<scp>D</scp>ynamics of bridge helix bending in RNA polymerase II

Wang, Zhanfeng; Fu, Yiben; Wang, Peng‐Ye; Xie, Ping

doi:10.1002/prot.25239

Cited by 5 publications

(4 citation statements)

References 57 publications

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“…Our MD simulation procedures were described in detail elsewhere, 32,41,42 which were redescribed briefly as follows. The MD simulations were performed using GROMACS4.6 43 with AMBER99SB force field.…”

Section: Simulationsmentioning

confidence: 99%

All‐atom molecular dynamics simulations reveal how kinesin transits from one‐head‐bound to two‐heads‐bound state

et al. 2019

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Kinesin dimer walks processively along a microtubule (MT) protofilament in a hand‐over‐hand manner, transiting alternately between one‐head‐bound (1HB) and two‐heads‐bound (2HB) states. In 1HB state, one head bound by adenosine diphosphate (ADP) is detached from MT and the other head is bound to MT. Here, using all‐atom molecular dynamics simulations we determined the position and orientation of the detached ADP‐head relative to the MT‐bound head in 1HB state. We showed that in 1HB state when the MT‐bound head is in ADP or nucleotide‐free state, with its neck linker being undocked, the detached ADP‐head and the MT‐bound head have the high binding energy, and after adenosine triphosphate (ATP) binds to the MT‐bound head, with its neck linker being docked, the binding energy between the two heads is reduced greatly. These results reveal how the kinesin dimer retains 1HB state before ATP binding and how the dimer transits from 1HB to 2HB state after ATP binding. Key residues involved in the head‐head interaction in 1HB state were identified.

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Section: Simulationsmentioning

confidence: 99%

All‐atom molecular dynamics simulations reveal how kinesin transits from one‐head‐bound to two‐heads‐bound state

et al. 2019

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“…We used similar methods and conditions to those in our previous works [34][35][36][37] to do MD simulations. For convenience of reading, we re-describe them as follows.…”

Section: Simulation Methodsmentioning

confidence: 99%

Investigating role of conformational changes of microtubule in regulating its binding affinity to kinesin by all‐atom molecular dynamics simulation

Shi

Guo

et al. 2018

Proteins

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Changes of affinity of kinesin head to microtubule regulated by changes in the nucleotide state are essential to processive movement of kinesin on microtubule. Here, using all-atom molecular dynamics simulations we show that besides the nucleotide state, large conformational changes of microtubule-tubulin heterodimers induced by strong interaction with the head in strongly binding state are also indispensable to regulate the affinity of the head to the tubulin. In strongly binding state the high affinity of the head to microtubule arises largely from mutual conformational changes of the microtubule and head induced by the specific interaction between them via an induced-fit mechanism. Moreover, the ADP-head has a much weaker affinity to the local microtubule-tubulin, whose conformation is largely altered by the interaction with the head in strongly binding state, than to other unperturbed tubulins. This indicates that upon Pi release the ADP-head temporarily has a much weaker affinity to the local tubulin than to other tubulins.

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“…We followed a similar procedure to that done in our previous works. [27,[44][45][46] to do the simulations. All of the MD simulations were performed using GROMACS 4.6 [47] and the Amber03 Force Field.…”

Section: Simulationsmentioning

confidence: 99%

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

Wang¹,

Liu²,

Wang³

et al. 2017

Chinese Phys. B

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Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate (NTP) selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre-and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre-and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson-Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA-RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTP.

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Dynamics of bridge helix bending in RNA polymerase II

Cited by 5 publications

References 57 publications

All‐atom molecular dynamics simulations reveal how kinesin transits from one‐head‐bound to two‐heads‐bound state

All‐atom molecular dynamics simulations reveal how kinesin transits from one‐head‐bound to two‐heads‐bound state

Investigating role of conformational changes of microtubule in regulating its binding affinity to kinesin by all‐atom molecular dynamics simulation

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

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