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The Biomolecular Dynamics group in the Innovation Academy for Precision Measurement Science and Technology (APM) of the Chinese Academy of Sciences has developed new methods to study protein dynamics

       Recently, Dr. Zhou Gong (an Associate Professor at the APM) and Tang Chun (a Professor at the APM) published a Resource article entitled "Tightening the crosslinking distance restraints for better resolution of protein structure and dynamics." They developed a new method to study protein structure and dynamics based on chemical crosslinking coupled with mass spectrometry (CXMS)

Characterizing protein dynamics can uncover the mechanism for protein function. Chemical crosslinking coupled with highly sensitive mass spectrometry is a structural biology technology developed in recent ten years. The distance information between specific amino acids in protein can be obtained by crosslinking. CXMS is becoming more popular owing to its high sensitivity and no limitation on the molecular weight of the protein system. CXMS distance restraints are usually applied to Cα or Cβ atoms of the crosslinked residues, with upper bounds over 20 ?. The incorporation of loose CXMS restraints only marginally improves the resolution of the calculated structures. The research group compared and analyzed published CXMS experimental data. With the inspiration from nuclear magnetic resonance, they developed a new method of using the Cω atom as the distance restraint point. With the flexible side-chain explicitly represented, the reformatted restraint can be applied to the modification group instead, with an upper bound of 6 ? or less. The use of the new type of restraints not only affords better-resolved structures but also uncovers protein dynamics.

Dr. Gong Zhou is the first author on this paper, and Dr. Tang Chun is the corresponding author. Shang-Xiang Ye is a Ph.D. student in the joint program of APM and Huazhong University of Science and Technology, also took part in this work. The research was supported by the Ministry of Science and Technology of China and the National Natural Science Foundation of China.

The Biomolecular Dynamics group has a keen interest in developing new methods for characterizing biomolecular dynamics. They have published several papers on the computational analysis of CXMS data, which include the development of CXMS calculation methods to study the dynamic structures of protein complexes (Biophys Rep, 2015,1:127-138), modeling of the protein excited-state structures from "over-length" chemical crosslinks (J Biol Chem, 2017,292:1187-1196), developing the new method integrates CXMS, Small-angle X-ray scattering, and single-molecule FRET data (Biochemistry, 2018, 57:305-313). Recently, they also systematically characterized the distribution characteristics of crosslinking distance, and proposed a more accurate crosslinking distance distribution model (J Phys Chem B, 2020, 123:4446-4453). It is worth mentioning that the bulk work of the two recent papers was done during the epidemic period of COVID-19 from February to April this year. At that time, Wuhan was in a lockdown, and the laboratory was also shut. The research group thus performed data analysis, structural calculation, and simulation all by working from home.

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