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Neighbor effect on conformational spaces of alanine residue in azapeptides.
Lee, Ho-Jin; Liu, Shi-Wei; Sulyok-Eiler, Máté; Harmat, Veronika; Farkas, Viktor; Bánóczi, Zoltán; El Khabchi, Mouna; Shawn Fan, Hua-Jun; Hirao, Kimihiko; Song, Jong-Won.
Afiliação
  • Lee HJ; Division of Natural and Mathematics Sciences, LeMoyne-Own College, Memphis, TN, 38126, USA.
  • Liu SW; Department of Natural Sciences, Southwest Tennessee Community College, Memphis, TN, 38015, USA.
  • Sulyok-Eiler M; College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, PR China.
  • Harmat V; Laboratory of Structural Biology and Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary.
  • Farkas V; Hevesy György PhD School of Chemistry, Eötvös Loránd University, Budapest, Hungary.
  • Bánóczi Z; Laboratory of Structural Biology and Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary.
  • El Khabchi M; HUN-REN - ELTE Protein Modeling Research Group, Budapest, Hungary.
  • Shawn Fan HJ; Laboratory of Structural Biology and Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary.
  • Hirao K; HUN-REN - ELTE Protein Modeling Research Group, Budapest, Hungary.
  • Song JW; Department of Organic Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, 1117, Budapest, Hungary.
Heliyon ; 10(12): e33159, 2024 Jun 30.
Article em En | MEDLINE | ID: mdl-39021983
ABSTRACT
The conformational properties of Alanine (Ala) residue have been investigated to understand protein folding and develop force fields. In this work, we examined the neighbor effect on the conformational spaces of Ala residue using model azapeptides, Ac-Ala-azaGly-NHMe (3, AaG), and Ac-azaGly-Ala-NHMe (4, aGA1). Ramachandran energy maps were generated by scanning (φ, ψ) dihedral angles of the Ala residues in models with the fixed dihedral angles (φ = ±90°, ψ = ±0° or ±180°) of azaGly residue using LCgau-BOP and LCgau-BOP + LRD functionals in the gas and water phases. The integral-equation-formalism polarizable continuum model (IEF-PCM) and a solvation model density (SMD) were employed to mimic the solvation effect. The most favorable conformation of Ala residue in azapeptide models is found as the polyproline II (ßP), inverse γ-turn (γ'), ß-sheet (ßS), right-handed helix (αR), or left-handed helix (αL) depending on the conformation of neighbor azaGly residue in isolated form. Solvation methods exhibit that the Ala residue favors the ßP, δR, and αR conformations regardless of its position in azapeptides 3 and 4 in water. Azapeptide 5, Ac-azaGly-Ala-NH2 (aGA2), was synthesized to evaluate the theoretical results. The X-ray structure showed that azaGly residue adopts the polyproline II (ßP) and Ala residue adopts the right-handed helical (αR) structure in aGA2. The conformational preferences of aGA2 and the dimer structure of aGA2 based on the X-ray structure were examined to assess the performance of DFT functionals. In addition, the local minima of azapeptide 6, Ac-Phe-azaGly-NH2 (FaG), were compared with the previous experimental results. SMD/LCgau-BOP + LRD methods agreed well with the reported experimental results. The results suggest the importance of weak dispersion interactions, neighbor effect, and solvent influence in the conformational preferences of Ala residue in model azapeptides.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Heliyon Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Estados Unidos País de publicação: Reino Unido
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Heliyon Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Estados Unidos País de publicação: Reino Unido