Molecular movie of nucleotide binding to a motor protein

Bondar, Ana‐Nicoleta; Mishima, Hirokazu; Okamoto, Yuko

doi:10.1016/j.bbagen.2020.129654

Cited by 3 publications

(1 citation statement)

References 55 publications

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“…ADP binding also stabilized allosterically regions of the flexibility arc that lie several nanometers away from the nucleotide: the scaffold (attached to the ATPase motor in trans) and the stem (rooted in NBD1), which associate with each other, and the PBD, which is an extension of the stem (Figure S1C, II). These regions provide a physical pathway for the motor to communicate with the clamp (Bondar et al, 2020). Moreover, the stem, a13, and the 3b tip were overstabilized only in SecA 2 (Figures 4C and S5A, IV), due to preexisting, interprotomeric contacts in the wide-open state that explain its stability (Figure S1C, II-III).…”

Section: Seca Monomers Display Enhanced Local Dynamicsmentioning

confidence: 99%

A nexus of intrinsic dynamics underlies translocase priming

et al. 2021

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Section: Seca Monomers Display Enhanced Local Dynamicsmentioning

confidence: 99%

A nexus of intrinsic dynamics underlies translocase priming

et al. 2021

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Editorial: Advances in computational molecular biophysics

Baudry

Bondar

Cournia

et al. 2021

Biochimica et Biophysica Acta (BBA) - General Subjects

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A nexus of intrinsic dynamics underlies translocase priming

Krisnamurthy

Eleftheriadis

Karathanou

et al. 2021

Preprint

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SummaryThe cytoplasmic ATPase SecA and the membrane-embedded SecYEG channel assemble to form the functional Sec translocase. How this interaction primes and catalytically activates the translocase remains unclear. We now show that priming exploits a sophisticated nexus of intrinsic dynamics in SecA. Using atomistic simulations, single molecule FRET and hydrogen/deuterium exchange mass spectrometry we reveal multiple distributed dynamic islands that cross-talk with domain and quaternary motions. These dynamic elements are highly conserved and essential for function. Central to the nexus is a slender Stem through which, motions in the helicase ATPase domain of SecA biases how the preprotein binding domain rotates between open-closed clamping states. Multi-tier dynamics are enabled by an H-bonded framework covering most of the SecA structure and allowing conformational alterations with minimal energy inputs. As a result, dimerization, the channel and nucleotides select pre-existing conformations, and alter local dynamics to restrict or promote catalytic activity and clamp motions. These events prime the translocase for high affinity reception of non-folded preprotein clients. Such dynamics nexuses are likely universal and essential in multi-liganded protein machines.

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Molecular movie of nucleotide binding to a motor protein

Cited by 3 publications

References 55 publications

A nexus of intrinsic dynamics underlies translocase priming

A nexus of intrinsic dynamics underlies translocase priming

Editorial: Advances in computational molecular biophysics

A nexus of intrinsic dynamics underlies translocase priming

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