Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 146, Issue 22, Pages -Publisher
AMER INST PHYSICS
DOI: 10.1063/1.4985221
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Funding
- National Science Center in Poland under the aegis of the EU Joint Programme in Neurodegenerative Diseases (JPND) [2014/15/Z/NZ1/00037]
- National Science Center [2014/15/B/ST3/01905]
- PL-GRID network
- European Regional Development Fund under the Operational Programme Innovative Economy NanoFun [POIG.02.02.00-00-025/09]
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We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both termini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK, and bacteriophytochrome. These proteins have been studied theoretically in their monomeric versions so far. The dimers are seen to separate on stretching through the tensile mechanism and the characteristic unraveling force depends on the pulling direction.
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