Fluorine in protein environments: a QM and MD study

The Journal of Physical Chemistry. B
Sergey A SamsonovM Teresa Pisabarro

Abstract

Noncanonical amino acids with newly designed side-chain functionalities represent powerful tools to improve structural, biological, and pharmacological properties of peptides and proteins. In this context, fluorinated amino acids have increasingly gained importance. Despite the current wide use of fluorination in protein engineering, the basic properties of fluorine in protein environments are still not completely understood. Our aim has been to characterize the physicochemical properties of fluorinated amino acids by using quantum mechanics (QM) and molecular dynamics (MD) approaches. We have analyzed geometry, charges, and hydrogen bonding abilities of several ethane fluorinated derivatives at different QM theory levels and have used them as simplified models for fluorinated amino acid side chains. We have parametrized four fluorinated L-amino acids for the AMBER ff94/99 force field: 4-monofluoroethylglycine (MfeGly), 4,4-difluoroethylglycine (DfeGly), 4,4,4-trifluoroethylglycine (TfeGly), and 4,4-difluoropropylglycine (DfpGly). We have characterized them in terms of molecular volumes, conformational preferences, and hydration properties. The obtained results illustrate that fluorine and hydrogen atoms of fluoromethyl groups ...Continue Reading

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Citations

May 1, 2010·Molecular BioSystems·Nediljko BudisaBirgit Wiltschi
Apr 7, 2012·Drug Discovery Today·Anna Vulpetti, Claudio Dalvit
Oct 28, 2009·Chembiochem : a European Journal of Chemical Biology·Mario Salwiczek, Beate Koksch
Mar 8, 2018·Chembiochem : a European Journal of Chemical Biology·Charlène GadaisThierry Brigaud
Oct 11, 2011·Angewandte Chemie·G K Surya PrakashGeorge A Olah
Feb 2, 2013·Chemistry : a European Journal·Camino BartoloméPablo Espinet
Mar 23, 2018·Beilstein Journal of Organic Chemistry·Susanne HuhmannBeate Koksch
Jul 22, 2014·Chemistry : a European Journal·Claudio DalvitAnna Vulpetti
Nov 10, 2013·Beilstein Journal of Organic Chemistry·Holger ErdbrinkConstantin Czekelius
Sep 1, 2015·Chemical Science·Shijie YeBeate Koksch
Jan 7, 2021·Chembiochem : a European Journal of Chemical Biology·Suvrat ChowdharyBeate Koksch

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