by Nicola Salvi, Anton Abyzov, and Martin Blackledge

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Presentation transcript:

by Nicola Salvi, Anton Abyzov, and Martin Blackledge Solvent-dependent segmental dynamics in intrinsically disordered proteins by Nicola Salvi, Anton Abyzov, and Martin Blackledge Science Volume 5(6):eaax2348 June 28, 2019 Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

Fig. 1 Comparison of experimental and simulated NMR relaxation rates at 278 to 298 K. Comparison of experimental and simulated NMR relaxation rates at 278 to 298 K. (A) Experimental 15N transverse spin relaxation rates R2 (gray bars) measured on Ntail at different magnetic fields (columns) and temperatures (rows) are compared with the results of simulations C3P (blue line), C4P (orange), and A4P (purple). At all temperatures and fields, simulations in TIP4P/2005 capture the dynamics of Ntail better than simulations in TIP3P water (RMSD given in figs. S4 to S6). All rates are reported in s−1. Rates at 950 MHz are not shown in the interests of space. (B) Experimental 15N longitudinal spin relaxation rates (R1) measured on Ntail at different magnetic fields (columns) and temperatures (rows) [color code as in (A)]. All simulations reproduce, at least qualitatively, the sequence dependence of R2 rates, although simulations are more accurate at room temperature than at lower temperature. All rates are reported in s−1. (C) Experimental 15N{1H} steady-state NOEs measured on Ntail at different magnetic fields (columns) and temperatures (rows) [color code as in (A)]. Simulations in TIP4P/2005 reproduce the experimental values better than C3P, at all temperatures and at all fields (RMSD given in figs. S4 to S6). Nicola Salvi et al. Sci Adv 2019;5:eaax2348 Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

Fig. 2 Average time scales resulted from fitting segmental dynamics correlation functions in C3P (blue), C4P (orange), and A4P (purple). Average time scales resulted from fitting segmental dynamics correlation functions in C3P (blue), C4P (orange), and A4P (purple). Nicola Salvi et al. Sci Adv 2019;5:eaax2348 Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

Fig. 3 Illustration of inter- and intrasegment dynamics contributing to NMR relaxation. Illustration of inter- and intrasegment dynamics contributing to NMR relaxation. (A) We consider a time-dependent gyration tensor for each segment (here represented by an ellipsoid), as defined in (36). The gyration tensor is diagonalized by a rotation matrix expressed as a function of time-dependent angles θ and φ that are used to compute a correlation function that reports on the time fluctuations of the orientation of the segment in the laboratory frame. (B) In the model presented in (30), all the information regarding segmental motions is encoded in the relative orientation of peptide planes. We label α1, α2 … αn the n = N(N − 1)/2 time-dependent angles identified by two Cα-Cα vectors in a segment of N residues. We compute n correlation functions reporting on intrasegment dynamics. Nicola Salvi et al. Sci Adv 2019;5:eaax2348 Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

Fig. 4 Comparison of intrasegment dynamics and longest relaxation active time scale. Comparison of intrasegment dynamics and longest relaxation active time scale. Time scales associated with intrasegment dynamics at 298 K (red circles) in C3P (top), C4P (middle), and A4P (bottom) are compared with the longest time scale resulting from fitting segmental dynamics correlation functions (gray squares, see also fig. S7). Nicola Salvi et al. Sci Adv 2019;5:eaax2348 Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

Fig. 5 Segmental motional models derived from C4P reproduce overall NMR relaxation rates better than segmental motional models derived from C3P. Segmental motional models derived from C4P reproduce overall NMR relaxation rates better than segmental motional models derived from C3P. (A) Top: Length and position of segments derived from C3P (green) and C4P (blue) at 278 K. Bottom: Difference in χ2 of the central residue in the segment between C3P- and C4P-derived segmental models (χ2C3P and χ2C4P). (B and C) Similar representation for segments derived from ensembles of trajectories determined from C3P and C4P at 288 K and 298 K. Nicola Salvi et al. Sci Adv 2019;5:eaax2348 Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

Fig. 6 Comparison of properties of water models. Comparison of properties of water models. Self-diffusion coefficients (A) and lifetime of hydrogen bonds (B) in TIP3P (blue circles) and TIP4P/2005 (orange squares) water. Nicola Salvi et al. Sci Adv 2019;5:eaax2348 Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).