Molecular dynamics simulations to investigate the effects of zinc ions on the structural stability of the c-Cbl RING domain

Hsuan Liang Liu, Ching Tao Yang, Jian Hua Zhao, Chih Hung Huang, Hsin Yi Lin, Hsu Wei Fang, Yih Ho, Wei Bor Tsai

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

In eukaryotic cells, ubiquitylation of proteins plays a critical role in regulating diverse cell processes by the ubiquitin activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin protein ligase (E3). E3 is the key component that confers specificity to ubiquitylation and directs the conjugation of ubiquitin to a specific target protein. RING domains are small structured protein domains that require the coordination of zinc ions for a stable tertiary fold and some of them are involved in the E3 family. In this study, we reported the detailed relationships between the two zinc ions and the structural stability of the c-Cbl RING domain by molecular dynamics simulations. Our results show that these two zinc ions play an important role in maintaining both the secondary and tertiary structural stabilities of the c-Cbl RING domain. Our results also reveal that the secondary structural stability of the c-Cbl RING domain is mainly determined by the hydrogen-bonding networks in or near the two zinc ion binding sites. Our results further demonstrate that zinc ion binding site 2 is more structurally stable than site 1.

Original languageEnglish
Pages (from-to)1231-1238
Number of pages8
JournalBiotechnology Progress
Volume23
Issue number5
DOIs
Publication statusPublished - Sep 2007

Fingerprint

molecular dynamics
Molecular Dynamics Simulation
Zinc
zinc
ubiquitin-protein ligase
Ions
ions
Ubiquitination
binding sites
Ubiquitin-Activating Enzymes
Binding Sites
Ubiquitin-Conjugating Enzymes
Ubiquitin-Protein Ligases
hydrogen bonding
proteins
Eukaryotic Cells
Hydrogen Bonding
ubiquitin
Ubiquitin
eukaryotic cells

ASJC Scopus subject areas

  • Food Science
  • Biotechnology
  • Microbiology

Cite this

Liu, H. L., Yang, C. T., Zhao, J. H., Huang, C. H., Lin, H. Y., Fang, H. W., ... Tsai, W. B. (2007). Molecular dynamics simulations to investigate the effects of zinc ions on the structural stability of the c-Cbl RING domain. Biotechnology Progress, 23(5), 1231-1238. https://doi.org/10.1021/bp0701665

Molecular dynamics simulations to investigate the effects of zinc ions on the structural stability of the c-Cbl RING domain. / Liu, Hsuan Liang; Yang, Ching Tao; Zhao, Jian Hua; Huang, Chih Hung; Lin, Hsin Yi; Fang, Hsu Wei; Ho, Yih; Tsai, Wei Bor.

In: Biotechnology Progress, Vol. 23, No. 5, 09.2007, p. 1231-1238.

Research output: Contribution to journalArticle

Liu, Hsuan Liang ; Yang, Ching Tao ; Zhao, Jian Hua ; Huang, Chih Hung ; Lin, Hsin Yi ; Fang, Hsu Wei ; Ho, Yih ; Tsai, Wei Bor. / Molecular dynamics simulations to investigate the effects of zinc ions on the structural stability of the c-Cbl RING domain. In: Biotechnology Progress. 2007 ; Vol. 23, No. 5. pp. 1231-1238.
@article{b3aa41a55bcc4f83b682a75cffd98fb3,
title = "Molecular dynamics simulations to investigate the effects of zinc ions on the structural stability of the c-Cbl RING domain",
abstract = "In eukaryotic cells, ubiquitylation of proteins plays a critical role in regulating diverse cell processes by the ubiquitin activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin protein ligase (E3). E3 is the key component that confers specificity to ubiquitylation and directs the conjugation of ubiquitin to a specific target protein. RING domains are small structured protein domains that require the coordination of zinc ions for a stable tertiary fold and some of them are involved in the E3 family. In this study, we reported the detailed relationships between the two zinc ions and the structural stability of the c-Cbl RING domain by molecular dynamics simulations. Our results show that these two zinc ions play an important role in maintaining both the secondary and tertiary structural stabilities of the c-Cbl RING domain. Our results also reveal that the secondary structural stability of the c-Cbl RING domain is mainly determined by the hydrogen-bonding networks in or near the two zinc ion binding sites. Our results further demonstrate that zinc ion binding site 2 is more structurally stable than site 1.",
author = "Liu, {Hsuan Liang} and Yang, {Ching Tao} and Zhao, {Jian Hua} and Huang, {Chih Hung} and Lin, {Hsin Yi} and Fang, {Hsu Wei} and Yih Ho and Tsai, {Wei Bor}",
year = "2007",
month = "9",
doi = "10.1021/bp0701665",
language = "English",
volume = "23",
pages = "1231--1238",
journal = "Biotechnology Progress",
issn = "8756-7938",
publisher = "John Wiley and Sons Ltd",
number = "5",

}

TY - JOUR

T1 - Molecular dynamics simulations to investigate the effects of zinc ions on the structural stability of the c-Cbl RING domain

AU - Liu, Hsuan Liang

AU - Yang, Ching Tao

AU - Zhao, Jian Hua

AU - Huang, Chih Hung

AU - Lin, Hsin Yi

AU - Fang, Hsu Wei

AU - Ho, Yih

AU - Tsai, Wei Bor

PY - 2007/9

Y1 - 2007/9

N2 - In eukaryotic cells, ubiquitylation of proteins plays a critical role in regulating diverse cell processes by the ubiquitin activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin protein ligase (E3). E3 is the key component that confers specificity to ubiquitylation and directs the conjugation of ubiquitin to a specific target protein. RING domains are small structured protein domains that require the coordination of zinc ions for a stable tertiary fold and some of them are involved in the E3 family. In this study, we reported the detailed relationships between the two zinc ions and the structural stability of the c-Cbl RING domain by molecular dynamics simulations. Our results show that these two zinc ions play an important role in maintaining both the secondary and tertiary structural stabilities of the c-Cbl RING domain. Our results also reveal that the secondary structural stability of the c-Cbl RING domain is mainly determined by the hydrogen-bonding networks in or near the two zinc ion binding sites. Our results further demonstrate that zinc ion binding site 2 is more structurally stable than site 1.

AB - In eukaryotic cells, ubiquitylation of proteins plays a critical role in regulating diverse cell processes by the ubiquitin activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin protein ligase (E3). E3 is the key component that confers specificity to ubiquitylation and directs the conjugation of ubiquitin to a specific target protein. RING domains are small structured protein domains that require the coordination of zinc ions for a stable tertiary fold and some of them are involved in the E3 family. In this study, we reported the detailed relationships between the two zinc ions and the structural stability of the c-Cbl RING domain by molecular dynamics simulations. Our results show that these two zinc ions play an important role in maintaining both the secondary and tertiary structural stabilities of the c-Cbl RING domain. Our results also reveal that the secondary structural stability of the c-Cbl RING domain is mainly determined by the hydrogen-bonding networks in or near the two zinc ion binding sites. Our results further demonstrate that zinc ion binding site 2 is more structurally stable than site 1.

UR - http://www.scopus.com/inward/record.url?scp=35348849005&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=35348849005&partnerID=8YFLogxK

U2 - 10.1021/bp0701665

DO - 10.1021/bp0701665

M3 - Article

C2 - 17691815

AN - SCOPUS:35348849005

VL - 23

SP - 1231

EP - 1238

JO - Biotechnology Progress

JF - Biotechnology Progress

SN - 8756-7938

IS - 5

ER -