Residues flanking the ARK^me3T/S motif allow binding of diverse
targets to the HP1 chromodomain: Insights from molecular
dynamics simulations

J 2021

Residues flanking the ARK^me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations

POKORNÁ, Pavlína, Miroslav KREPL a Jiří ŠPONER

Základní údaje

Originální název

Residues flanking the ARK^me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations

Autoři

POKORNÁ, Pavlína (203 Česká republika, domácí), Miroslav KREPL (203 Česká republika) a Jiří ŠPONER (203 Česká republika, garant)

Vydání

Biochimica et Biophysica Acta - General Subjects, Amsterdam, Elsevier B.V. 2021, 0304-4165

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.117

Kód RIV

RIV/00216224:14310/21:00118823

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1016/j.bbagen.2020.129771

UT WoS

000594131800032

Klíčová slova anglicky

MD simulations; HP1; Chromodomain; Peptide recognition; Protein-protein interaction

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 11. 2. 2021 14:31, Mgr. Marie Šípková, DiS.

Anotace

V originále

Background: The chromodomain (CD) of HP1 proteins is an established H3K9(me3) reader that also binds H1, EHMT2 and H3K23 lysine-methylated targets. Structural experiments have provided atomistic pictures of its recognition of the conserved ARK(me3)S/T motif, but structural dynamics' contribution to the recognition may have been masked by ensemble averaging. Methods: We acquired similar to 350 mu s of explicit solvent molecular dynamics (MD) simulations of the CD domain interacting with several peptides using the latest AMBER force fields. Results: The simulations reproduced the experimentally observed static binding patterns well but also revealed visible structural dynamics at the interfaces. While the buried K-0(me3) and A(-2) target residues are tightly bound, several flanking sidechains sample diverse sites on the CD surface. Different amino acid positions of the targets can substitute for each other by forming mutually replaceable interactions with CD, thereby explaining the lack of strict requirement for cationic H3 target residues at the -3 position. The Q(-4) residue of H3 targets further stabilizes the binding. The recognition pattern of the H3K23 ATK(me3)A motif, for which no structure is available, is predicted. Conclusions: The CD reads a longer target segment than previously thought, ranging from positions -7 to +3. The CD anionic clamp can be neutralized not only by the -3 and -1 residues, but also by -7, -6, -5 and +3 residues. General Significance: Structural dynamics, not immediately apparent from the structural data, contribute to molecular recognition between the HP1 CD domain and its targets. Mutual replaceability of target residues increases target sequence flexibility.

Návaznosti

GA18-07384S, projekt VaV

Název: Od konformace po biologické funkce proteinu HP1

Investor: Grantová agentura ČR, Od konformace po biologické funkce proteinu HP1

Citovat

POKORNÁ, Pavlína, Miroslav KREPL a Jiří ŠPONER. Residues flanking the ARK^me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations. Biochimica et Biophysica Acta - General Subjects. Amsterdam: Elsevier B.V., 2021, roč. 1865, č. 1, s. 1-12. ISSN 0304-4165. Dostupné z: https://dx.doi.org/10.1016/j.bbagen.2020.129771.

@article{1728139,
   author = {Pokorná, Pavlína and Krepl, Miroslav and Šponer, Jiří},
   article_location = {Amsterdam},
   article_number = {1},
   doi = {http://dx.doi.org/10.1016/j.bbagen.2020.129771},
   keywords = {MD simulations; HP1; Chromodomain; Peptide recognition; Protein-protein interaction},
   language = {eng},
   issn = {0304-4165},
   journal = {Biochimica et Biophysica Acta - General Subjects},
   title = {Residues flanking the ARK^me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations},
   url = {https://doi.org/10.1016/j.bbagen.2020.129771},
   volume = {1865},
   year = {2021}
}

TY  - JOUR
ID  - 1728139
AU  - Pokorná, Pavlína - Krepl, Miroslav - Šponer, Jiří
PY  - 2021
TI  - Residues flanking the ARK^me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations
JF  - Biochimica et Biophysica Acta - General Subjects
VL  - 1865
IS  - 1
SP  - 1-12
EP  - 1-12
PB  - Elsevier B.V.
SN  - 03044165
KW  - MD simulations
KW  - HP1
KW  - Chromodomain
KW  - Peptide recognition
KW  - Protein-protein interaction
UR  - https://doi.org/10.1016/j.bbagen.2020.129771
L2  - https://doi.org/10.1016/j.bbagen.2020.129771
N2  - Background: The chromodomain (CD) of HP1 proteins is an established H3K9(me3) reader that also binds H1, EHMT2 and H3K23 lysine-methylated targets. Structural experiments have provided atomistic pictures of its recognition of the conserved ARK(me3)S/T motif, but structural dynamics' contribution to the recognition may have been masked by ensemble averaging. Methods: We acquired similar to 350 mu s of explicit solvent molecular dynamics (MD) simulations of the CD domain interacting with several peptides using the latest AMBER force fields. Results: The simulations reproduced the experimentally observed static binding patterns well but also revealed visible structural dynamics at the interfaces. While the buried K-0(me3) and A(-2) target residues are tightly bound, several flanking sidechains sample diverse sites on the CD surface. Different amino acid positions of the targets can substitute for each other by forming mutually replaceable interactions with CD, thereby explaining the lack of strict requirement for cationic H3 target residues at the -3 position. The Q(-4) residue of H3 targets further stabilizes the binding. The recognition pattern of the H3K23 ATK(me3)A motif, for which no structure is available, is predicted. Conclusions: The CD reads a longer target segment than previously thought, ranging from positions -7 to +3. The CD anionic clamp can be neutralized not only by the -3 and -1 residues, but also by -7, -6, -5 and +3 residues. General Significance: Structural dynamics, not immediately apparent from the structural data, contribute to molecular recognition between the HP1 CD domain and its targets. Mutual replaceability of target residues increases target sequence flexibility.
ER  -

POKORNÁ, Pavlína, Miroslav KREPL a Jiří ŠPONER. Residues flanking the ARK\^{}me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations. \textit{Biochimica et Biophysica Acta - General Subjects}. Amsterdam: Elsevier B.V., 2021, roč.~1865, č.~1, s.~1-12. ISSN~0304-4165. Dostupné z: https://dx.doi.org/10.1016/j.bbagen.2020.129771.

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