Quantum chemical quantification of weakly polar interaction energies in the TC5b miniprotein

Marcus P D Hatfield, Nicholas Y. Palermo, József Csontos, Richard F. Murphy, Sándor Lovas

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

The tertiary structure of the TC5b miniprotein is stabilized by inter-residue interactions of the Trp-cage, which is composed of a Tyr and several Pro residues surrounding a central Trp residue. The interactions include Ar - Ar (aromatic side-chain-aromatic side-chain), Ar - NH (aromatic side-chain - backbone amide), and CH - π (aromatic side-chain-aliphatic hydrogen) interactions. In the present work, the strength of the weakly polar interactions found in the TC5b miniprotein was quantified using all of the available 38 NMR structures (1L2Y) from the Protein Data Bank with DFT quantum chemical calculations at the BHandHLYP/ cc-pVTZ level of theory and molecular fragmentation with capping of the partial structures. The energies of interaction between the individual residues of the Trp-cage range between -5.85 ± 1.41 and -21.30 ± 0.88 kcal mol-1, leading to a significant total structural stabilization energy of -52.13 ± 2.56 kcal mol-1 of which about 50% is from the weakly polar interactions. Furthermore, the strengths of the individual weakly polar interactions are between -2.32 ± 0.17 and -2.93 ± 0.12 kcal mol-1 for the CH - π interactions, between -2.48 ± 0.97 and -3.09 ± 1.02 kcal mol-1 for the Ar - NH interaction and -2.74 ± 1.06 kcal mol-1 for the Ar - Ar interaction.

Original languageEnglish
Pages (from-to)3503-3508
Number of pages6
JournalJournal of Physical Chemistry B
Volume112
Issue number11
DOIs
StatePublished - Mar 20 2008

Fingerprint

Amides
Discrete Fourier transforms
Hydrogen
Stabilization
Nuclear magnetic resonance
Proteins
interactions
energy
methylidyne
amides
fragmentation
stabilization
proteins
nuclear magnetic resonance
hydrogen

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry

Cite this

Quantum chemical quantification of weakly polar interaction energies in the TC5b miniprotein. / Hatfield, Marcus P D; Palermo, Nicholas Y.; Csontos, József; Murphy, Richard F.; Lovas, Sándor.

In: Journal of Physical Chemistry B, Vol. 112, No. 11, 20.03.2008, p. 3503-3508.

Research output: Contribution to journalArticle

Hatfield, Marcus P D ; Palermo, Nicholas Y. ; Csontos, József ; Murphy, Richard F. ; Lovas, Sándor. / Quantum chemical quantification of weakly polar interaction energies in the TC5b miniprotein. In: Journal of Physical Chemistry B. 2008 ; Vol. 112, No. 11. pp. 3503-3508.
@article{ee4f782fe01747e6b344268d7a1c59de,
title = "Quantum chemical quantification of weakly polar interaction energies in the TC5b miniprotein",
abstract = "The tertiary structure of the TC5b miniprotein is stabilized by inter-residue interactions of the Trp-cage, which is composed of a Tyr and several Pro residues surrounding a central Trp residue. The interactions include Ar - Ar (aromatic side-chain-aromatic side-chain), Ar - NH (aromatic side-chain - backbone amide), and CH - π (aromatic side-chain-aliphatic hydrogen) interactions. In the present work, the strength of the weakly polar interactions found in the TC5b miniprotein was quantified using all of the available 38 NMR structures (1L2Y) from the Protein Data Bank with DFT quantum chemical calculations at the BHandHLYP/ cc-pVTZ level of theory and molecular fragmentation with capping of the partial structures. The energies of interaction between the individual residues of the Trp-cage range between -5.85 ± 1.41 and -21.30 ± 0.88 kcal mol-1, leading to a significant total structural stabilization energy of -52.13 ± 2.56 kcal mol-1 of which about 50{\%} is from the weakly polar interactions. Furthermore, the strengths of the individual weakly polar interactions are between -2.32 ± 0.17 and -2.93 ± 0.12 kcal mol-1 for the CH - π interactions, between -2.48 ± 0.97 and -3.09 ± 1.02 kcal mol-1 for the Ar - NH interaction and -2.74 ± 1.06 kcal mol-1 for the Ar - Ar interaction.",
author = "Hatfield, {Marcus P D} and Palermo, {Nicholas Y.} and J{\'o}zsef Csontos and Murphy, {Richard F.} and S{\'a}ndor Lovas",
year = "2008",
month = "3",
day = "20",
doi = "10.1021/jp077674h",
language = "English",
volume = "112",
pages = "3503--3508",
journal = "Journal of Physical Chemistry B Materials",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "11",

}

TY - JOUR

T1 - Quantum chemical quantification of weakly polar interaction energies in the TC5b miniprotein

AU - Hatfield, Marcus P D

AU - Palermo, Nicholas Y.

AU - Csontos, József

AU - Murphy, Richard F.

AU - Lovas, Sándor

PY - 2008/3/20

Y1 - 2008/3/20

N2 - The tertiary structure of the TC5b miniprotein is stabilized by inter-residue interactions of the Trp-cage, which is composed of a Tyr and several Pro residues surrounding a central Trp residue. The interactions include Ar - Ar (aromatic side-chain-aromatic side-chain), Ar - NH (aromatic side-chain - backbone amide), and CH - π (aromatic side-chain-aliphatic hydrogen) interactions. In the present work, the strength of the weakly polar interactions found in the TC5b miniprotein was quantified using all of the available 38 NMR structures (1L2Y) from the Protein Data Bank with DFT quantum chemical calculations at the BHandHLYP/ cc-pVTZ level of theory and molecular fragmentation with capping of the partial structures. The energies of interaction between the individual residues of the Trp-cage range between -5.85 ± 1.41 and -21.30 ± 0.88 kcal mol-1, leading to a significant total structural stabilization energy of -52.13 ± 2.56 kcal mol-1 of which about 50% is from the weakly polar interactions. Furthermore, the strengths of the individual weakly polar interactions are between -2.32 ± 0.17 and -2.93 ± 0.12 kcal mol-1 for the CH - π interactions, between -2.48 ± 0.97 and -3.09 ± 1.02 kcal mol-1 for the Ar - NH interaction and -2.74 ± 1.06 kcal mol-1 for the Ar - Ar interaction.

AB - The tertiary structure of the TC5b miniprotein is stabilized by inter-residue interactions of the Trp-cage, which is composed of a Tyr and several Pro residues surrounding a central Trp residue. The interactions include Ar - Ar (aromatic side-chain-aromatic side-chain), Ar - NH (aromatic side-chain - backbone amide), and CH - π (aromatic side-chain-aliphatic hydrogen) interactions. In the present work, the strength of the weakly polar interactions found in the TC5b miniprotein was quantified using all of the available 38 NMR structures (1L2Y) from the Protein Data Bank with DFT quantum chemical calculations at the BHandHLYP/ cc-pVTZ level of theory and molecular fragmentation with capping of the partial structures. The energies of interaction between the individual residues of the Trp-cage range between -5.85 ± 1.41 and -21.30 ± 0.88 kcal mol-1, leading to a significant total structural stabilization energy of -52.13 ± 2.56 kcal mol-1 of which about 50% is from the weakly polar interactions. Furthermore, the strengths of the individual weakly polar interactions are between -2.32 ± 0.17 and -2.93 ± 0.12 kcal mol-1 for the CH - π interactions, between -2.48 ± 0.97 and -3.09 ± 1.02 kcal mol-1 for the Ar - NH interaction and -2.74 ± 1.06 kcal mol-1 for the Ar - Ar interaction.

UR - http://www.scopus.com/inward/record.url?scp=45949106993&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=45949106993&partnerID=8YFLogxK

U2 - 10.1021/jp077674h

DO - 10.1021/jp077674h

M3 - Article

VL - 112

SP - 3503

EP - 3508

JO - Journal of Physical Chemistry B Materials

JF - Journal of Physical Chemistry B Materials

SN - 1520-6106

IS - 11

ER -