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2.6. Redesigning the protein–protein interface

JY Jingyi Yang
ZZ Zhao Zhang
FY Fengyuan Yang
HZ Haiwei Zhang
HW Haibo Wu
FZ Feng Zhu
WX Weiwei Xue
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The protein–protein interface redesign was carried out by RosettaDesign (Mandell et al., 2009; Wang et al., 2007) in two steps. First, Rosetta fast relax (Nivon et al., 2013) was performed on the PDB files of Nb bound RBD complex taken from the MD simulations. The chain ID of the complex was deleted before running the relax protocol. Then, a resfile which specifies the residues need to be redesigned was used to run the fixbb protocol (Huang et al., 2011) in the Rosetta. For each Nb‐RBD complex, sequence alignment shows that the interface redesign may generate the same Nb sequences, and Nbs with different sequences among the top 5 redesigned structures were selected for further MD simulations and binding free energies calculation analysis using the same setup as mentioned above.

Copyright and License information:  ©2021 John Wiley & Sons A/S.
This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.

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