Randomizing the unfolded state of peptides (and proteins) by nearest neighbor interactions between unlike residues

Chemistry : a European Journal
Siobhan E ToalReinhard Schweitzer-Stenner

Abstract

To explore the influence of nearest neighbors on conformational biases in unfolded peptides, we combined vibrational and 2D NMR spectroscopy to obtain the conformational distributions of selected "GxyG" host-guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y=A, K, L, V. Large changes of conformational propensities were observed due to nearest-neighbor interactions, at variance with the isolated pair hypothesis. We found that protonated aspartic acid and serine lose their above-the-average preference for turn-like structures in favor of polyproline II (pPII) populations in the presence of neighbors with bulky side chains. Such residues also decrease the above-the-average pPII preference of alanine. These observations suggest that the underlying mechanism involves a disruption of the hydration shell. Thermodynamic analysis of (3) J(H(N) ,H(α) ) (T) data for each x,y residue reveals that modest changes in the conformational ensemble masks larger changes of enthalpy and entropy governing the pPII↔β equilibrium indicating a significant residue dependent temperature dependence of the peptides' conformational ensembles. These results suggest that nearest-neighbor interactions between unlike residues act as conformat...Continue Reading

References

Jan 1, 1968·Advances in Protein Chemistry·C Tanford
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Jul 1, 1995·Nature Structural Biology·M B SwindellsJ M Thornton
May 1, 1994·Protein Science : a Publication of the Protein Society·A ChakrabarttyR L Baldwin
Feb 12, 1998·Journal of Molecular Biology·C J PenkettL J Smith
Nov 9, 2000·Proceedings of the National Academy of Sciences of the United States of America·R V PappuG D Rose
Jul 18, 2001·Journal of the American Chemical Society·S SchwarzingerH J Dyson
Nov 29, 2001·Biochemistry·M A KellyT P Creamer
Jul 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Zhengshuang ShiNeville R Kallenbach
Nov 7, 2002·Advances in Protein Chemistry·Zhengshuang ShiNeville R Kallenbach
Jul 3, 2003·Journal of the American Chemical Society·Liang DingNeville R Kallenbach
Jul 1, 1963·Journal of Molecular Biology·G N RAMACHANDRANV SASISEKHARAN
Jan 1, 1959·Advances in Protein Chemistry·W KAUZMANN
Mar 5, 2004·Journal of the American Chemical Society·Reinhard Schweitzer-StennerLaurence A Nafie
Apr 22, 2004·Journal of the American Chemical Society·Iain H McCollLaurence D Barron
Jul 16, 2004·Proceedings of the National Academy of Sciences of the United States of America·Franc Avbelj, Robert L Baldwin
Oct 2, 2004·Protein Science : a Publication of the Protein Society·William J DuddyE James Milner-White
Oct 19, 2004·Proceedings of the National Academy of Sciences of the United States of America·Kang ChenNeville R Kallenbach
Aug 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Bojan ZagrovicVijay S Pande
Sep 1, 2005·Proceedings of the National Academy of Sciences of the United States of America·Abhishek K JhaTobin R Sosnick
Nov 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·Pau BernadóMartin Blackledge
Dec 7, 2005·Proceedings of the National Academy of Sciences of the United States of America·Zhengshuang ShiNeville R Kallenbach
Dec 22, 2005·Journal of the American Chemical Society·Pau BernadóMartin Blackledge
Jan 21, 2006·Proceedings of the National Academy of Sciences of the United States of America·Franc AvbeljRobert L Baldwin
Feb 1, 2006·Proceedings of the National Academy of Sciences of the United States of America·Joanna MakowskaHarold A Scheraga
May 11, 2006·Chemical Reviews·Zhengshuang ShiNeville R Kallenbach
Feb 1, 2007·Journal of the American Chemical Society·Jürgen GrafHarald Schwalbe
Feb 6, 2007·Biophysical Journal·Joanna MakowskaHarold A Scheraga
Apr 7, 2007·Journal of the American Chemical Society·Pau BernadóDmitri I Svergun
Apr 10, 2007·Proceedings of the National Academy of Sciences of the United States of America·Reinhard Schweitzer-Stenner, Thomas J Measey
Jul 20, 2007·Journal of the American Chemical Society·Sebastian MeierMartin Blackledge
Feb 12, 2008·The Journal of Physical Chemistry. B·Joze GrdadolnikFranc Avbelj
Jun 11, 2009·The Journal of Physical Chemistry. B·Gerhard König, Stefan Boresch
Oct 2, 2009·The Journal of Chemical Physics·Pavol BodisSander Woutersen

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Citations

Sep 29, 2015·Chemical Communications : Chem Comm·Bridget MiloreyReinhard Schweitzer-Stenner
Jul 22, 2016·Molecular BioSystems·Maodong LiZhirong Liu
May 22, 2018·Chemical Communications : Chem Comm·Yan ZhangZhengshuang Shi
Sep 9, 2017·Protein Science : a Publication of the Protein Society·Yang ShenAd Bax
Mar 15, 2018·Biophysical Journal·Reinhard Schweitzer-Stenner, Siobhan E Toal
Apr 3, 2021·The Journal of Physical Chemistry. B·David RosenbergerAngel E Garcia
Dec 8, 2020·Journal of Chemical Information and Modeling·Adolfo BastidaJavier Cerezo
Dec 11, 2020·The Journal of Physical Chemistry. B·Shuting ZhangBrigita Urbanc
Mar 28, 2018·The Journal of Physical Chemistry. B·Giuseppe Lanza, Maria A Chiacchio
Nov 22, 2019·Journal of Chemical Theory and Computation·Shuting ZhangBrigita Urbanc
Jan 5, 2019·The Journal of Physical Chemistry. B·Reinhard Schweitzer-StennerCunlan Guo
Oct 8, 2021·The Journal of Physical Chemistry. B·Bridget MiloreyReinhard Schweitzer-Stenner

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