Predicting protein folding cores by empirical potential functions

Mingzhi Chen, Athanasios D. Dousis, Yinghao Wu, Pernilla Wittung-Stafshede, Jianpeng Ma

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Theoretical and in vitro experiments suggest that protein folding cores form early in the process of folding, and that proteins may have evolved to optimize both folding speed and native-state stability. In our previous work (Chen et al., Structure, 14 (2006) 1401), we developed a set of empirical potential functions and used them to analyze interaction energies among secondary-structure elements in two β-sandwich proteins. Our work on this group of proteins demonstrated that the predicted folding core also harbors residues that form native-like interactions early in the folding reaction. In the current work, we have tested our empirical potential functions on structurally-different proteins for which the folding cores have been revealed by protein hydrogen-deuterium exchange experiments. Using a set of 29 unrelated proteins, which have been extensively studied in the literature, we demonstrate that the average prediction result from our method is significantly better than predictions based on other computational methods. Our study is an important step towards the ultimate goal of understanding the correlation between folding cores and native structures.

Original languageEnglish (US)
Pages (from-to)16-22
Number of pages7
JournalArchives of Biochemistry and Biophysics
Volume483
Issue number1
DOIs
StatePublished - Mar 1 2009
Externally publishedYes

Fingerprint

Protein folding
Protein Folding
Proteins
Deuterium
Hydrogen
Ports and harbors
Computational methods
Experiments

Keywords

  • Folding cores
  • Folding nuclei
  • HX
  • Hydrogen exchange
  • phi-value
  • Protein folding

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

Cite this

Predicting protein folding cores by empirical potential functions. / Chen, Mingzhi; Dousis, Athanasios D.; Wu, Yinghao; Wittung-Stafshede, Pernilla; Ma, Jianpeng.

In: Archives of Biochemistry and Biophysics, Vol. 483, No. 1, 01.03.2009, p. 16-22.

Research output: Contribution to journalArticle

Chen, Mingzhi ; Dousis, Athanasios D. ; Wu, Yinghao ; Wittung-Stafshede, Pernilla ; Ma, Jianpeng. / Predicting protein folding cores by empirical potential functions. In: Archives of Biochemistry and Biophysics. 2009 ; Vol. 483, No. 1. pp. 16-22.
@article{03c8426c2ebe4585893f5bdbaacd77cc,
title = "Predicting protein folding cores by empirical potential functions",
abstract = "Theoretical and in vitro experiments suggest that protein folding cores form early in the process of folding, and that proteins may have evolved to optimize both folding speed and native-state stability. In our previous work (Chen et al., Structure, 14 (2006) 1401), we developed a set of empirical potential functions and used them to analyze interaction energies among secondary-structure elements in two β-sandwich proteins. Our work on this group of proteins demonstrated that the predicted folding core also harbors residues that form native-like interactions early in the folding reaction. In the current work, we have tested our empirical potential functions on structurally-different proteins for which the folding cores have been revealed by protein hydrogen-deuterium exchange experiments. Using a set of 29 unrelated proteins, which have been extensively studied in the literature, we demonstrate that the average prediction result from our method is significantly better than predictions based on other computational methods. Our study is an important step towards the ultimate goal of understanding the correlation between folding cores and native structures.",
keywords = "Folding cores, Folding nuclei, HX, Hydrogen exchange, phi-value, Protein folding",
author = "Mingzhi Chen and Dousis, {Athanasios D.} and Yinghao Wu and Pernilla Wittung-Stafshede and Jianpeng Ma",
year = "2009",
month = "3",
day = "1",
doi = "10.1016/j.abb.2008.12.011",
language = "English (US)",
volume = "483",
pages = "16--22",
journal = "Archives of Biochemistry and Biophysics",
issn = "0003-9861",
publisher = "Academic Press Inc.",
number = "1",

}

TY - JOUR

T1 - Predicting protein folding cores by empirical potential functions

AU - Chen, Mingzhi

AU - Dousis, Athanasios D.

AU - Wu, Yinghao

AU - Wittung-Stafshede, Pernilla

AU - Ma, Jianpeng

PY - 2009/3/1

Y1 - 2009/3/1

N2 - Theoretical and in vitro experiments suggest that protein folding cores form early in the process of folding, and that proteins may have evolved to optimize both folding speed and native-state stability. In our previous work (Chen et al., Structure, 14 (2006) 1401), we developed a set of empirical potential functions and used them to analyze interaction energies among secondary-structure elements in two β-sandwich proteins. Our work on this group of proteins demonstrated that the predicted folding core also harbors residues that form native-like interactions early in the folding reaction. In the current work, we have tested our empirical potential functions on structurally-different proteins for which the folding cores have been revealed by protein hydrogen-deuterium exchange experiments. Using a set of 29 unrelated proteins, which have been extensively studied in the literature, we demonstrate that the average prediction result from our method is significantly better than predictions based on other computational methods. Our study is an important step towards the ultimate goal of understanding the correlation between folding cores and native structures.

AB - Theoretical and in vitro experiments suggest that protein folding cores form early in the process of folding, and that proteins may have evolved to optimize both folding speed and native-state stability. In our previous work (Chen et al., Structure, 14 (2006) 1401), we developed a set of empirical potential functions and used them to analyze interaction energies among secondary-structure elements in two β-sandwich proteins. Our work on this group of proteins demonstrated that the predicted folding core also harbors residues that form native-like interactions early in the folding reaction. In the current work, we have tested our empirical potential functions on structurally-different proteins for which the folding cores have been revealed by protein hydrogen-deuterium exchange experiments. Using a set of 29 unrelated proteins, which have been extensively studied in the literature, we demonstrate that the average prediction result from our method is significantly better than predictions based on other computational methods. Our study is an important step towards the ultimate goal of understanding the correlation between folding cores and native structures.

KW - Folding cores

KW - Folding nuclei

KW - HX

KW - Hydrogen exchange

KW - phi-value

KW - Protein folding

UR - http://www.scopus.com/inward/record.url?scp=60049093576&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=60049093576&partnerID=8YFLogxK

U2 - 10.1016/j.abb.2008.12.011

DO - 10.1016/j.abb.2008.12.011

M3 - Article

C2 - 19135974

AN - SCOPUS:60049093576

VL - 483

SP - 16

EP - 22

JO - Archives of Biochemistry and Biophysics

JF - Archives of Biochemistry and Biophysics

SN - 0003-9861

IS - 1

ER -