Residence times of water molecules in the hydration sites of myoglobin

Vladimir A. Makarov, B. Kim Andrews, Paul E. Smith, Bernard Pettitt

Research output: Contribution to journalArticle

209 Citations (Scopus)

Abstract

Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.

Original languageEnglish (US)
Pages (from-to)2966-2974
Number of pages9
JournalBiophysical Journal
Volume79
Issue number6
StatePublished - Dec 2000
Externally publishedYes

Fingerprint

Myoglobin
Water
Sperm Whale
Proteins
Neutrons
Molecular Dynamics Simulation
Hydrophobic and Hydrophilic Interactions
Hydrogen
X-Rays

ASJC Scopus subject areas

  • Biophysics

Cite this

Makarov, V. A., Andrews, B. K., Smith, P. E., & Pettitt, B. (2000). Residence times of water molecules in the hydration sites of myoglobin. Biophysical Journal, 79(6), 2966-2974.

Residence times of water molecules in the hydration sites of myoglobin. / Makarov, Vladimir A.; Andrews, B. Kim; Smith, Paul E.; Pettitt, Bernard.

In: Biophysical Journal, Vol. 79, No. 6, 12.2000, p. 2966-2974.

Research output: Contribution to journalArticle

Makarov, VA, Andrews, BK, Smith, PE & Pettitt, B 2000, 'Residence times of water molecules in the hydration sites of myoglobin', Biophysical Journal, vol. 79, no. 6, pp. 2966-2974.
Makarov, Vladimir A. ; Andrews, B. Kim ; Smith, Paul E. ; Pettitt, Bernard. / Residence times of water molecules in the hydration sites of myoglobin. In: Biophysical Journal. 2000 ; Vol. 79, No. 6. pp. 2966-2974.
@article{de2a15b9a89b493bad2cf658f4f1d225,
title = "Residence times of water molecules in the hydration sites of myoglobin",
abstract = "Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.",
author = "Makarov, {Vladimir A.} and Andrews, {B. Kim} and Smith, {Paul E.} and Bernard Pettitt",
year = "2000",
month = "12",
language = "English (US)",
volume = "79",
pages = "2966--2974",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "6",

}

TY - JOUR

T1 - Residence times of water molecules in the hydration sites of myoglobin

AU - Makarov, Vladimir A.

AU - Andrews, B. Kim

AU - Smith, Paul E.

AU - Pettitt, Bernard

PY - 2000/12

Y1 - 2000/12

N2 - Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.

AB - Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.

UR - http://www.scopus.com/inward/record.url?scp=0033636839&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0033636839&partnerID=8YFLogxK

M3 - Article

VL - 79

SP - 2966

EP - 2974

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 6

ER -