Validation and Comparison of Force Fields for Native Cyclodextrins in Aqueous Solution

The Journal of Physical Chemistry. B
Julia GebhardtNiels Hansen

Abstract

Molecular dynamics simulations of native α-, β-, and γ-cyclodextrin in aqueous solution have been conducted with the goal to investigate the performance of the CHARMM36 force field, the AMBER-compatible q4md-CD force field, and five variants of the GROMOS force field. The properties analyzed are structural parameters derived from X-ray diffraction and NMR experiments as well as hydrogen bonds and hydration patterns, including hydration free enthalpies. Recent revisions of the torsional-angle parameters for carbohydrate systems within the GROMOS family of force fields lead to a significant improvement of the agreement between simulated and experimental NMR data. Therefore, we recommend using the variant 53A6GLYC instead of 53A6 and 56A6CARBO_R or 2016H66 instead of 56A6CARBO to simulate cyclodextrins in solution. The CHARMM36 and q4md-CD force fields show a similar performance as the three recommended GROMOS parameter sets. A significant difference is the more flexible nature of the cyclodextrins modeled with the CHARMM36 and q4md-CD force fields compared to the three recommended GROMOS parameter sets.

References

Jan 1, 1986·Annals of the New York Academy of Sciences·H J BerendsenR G Geurtsen
Aug 30, 2001·Proceedings of the National Academy of Sciences of the United States of America·K N Kirschner, R J Woods
Feb 19, 2002·Chemical Reviews·József Szejtli
Feb 19, 2002·Chemical Reviews·Hans-Jörg SchneiderHiroshi Ikeda
Feb 19, 2002·Chemical Reviews·Wolfram SaengerTakeshi Takaha
Feb 19, 2002·Chemical Reviews·Kenny B. Lipkowitz
Oct 9, 2002·Journal of Computational Chemistry·D KonyW F Van Gunsteren
Mar 1, 2003·Biophysical Journal·Swarnalatha Y ReddyMartin Karplus
Mar 13, 2003·European Biophysics Journal : EBJ·Indira ChandrasekharWilfred F van Gunsteren
Aug 22, 2003·Protein Science : a Publication of the Protein Society·Nikos PinotsisIrene M Mavridis
Jul 21, 2004·Journal of Computational Chemistry·Chris OostenbrinkWilfred F van Gunsteren
Jul 22, 2005·Journal of Computational Chemistry·Roberto D Lins, Philippe H Hünenberger
Oct 8, 2005·Journal of Computational Chemistry·Markus ChristenWilfred F van Gunsteren
Mar 7, 2006·The Journal of Physical Chemistry. a·K N Kirschner, R J Woods
Mar 24, 2006·The Journal of Physical Chemistry. B·Yanmin YuXueguang Shao
May 6, 2006·The Journal of Chemical Physics·Dietmar PaschekDieter Suter
Sep 13, 2007·Journal of Computational Chemistry·Karl N KirschnerRobert J Woods
Sep 21, 2007·Journal of Computational Chemistry·M BasmaR J Woods
May 27, 2008·Physical Chemistry Chemical Physics : PCCP·Wensheng CaiChristophe Chipot
Jun 26, 2008·The Journal of Physical Chemistry. B·Johan ThaningArnold Maliniak
Sep 12, 2008·Journal of Computational Chemistry·Amanda M SalisburgKarl N Kirschner
Jan 16, 2009·The Journal of Physical Chemistry. B·Javier Rodriguez, M Dolores Elola
May 16, 2009·Journal of Computational Chemistry·B R BrooksM Karplus
Jun 6, 2009·The FEBS Journal·Naoki MatsumotoTakashi Tonozuka
Aug 22, 2009·The Journal of Physical Chemistry. B·Elizabeth HatcherAlexander D Mackerell
Sep 18, 2009·Carbohydrate Research·Carlos A StortzGábor I Csonka
Feb 18, 2010·Journal of Chemical Theory and Computation·Elizabeth HatcherAlexander D Mackerell
Feb 18, 2010·Journal of Chemical Theory and Computation·Olgun GuvenchAlexander D Mackerell
Feb 26, 2010·Organic Letters·Kazuhiro YamauchiAkira Harada
Jul 10, 2010·The Journal of Physical Chemistry. B·Clarisse G RicciPaulo A Netz
Sep 10, 2010·The Journal of Physical Chemistry. B·Abil E Aliev, Denis Courtier-Murias
Sep 18, 2010·The Journal of Physical Chemistry. B·E Prabhu RamanAlexander D MacKerell
Apr 2, 2011·PLoS Computational Biology·Cesar A LópezSiewert J Marrink
May 3, 2011·European Biophysics Journal : EBJ·Nathan SchmidWilfred F van Gunsteren
Jul 28, 2011·Physical Chemistry Chemical Physics : PCCP·Christine CézardFrançois-Yves Dupradeau

❮ Previous
Next ❯

Citations

Feb 26, 2019·Chemistry : a European Journal·Stella A VerkhnyatskayaMarthe T C Walvoort
Mar 29, 2019·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Aysegül TurupcuChris Oostenbrink
Dec 22, 2019·International Journal of Molecular Sciences·Aysegül TurupcuChris Oostenbrink
Dec 31, 2020·International Journal of Molecular Sciences·Magdalena Paczkowska-WalendowskaJudyta Cielecka-Piontek
May 1, 2021·International Journal of Molecular Sciences·Anna StasiłowiczJudyta Cielecka-Piontek
Jul 3, 2021·The Journal of Physical Chemistry. B·Andrea ArsiccioRoberto Pisano
Feb 26, 2020·The Journal of Physical Chemistry. B·Alessandro TrioloOlga Russina
Oct 12, 2019·Journal of Chemical Theory and Computation·David R SlochowerMichael K Gilson
Mar 16, 2019·Journal of Chemical Information and Modeling·Mayk C RamosBruno A C Horta
Oct 20, 2020·ACS Omega·Avilasha A SandilyaM Hamsa Priya
Sep 12, 2019·The Journal of Physical Chemistry. B·Peng HeLauren Wickstrom

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Protein Science : a Publication of the Protein Society
Wei HuangWilfred F van Gunsteren
Journal of Computational Chemistry
T A SoaresWilfred F van Gunsteren
Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
Daan P Geerke, Wilfred F van Gunsteren
© 2022 Meta ULC. All rights reserved