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Patterns in Protein Flexibility: A Comparison of NMR "Ensembles", MD Trajectories, and Crystallographic B-Factors.
Reinknecht, Christopher; Riga, Anthony; Rivera, Jasmin; Snyder, David A.
Afiliação
  • Reinknecht C; Department of Chemistry, College of Science and Health, William Paterson University, 300 Pompton Rd, Wayne, NJ 07470, USA.
  • Riga A; Department of Chemistry, College of Science and Health, William Paterson University, 300 Pompton Rd, Wayne, NJ 07470, USA.
  • Rivera J; Department of Chemistry, College of Science and Health, William Paterson University, 300 Pompton Rd, Wayne, NJ 07470, USA.
  • Snyder DA; Department of Chemistry, College of Science and Health, William Paterson University, 300 Pompton Rd, Wayne, NJ 07470, USA.
Molecules ; 26(5)2021 Mar 09.
Article em En | MEDLINE | ID: mdl-33803249
ABSTRACT
Proteins are molecular machines requiring flexibility to function. Crystallographic B-factors and Molecular Dynamics (MD) simulations both provide insights into protein flexibility on an atomic scale. Nuclear Magnetic Resonance (NMR) lacks a universally accepted analog of the B-factor. However, a lack of convergence in atomic coordinates in an NMR-based structure calculation also suggests atomic mobility. This paper describes a pattern in the coordinate uncertainties of backbone heavy atoms in NMR-derived structural "ensembles" first noted in the development of FindCore2 (previously called Expanded FindCore DA Snyder, J Grullon, YJ Huang, R Tejero, GT Montelione, Proteins Structure, Function, and Bioinformatics 82 (S2), 219-230) and demonstrates that this pattern exists in coordinate variances across MD trajectories but not in crystallographic B-factors. This either suggests that MD trajectories and NMR "ensembles" capture motional behavior of peptide bond units not captured by B-factors or indicates a deficiency common to force fields used in both NMR and MD calculations.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Proteínas / Elasticidade / Resistência à Flexão Idioma: En Revista: Molecules Assunto da revista: BIOLOGIA Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Proteínas / Elasticidade / Resistência à Flexão Idioma: En Revista: Molecules Assunto da revista: BIOLOGIA Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos