2024-01-25 マサチューセッツ大学アマースト校
◆新しい手法は、IDPによって仲介される相分離をシミュレートするためのもので、これは研究と説明が難しいプロセスでした。これにより、IDP相分離の分子レベルでの理解が進み、がんや神経変性疾患と関連する重要なタンパク質に関与する多くのプロセスが明らかになります。
<関連情報>
- https://www.umass.edu/news/article/umass-amherst-research-advances-molecular-modeling-biomolecular-condensates
- https://pubs.acs.org/doi/full/10.1021/jacs.3c09195
タンパク質の二次構造と相分離のカップリングの正確なシミュレーションに向けて Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation
Yumeng Zhang, Shanlong Li, Xiping Gong, and Jianhan Chen
Journal of the American Chemical Society Published:December 19, 2023
DOI:https://doi.org/10.1021/jacs.3c09195
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.
