Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: Insights from accelerated molecular dynamics simulations

Juan Bueren-Calabuig (Lead / Corresponding author), Marcus Bage, Victoria Cowling, Andrei Pisliakov (Lead / Corresponding author)

Research output: Contribution to journalArticle

22 Downloads (Pure)

Abstract

The RNA guanine-N7 methyltransferase (RNMT) in complex with RNMT-Activating Miniprotein (RAM) catalyses the formation of a N7-methylated guanosine cap structure on the 5’ end of nascent RNA polymerase II transcripts. The mRNA cap protects the primary transcript from exonucleases and recruits cap-binding complexes that mediate RNA processing, export and translation. By using microsecond standard and accelerated molecular dynamics simulations, we provide for the first time a detailed molecular mechanism of allosteric regulation of RNMT by RAM. We show that RAM selects the RNMT active site conformations that are optimal for binding of substrates (AdoMet and the cap), thus enhancing their affinity. Furthermore, our results strongly suggest the likely scenario in which the cap binding promotes the subsequent AdoMet binding, consistent with the previously suggested cooperative binding model. By employing the network community analyses, we revealed the underlying long-range allosteric networks and paths that are crucial for allosteric regulation by RAM. Our findings complement and explain previous experimental data on RNMT activity. Moreover, this study provides the most complete description of the cap and AdoMet binding poses and interactions within the enzyme’s active site. This information is critical for the drug discovery efforts that consider RNMT as a promising anti-cancer target.
Original languageEnglish
Article numbergkz613
JournalNucleic Acids Research
Volume1
DOIs
Publication statusPublished - 22 Jul 2019

Fingerprint

Guanine
Methyltransferases
Molecular Dynamics Simulation
RNA
S-Adenosylmethionine
Allosteric Regulation
Catalytic Domain
Exonucleases
RNA Polymerase II
Guanosine
Drug Discovery
mRNA (guanine(N7))-methyltransferase
Messenger RNA
Enzymes
Neoplasms

Keywords

  • RNMT
  • allosteric activation
  • accelerated molecular dynamics
  • conformational selection
  • mRNA cap

Cite this

@article{c67a2e6b59db400c804f6d913de05201,
title = "Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: Insights from accelerated molecular dynamics simulations",
abstract = "The RNA guanine-N7 methyltransferase (RNMT) in complex with RNMT-Activating Miniprotein (RAM) catalyses the formation of a N7-methylated guanosine cap structure on the 5’ end of nascent RNA polymerase II transcripts. The mRNA cap protects the primary transcript from exonucleases and recruits cap-binding complexes that mediate RNA processing, export and translation. By using microsecond standard and accelerated molecular dynamics simulations, we provide for the first time a detailed molecular mechanism of allosteric regulation of RNMT by RAM. We show that RAM selects the RNMT active site conformations that are optimal for binding of substrates (AdoMet and the cap), thus enhancing their affinity. Furthermore, our results strongly suggest the likely scenario in which the cap binding promotes the subsequent AdoMet binding, consistent with the previously suggested cooperative binding model. By employing the network community analyses, we revealed the underlying long-range allosteric networks and paths that are crucial for allosteric regulation by RAM. Our findings complement and explain previous experimental data on RNMT activity. Moreover, this study provides the most complete description of the cap and AdoMet binding poses and interactions within the enzyme’s active site. This information is critical for the drug discovery efforts that consider RNMT as a promising anti-cancer target.",
keywords = "RNMT, allosteric activation, accelerated molecular dynamics, conformational selection, mRNA cap",
author = "Juan Bueren-Calabuig and Marcus Bage and Victoria Cowling and Andrei Pisliakov",
note = "Research was funded by the Institutional Strategic Support Fund 204816 at the University of Dundee and Scottish Universities Physics Alliance (AVP), UK Medical Research Council Doctoral Training Programme (MB), and Medical Research Council MR/K024213/1 (VHC). Medical Research Council Senior Fellowship (MR/K024213/1), Royal Society Wolfson Research Merit Award (WRM\R1\180008), ERC Consolidator Grant 769080 TCAPS.",
year = "2019",
month = "7",
day = "22",
doi = "10.1093/nar/gkz613",
language = "English",
volume = "1",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",

}

TY - JOUR

T1 - Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM

T2 - Insights from accelerated molecular dynamics simulations

AU - Bueren-Calabuig, Juan

AU - Bage, Marcus

AU - Cowling, Victoria

AU - Pisliakov, Andrei

N1 - Research was funded by the Institutional Strategic Support Fund 204816 at the University of Dundee and Scottish Universities Physics Alliance (AVP), UK Medical Research Council Doctoral Training Programme (MB), and Medical Research Council MR/K024213/1 (VHC). Medical Research Council Senior Fellowship (MR/K024213/1), Royal Society Wolfson Research Merit Award (WRM\R1\180008), ERC Consolidator Grant 769080 TCAPS.

PY - 2019/7/22

Y1 - 2019/7/22

N2 - The RNA guanine-N7 methyltransferase (RNMT) in complex with RNMT-Activating Miniprotein (RAM) catalyses the formation of a N7-methylated guanosine cap structure on the 5’ end of nascent RNA polymerase II transcripts. The mRNA cap protects the primary transcript from exonucleases and recruits cap-binding complexes that mediate RNA processing, export and translation. By using microsecond standard and accelerated molecular dynamics simulations, we provide for the first time a detailed molecular mechanism of allosteric regulation of RNMT by RAM. We show that RAM selects the RNMT active site conformations that are optimal for binding of substrates (AdoMet and the cap), thus enhancing their affinity. Furthermore, our results strongly suggest the likely scenario in which the cap binding promotes the subsequent AdoMet binding, consistent with the previously suggested cooperative binding model. By employing the network community analyses, we revealed the underlying long-range allosteric networks and paths that are crucial for allosteric regulation by RAM. Our findings complement and explain previous experimental data on RNMT activity. Moreover, this study provides the most complete description of the cap and AdoMet binding poses and interactions within the enzyme’s active site. This information is critical for the drug discovery efforts that consider RNMT as a promising anti-cancer target.

AB - The RNA guanine-N7 methyltransferase (RNMT) in complex with RNMT-Activating Miniprotein (RAM) catalyses the formation of a N7-methylated guanosine cap structure on the 5’ end of nascent RNA polymerase II transcripts. The mRNA cap protects the primary transcript from exonucleases and recruits cap-binding complexes that mediate RNA processing, export and translation. By using microsecond standard and accelerated molecular dynamics simulations, we provide for the first time a detailed molecular mechanism of allosteric regulation of RNMT by RAM. We show that RAM selects the RNMT active site conformations that are optimal for binding of substrates (AdoMet and the cap), thus enhancing their affinity. Furthermore, our results strongly suggest the likely scenario in which the cap binding promotes the subsequent AdoMet binding, consistent with the previously suggested cooperative binding model. By employing the network community analyses, we revealed the underlying long-range allosteric networks and paths that are crucial for allosteric regulation by RAM. Our findings complement and explain previous experimental data on RNMT activity. Moreover, this study provides the most complete description of the cap and AdoMet binding poses and interactions within the enzyme’s active site. This information is critical for the drug discovery efforts that consider RNMT as a promising anti-cancer target.

KW - RNMT

KW - allosteric activation

KW - accelerated molecular dynamics

KW - conformational selection

KW - mRNA cap

U2 - 10.1093/nar/gkz613

DO - 10.1093/nar/gkz613

M3 - Article

C2 - 31329932

VL - 1

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

M1 - gkz613

ER -