA template.^[1] PCNA then associates with DNA polymerase δ (pol δ) creating a holoenzyme so that pol δ synthesizes new DNA strands without dissociating from the DNA template. ^[2]

Structural Highlights

consist of 258 residues each and are a mass of 28.916 kDa. Each monomer contributes two domains to the trimeric ring. These domains possess anti-parallel beta sheets (blue) which approach each other on one end, but are separated by two alpha helices at the other (red), creating a 45 degree wedge in the sheets with alpha helices at the blunt end. The domains are connected by an extended beta sheet. This creates a and it also creates a β-α-β-β-β motif going around the ring. ^[3]

Interactions with DNA

Other structural features of PCNA elucidate how it functions as a sliding clamp protein, and how PCNA is able to loosely interact with DNA. Firstly, b-DNA and a-DNA have cross sectional diameters of about 18 and 21 Angstroms. PCNA has an internal diameter of approximately 34 Angstroms. [3] The diameter of PCNA being a little less than twice the size of the two most common forms of DNA suggests that size of the clamp plays a role in how tightly it associates with DNA. Specifically, if the difference in diameters was were greater, there would be little association, but if it were smaller, there would be a tighter association, which would not allow for the "sliding" of the sliding clamp.

Another factor that plays a role in association with DNA is the polarity of PCNA. Firstly, PCNA also giving it a charge of -60. This creates a negative electrostatic potential around the ring. However, in the center of the ring there is a positive electrostatic potential due to the the presence of 9 lysine and arginine residues in or adjacent to the helices of each monomer. [3] Below is an electrostatic map of PCNA showing this with positive potential in blue and negative in red.

Media:https://scontent-ort2-1.xx.fbcdn.net/v/t1.0-9/14702231_10153842197437539_1637277020294120554_n.jpg?oh=867feaedbf7a6f8ce87ac32cb9ed696e&oe=587088D3

^[4]

The positive potential and positively charged residues attract the negatively charged DNA backbone. (positively charged residues shown in yellow, DNA shown in lime green). ^[5] In general, both the size of PCNA and the charge distribution allow for a facilitated but loose reaction with DNA, allowing for PCNA to function as a "sliding clamp".