Evaluation of Selected Classical Force Fields for Alchemical
Binding Free Energy Calculations of Protein-Carbohydrate
Complexes

J 2015

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

MISHRA, Sushil Kumar; Gaetano CALABRO; Hannes H. LOEFFLER; Julien MICHEL; Jaroslav KOČA et al.

Základní údaje

Originální název

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

Název česky

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

Autoři

MISHRA, Sushil Kumar; Gaetano CALABRO; Hannes H. LOEFFLER; Julien MICHEL a Jaroslav KOČA

Vydání

Journal of Chemical Theory and Computation, Washington D.C. American Chemical Society, 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/00216224:14740/15:00081013

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

MOLECULAR-DYNAMICS SIMULATIONS; THERMODYNAMIC INTEGRATION; DRUG DESIGN; RALSTONIA-SOLANACEARUM; EFFICIENT GENERATION; CONCANAVALIN-A; AM1-BCC MODEL; SUGAR BINDING; LECTIN; AFFINITIES

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 3. 2016 16:36, Mgr. Eva Špillingová

Anotace

V originále

Protein carbohydrate recognition is crucial in many vital biological processes including host-pathogen recognition, cell-signaling, and catalysis. Accordingly, computational prediction of protein-carbohydrate binding free energies is of enormous interest for drug design. However, the accuracy of current force fields (FFs) for predicting binding free energies of protein-carbohydrate complexes is not well understood owing to technical challenges such as the highly polar nature of the complexes, anomerization, and conformational flexibility of carbohydrates. The present study evaluated the performance of alchemical predictions of binding free energies with the GAFF1.7/AM1-BCC and GLYCAMO6j force fields for modeling protein carbohydrate complexes. Mean unsigned errors of 1.1 +/- 0.06 (GLYCAMO6j) and 2.6 +/- 0.08 (GAFF1.7/AM1-BCC) kcal.mol(-1) are achieved for a large data set of monosaccharide ligands for Ralstonia solanacearum lectin (RSL). The level of accuracy provided by GLYCAMO6j is sufficient to discriminate potent, moderate, and weak binders, a goal that has been difficult to achieve through other scoring approaches. Accordingly, the protocols presented here could find useful applications in carbohydrate-based drug and vaccine developments.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

EE2.3.30.0009, projekt VaV

Název: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

GA13-25401S, projekt VaV

Název: Studium proteinů z patogenů zapojených do rozpoznávání hostitelského organismu

Investor: Grantová agentura ČR, Studium proteinu z patogenu zapojených do rozpoznávání hostitelského organismu

Citovat

MISHRA, Sushil Kumar; Gaetano CALABRO; Hannes H. LOEFFLER; Julien MICHEL a Jaroslav KOČA. Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes. Journal of Chemical Theory and Computation. Washington D.C.: American Chemical Society, 2015, roč. 11, č. 7, s. 3333-3345. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.5b00159.

@article{1310522,
   author = {Mishra, Sushil Kumar and Calabro, Gaetano and Loeffler, Hannes H. and Michel, Julien and Koča, Jaroslav},
   article_location = {Washington D.C.},
   article_number = {7},
   doi = {https://doi.org/10.1021/acs.jctc.5b00159},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; THERMODYNAMIC INTEGRATION; DRUG DESIGN; RALSTONIA-SOLANACEARUM; EFFICIENT GENERATION; CONCANAVALIN-A; AM1-BCC MODEL; SUGAR BINDING; LECTIN; AFFINITIES},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes},
   url = {http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b00159},
   volume = {11},
   year = {2015}
}

TY  - JOUR
ID  - 1310522
AU  - Mishra, Sushil Kumar - Calabro, Gaetano - Loeffler, Hannes H. - Michel, Julien - Koča, Jaroslav
PY  - 2015
TI  - Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes
JF  - Journal of Chemical Theory and Computation
VL  - 11
IS  - 7
SP  - 3333-3345
EP  - 3333-3345
PB  - American Chemical Society
SN  - 15499618
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - THERMODYNAMIC INTEGRATION
KW  - DRUG DESIGN
KW  - RALSTONIA-SOLANACEARUM
KW  - EFFICIENT GENERATION
KW  - CONCANAVALIN-A
KW  - AM1-BCC MODEL
KW  - SUGAR BINDING
KW  - LECTIN
KW  - AFFINITIES
UR  - http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b00159
L2  - http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b00159
N2  - Protein carbohydrate recognition is crucial in many vital biological processes including host-pathogen recognition, cell-signaling, and catalysis. Accordingly, computational prediction of protein-carbohydrate binding free energies is of enormous interest for drug design. However, the accuracy of current force fields (FFs) for predicting binding free energies of protein-carbohydrate complexes is not well understood owing to technical challenges such as the highly polar nature of the complexes, anomerization, and conformational flexibility of carbohydrates. The present study evaluated the performance of alchemical predictions of binding free energies with the GAFF1.7/AM1-BCC and GLYCAMO6j force fields for modeling protein carbohydrate complexes. Mean unsigned errors of 1.1 +/- 0.06 (GLYCAMO6j) and 2.6 +/- 0.08 (GAFF1.7/AM1-BCC) kcal.mol(-1) are achieved for a large data set of monosaccharide ligands for Ralstonia solanacearum lectin (RSL). The level of accuracy provided by GLYCAMO6j is sufficient to discriminate potent, moderate, and weak binders, a goal that has been difficult to achieve through other scoring approaches. Accordingly, the protocols presented here could find useful applications in carbohydrate-based drug and vaccine developments.
ER  -

MISHRA, Sushil Kumar; Gaetano CALABRO; Hannes H. LOEFFLER; Julien MICHEL a Jaroslav KOČA. Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes. \textit{Journal of Chemical Theory and Computation}. Washington D.C.: American Chemical Society, 2015, roč.~11, č.~7, s.~3333-3345. ISSN~1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.5b00159.

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