Combining Free Energy Simulations and NMR Chemical-Shift Perturbation To Identify Transient Cation-pi Contacts in Proteins

Autor(es)

Reis, Andre A. O. ^[1] ; Sayegh, Raphael S. R. ^[1] ; Marana, Sandro R. ^[1] ; Arantes, Guilherme M. ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Inst Quim, Dept Biochem, Av Prof Lineu Prestes 748, BR-05508900 Sao Paulo, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: JOURNAL OF CHEMICAL INFORMATION AND MODELING; v. 60, n. 2, p. 890-897, FEB 2020.
• Citações Web of Science: 1

Resumo

Flexible protein regions containing cationic and aromatic side-chains exposed to solvent may form transient cation-pi interactions with structural and functional roles. To evaluate their stability and identify important intramolecular cation-pi contacts, a combination of free energy profiles estimated from umbrella sampling with molecular dynamics simulations and chemical shift perturbations (CSP) obtained from nuclear magnetic resonance (NMR) experiments is applied here to the complete catalytic domain of human phosphatase Cdc25B. This protein is a good model system for transient cation-pi interactions as it contains only one Trp residue (W550) in the disordered C-terminal segment and a total of 17 Arg residues, many exposed to solvent. Eight putative Arg-Trp pairs were simulated here. Only R482 and R544 show bound profiles corresponding to important transient cation-pi interactions, while the others have dissociative or almost flat profiles. These results are corroborated by CSP analysis of three Cdc25B point mutants (W550A, R482A, and R544A) disrupting cation-pi contacts. The proposed validation of statistically representative molecular simulations by NMR spectroscopy could be applied to identify transient contacts of proteins in general but carefully, as NMR chemical shifts are sensitive to changes in both molecular contacts and conformational distributions. (AU)

• Processo FAPESP: 18/25952-8 - Catálise e Termoestabilidade em Enzimas: Efeitos da Oligomerização, Redes Estruturais e Dinâmica
• Beneficiário: Sandro Roberto Marana
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 16/22365-9 - Redes estruturais e dinâmica em enzimas
• Beneficiário: Sandro Roberto Marana
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 16/24096-5 - Simulação computacional de metaloenzimas e de proteínas flexíveis
• Beneficiário: Guilherme Menegon Arantes
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 12/00543-1 - Reconhecimento de Inibidores e Flexibilidade da Fosfatase Cdc25B
• Beneficiário: Raphael Santa Rosa Sayegh
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 18/08311-9 - Bioquímica inorgânica computacional & computação de alta-performance
• Beneficiário: Guilherme Menegon Arantes
• Modalidade de apoio: Auxílio à Pesquisa - Regular