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QM/MM study of N501 involved intermolecular interaction between SARS-CoV-2 receptor binding domain and antibody of human origin.
Liu, Yuemin; Sulaiman, Hana F; Johnson, Bruce R; Ma, Rulong; Gao, Yunxiang; Fernando, Harshica; Amarasekara, Ananda; Ashley-Oyewole, Andrea; Fan, Huajun; Ingram, Heaven N; Briggs, James M.
  • Liu Y; Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America; Department of Chemistry, Rice University, Houston, TX 77005, the United States of America. Electronic address: yeliu@pvamu.edu.
  • Sulaiman HF; Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America.
  • Johnson BR; Department of Chemistry, Rice University, Houston, TX 77005, the United States of America.
  • Ma R; Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, the United States of America.
  • Gao Y; Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America.
  • Fernando H; Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America.
  • Amarasekara A; Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America.
  • Ashley-Oyewole A; Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America.
  • Fan H; College of Chemical Engineering, Sichuan University Science and Engineering, Zigong, Sichuan 643000, PR China.
  • Ingram HN; Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America.
  • Briggs JM; Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, the United States of America.
Comput Biol Chem ; 102: 107810, 2023 Feb.
Article in English | MEDLINE | ID: covidwho-2165190
ABSTRACT
Intermolecular interaction between key residue N501 of the epitope on SARS-CoV-2 RBD and screening antibody B38 was studied using the QM/MM and QM approach. The QM/MM optimized geometry shows that angle X-H---Y is 165° for O-H---O between mAb light chain S30 and RBD N501. High level MP2 calculations indicated the interaction between RBD N501 and S30 of B38 Fab light chain provide a relatively strong attractive force of - 3.32 kcal/mol, whereas the hydrogen bond between RBD Q498 and S30 was quantified as 0.10 kcal/mol. The decrease in ESP partial charge on hydrogen atom of hydroxyl group on S30 drops from 0.38 a.u. to 0.31 a.u., exhibiting the sharing of 0.07 a.u. from the lone pair electron oxygen of N501 due to hydrogen bond formation. The NBO occupancy of hydrogen atom also decreases from 25.79 % to 22.93 % in the hydroxyl H-O NBO bond of S30. However, the minor change of NBO hybridization of hydroxyl oxygen of S30 from sp3.00 to sp3.05 implies the rigidity of hydrogen bond tetrahedral geometry in the relative dynamic protein complex. The O-H---O angle is 165° which is close but not exactly linear. The structural requirement for sp3 hybridization of oxygen for hydroxyl group on S30 and dimension of protein likely prevent O-H---O from adopting linear geometry. The hydrogen bond strengths were also calculated using a variety of DFT methods, and the result of - 3.33 kcal/mol from the M06L method is the closest to that of the MP2 calculation. Results of this work may aid in the COVID-19 vaccine and drug screening.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Topics: Vaccines Limits: Humans Language: English Journal: Comput Biol Chem Journal subject: Biology / Medical Informatics / Chemistry Year: 2023 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Topics: Vaccines Limits: Humans Language: English Journal: Comput Biol Chem Journal subject: Biology / Medical Informatics / Chemistry Year: 2023 Document Type: Article