Analytical and functional aspects of protein-ligand interactions: Beyond induced fit and conformational selection.
Sign Up to like & getrecommendations! Published in 2021 at "Archives of biochemistry and biophysics"
DOI: 10.1016/j.abb.2021.109064
Abstract: Ligand-dependent changes in protein conformation are foundational to biology. Historical mechanistic models for substrate-specific proteins are induced fit (IF) and conformational selection (CS), which invoke a change in protein conformation after ligand binds or before… read more here.
Keywords: protein; conformational selection; analytical functional; induced fit ... See more keywords
Conformational selection and induced fit as a useful framework for molecular motor mechanisms.
Sign Up to like & getrecommendations! Published in 2017 at "Biophysical chemistry"
DOI: 10.1016/j.bpc.2017.01.004
Abstract: The linkage between macromolecular binding and conformational change that is ubiquitous in biological molecules can be understood in the context of the mechanisms of conformational selection and induced fit. Here, we explore mappings between these… read more here.
Keywords: conformational selection; fit useful; selection induced; mechanisms conformational ... See more keywords
Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00371
Abstract: Homology models have been used for virtual screening and to understand the binding mode of a known active compound; however, rarely have the models been shown to be of sufficient accuracy, comparable to crystal structures,… read more here.
Keywords: energy perturbation; induced fit; homology models; free energy ... See more keywords
Expanding Coefficient: A Parameter To Assess the Stability of Induced-Fit Complexes
Sign Up to like & getrecommendations! Published in 2021 at "Organic Letters"
DOI: 10.1021/acs.orglett.1c00165
Abstract: Here we propose a new parameter, the Expanding Coefficient (EC), that can be correlated with the thermodynamic stability of supramolecular complexes governed by weak secondary interactions and obeying the induced-fit model. The EC values show… read more here.
Keywords: expanding coefficient; stability; induced fit; coefficient parameter ... See more keywords
An induced-fit model for asymmetric organocatalytic reactions: a case study of the activation of olefins via chiral Brønsted acid catalysts
Sign Up to like & getrecommendations! Published in 2022 at "Chemical Science"
DOI: 10.1039/d2sc02274e
Abstract: We elucidate the stereo-controlling factors of the asymmetric intramolecular hydroalkoxylation of terminal olefins catalyzed by bulky Brønsted acids [Science2018, 359 (6383), 1501–1505] using high-level electronic structure methods. The catalyst–substrate interaction is described using a dispersion-driven… read more here.
Keywords: induced fit; dispersion; model; model asymmetric ... See more keywords
An induced-fit de novo initiation mechanism suggested by a pestivirus RNA-dependent RNA polymerase
Sign Up to like & getrecommendations! Published in 2021 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkab666
Abstract: Abstract Viral RNA-dependent RNA polymerases (RdRPs) play central roles in the genome replication and transcription processes of RNA viruses. RdRPs initiate RNA synthesis either in primer-dependent or de novo mechanism, with the latter often assisted… read more here.
Keywords: initiation; rna dependent; rna; dependent rna ... See more keywords
Crystal structures of PigF, an O-methyltransferase involved in the prodigiosin synthetic pathway, reveal an induced-fit substrate-recognition mechanism
Sign Up to like & getrecommendations! Published in 2022 at "IUCrJ"
DOI: 10.1107/s2052252521011696
Abstract: Crystal structures of apo and SAH-bound PigF were determined and structural analyses revealed an induced-fit substrate-recognition model. read more here.
Keywords: substrate recognition; crystal structures; induced fit; fit substrate ... See more keywords
High-speed AFM reveals accelerated binding of agitoxin-2 to a K+ channel by induced fit
Sign Up to like & getrecommendations! Published in 2019 at "Science Advances"
DOI: 10.1126/sciadv.aax0495
Abstract: We revealed that binding of agitoxin-2 to a K+ channel uses an induced-fit pathway by single-molecule analysis via high-speed AFM. Agitoxin-2 (AgTx2) from scorpion venom is a potent blocker of K+ channels. The docking model… read more here.
Keywords: agitoxin; channel; induced fit; agtx2 ... See more keywords