Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps.
Sliding clamp proteins encircle duplex DNA and are involved in processive DNA replication and the DNA damage response. Clamp proteins are ring-shaped oligomers (dimers or trimers) and are loaded onto DNA by an ATP-dependent clamp loader complex that ruptures the interface between two adjacent subunits. Here we measured the solution dynamics of the human clamp protein, proliferating cell nuclear antigen, by monitoring the change in the fluorescence of a site-specifically labeled. To unravel the origins of clamp subunit interface stability, we carried out comprehensive comparative analysis of the interfaces of seven sliding clamps. We used computational modeling (molecular dynamic simulations and MM/GBSA binding energy decomposition analyses) to identify conserved networks of hydrophobic residues critical for clamp stability and ring-opening dynamics. The hydrophobic network is shared among clamp proteins and exhibits a "key in a keyhole" pattern where a bulky aromatic residue from one clamp subunit is anchored into a hydrophobic pocket of the opposing subunit. Bioinformatics and dynamic network analyses showed that this oligomeric latch is conserved across DNA sliding clamps from all domains of life and dictates the dynamics of clamp opening and closing.
['Perumal|Senthil K|SK|', 'Xu|Xiaojun|X|', 'Yan|Chunli|C|', 'Ivanov|Ivaylo|I|', 'Benkovic|Stephen J|SJ|']
D004247:DNA D004261:DNA Replication D006801:Humans D057927:Hydrophobic and Hydrophilic Interactions D056004:Molecular Dynamics Simulation D016297:Mutagenesis, Site-Directed D009154:Mutation D018809:Proliferating Cell Nuclear Antigen D011485:Protein Binding D011487:Protein Conformation D060066:Protein Interaction Maps D021122:Protein Subunits D051818:Replication Protein C
DNA damage response proliferating cell nuclear antigen molecular dynamics binding energy replication factor C