DOI: 10.1002/bip.22034. β‐turn tendency in <i>N</i>‐methylated peptides with dehydrophenylalanine residue: DFT study

β‐turn tendency in N‐methylated peptides with dehydrophenylalanine residue: DFT study

10.1002/bip.22034

Crossref journal-article

Wiley

Biopolymers (311)

Abstract

AbstractThe tendency to adopt β‐turn conformation by model dipeptides with α,β‐dehydrophenylalanine (ΔPhe) residue in the gas phase and in solution is investigated by theoretical methods. We pay special attention to a dependence of conformational properties on the side‐chain configuration of dehydro residue and the influence of N‐methylation on β‐turn stability. An extensive computational study of the conformational preferences of Z and E isomers of dipeptides Ac‐Gly‐(E/Z)‐ΔPhe‐NHMe (1a / 1b) and Ac‐Gly‐(E/Z)‐ΔPhe‐NMe2 (2a/2b) by B3LYP/6‐311++G(d,p) and MP2/6‐311++G(d,p) methods is reported. It is shown that, in agreement with experimental data, Ac‐Gly‐(Z)‐ΔPhe‐NHMe has a great tendency to adopt β‐turn conformation. In the gas phase the type II β‐turn is preferred, whereas in the polar environment, the type I. On the other hand, dehydro residue in Ac‐Gly‐(E)‐ΔPhe‐NHMe has a preference to adopt extended conformations in all environments. N‐methylation of C‐terminal amide group, which prevents the formation of 1←4 intramolecular hydrogen bond, change dramatically the conformational properties of studied dehydropeptides. Especially, the tendency to adopt β‐turn conformations is much weaker for the N‐methylated Z isomer (Ac‐Gly‐(Z)‐ΔPhe‐NMe2), both in vacuo and in the polar environment. On the contrary, N‐methylated E isomer (Ac‐Gly‐(E)‐ΔPhe‐NMe2) can easier adopt β‐turn conformation, but the backbone torsion angles (ϕ1, ψ1, ϕ2, ψ2) are off the limits for common β‐turn types. © 2012 Wiley Periodicals, Inc. Biopolymers 97:518–528, 2012.

Bibliography

Buczek, A., WaÅÄsa, R., & Broda, M. A. (2012). Î²âturn tendency in Nâmethylated peptides with dehydrophenylalanine residue: DFT study. Biopolymers, 97(7), 518â528. Portico.

Authors 3

Aneta Buczek (first)
Roksana Wałęsa (additional)
Małgorzata A. Broda (additional)

References 46 Referenced 14

10.1016/S0065-3233(08)60063-7
10.1021/cr000100n
10.3109/10409238009105471
10.1002/bip.21561
10.1002/bip.10571
{'key': 'e_1_2_5_7_2', 'first-page': '33', 'volume-title': 'Chemistry and Biochemistry of Amino Acid, Peptides and Proteins', 'author': 'Stammer C.H.', 'year': '1982'} / Chemistry and Biochemistry of Amino Acid, Peptides and Proteins by Stammer C.H. (1982)
{'key': 'e_1_2_5_8_2', 'first-page': '285', 'volume-title': 'The Peptides', 'author': 'Noda K.', 'year': '1983'} / The Peptides by Noda K. (1983)
{'key': 'e_1_2_5_9_2', 'first-page': '1595', 'volume': '69', 'author': 'Pietrzyński G.', 'year': '1995', 'journal-title': 'Polish J Chem'} / Polish J Chem by Pietrzyński G. (1995)
10.1016/S0079-6107(97)85628-3
10.1002/(SICI)1097-0282(1996)40:1<105::AID-BIP5>3.0.CO;2-#
10.1002/(SICI)1097-0282(199609)39:3<287::AID-BIP2>3.0.CO;2-K
10.1021/jo961661a
10.1039/B601634K
10.1016/j.molstruc.2008.06.023
10.1002/bip.21522
10.1002/mrc.2753
10.1107/S1600536806049841
10.1107/S1600536806002273
10.1107/S0108270105015258
10.1002/psc.601
10.1021/jp200949t
10.1021/ar8000603
10.1021/bi060837s
{'key': 'e_1_2_5_25_2', 'volume-title': 'Gaussian 09, Revision B.01', 'author': 'Frisch M. J.', 'year': '2009'} / Gaussian 09, Revision B.01 by Frisch M. J. (2009)
10.1021/ja00016a049
10.1021/ja00016a010
10.1021/ja00099a048
10.1021/ct8005437
10.1016/0301-0104(82)85072-6
10.1021/cr9904009
10.1002/jcc.20073
10.1021/ja00064a053
10.1002/chem.200204393
10.1021/ja0435788
10.1021/ja806951r
10.1016/j.theochem.2003.12.048
10.1021/ma60055a001
10.1021/jp013952f
10.1002/prot.21630
10.1002/1521-3773(20020104)41:1<48::AID-ANIE48>3.0.CO;2-U
10.1107/S0108768198001463
10.1002/psc.763
10.1016/S0166-1280(97)00422-3
10.1039/b923041f
10.1002/bip.360280709
10.1002/psc.433

Dates

Type	When
Created	13 years, 6 months ago (Feb. 10, 2012, 8:31 a.m.)
Deposited	1 year, 10 months ago (Oct. 10, 2023, 10:28 a.m.)
Indexed	2 months, 2 weeks ago (June 16, 2025, 10:09 a.m.)
Issued	13 years, 6 months ago (Feb. 10, 2012)
Published	13 years, 6 months ago (Feb. 10, 2012)
Published Online	13 years, 6 months ago (Feb. 10, 2012)
Published Print	13 years, 2 months ago (July 1, 2012)

Funders 0

None

BibTeX

@article{Buczek_2012, title={β‐turn tendency in N‐methylated peptides with dehydrophenylalanine residue: DFT study}, volume={97}, ISSN={1097-0282}, url={http://dx.doi.org/10.1002/bip.22034}, DOI={10.1002/bip.22034}, number={7}, journal={Biopolymers}, publisher={Wiley}, author={Buczek, Aneta and Wałęsa, Roksana and Broda, Małgorzata A.}, year={2012}, month=feb, pages={518–528} }

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  "abstract": "<jats:title>Abstract</jats:title><jats:p>The tendency to adopt \u03b2\u2010turn conformation by model dipeptides with \u03b1,\u03b2\u2010dehydrophenylalanine (\u0394Phe) residue in the gas phase and in solution is investigated by theoretical methods. We pay special attention to a dependence of conformational properties on the side\u2010chain configuration of dehydro residue and the influence of <jats:italic>N</jats:italic>\u2010methylation on \u03b2\u2010turn stability. An extensive computational study of the conformational preferences of <jats:italic>Z</jats:italic> and <jats:italic>E</jats:italic> isomers of dipeptides Ac\u2010Gly\u2010(<jats:italic>E</jats:italic>/<jats:italic>Z</jats:italic>)\u2010\u0394Phe\u2010NHMe (<jats:bold>1a</jats:bold> / <jats:bold>1b</jats:bold>) and Ac\u2010Gly\u2010(<jats:italic>E</jats:italic>/<jats:italic>Z</jats:italic>)\u2010\u0394Phe\u2010NMe<jats:sub>2</jats:sub> (<jats:bold>2a</jats:bold>/<jats:bold>2b</jats:bold>) by B3LYP/6\u2010311++G(d,p) and MP2/6\u2010311++G(d,p) methods is reported. It is shown that, in agreement with experimental data, Ac\u2010Gly\u2010(<jats:italic>Z</jats:italic>)\u2010\u0394Phe\u2010NHMe has a great tendency to adopt \u03b2\u2010turn conformation. In the gas phase the type II \u03b2\u2010turn is preferred, whereas in the polar environment, the type I. On the other hand, dehydro residue in Ac\u2010Gly\u2010(<jats:italic>E</jats:italic>)\u2010\u0394Phe\u2010NHMe has a preference to adopt extended conformations in all environments. <jats:italic>N</jats:italic>\u2010methylation of C\u2010terminal amide group, which prevents the formation of 1\u21904 intramolecular hydrogen bond, change dramatically the conformational properties of studied dehydropeptides. Especially, the tendency to adopt \u03b2\u2010turn conformations is much weaker for the <jats:italic>N</jats:italic>\u2010methylated <jats:italic>Z</jats:italic> isomer (Ac\u2010Gly\u2010(<jats:italic>Z</jats:italic>)\u2010\u0394Phe\u2010NMe<jats:sub>2</jats:sub>), both in vacuo and in the polar environment. On the contrary, <jats:italic>N</jats:italic>\u2010methylated <jats:italic>E</jats:italic> isomer (Ac\u2010Gly\u2010(<jats:italic>E</jats:italic>)\u2010\u0394Phe\u2010NMe<jats:sub>2</jats:sub>) can easier adopt \u03b2\u2010turn conformation, but the backbone torsion angles (\u03d5<jats:sub>1</jats:sub>, \u03c8<jats:sub>1</jats:sub>, \u03d5<jats:sub>2</jats:sub>, \u03c8<jats:sub>2</jats:sub>) are off the limits for common \u03b2\u2010turn types. \u00a9 2012 Wiley Periodicals, Inc. Biopolymers 97:518\u2013528, 2012.</jats:p>",
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