CHARMM force field parameterization protocol for self-assembling peptide amphiphiles: the Fmoc moiety

Physical Chemistry Chemical Physics : PCCP
I Ramos SasselliTell Tuttle

Abstract

Aromatic peptide amphiphiles are known to self-assemble into nanostructures but the molecular level structure and the mechanism of formation of these nanostructures is not yet understood in detail. Molecular dynamic simulations using the CHARMM force field have been applied to a wide variety of peptide-based systems to obtain molecular level details of processes that are inaccessible with experimental techniques. However, this force field does not include parameters for the aromatic moieties which dictate the self-assembly of these systems. The standard CHARMM force field parameterization protocol uses hydrophilic interactions for the non-bonding parameters evaluation. However, to effectively reproduce the self-assembling behaviour of these molecules, the balance between the hydrophilic and hydrophobic nature of the molecule is essential. In this work, a modified parameterization protocol for the CHARMM force field for these aromatic moieties is presented. This protocol is applied for the specific case of the Fmoc moiety. The resulting set of parameters satisfies the conformational and interactions analysis and is able to reproduce experimental results such as the Fmoc-S-OMe water/octanol partition free energy and the self-asse...Continue Reading

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Nov 27, 2001·Science·J D HartgerinkS I Stupp
Mar 30, 2002·Science·George M Whitesides, Bartosz Grzybowski
Apr 26, 2003·Science·Meital Reches, Ehud Gazit
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
May 11, 2006·Chemical Reviews·Stewart A Adcock, J Andrew McCammon
Jun 9, 2006·Angewandte Chemie·Wilfred F van GunsterenHaibo B Yu
Sep 7, 2006·Journal of Computational Chemistry·Stefan Grimme
Feb 7, 2008·The Journal of Physical Chemistry. B·Yuri S VelichkoMonica Olvera de la Cruz
Mar 26, 2008·Chemical Society Reviews·Rein V Ulijn, Andrew M Smith
Jul 19, 2008·The Journal of Physical Chemistry. B·Martin McCullaghGeorge C Schatz
May 16, 2009·Journal of Computational Chemistry·B R BrooksM Karplus
Jun 9, 2009·Langmuir : the ACS Journal of Surfaces and Colloids·Sam SuttonDave J Adams
Jul 21, 2010·Chemical Society Reviews·Frank VersluisAlexander Kros
Feb 24, 2011·Journal of the American Chemical Society·One-Sun LeeGeorge C Schatz
Oct 15, 2011·Langmuir : the ACS Journal of Surfaces and Colloids·Claire TangAlberto Saiani
Aug 15, 2012·Journal of Cheminformatics·Marcus D HanwellGeoffrey R Hutchison
Oct 6, 2011·The Journal of Physical Chemistry Letters·Pim W J M FrederixTell Tuttle
Sep 13, 2013·Small·Yousef M Abul-HaijaRein V Ulijn
Oct 3, 2013·The European Physical Journal. E, Soft Matter·Claire TangAlberto Saiani
Oct 5, 2013·Langmuir : the ACS Journal of Surfaces and Colloids·Yurong ZhaoJian R Lu
Oct 5, 2013·Chemical Communications : Chem Comm·Scott FlemingRein V Ulijn
Oct 23, 2013·The Journal of Physical Chemistry. B·Tao Yu, George C Schatz
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
Sep 10, 2014·Chemical Society Reviews·Scott Fleming, Rein V Ulijn
Aug 14, 2012·Journal of Chemical Theory and Computation·Peng LiuChristophe Chipot

❮ Previous
Next ❯

Citations

Feb 26, 2016·Soft Matter·Inês P MoreiraRein V Ulijn
Aug 10, 2016·Journal of the American Chemical Society·Marc P CoonsJohn M Herbert
May 12, 2018·Chemical Society Reviews·A LampelT Tuttle
May 26, 2017·Physical Chemistry Chemical Physics : PCCP·Chengqian YuanXuehai Yan
Apr 25, 2018·Chemical Society Reviews·Pim W J M FrederixSiewert J Marrink
Nov 20, 2020·The Journal of Physical Chemistry. B·Vivek SundaramBjörn Baumeier
May 5, 2017·ACS Omega·Seyed Meysam HashemnejadSantanu Kundu

❮ 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.