Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins

Maiti, Snigdha; Singh, Aakanksha; Maji, Tanisha; Saibo, Nikita V.; De, Soumya

doi:10.1016/j.crstbi.2024.100138

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Cited by 6 publications

(2 citation statements)

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“…The residue-wise stability of both EXD WT and EXD G290A was determined by NMR-based hydrogen exchange (HX) experiments ( Saibo et al, 2023 ; Maiti, 2024 ). For both EXD WT and EXD G290A protium-deuterium exchange rates were measured for the backbone amides at 25 °C and pH 5.5.…”

Section: Resultsmentioning

confidence: 99%

Stability and dynamics of extradenticle modulates its function

Singh,

Acharya,

Mukherjee

et al. 2024

Current Research in Structural Biology

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Section: Resultsmentioning

confidence: 99%

Stability and dynamics of extradenticle modulates its function

Singh,

Acharya,

Mukherjee

et al. 2024

Current Research in Structural Biology

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“…X-ray crystallography and cryo-EM are fairly impotent when characterizing IDRs, although cryo-EM maps do provide some information about IDRs approximate averaged location. Instead, nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET) are the methods of choice when it comes to experimental studies of IDRs. − …”

Section: Experimental Methodsmentioning

confidence: 99%

Predicting Conformational Ensembles of Intrinsically Disordered Proteins: From Molecular Dynamics to Machine Learning

Aupič,

Pokorná,

Ruthstein

et al. 2024

J. Phys. Chem. Lett.

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Intrinsically disordered proteins and regions (IDP/IDRs) are ubiquitous across all domains of life. Characterized by a lack of a stable tertiary structure, IDP/IDRs populate a diverse set of transiently formed structural states that can promiscuously adapt upon binding with specific interaction partners and/or certain alterations in environmental conditions. This malleability is foundational for their role as tunable interaction hubs in core cellular processes such as signaling, transcription, and translation. Tracing the conformational ensemble of an IDP/IDR and its perturbation in response to regulatory cues is thus paramount for illuminating its function. However, the conformational heterogeneity of IDP/IDRs poses several challenges. Here, we review experimental and computational methods devised to disentangle the conformational landscape of IDP/IDRs, highlighting recent computational advances that permit proteome-wide scans of IDP/IDRs conformations. We briefly evaluate selected computational methods using the disordered N-terminal of the human copper transporter 1 as a test case and outline further challenges in IDP/IDRs ensemble prediction.

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