Molecular dynamics simulation to investigate structural characteristics of aggrecan in degenerated intervertebral discs

Kiwoon Kwon, Hyoseon Kim, Taewoo Lee, Dae Sung Yoon, Han Sung Kim

Research output: Contribution to journalArticle

Abstract

Purpose: Intervertebral discs (IDs) in human and animal backbones resist compression and shear due to the nucleus pulposus (NP). The NP is mainly composed of water and aggrecan protein. As humans age, IDs degenerate, and aggrecan and water in the NP decrease; however, the relative water density with respect to fixed aggrecan density increases. In this paper, changes in aggrecan’s structure with respect to changes in water density in the NP were explored. Methods: The atomic coordinates in aggreacan were taken from the Protein Data Bank. The molecular dynamics simulation was implemented by using NAMD and VMD softwares To investigate the effect of water density in the NP, we used cubic water boxes with thickness 6, 20, and 30 Å. Results: We found that the number of hydrophilic hydrogen bonds increase, the RMSD(root-mean-square density) of amino acid residues decrease, and random coil secondary structures with low RMSD appears, as the thickness of water boxes increase from 6 to 30 Å. Conclusions: According to the simulation study, as the relative water density in NP increases, highly fluctuating secondary structures are changed into low-fluctuation and low-energy random coil structures.

Original languageEnglish
Pages (from-to)65-69
Number of pages5
JournalBiomedical Engineering Letters
Volume5
Issue number1
DOIs
Publication statusPublished - 2015 Mar 1

Fingerprint

Molecular dynamics
Computer simulation
Water
Proteins
Amino acids
Hydrogen bonds
Animals

Keywords

  • Aggrecan
  • Intervertebral disc
  • Molecular dynamics

ASJC Scopus subject areas

  • Biomedical Engineering

Cite this

Molecular dynamics simulation to investigate structural characteristics of aggrecan in degenerated intervertebral discs. / Kwon, Kiwoon; Kim, Hyoseon; Lee, Taewoo; Yoon, Dae Sung; Kim, Han Sung.

In: Biomedical Engineering Letters, Vol. 5, No. 1, 01.03.2015, p. 65-69.

Research output: Contribution to journalArticle

@article{3a0d867d9bcc4ff39359684eefa86ef6,
title = "Molecular dynamics simulation to investigate structural characteristics of aggrecan in degenerated intervertebral discs",
abstract = "Purpose: Intervertebral discs (IDs) in human and animal backbones resist compression and shear due to the nucleus pulposus (NP). The NP is mainly composed of water and aggrecan protein. As humans age, IDs degenerate, and aggrecan and water in the NP decrease; however, the relative water density with respect to fixed aggrecan density increases. In this paper, changes in aggrecan’s structure with respect to changes in water density in the NP were explored. Methods: The atomic coordinates in aggreacan were taken from the Protein Data Bank. The molecular dynamics simulation was implemented by using NAMD and VMD softwares To investigate the effect of water density in the NP, we used cubic water boxes with thickness 6, 20, and 30 {\AA}. Results: We found that the number of hydrophilic hydrogen bonds increase, the RMSD(root-mean-square density) of amino acid residues decrease, and random coil secondary structures with low RMSD appears, as the thickness of water boxes increase from 6 to 30 {\AA}. Conclusions: According to the simulation study, as the relative water density in NP increases, highly fluctuating secondary structures are changed into low-fluctuation and low-energy random coil structures.",
keywords = "Aggrecan, Intervertebral disc, Molecular dynamics",
author = "Kiwoon Kwon and Hyoseon Kim and Taewoo Lee and Yoon, {Dae Sung} and Kim, {Han Sung}",
year = "2015",
month = "3",
day = "1",
doi = "10.1007/s13534-015-0177-z",
language = "English",
volume = "5",
pages = "65--69",
journal = "Biomedical Engineering Letters",
issn = "2093-9868",
publisher = "Springer Verlag",
number = "1",

}

TY - JOUR

T1 - Molecular dynamics simulation to investigate structural characteristics of aggrecan in degenerated intervertebral discs

AU - Kwon, Kiwoon

AU - Kim, Hyoseon

AU - Lee, Taewoo

AU - Yoon, Dae Sung

AU - Kim, Han Sung

PY - 2015/3/1

Y1 - 2015/3/1

N2 - Purpose: Intervertebral discs (IDs) in human and animal backbones resist compression and shear due to the nucleus pulposus (NP). The NP is mainly composed of water and aggrecan protein. As humans age, IDs degenerate, and aggrecan and water in the NP decrease; however, the relative water density with respect to fixed aggrecan density increases. In this paper, changes in aggrecan’s structure with respect to changes in water density in the NP were explored. Methods: The atomic coordinates in aggreacan were taken from the Protein Data Bank. The molecular dynamics simulation was implemented by using NAMD and VMD softwares To investigate the effect of water density in the NP, we used cubic water boxes with thickness 6, 20, and 30 Å. Results: We found that the number of hydrophilic hydrogen bonds increase, the RMSD(root-mean-square density) of amino acid residues decrease, and random coil secondary structures with low RMSD appears, as the thickness of water boxes increase from 6 to 30 Å. Conclusions: According to the simulation study, as the relative water density in NP increases, highly fluctuating secondary structures are changed into low-fluctuation and low-energy random coil structures.

AB - Purpose: Intervertebral discs (IDs) in human and animal backbones resist compression and shear due to the nucleus pulposus (NP). The NP is mainly composed of water and aggrecan protein. As humans age, IDs degenerate, and aggrecan and water in the NP decrease; however, the relative water density with respect to fixed aggrecan density increases. In this paper, changes in aggrecan’s structure with respect to changes in water density in the NP were explored. Methods: The atomic coordinates in aggreacan were taken from the Protein Data Bank. The molecular dynamics simulation was implemented by using NAMD and VMD softwares To investigate the effect of water density in the NP, we used cubic water boxes with thickness 6, 20, and 30 Å. Results: We found that the number of hydrophilic hydrogen bonds increase, the RMSD(root-mean-square density) of amino acid residues decrease, and random coil secondary structures with low RMSD appears, as the thickness of water boxes increase from 6 to 30 Å. Conclusions: According to the simulation study, as the relative water density in NP increases, highly fluctuating secondary structures are changed into low-fluctuation and low-energy random coil structures.

KW - Aggrecan

KW - Intervertebral disc

KW - Molecular dynamics

UR - http://www.scopus.com/inward/record.url?scp=84928160340&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84928160340&partnerID=8YFLogxK

U2 - 10.1007/s13534-015-0177-z

DO - 10.1007/s13534-015-0177-z

M3 - Article

AN - SCOPUS:84928160340

VL - 5

SP - 65

EP - 69

JO - Biomedical Engineering Letters

JF - Biomedical Engineering Letters

SN - 2093-9868

IS - 1

ER -