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| 001 | 1025182 | ||
| 005 | 20250204113838.0 | ||
| 024 | 7 | _ | |a 10.1016/j.bpj.2023.11.1698 |2 doi |
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| 037 | _ | _ | |a FZJ-2024-02759 |
| 082 | _ | _ | |a 570 |
| 100 | 1 | _ | |a Kelly, Maria S. |0 P:(DE-HGF)0 |b 0 |
| 111 | 2 | _ | |a Biophysical Society Meeting |c Philadelphia |d 2024-02-10 - 2024-02-14 |w USA |
| 245 | _ | _ | |a Optimizing biophysical predictor selection for katanin allosteric transitions via metadynamics and machine learning |
| 260 | _ | _ | |c 2024 |
| 336 | 7 | _ | |a Abstract |b abstract |m abstract |0 PUB:(DE-HGF)1 |s 1714556723_354 |2 PUB:(DE-HGF) |
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| 520 | _ | _ | |a Katanin, a microtubule-severing enzyme, plays a pivotal role in regulating cytoskeletal dynamics, cell division, and intracellular transport. Katanin does this by forming a hexamer and undergoing a conformational change from its open “spiral” to closed “ring” state, which enacts mechanical forces required for the removal of tubulin dimers from the microtubule lattice. Allosteric regulation has emerged as a critical aspect of katanin’s functionality, where binding of ATP and tubulin carboxy-terminal tails (CTTs) allows katanin to transition from spiral to ring. Additionally, CTT sequence diversity and post-translational modifications are known to modulate katanin activity. Thus, there is a need to learn more about katanin’s allosteric response to ligand binding to understand its full mechanism. Here, we ran molecular dynamics simulations of katanin and surveyed a wide range of biophysical descriptors that reduce the dimensionality of the all-atomistic output while allowing us to identify katanin’s allosteric responses to ligand binding. We studied many physical and chemical predictors within katanin’s monomeric and hexameric form, such as solvent accessibility and salt bridge distances, using machine learning classification algorithms to attribute large descriptor differences to allosteric responses from the binding of either ATP or the CTT. Effective predictors were then utilized as collective variables for metadynamics simulations, that introduce bias potentials to aid in the exploration of the free energy landscape to simulate katanin’s transition from its spiral to ring configuration. We can then test how the binding of relevant CTT sequences affects katanin’s free energy landscape during this transition. In total, we can study the complexity of allosteric regulation through various applications using multiple biophysical features of katanin. |
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| 700 | 1 | _ | |a Capelli, Riccardo |0 P:(DE-Juel1)174546 |b 1 |
| 700 | 1 | _ | |a Kahawatte, Shehani |0 P:(DE-HGF)0 |b 2 |
| 700 | 1 | _ | |a Wijethunga, Hesaree |0 P:(DE-HGF)0 |b 3 |
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| 700 | 1 | _ | |a Dima, Ruxandra I. |0 P:(DE-HGF)0 |b 5 |
| 773 | _ | _ | |a 10.1016/j.bpj.2023.11.1698 |0 PERI:(DE-600)1477214-0 |y 2024 |g Vol. 123, no. 3, p. 273a - |x 0006-3495 |
| 856 | 4 | _ | |u https://www.sciencedirect.com/science/article/pii/S0006349523023986/pdfft?md5=604e1f41185155579621d3b9e4ff276a&pid=1-s2.0-S0006349523023986-main.pdf |
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