Can We Execute Stable Microsecond-Scale Atomistic Simulations
of Protein-RNA Complexes?

J 2015

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

KREPL, Miroslav; Marek HAVRILA; Petr STADLBAUER; Pavel BANÁŠ; Michal OTYEPKA et al.

Základní údaje

Originální název

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

Autoři

KREPL, Miroslav; Marek HAVRILA; Petr STADLBAUER; Pavel BANÁŠ; Michal OTYEPKA; Josef PASULKA; Richard ŠTEFL a Jiří ŠPONER

Vydání

Journal of Chemical Theory and Computation, WASHINGTON, AMER CHEMICAL SOC, 2015, 1549-9618

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.301

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/15:00080801

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

MOLECULAR-DYNAMICS SIMULATIONS; PARTICLE MESH EWALD; MECHANICS FORCE-FIELDS; RIBOSOMAL L1 STALK; BINDING PROTEINS; NUCLEIC-ACIDS; CAENORHABDITIS-ELEGANS; CRYSTAL-STRUCTURE; NONCODING RNAS; ANIMAL VIRUS

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 5. 2015 12:26, Martina Prášilová

Anotace

V originále

We report over 30 mu s of unrestrained molecular dynamics simulations of six protein-RNA complexes in explicit solvent. We utilize the AMBER ff99bsc0 chi(OL3) RNA force field combined with the ff99SB protein force field and its more recent ff12SB version with reparametrized side-chain dihedrals. The simulations show variable behavior, ranging from systems that are essentially stable to systems with progressive deviations from the experimental structure, which we could not stabilize anywhere close to the starting experimental structure. For some systems, microsecond-scale simulations are necessary to achieve stabilization after initial sizable structural perturbations. The results show that simulations of protein-RNA complexes are challenging and every system should be treated individually. The simulations are affected by numerous factors, including properties of the starting structures (the initially high force field potential energy, resolution limits, conformational averaging, crystal packing, etc.), force field imbalances, and real flexibility of the studied systems. These factors, and thus the simulation behavior, differ from system to system. The structural stability of simulated systems does not correlate with the size of buried interaction surface or experimentally determined binding affinities but reflects the type of protein-RNA recognition. Protein-RNA interfaces involving shape-specific recognition of RNA are more stable than those relying on sequence-specific RNA recognition. The differences between the protein force fields are considerably smaller than the uncertainties caused by sampling and starting structures. The ff12SB improves description of the tyrosine side-chain group, which eliminates some problems associated with tyrosine dynamics.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

GBP305/12/G034, projekt VaV

Název: Centrum biologie RNA

Citovat

KREPL, Miroslav; Marek HAVRILA; Petr STADLBAUER; Pavel BANÁŠ; Michal OTYEPKA; Josef PASULKA; Richard ŠTEFL a Jiří ŠPONER. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 11, č. 3, s. 1220-1243. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/ct5008108.

@article{1299537,
   author = {Krepl, Miroslav and Havrila, Marek and Stadlbauer, Petr and Banáš, Pavel and Otyepka, Michal and Pasulka, Josef and Štefl, Richard and Šponer, Jiří},
   article_location = {WASHINGTON},
   article_number = {3},
   doi = {https://doi.org/10.1021/ct5008108},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; PARTICLE MESH EWALD; MECHANICS FORCE-FIELDS; RIBOSOMAL L1 STALK; BINDING PROTEINS; NUCLEIC-ACIDS; CAENORHABDITIS-ELEGANS; CRYSTAL-STRUCTURE; NONCODING RNAS; ANIMAL VIRUS},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?},
   url = {http://pubs.acs.org/doi/pdf/10.1021/ct5008108},
   volume = {11},
   year = {2015}
}

TY  - JOUR
ID  - 1299537
AU  - Krepl, Miroslav - Havrila, Marek - Stadlbauer, Petr - Banáš, Pavel - Otyepka, Michal - Pasulka, Josef - Štefl, Richard - Šponer, Jiří
PY  - 2015
TI  - Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?
JF  - Journal of Chemical Theory and Computation
VL  - 11
IS  - 3
SP  - 1220-1243
EP  - 1220-1243
PB  - AMER CHEMICAL SOC
SN  - 15499618
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - PARTICLE MESH EWALD
KW  - MECHANICS FORCE-FIELDS
KW  - RIBOSOMAL L1 STALK
KW  - BINDING PROTEINS
KW  - NUCLEIC-ACIDS
KW  - CAENORHABDITIS-ELEGANS
KW  - CRYSTAL-STRUCTURE
KW  - NONCODING RNAS
KW  - ANIMAL VIRUS
UR  - http://pubs.acs.org/doi/pdf/10.1021/ct5008108
L2  - http://pubs.acs.org/doi/pdf/10.1021/ct5008108
N2  - We report over 30 mu s of unrestrained molecular dynamics simulations of six protein-RNA complexes in explicit solvent. We utilize the AMBER ff99bsc0 chi(OL3) RNA force field combined with the ff99SB protein force field and its more recent ff12SB version with reparametrized side-chain dihedrals. The simulations show variable behavior, ranging from systems that are essentially stable to systems with progressive deviations from the experimental structure, which we could not stabilize anywhere close to the starting experimental structure. For some systems, microsecond-scale simulations are necessary to achieve stabilization after initial sizable structural perturbations. The results show that simulations of protein-RNA complexes are challenging and every system should be treated individually. The simulations are affected by numerous factors, including properties of the starting structures (the initially high force field potential energy, resolution limits, conformational averaging, crystal packing, etc.), force field imbalances, and real flexibility of the studied systems. These factors, and thus the simulation behavior, differ from system to system. The structural stability of simulated systems does not correlate with the size of buried interaction surface or experimentally determined binding affinities but reflects the type of protein-RNA recognition. Protein-RNA interfaces involving shape-specific recognition of RNA are more stable than those relying on sequence-specific RNA recognition. The differences between the protein force fields are considerably smaller than the uncertainties caused by sampling and starting structures. The ff12SB improves description of the tyrosine side-chain group, which eliminates some problems associated with tyrosine dynamics.
ER  -

KREPL, Miroslav; Marek HAVRILA; Petr STADLBAUER; Pavel BANÁŠ; Michal OTYEPKA; Josef PASULKA; Richard ŠTEFL a Jiří ŠPONER. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? \textit{Journal of Chemical Theory and Computation}. WASHINGTON: AMER CHEMICAL SOC, 2015, roč.~11, č.~3, s.~1220-1243. ISSN~1549-9618. Dostupné z: https://doi.org/10.1021/ct5008108.

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