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Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries

Cell. 2024-02; 
Yu-Xi Tsai, Ning-En Chang, Klaus Reuter, Hao-Ting Chang, Tzu-Jing Yang, Sören von Bülow, Vidhi Sehrawat, Noémie Zerrouki, Matthieu Tuffery, Michae Gecht, Isabell Louise Grothaus, Lucio Colombi Ciacchi, Yong-Sheng Wang, Min-Feng Hsu, Kay-Hooi Khoo, Gerhard Hummer, Shang-Te Danny Hsu, Cyril Hanus , Mateusz Sikora
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Gene Synthesis The open reading frame of mouse N-cadherin cDNA (NCBI accession number: NP_031690.3) encompassing its entire ectodomain (EC1-EC5, residues 160-712) and domains EC4-EC5 (residues 331 to 542) were synthesized by GenScript. Get A Quote

摘要

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using... More

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