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Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL

Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross...

Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase

of labor, the RNA- RNA modification; N6-methyladenosine; METTL3; target recognition domain; zinc finger; paramagnetic relaxation enhancement - Jinbo Huang, Xu Dong and Zhou Gong have contributed ... ; ZFD, zinc finger domain. COMPLIANCE WITH ETHICS GUIDELINES Jinbo Huang, Xu Dong, Zhou Gong, Ling-Yun Qin, Shuai Yang, YueLing Zhu, Xiang Wang, Delin Zhang, Tingting Zou, Ping Yin and Chun Tang declare

Conjoined Use of EM and NMR in RNA Structure Refinement

More than 40% of the RNA structures have been determined using nuclear magnetic resonance (NMR) technique. NMR mainly provides local structural information of protons and works most effectively on relatively small biomacromolecules. Hence structural characterization of large RNAs can be difficult for NMR alone. Electron microscopy (EM) provides global shape information of...

Visualizing the Ensemble Structures of Protein Complexes Using Chemical Cross-Linking Coupled with Mass Spectrometry

intermolecular cross-links identified for a stable seemingly incompatible cross-links identified with high complex with sub-lmol/L binding affinity. In contrast, we Zhou Gong and Yue-He Ding have contributed ... ). The research of C.T. was supported in part by an International Early Career Scientist Grant from the Howard Hughes Medical Institute. Compliance with Ethical Standards Conflict of Interest Zhou Gong

Insights into Ligand Binding to PreQ1 Riboswitch Aptamer from Molecular Dynamics Simulations

Riboswitches play roles in transcriptional or translational regulation through specific ligand binding of their aptamer domains. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, preQ1 riboswitch aptamer...

Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition

ScholarSearch for Wenxian Lan in:Nature Research journals • PubMed • Google ScholarSearch for Zhou Gong in:Nature Research journals • PubMed • Google ScholarSearch for Chun Tang in:Nature Research journals

Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition

A polyubiquitin comprises multiple covalently linked ubiquitins and recognizes myriad targets. Free or bound to ligands, polyubiquitins are found in different arrangements of ubiquitin subunits. To understand the structural basis for polyubiquitin quaternary plasticity and to explore the target recognition mechanism, we characterize the conformational space of Lys63-linked...

Computational Study of Unfolding and Regulation Mechanism of preQ1 Riboswitches

Riboswitches are novel RNA regulatory elements. Each riboswitch molecule consists of two domains: aptamer and express platform. The three-dimensional (3D) structure of the aptamer domain, depending on ligand binding or not, controls that of the express platform, which then switches on or off transcriptional or translational process. Here we study the two types of preQ1 riboswitch...

Automated and fast building of three-dimensional RNA structures

, Wuhan 430074, Hubei, ChinaYunjie Zhao, Yangyu Huang, Zhou Gong, Yanjie Wang, Jianfen Man & Yi Xiao AuthorsSearch for Yunjie Zhao in:Nature Research journals • PubMed • Google ScholarSearch for Yangyu ... Huang in:Nature Research journals • PubMed • Google ScholarSearch for Zhou Gong in:Nature Research journals • PubMed • Google ScholarSearch for Yanjie Wang in:Nature Research journals • PubMed • Google