Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling.

The biological function of proteins is determined not only by their static structures but also by the dynamic properties of their conformational ensembles. Numerous high-accuracy static structure prediction tools have been recently developed based on deep learning; however, there remains a lack of efficient and accurate methods for exploring protein dynamic conformations. Traditionally, studies concerning protein dynamics have relied on molecular dynamics (MD) simulations, which incur significant computational costs for all-atom precision and struggle to adequately sample conformational spaces with high energy barriers. To overcome these limitations, various enhanced sampling techniques have been developed to accelerate sampling in MD. Traditional enhanced sampling approaches like replica exchange molecular dynamics (REMD) and frontier expansion sampling (FEXS) often follow the MD simulation approach and still cost a lot of computational resources and time. Variational autoencoders (VAEs), as a classic deep generative model, are not restricted by potential energy landscapes and can explore conformational spaces more efficiently than traditional methods. However, VAEs often face challenges in generating reasonable conformations for complex proteins, especially intrinsically disordered proteins (IDPs), which limits their application as an enhanced sampling method. In this study, we presented a novel deep learning model (named Phanto-IDP) that utilizes a graph-based encoder to extract protein features and a transformer-based decoder combined with variational sampling to generate highly accurate protein backbones. Ten IDPs and four structured proteins were used to evaluate the sampling ability of Phanto-IDP. The results demonstrate that Phanto-IDP has high fidelity and diversity in the generated conformation ensembles, making it a suitable tool for enhancing the efficiency of MD simulation, generating broader protein conformational space and a continuous protein transition path.

Direct and Detailed Site-Specific Glycopeptide Characterization by Higher-Energy Electron-Activated Dissociation Tandem Mass Spectrometry.

Glycosylation is widely recognized as the most complex post-translational modification due to the widespread presence of macro- and microheterogeneities, wherein its biological consequence is closely related to both the glycosylation sites and the glycan fine structures. Yet, efficient site-specific detailed glycan characterization remains a significant analytical challenge. Here, utilizing an Orbitrap-Omnitrap platform, higher-energy electron-activated dissociation (heExD) tandem mass spectrometry (MS/MS) revealed extraordinary efficacy for the structural characterization of intact glycopeptides. HeExD produced extensive fragmentation within both the glycan and the peptide, including A-/B-/C-/Y-/Z-/X-ions from the glycan motif and a-/b-/c-/x-/y-/z-type peptide fragments (with or without the glycan). The intensity of cross-ring cleavage and backbone fragments retaining the intact glycan was highly dependent on the electron energy. Among the four electron energy levels investigated, electronic excitation dissociation (EED) provided the most comprehensive structural information, yielding a complete series of glycosidic fragments for accurate glycan topology determination, a wealth of cross-ring fragments for linkage definition, and the most extensive peptide backbone fragments for accurate peptide sequencing and glycosylation site localization. The glycan fragments observed in the EED spectrum correlated well with the fragmentation patterns observed in EED MS/MS of the released glycans. The advantages of EED over higher-energy collisional dissociation (HCD), stepped collision energy HCD (sceHCD), and electron-transfer/higher-energy collisional dissociation (EThcD) were demonstrated for the characterization of a glycopeptide bearing a biantennary disialylated glycan. EED can produce a complete peptide backbone and glycan sequence coverage even for doubly protonated precursors. The exceptional performance of heExD MS/MS, particularly EED MS/MS, in site-specific detailed glycan characterization on an Orbitrap-Omnitrap hybrid instrument presents a novel option for in-depth glycosylation analysis.

p-TAK1 acts as a switch between myoblast proliferation phase and differentiation phase in mdx mice via regulating HO-1 expression.

Skeletal muscle transforming growth factor-ß-activated kinase 1 (TAK1) continuous excessive phosphorylation was observed in Duchenne muscular dystrophy (DMD) patients and mdx mice. Inhibiting TAK1 phosphorylation ameliorated fibrosis and muscular atrophy, while TAK1 knockout also impaired muscle regeneration. The definite effect and mechanism of p-TAK1 in muscle regeneration disorder is still obscure. In this study, BaCl2-induced acute muscle injury model was used to investigate the role of p-TAK1 in myoblast proliferation and differentiation phase. The results showed that TAK1 phosphorylation was significantly up-regulated in proliferation phase along with Keap1/Nrf2/HO-1 signaling pathway activation, which was down-regulated in differentiation phase yet. In C2C12 cells, inhibiting TAK1 phosphorylation markedly suppressed the expression of heme oxygenase-1 (HO-1), and both myoblast proliferation and differentiation were inhibited. As for activation, p-TAK1 promoted myoblast proliferation via up-regulating HO-1 level. However, excessive TAK1 phosphorylation (induced by 20 ng·mL-1 TGF-ß1) notably up-regulated HO-1 expression, inhibiting myogenic differentiation antigen (MyOD) and myogenic differentiation. A mild p-TAK1 level (induced by 5 or 10 ng·mL-1 TGF-ß1) was beneficial for myoblast differentiation. In mdx mice, robust myoblast proliferation and differentiation arrest were observed with high p-TAK1 level in skeletal muscle. HO-1 expression was significantly up-regulated. TAK1 phosphorylation inhibitor NG25 (N-[4-[(4-ethylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl]-4-methyl-3-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)benzamide) significantly inhibited HO-1 expression, relieved excessive myoblast proliferation and differentiation arrest, promoted new myofiber formation, and eventually improved muscle function. In conclusion, p-TAK1 acted as "a switch" between proliferation and differentiation phase. Mitigating p-TAK1 level transformed myoblast excessive proliferation phase into differentiation phase in mdx mouse via regulating HO-1 expression.