Elucidating the mechanisms underlying protein conformational switching using NMR spectroscopy

Jain, Srishti; Sekhar, Ashok

doi:10.1016/j.jmro.2022.100034

Cited by 3 publications

(3 citation statements)

References 135 publications

(101 reference statements)

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“…The present simulations require prior knowledge of all the microscopic forward and reverse rate constants. Those can be purely theoretical, but they can also be obtained owing to recent advances in molecular dynamics simulations [43] and in experimental techniques like fluorescence and nuclear magnetic resonance spectroscopy [56].…”

Section: Discussionmentioning

confidence: 99%

Competition in drug binding and … the race to equilibrium

Vauquelin

Maes

2022

Fundamemntal Clinical Pharma

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Binding kinetics has become a popular topic in pharmacology due to its potential contribution to the selectivity and duration of drug action. Yet, the overall kinetic aspects of complex binding mechanisms are still merely described in terms of elaborate algebraic equations. Interestingly, it has been recommended some 10 years ago to examine such mechanisms in terms of binding fluxes instead of the conventional rate constants. Alike the velocity of product formation in enzymology, those fluxes refer to the velocity by which one target species converts into another one. Novel binding flux‐based approaches are utilized to get a better visual insight into the “competition” between two drugs/ligands for a single target as well as between induced fit‐ and conformational selection pathways for a single ligand within a thermodynamic cycle. The present data were obtained by differential equation‐based simulations. Early on, the ligand‐binding steps “race” to equilibrium (i.e., when their forward and reverse fluxes are equal) at their individual pace. The overall/global equilibrium is only reached later on. For the competition association assays, this parting might produce a transient “overshoot” of one of the bound target species. A similar overshoot may also show up within a thermodynamic cycle and, at first glance, suggest that the induced fit pathway dominates. Yet, present findings show that under certain circumstances, it could rather be the other way round. Novel binding flux‐based approaches offer visually attractive insights into crucial aspects of “complex” binding mechanisms under non‐equilibrium conditions.

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Section: Discussionmentioning

confidence: 99%

Competition in drug binding and … the race to equilibrium

Vauquelin

Maes

2022

Fundamemntal Clinical Pharma

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“…1,2 In the case of NMR spectroscopy, the obtained spectra carry information related to the quantum mechanical properties of the nucleus of each atom present and can be used to provide crucial details about the structural configurations, reaction mechanisms, molecular dynamics, chemical equilibrium and even crystalline structures in solids. [3][4][5][6][7][8][9][10] Since the spectrum digitalization carries relevant information from the compound at the molecular level, it can be useful as an input parameter for the development of mathematical models to perform the prediction of important physicochemical properties. [11][12][13] The chemical information of the NMR technique is presented through chemical shift, intensity and multiplicity.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

SpectraFP: a new spectra-based descriptor to aid in cheminformatics, molecular characterization and search algorithm applications

Dias-Silva

Oliveira

Sanches-Neto

et al. 2023

Phys. Chem. Chem. Phys.

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Transient excited states of the metamorphic protein Mad2 and their implications for function

Jain,

Sekhar

2024

Proteins

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The spindle checkpoint complex is a key surveillance mechanism in cell division that prevents premature separation of sister chromatids. Mad2 is an integral component of this spindle checkpoint complex that recognizes cognate substrates such as Mad1 and Cdc20 in its closed (C‐Mad2) conformation by fastening a “seatbelt” around short peptide regions that bind to the substrate recognition site. Mad2 is also a metamorphic protein that adopts not only the fold found in C‐Mad2, but also a structurally distinct open conformation (O‐Mad2) which is incapable of binding substrates. Here, we show using chemical exchange saturation transfer (CEST) and relaxation dispersion (CPMG) NMR experiments that Mad2 transiently populates three other higher free energy states with millisecond lifetimes, two in equilibrium with C‐Mad2 (E1 and E2) and one with O‐Mad2 (E3). E1 is a mimic of substrate‐bound C‐Mad2 in which the N‐terminus of one C‐Mad2 molecule inserts into the seatbelt region of a second molecule of C‐Mad2, providing a potential pathway for autoinhibition of C‐Mad2. E2 is the “unbuckled” conformation of C‐Mad2 that facilitates the triage of molecules along competing fold‐switching and substrate binding pathways. The E3 conformation that coexists with O‐Mad2 shows fluctuations at a hydrophobic lock that is required for stabilizing the O‐Mad2 fold and we hypothesize that E3 represents an early intermediate on‐pathway towards conversion to C‐Mad2. Collectively, the NMR data highlight the rugged free energy landscape of Mad2 with multiple low‐lying intermediates that interlink substrate‐binding and fold‐switching, and also emphasize the role of molecular dynamics in its function.

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Elucidating the mechanisms underlying protein conformational switching using NMR spectroscopy

Cited by 3 publications

References 135 publications

Competition in drug binding and … the race to equilibrium

Competition in drug binding and … the race to equilibrium

SpectraFP: a new spectra-based descriptor to aid in cheminformatics, molecular characterization and search algorithm applications

Transient excited states of the metamorphic protein Mad2 and their implications for function

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