Change in binding states between catabolite activating protein and DNA induced by ligand-binding: molecular dynamics and ab initio fragment molecular orbital calculations

Anan, Ryo; Nakamura, Toshiya; Shimamura, Kanako; Matsushita, Yushu; Ohyama, Tatsuya; Kurita, Noriyuki

doi:10.1007/s00894-019-4087-3

Cited by 6 publications

(4 citation statements)

References 30 publications

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“…This method was recently used to analyze the interaction energy in different biomolecular systems. 33,62–66…”

Section: Methodsmentioning

confidence: 99%

“…This method was recently used to analyze the interaction energy in different biomolecular systems. 33,[62][63][64][65][66] To understand the inhibitory effect of the aromatic naphthyl linker of 17 and 18 and compare the differences in interactions between 17 (or 18) and dGMII, and JBMan, the inhibitors were divided into two fragments, the pyrrolidine ring structure (I ring ) and the naphthyl linker (I linker ). Then, the interaction energy between the inhibitor and the enzyme (ΔE I-E ) consists of the interaction energy between the pyrrolidine ring of the inhibitor and the enzyme (ΔE ring-E ) and the interaction energy between the linker of the inhibitor and the enzyme (ΔE linker-E ):…”

Section: Papermentioning

confidence: 99%

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1,4-Dideoxy-1,4-imino-d- andl-lyxitol-based inhibitors bind to Golgi α-mannosidase II in different protonation forms

et al. 2022

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“…This method was recently used to analyze the interaction energy in different biomolecular systems. 33,62–66…”

Section: Methodsmentioning

confidence: 99%

Section: Papermentioning

confidence: 99%

1,4-Dideoxy-1,4-imino-d- andl-lyxitol-based inhibitors bind to Golgi α-mannosidase II in different protonation forms

et al. 2022

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“…ΔGR:L sol is solute-solvent solvation free energy. This method was recently used to analyze interaction energy in different biomolecular systems (Lim et al 2019;Sogawa et al 2020;Anan et al 2019;Sladek et al 2017;Sladek et al 2018;Takaya et al 2020;Sladek and Fedorov 2022;Kalník et al 2023;Mironov et al 2022).…”

Section: Methodsmentioning

confidence: 99%

Comparative study of interaction energies between αIIbβ3 integrin and the peptidic, peptidomimetic and non-peptidic ligands by quantum mechanics FMO-PIEDA calculations

Kóňa

2023

Preprint

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Integrins are one of the major families of cell adhesion receptors. The recognition of the vital roles of integrins in various diseases revealed their therapeutic potential. To better understand an adhesion mechanism of integrins, pair interaction energy decomposition analysis (PIEDA) along the two-body fragmented molecular orbital (FMO) method was used. Interaction energies were evaluated between the amino acid residues including Mg2+ and Ca2+ ions at ligand-binding site of αIIbβ3 integrin and two peptide chains with the Ala-Gly-Asp and the Arg-Gly-Asp binding motifs, a cyclic peptide (eptifibatide), peptidomimetic ligands (tirofiban and L-739758) and poly(L-lactic acid) chain (PLA). The results indicate that Mg2+ and Ca2+ ions together with Asp224A, Asn215B, Asp159A and Lys125B of αIIbβ3 are the most important residues for a binding of the peptidic ligands while for the peptidomimetic ligands and PLA, interactions with Ca2+ ions are less significant than those with amino acid residues of αIIbβ3. For all complexes a dominant part of interaction energy comes from electrostatic interactions. Based on optimized geometries at the quantum mechanics/molecular mechanics (QM/MM) level an interaction pattern predicted for PLA was compared with the native peptidic ligands.

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“…A large number of experimental − and computational ,− studies examining the allosteric coupling between cAMP binding sites and the DNA binding domains have shown that upon binding to cAMP-loaded CAP the DNA duplex is bent to optimize the electrostatic complementarity between the DNA and CAP . Although earlier studies have shown that the apo- and singly loaded CAP have been known to recognize and bind to DNA, their binding affinity for DNA is significantly lower than that of doubly loaded CAP .…”

Section: Introductionmentioning

confidence: 99%

Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding

Prabhakant

Panigrahi

Krishnan

2020

J. Chem. Inf. Model.

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The homodimeric catabolite activator protein (CAP) regulates the transcription of several bacterial genes based on the cellular concentration of cyclic adenosine monophosphate (cAMP). The binding of cAMP to CAP triggers allosteric communication between the cAMP binding domains (CBD) and DNA binding domains (DBD) of CAP, which entails repositioning of DNA recognition helices (F-helices) in the DBD to dock favorably to the target DNA. Despite considerable progress, much remains to be understood about the mechanistic details of DNA recognition by CAP and about the map of allosteric pathways involved in CAP-mediated gene transcription. The present study uses molecular dynamics and umbrella sampling simulations to investigate the mechanism of cAMP-and DNAinduced changes in the conformation and energetics of F-helices observed during the allosteric regulation of CAP by cAMP and the subsequent binding to the DNA promoter region. Using novel collective variables, the free energy profiles associated with the orientation and dynamics of F-helices in the unliganded, cAMP-bound, and cAMP-DNA-bound states of CAP are calculated and compared. The binding-induced alterations in the resultant free energy profiles reveal important flexibility constraints imposed on DBD upon cAMP and DNA binding. A comprehensive analysis of residue-wise interaction maps reveals potential allosteric pathways between CBD and DBD that facilitate the allosteric transduction of regulatory signals in CAP. The revelation that the predicted allosteric pathways crisscross the intersubunit interface offers important clues on the microscopic origin of the intersubunit cooperativity and dimer stability of CAP.

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Change in binding states between catabolite activating protein and DNA induced by ligand-binding: molecular dynamics and ab initio fragment molecular orbital calculations

Cited by 6 publications

References 30 publications

1,4-Dideoxy-1,4-imino-d- andl-lyxitol-based inhibitors bind to Golgi α-mannosidase II in different protonation forms

1,4-Dideoxy-1,4-imino-d- andl-lyxitol-based inhibitors bind to Golgi α-mannosidase II in different protonation forms

Comparative study of interaction energies between αIIbβ3 integrin and the peptidic, peptidomimetic and non-peptidic ligands by quantum mechanics FMO-PIEDA calculations

Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding

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