A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints

Lei Shi, Nathaniel Traaseth, Raffaello Verardi, Alessandro Cembran, Jiali Gao, Gianluigi Veglia

Research output: Contribution to journalArticle

Abstract

To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, Ez (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use.

Original languageEnglish (US)
Pages (from-to)195-205
Number of pages11
JournalJournal of Biomolecular NMR
Volume44
Issue number4
DOIs
StatePublished - 2009

Fingerprint

Membrane Proteins
Nuclear magnetic resonance
Topology
Membranes
Lipid bilayers
X ray crystallography
Chemical shift
Micelles
Simulated annealing
Detergents
X Ray Crystallography
Anisotropy
Lipid Bilayers
Software
Proteins

Keywords

  • Hybrid method
  • Membrane protein
  • Molecular modeling
  • PISEMA
  • Solid-state NMR
  • Structural topology

ASJC Scopus subject areas

  • Spectroscopy
  • Biochemistry

Cite this

A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints. / Shi, Lei; Traaseth, Nathaniel; Verardi, Raffaello; Cembran, Alessandro; Gao, Jiali; Veglia, Gianluigi.

In: Journal of Biomolecular NMR, Vol. 44, No. 4, 2009, p. 195-205.

Research output: Contribution to journalArticle

@article{43238f9df0494e09bf2cce91c1fa1148,
title = "A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints",
abstract = "To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, Ez (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use.",
keywords = "Hybrid method, Membrane protein, Molecular modeling, PISEMA, Solid-state NMR, Structural topology",
author = "Lei Shi and Nathaniel Traaseth and Raffaello Verardi and Alessandro Cembran and Jiali Gao and Gianluigi Veglia",
year = "2009",
doi = "10.1007/s10858-009-9328-9",
language = "English (US)",
volume = "44",
pages = "195--205",
journal = "Journal of Biomolecular NMR",
issn = "0925-2738",
publisher = "Springer Netherlands",
number = "4",

}

TY - JOUR

T1 - A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints

AU - Shi, Lei

AU - Traaseth, Nathaniel

AU - Verardi, Raffaello

AU - Cembran, Alessandro

AU - Gao, Jiali

AU - Veglia, Gianluigi

PY - 2009

Y1 - 2009

N2 - To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, Ez (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use.

AB - To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, Ez (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use.

KW - Hybrid method

KW - Membrane protein

KW - Molecular modeling

KW - PISEMA

KW - Solid-state NMR

KW - Structural topology

UR - http://www.scopus.com/inward/record.url?scp=68349122607&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=68349122607&partnerID=8YFLogxK

U2 - 10.1007/s10858-009-9328-9

DO - 10.1007/s10858-009-9328-9

M3 - Article

VL - 44

SP - 195

EP - 205

JO - Journal of Biomolecular NMR

JF - Journal of Biomolecular NMR

SN - 0925-2738

IS - 4

ER -