Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water: Singular value decomposition analysis

Kwang Im Oh, Kyung Koo Lee, Eun Kyung Park, Dong Geun Yoo, Geum Sook Hwang, Minhaeng Cho

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

Despite that a number of experimental and theoretical investigations have been carried out to determine the structure of trialanine in water, the reported populations of polyproline II (PPII) and β-strand conformers vary and were found to be dependent on which spectroscopic method was used. Such discrepancies are due to limitations of different spectroscopic methods used. Here, the temperature- and pH-dependent circular dichroism (CD) and NMR experiments have been carried out to develop a self-consistent singular value decomposition procedure. The temperature-dependent CD spectra indicate the presence of two conformers, but due to the two peptide bonds in a trialanine, one should take into consideration of four different conformers to fully interpret the NMR results. From the pH-dependent NMR coupling constant measurements, the conformation of zwitterionic trialanine is little different from that of cationic one. The strong pH dependency of CD spectrum is likely due to charge transfer transitions between carboxylate and nearby peptide groups or internal field effects not to pH-dependent conformational change. To simultaneously analyze the temperature-dependent CD and NMR data, a self-consistent procedure was used to newly determine the reference NMR coupling constants required to estimate one of the peptide dihedral angles. From the estimated enthalpy and entropy changes associated with the transition from enthalpically favorable PPII conformer to entropically favorable β-strand conformer, the relative populations of the four possible conformers of trialanine were determined and compared with the previous experimental findings. We anticipate that the present experimental results and interpretation procedure would be of use in determining the solution structures of small oligopeptides in the future. Chirality, 2010. © 2010 Wiley-Liss, Inc. ©

Original languageEnglish
JournalChirality
Volume22
Issue number1 E
DOIs
Publication statusPublished - 2010 Nov 22

Fingerprint

Dichroism
Singular value decomposition
Circular Dichroism
Nuclear magnetic resonance
Water
Peptides
Temperature
Population
Oligopeptides
Chirality
Entropy
Dihedral angle
Conformations
Charge transfer
Enthalpy
alanyl-alanyl-alanine
polyproline
Experiments

Keywords

  • circular dichroism
  • poyproline II
  • singular value decomposition
  • trialanine

ASJC Scopus subject areas

  • Organic Chemistry
  • Analytical Chemistry
  • Drug Discovery
  • Pharmacology
  • Catalysis
  • Spectroscopy

Cite this

Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water : Singular value decomposition analysis. / Oh, Kwang Im; Lee, Kyung Koo; Park, Eun Kyung; Yoo, Dong Geun; Hwang, Geum Sook; Cho, Minhaeng.

In: Chirality, Vol. 22, No. 1 E, 22.11.2010.

Research output: Contribution to journalArticle

Oh, Kwang Im ; Lee, Kyung Koo ; Park, Eun Kyung ; Yoo, Dong Geun ; Hwang, Geum Sook ; Cho, Minhaeng. / Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water : Singular value decomposition analysis. In: Chirality. 2010 ; Vol. 22, No. 1 E.
@article{47bad1a256054224bf01bb4e2f89a060,
title = "Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water: Singular value decomposition analysis",
abstract = "Despite that a number of experimental and theoretical investigations have been carried out to determine the structure of trialanine in water, the reported populations of polyproline II (PPII) and β-strand conformers vary and were found to be dependent on which spectroscopic method was used. Such discrepancies are due to limitations of different spectroscopic methods used. Here, the temperature- and pH-dependent circular dichroism (CD) and NMR experiments have been carried out to develop a self-consistent singular value decomposition procedure. The temperature-dependent CD spectra indicate the presence of two conformers, but due to the two peptide bonds in a trialanine, one should take into consideration of four different conformers to fully interpret the NMR results. From the pH-dependent NMR coupling constant measurements, the conformation of zwitterionic trialanine is little different from that of cationic one. The strong pH dependency of CD spectrum is likely due to charge transfer transitions between carboxylate and nearby peptide groups or internal field effects not to pH-dependent conformational change. To simultaneously analyze the temperature-dependent CD and NMR data, a self-consistent procedure was used to newly determine the reference NMR coupling constants required to estimate one of the peptide dihedral angles. From the estimated enthalpy and entropy changes associated with the transition from enthalpically favorable PPII conformer to entropically favorable β-strand conformer, the relative populations of the four possible conformers of trialanine were determined and compared with the previous experimental findings. We anticipate that the present experimental results and interpretation procedure would be of use in determining the solution structures of small oligopeptides in the future. Chirality, 2010. {\circledC} 2010 Wiley-Liss, Inc. {\circledC}",
keywords = "circular dichroism, poyproline II, singular value decomposition, trialanine",
author = "Oh, {Kwang Im} and Lee, {Kyung Koo} and Park, {Eun Kyung} and Yoo, {Dong Geun} and Hwang, {Geum Sook} and Minhaeng Cho",
year = "2010",
month = "11",
day = "22",
doi = "10.1002/chir.20870",
language = "English",
volume = "22",
journal = "Chirality",
issn = "0899-0042",
publisher = "Wiley-Liss Inc.",
number = "1 E",

}

TY - JOUR

T1 - Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water

T2 - Singular value decomposition analysis

AU - Oh, Kwang Im

AU - Lee, Kyung Koo

AU - Park, Eun Kyung

AU - Yoo, Dong Geun

AU - Hwang, Geum Sook

AU - Cho, Minhaeng

PY - 2010/11/22

Y1 - 2010/11/22

N2 - Despite that a number of experimental and theoretical investigations have been carried out to determine the structure of trialanine in water, the reported populations of polyproline II (PPII) and β-strand conformers vary and were found to be dependent on which spectroscopic method was used. Such discrepancies are due to limitations of different spectroscopic methods used. Here, the temperature- and pH-dependent circular dichroism (CD) and NMR experiments have been carried out to develop a self-consistent singular value decomposition procedure. The temperature-dependent CD spectra indicate the presence of two conformers, but due to the two peptide bonds in a trialanine, one should take into consideration of four different conformers to fully interpret the NMR results. From the pH-dependent NMR coupling constant measurements, the conformation of zwitterionic trialanine is little different from that of cationic one. The strong pH dependency of CD spectrum is likely due to charge transfer transitions between carboxylate and nearby peptide groups or internal field effects not to pH-dependent conformational change. To simultaneously analyze the temperature-dependent CD and NMR data, a self-consistent procedure was used to newly determine the reference NMR coupling constants required to estimate one of the peptide dihedral angles. From the estimated enthalpy and entropy changes associated with the transition from enthalpically favorable PPII conformer to entropically favorable β-strand conformer, the relative populations of the four possible conformers of trialanine were determined and compared with the previous experimental findings. We anticipate that the present experimental results and interpretation procedure would be of use in determining the solution structures of small oligopeptides in the future. Chirality, 2010. © 2010 Wiley-Liss, Inc. ©

AB - Despite that a number of experimental and theoretical investigations have been carried out to determine the structure of trialanine in water, the reported populations of polyproline II (PPII) and β-strand conformers vary and were found to be dependent on which spectroscopic method was used. Such discrepancies are due to limitations of different spectroscopic methods used. Here, the temperature- and pH-dependent circular dichroism (CD) and NMR experiments have been carried out to develop a self-consistent singular value decomposition procedure. The temperature-dependent CD spectra indicate the presence of two conformers, but due to the two peptide bonds in a trialanine, one should take into consideration of four different conformers to fully interpret the NMR results. From the pH-dependent NMR coupling constant measurements, the conformation of zwitterionic trialanine is little different from that of cationic one. The strong pH dependency of CD spectrum is likely due to charge transfer transitions between carboxylate and nearby peptide groups or internal field effects not to pH-dependent conformational change. To simultaneously analyze the temperature-dependent CD and NMR data, a self-consistent procedure was used to newly determine the reference NMR coupling constants required to estimate one of the peptide dihedral angles. From the estimated enthalpy and entropy changes associated with the transition from enthalpically favorable PPII conformer to entropically favorable β-strand conformer, the relative populations of the four possible conformers of trialanine were determined and compared with the previous experimental findings. We anticipate that the present experimental results and interpretation procedure would be of use in determining the solution structures of small oligopeptides in the future. Chirality, 2010. © 2010 Wiley-Liss, Inc. ©

KW - circular dichroism

KW - poyproline II

KW - singular value decomposition

KW - trialanine

UR - http://www.scopus.com/inward/record.url?scp=78349293761&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78349293761&partnerID=8YFLogxK

U2 - 10.1002/chir.20870

DO - 10.1002/chir.20870

M3 - Article

C2 - 21038390

AN - SCOPUS:78349293761

VL - 22

JO - Chirality

JF - Chirality

SN - 0899-0042

IS - 1 E

ER -