Dynamics of internal water in fatty acid binding protein

Computer simulations and comparison with experiments

Vladimir A. Likić, Franklyn G. Prendergast

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Multiple molecular dynamics (MD) simulations of fully solvated rat intestinal fatty acid binding protein (I-FABP) were conducted to investigate the dynamics of internal water molecules. Although the long time average of the number of internal water molecules in I-FABP is 22 as shown by the X-ray crystal structure, MD simulations predict large variations in the instantaneous number of internal water molecules on the nanosecond time scale. The computational model employed predicts that w135 (internal) and w217 (located on the protein surface) may be the water molecules with long residence times observed in previously reported magnetic relaxation dispersion studies. The average residence time of ∼20 internal water molecules occupying the fatty acid binding cavity is estimated to be between 0.6 and 2.0 nanoseconds. Exchange of internal water in I-FABP appears to occur almost exclusively through the interface of β-strands EF with the rest of the protein, which has significant implications for the pathways of the fatty acid entry and exit from the binding cavity.

Original languageEnglish (US)
Pages (from-to)65-72
Number of pages8
JournalProteins: Structure, Function and Genetics
Volume43
Issue number1
DOIs
StatePublished - Apr 1 2001

Fingerprint

Fatty Acid-Binding Proteins
Computer Simulation
Water
Computer simulation
Molecules
Experiments
Molecular Dynamics Simulation
Molecular dynamics
Fatty Acids
Magnetic relaxation
Rats
Membrane Proteins
Crystal structure
X-Rays
X rays
Proteins

Keywords

  • Buried water
  • I-FABP
  • Internal water cluster
  • MD simulations
  • Protein hydration

ASJC Scopus subject areas

  • Biochemistry
  • Genetics
  • Structural Biology

Cite this

Dynamics of internal water in fatty acid binding protein : Computer simulations and comparison with experiments. / Likić, Vladimir A.; Prendergast, Franklyn G.

In: Proteins: Structure, Function and Genetics, Vol. 43, No. 1, 01.04.2001, p. 65-72.

Research output: Contribution to journalArticle

@article{ef1700158a1042c1ba4fd79b9af9cb92,
title = "Dynamics of internal water in fatty acid binding protein: Computer simulations and comparison with experiments",
abstract = "Multiple molecular dynamics (MD) simulations of fully solvated rat intestinal fatty acid binding protein (I-FABP) were conducted to investigate the dynamics of internal water molecules. Although the long time average of the number of internal water molecules in I-FABP is 22 as shown by the X-ray crystal structure, MD simulations predict large variations in the instantaneous number of internal water molecules on the nanosecond time scale. The computational model employed predicts that w135 (internal) and w217 (located on the protein surface) may be the water molecules with long residence times observed in previously reported magnetic relaxation dispersion studies. The average residence time of ∼20 internal water molecules occupying the fatty acid binding cavity is estimated to be between 0.6 and 2.0 nanoseconds. Exchange of internal water in I-FABP appears to occur almost exclusively through the interface of β-strands EF with the rest of the protein, which has significant implications for the pathways of the fatty acid entry and exit from the binding cavity.",
keywords = "Buried water, I-FABP, Internal water cluster, MD simulations, Protein hydration",
author = "Likić, {Vladimir A.} and Prendergast, {Franklyn G.}",
year = "2001",
month = "4",
day = "1",
doi = "10.1002/1097-0134(20010401)43:1<65::AID-PROT1018>3.0.CO;2-F",
language = "English (US)",
volume = "43",
pages = "65--72",
journal = "Proteins: Structure, Function and Bioinformatics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "1",

}

TY - JOUR

T1 - Dynamics of internal water in fatty acid binding protein

T2 - Computer simulations and comparison with experiments

AU - Likić, Vladimir A.

AU - Prendergast, Franklyn G.

PY - 2001/4/1

Y1 - 2001/4/1

N2 - Multiple molecular dynamics (MD) simulations of fully solvated rat intestinal fatty acid binding protein (I-FABP) were conducted to investigate the dynamics of internal water molecules. Although the long time average of the number of internal water molecules in I-FABP is 22 as shown by the X-ray crystal structure, MD simulations predict large variations in the instantaneous number of internal water molecules on the nanosecond time scale. The computational model employed predicts that w135 (internal) and w217 (located on the protein surface) may be the water molecules with long residence times observed in previously reported magnetic relaxation dispersion studies. The average residence time of ∼20 internal water molecules occupying the fatty acid binding cavity is estimated to be between 0.6 and 2.0 nanoseconds. Exchange of internal water in I-FABP appears to occur almost exclusively through the interface of β-strands EF with the rest of the protein, which has significant implications for the pathways of the fatty acid entry and exit from the binding cavity.

AB - Multiple molecular dynamics (MD) simulations of fully solvated rat intestinal fatty acid binding protein (I-FABP) were conducted to investigate the dynamics of internal water molecules. Although the long time average of the number of internal water molecules in I-FABP is 22 as shown by the X-ray crystal structure, MD simulations predict large variations in the instantaneous number of internal water molecules on the nanosecond time scale. The computational model employed predicts that w135 (internal) and w217 (located on the protein surface) may be the water molecules with long residence times observed in previously reported magnetic relaxation dispersion studies. The average residence time of ∼20 internal water molecules occupying the fatty acid binding cavity is estimated to be between 0.6 and 2.0 nanoseconds. Exchange of internal water in I-FABP appears to occur almost exclusively through the interface of β-strands EF with the rest of the protein, which has significant implications for the pathways of the fatty acid entry and exit from the binding cavity.

KW - Buried water

KW - I-FABP

KW - Internal water cluster

KW - MD simulations

KW - Protein hydration

UR - http://www.scopus.com/inward/record.url?scp=0035314045&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0035314045&partnerID=8YFLogxK

U2 - 10.1002/1097-0134(20010401)43:1<65::AID-PROT1018>3.0.CO;2-F

DO - 10.1002/1097-0134(20010401)43:1<65::AID-PROT1018>3.0.CO;2-F

M3 - Article

VL - 43

SP - 65

EP - 72

JO - Proteins: Structure, Function and Bioinformatics

JF - Proteins: Structure, Function and Bioinformatics

SN - 0887-3585

IS - 1

ER -