User:Wally Novak/Sandbox Hicks: Difference between revisions
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== Structural Highlights == | == Structural Highlights == | ||
<scene name='74/744126/Pcna_monomer_helixfront_2/1'> The PCNA monomers </scene> 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 <scene name='74/744126/6_fold_symmetry/1'> six-fold symmetry within the trimeric ring </scene> and it also creates a β-α-β-β-β motif going around the ring. <ref>PMID:8001157</ref> | <scene name='74/744126/Pcna_monomer_helixfront_2/1'> The PCNA monomers </scene> 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 <scene name='74/744126/6_fold_symmetry/1'> six-fold symmetry within the trimeric ring </scene> and it also creates a β-α-β-β-β motif going around the ring. <ref>PMID:8001157</ref> | ||
== | == 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. | |||
<ref>doi:10.1006</ref> | |||
Another factor that plays a role in association with DNA is the polarity of PCNA. Firstly, PCNA also <scene name='74/744126/Acidic_residues_pcna/2'> has a relatively large number of acidic residues </scene> 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]] | |||
<ref>doi:10.1006</ref> | |||
The positive potential and positively charged residues attract the negatively charged DNA backbone. <scene name='74/744126/Pcna_with_dna/2'> DNA enters the PCNA-RFC complex at an angle while interacting with positively charged residues </scene> (positively charged residues shown in yellow, DNA shown in lime green). <ref>PMCID:PMC2824762</ref> 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". | |||
