A preliminary survey of the peptoid folding landscape

Journal of the American Chemical Society
Glenn L ButterfossRichard Bonneau

Abstract

We present an analysis of the conformational preferences of N-substituted glycine peptoid oligomers. We survey the backbone conformations observed in experimentally determined peptoid structures and provide a comparison with high-level quantum mechanics calculations of short peptoid oligomers. The dominant sources of structural variation derive from: side-chain dependent cis/trans isomerization of backbone amide bonds, side chain stereochemistry, and flexibility in the psi dihedral angle. We find good agreement between the clustering of experimentally determined peptoid torsion angles and local torsional minima predicted by theory for a disarcosine model. The calculations describe a well-defined conformational map featuring distinct energy minima. The general features of the peptoid backbone conformational landscape are consistent across a range of N-alkyl glycine side chains. Alteration of side chain types, however, creates subtle but potentially significant variations in local folding propensities. We identify a limited number of low energy local conformations, which may be preferentially favored by incorporation of particular monomer units. Greater variation in backbone dihedral angles are accessible in peptoids featuring tr...Continue Reading

References

Oct 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·R J SimonC K Marlowe
Jul 14, 1971·Journal of Molecular Biology·F K Winkler, J D Dunitz
Oct 1, 1968·Biopolymers·G N Ramachandran
Dec 20, 1996·Journal of Molecular Biology·M W MacArthur, J M Thornton
Jan 1, 1997·Folding & Design·P ArmandF E Cohen
May 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·P ArmandE K Bradley
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Feb 27, 2001·Nature Structural Biology·A S Edison
Mar 11, 1953·Proceedings of the Royal Society of London. Series B, Containing Papers of a Biological Character·R B COREY, L PAULING
Jul 1, 1963·Journal of Molecular Biology·G N RAMACHANDRANV SASISEKHARAN
Oct 30, 2003·Journal of the American Chemical Society·Cindy W WuAnnelise E Barron
Nov 25, 2003·Protein Science : a Publication of the Protein Society·Glenn L Butterfoss, Jan Hermans
Apr 1, 1951·Proceedings of the National Academy of Sciences of the United States of America·L PAULINGH R BRANSON
Apr 6, 2004·Methods in Enzymology·Carol A RohlDavid Baker
Nov 13, 2004·Journal of the American Chemical Society·Brian W Chellgren, Trevor P Creamer
Nov 19, 2004·Journal of the American Chemical Society·Zhigang LiuNeville R Kallenbach
Jul 19, 2005·Bioorganic Chemistry·P Selvarengan, P Kolandaivel
Dec 24, 2005·Protein Science : a Publication of the Protein Society·Jia-Cherng Horng, Ronald T Raines
Feb 2, 2006·Journal of the American Chemical Society·Kai HuangIshwar Radhakrishnan
Apr 4, 2006·Physical Biology·Carsten BaldaufHans-Jörg Hofmann
Sep 1, 2006·The Journal of Physical Chemistry. B·Young Kee KangHae Sook Park
Feb 28, 2007·Journal of the American Chemical Society·Sung Bin Y ShinKent Kirshenbaum
Apr 18, 2007·Nature Chemical Biology·Catherine M GoodmanWilliam F DeGrado
Jul 5, 2007·Journal of the American Chemical Society·Benjamin C GorskeHelen E Blackwell
Aug 10, 2007·Chirality·Lucie BednárováPetr Bour
Sep 11, 2007·Journal of the American Chemical Society·Qiang SuiDallas L Rabenstein
Dec 4, 2008·Journal of the American Chemical Society·Neel H ShahKent Kirshenbaum
May 28, 2009·Journal of the American Chemical Society·Amit ChoudharyRonald T Raines
Aug 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·Galia MaayanKent Kirshenbaum

❮ Previous
Next ❯

Citations

Oct 1, 2011·ACS Chemical Biology·Byoung-Chul Lee, Ronald N Zuckermann
Jun 4, 2011·Journal of the American Chemical Society·Bishwajit PaulKent Kirshenbaum
May 23, 2012·Journal of the American Chemical Society·Cécile CaumesClaude Taillefumier
Jan 25, 2013·Journal of the American Chemical Society·Jonas S LaursenChristian A Olsen
Oct 30, 2012·Langmuir : the ACS Journal of Surfaces and Colloids·King Hang Aaron LauPhillip B Messersmith
Jun 1, 2013·ACS Nano·Jing Sun, Ronald N Zuckermann
Jan 26, 2012·Organic Letters·Bishwajit PaulKent Kirshenbaum
Jan 22, 2013·Organic Letters·Irene IzzoFrancesco De Riccardis
Aug 22, 2012·Proceedings of the National Academy of Sciences of the United States of America·Glenn L ButterfossVincent A Voelz
May 7, 2014·Organic Letters·Adrian S CulfAndreas Decken
Jun 1, 2012·Expert Opinion on Drug Discovery·W Seth Horne
Dec 25, 2015·Chemical Reviews·Niklas GangloffRobert Luxenhofer
Nov 20, 2015·The Journal of Physical Chemistry. B·Sudipto MukherjeeVincent Alvin Voelz
Feb 3, 2015·Journal of Peptide Science : an Official Publication of the European Peptide Society·Marco CrismaClaudio Toniolo
Feb 13, 2014·Journal of Peptide Science : an Official Publication of the European Peptide Society·Roksana Wałęsa, Małgorzata A Broda
May 7, 2015·Nature Communications·Jonas S LaursenChristian A Olsen
Feb 13, 2016·Chemical Communications : Chem Comm·Dillon FloodRonald N Zuckermann
Nov 23, 2017·Organic & Biomolecular Chemistry·A D'AmatoF De Riccardis
Oct 13, 2011·ChemMedChem·Mia Lace HuangKent Kirshenbaum
Apr 24, 2010·Chemistry : a European Journal·Barney YooKent Kirshenbaum
Aug 18, 2010·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Adrian S Culf, Rodney J Ouellette
Mar 6, 2019·Biopolymers·Ryan K SpencerRonald N Zuckermann
Oct 8, 2015·Nature·Ranjan V MannigeStephen Whitelam
Jul 14, 2011·Chembiochem : a European Journal of Chemical Biology·Rob M J LiskampJohan Kemmink
Oct 21, 2011·Chemical Society Reviews·Søren L PedersenKnud J Jensen
Dec 3, 2013·Journal of Computational Chemistry·Dina T MirijanianStephen Whitelam
Apr 30, 2020·Expert Opinion on Drug Discovery·Vikram K Mulligan
Dec 20, 2011·Biopolymers·Wolfgang BrandtLudger Wessjohann
Feb 13, 2013·Chemical Communications : Chem Comm·Sidonie B L VollrathKent Kirshenbaum
Apr 10, 2015·Advanced Materials·Abigail S KnightRonald N Zuckermann
May 1, 2016·Chemical Science·Julian VastlDavid A Spiegel
May 8, 2019·Journal of Computational Chemistry·Laura J Weiser, Erik E Santiso
Dec 20, 2011·Biopolymers·Jared C HooksD Gomika Udugamasooriya
Dec 20, 2011·Biopolymers·Modi Wetzler, Annelise E Barron
Jun 13, 2014·Biopolymers·Glenn L ButterfossRichard Bonneau
Aug 20, 2016·Chembiochem : a European Journal of Chemical Biology·Timothy W CravenKent Kirshenbaum
Jul 25, 2018·Nature Communications·Xiaopeng YuRobert A DiStasio
Dec 20, 2011·Biopolymers·Peter A JordanKent Kirshenbaum

❮ 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.