Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA
Approaches on Protein/Carbohydrate Complexes: Effect of
Implicit Solvent Models, QM Methods, and Entropic Contributions

J 2018

Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions

MISHRA, Sushil Kumar a Jaroslav KOČA

Základní údaje

Originální název

Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions

Autoři

MISHRA, Sushil Kumar a Jaroslav KOČA

Vydání

Journal of Physical Chemistry B, WASHINGTON, AMER CHEMICAL SOC, 2018, 1520-6106

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

Impakt faktor

Impact factor: 2.923

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/18:00106636

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

FREE-ENERGY CALCULATIONS; GENERALIZED BORN MODEL; BINDING FREE-ENERGIES; RALSTONIA-SOLANACEARUM; MOLECULAR-DYNAMICS; FORCE-FIELD; PARAMETERS; LECTINS; RECOGNITION; APPROXIMATIONS

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 24. 4. 2019 16:34, prof. RNDr. Jaroslav Koča, DrSc.

Anotace

V originále

Rapid and accurate binding affinity prediction of protein-carbohydrate complexes is a major challenge in glycomimetics design. Among the existing computational techniques, endpoint methods have received considerable interest because of their low computational cost. However, significant obstacles remain when such methods are applied to protein-glycan complexes. This article reports the performance of end-point free-energy calculation methods: molecular mechanics/Poisson-Boltzmann surface area (MM/ PBSA), MM/generalized Born surface area (MM/GBSA), and quantum mechanics-MM/GBSA (QM-MM/GBSA) on monosaccharides bound to RSL lectin from Ralstonia solanacearum. A careful investigation of the molecular dynamics simulation length, van der Waals radii sets, GB models, QM Hamiltonians, and entropic compensation has been made, and the results are compared with the experimental binding free energies from isothermal titration calorimetry/surface plasmon resonance measurements. The binding free energies using implicit solvent methods are found to be sensitive to the simulation length, radii set, GB model, and QM Hamiltonian. A simulation length of 10 ns using the radii set mbondi provides the best agreement with the experimental values (r(2) = 0.96) by MM/PBSA. The GB(HCT) model is in accord with the experimental values in MM/GBSA (r(2) = 0.91) or in combination with parameterized model number 6 (PM6) (r(2) = 0.98) in QM-MM/GBSA. Out of 12 QM Hamiltonians tested, PM6, density functional theory-based tight binding (DFTB), and their variants proved to be more efficient than other semiempirical methods. These methods perform equally well in predicting both absolute and relative binding free energies.

Návaznosti

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

LTC17076, projekt VaV

Název: Interdisciplinární přístup ke studiu biologických systémů na molekulární úrovni

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Interdisciplinární přístup ke studiu biologických systémů na molekulární úrovni, INTER-COST

Citovat

MISHRA, Sushil Kumar a Jaroslav KOČA. Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2018, roč. 122, č. 34, s. 8113-8121. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/acs.jpcb.8b03655.

@article{1506857,
   author = {Mishra, Sushil Kumar and Koča, Jaroslav},
   article_location = {WASHINGTON},
   article_number = {34},
   doi = {https://doi.org/10.1021/acs.jpcb.8b03655},
   keywords = {FREE-ENERGY CALCULATIONS; GENERALIZED BORN MODEL; BINDING FREE-ENERGIES; RALSTONIA-SOLANACEARUM; MOLECULAR-DYNAMICS; FORCE-FIELD; PARAMETERS; LECTINS; RECOGNITION; APPROXIMATIONS},
   language = {eng},
   issn = {1520-6106},
   journal = {Journal of Physical Chemistry B},
   title = {Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions},
   volume = {122},
   year = {2018}
}

TY  - JOUR
ID  - 1506857
AU  - Mishra, Sushil Kumar - Koča, Jaroslav
PY  - 2018
TI  - Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions
JF  - Journal of Physical Chemistry B
VL  - 122
IS  - 34
SP  - 8113-8121
EP  - 8113-8121
PB  - AMER CHEMICAL SOC
SN  - 15206106
KW  - FREE-ENERGY CALCULATIONS
KW  - GENERALIZED BORN MODEL
KW  - BINDING FREE-ENERGIES
KW  - RALSTONIA-SOLANACEARUM
KW  - MOLECULAR-DYNAMICS
KW  - FORCE-FIELD
KW  - PARAMETERS
KW  - LECTINS
KW  - RECOGNITION
KW  - APPROXIMATIONS
N2  - Rapid and accurate binding affinity prediction of protein-carbohydrate complexes is a major challenge in glycomimetics design. Among the existing computational techniques, endpoint methods have received considerable interest because of their low computational cost. However, significant obstacles remain when such methods are applied to protein-glycan complexes. This article reports the performance of end-point free-energy calculation methods: molecular mechanics/Poisson-Boltzmann surface area (MM/ PBSA), MM/generalized Born surface area (MM/GBSA), and quantum mechanics-MM/GBSA (QM-MM/GBSA) on monosaccharides bound to RSL lectin from Ralstonia solanacearum. A careful investigation of the molecular dynamics simulation length, van der Waals radii sets, GB models, QM Hamiltonians, and entropic compensation has been made, and the results are compared with the experimental binding free energies from isothermal titration calorimetry/surface plasmon resonance measurements. The binding free energies using implicit solvent methods are found to be sensitive to the simulation length, radii set, GB model, and QM Hamiltonian. A simulation length of 10 ns using the radii set mbondi provides the best agreement with the experimental values (r(2) = 0.96) by MM/PBSA. The GB(HCT) model is in accord with the experimental values in MM/GBSA (r(2) = 0.91) or in combination with parameterized model number 6 (PM6) (r(2) = 0.98) in QM-MM/GBSA. Out of 12 QM Hamiltonians tested, PM6, density functional theory-based tight binding (DFTB), and their variants proved to be more efficient than other semiempirical methods. These methods perform equally well in predicting both absolute and relative binding free energies.
ER  -

MISHRA, Sushil Kumar a Jaroslav KOČA. Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions. \textit{Journal of Physical Chemistry B}. WASHINGTON: AMER CHEMICAL SOC, 2018, roč.~122, č.~34, s.~8113-8121. ISSN~1520-6106. Dostupné z: https://doi.org/10.1021/acs.jpcb.8b03655.

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