High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data

Ming Tang, Lindsay J. Sperling, Deborah A. Berthold, Charles D. Schwieters, Anna E. Nesbitt, Andrew J. Nieuwkoop, Robert B. Gennis, Chad M. Rienstra

Research output: Contribution to journalArticle

Abstract

X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.

Original languageEnglish (US)
Pages (from-to)227-233
Number of pages7
JournalJournal of Biomolecular NMR
Volume51
Issue number3
DOIs
StatePublished - Nov 1 2011

Fingerprint

Nuclear magnetic resonance spectroscopy
Membrane Proteins
Magnetic Resonance Spectroscopy
Joints
X-Rays
X rays
Crystal structure
Crystal atomic structure
Barreling
Crystals
X-Ray Diffraction
Proteins
X ray diffraction

Keywords

  • High resolution
  • Joint calculation
  • Membrane protein
  • Solid-state NMR
  • X-ray reflections

ASJC Scopus subject areas

  • Biochemistry
  • Spectroscopy

Cite this

High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. / Tang, Ming; Sperling, Lindsay J.; Berthold, Deborah A.; Schwieters, Charles D.; Nesbitt, Anna E.; Nieuwkoop, Andrew J.; Gennis, Robert B.; Rienstra, Chad M.

In: Journal of Biomolecular NMR, Vol. 51, No. 3, 01.11.2011, p. 227-233.

Research output: Contribution to journalArticle

Tang, Ming ; Sperling, Lindsay J. ; Berthold, Deborah A. ; Schwieters, Charles D. ; Nesbitt, Anna E. ; Nieuwkoop, Andrew J. ; Gennis, Robert B. ; Rienstra, Chad M. / High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. In: Journal of Biomolecular NMR. 2011 ; Vol. 51, No. 3. pp. 227-233.
@article{5beb3cb2134b418bba87ba03eb3f0d44,
title = "High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data",
abstract = "X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 {\AA} crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 {\AA} in the transmembrane region, a 58{\%} enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22{\%} of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.",
keywords = "High resolution, Joint calculation, Membrane protein, Solid-state NMR, X-ray reflections",
author = "Ming Tang and Sperling, {Lindsay J.} and Berthold, {Deborah A.} and Schwieters, {Charles D.} and Nesbitt, {Anna E.} and Nieuwkoop, {Andrew J.} and Gennis, {Robert B.} and Rienstra, {Chad M.}",
year = "2011",
month = "11",
day = "1",
doi = "10.1007/s10858-011-9565-6",
language = "English (US)",
volume = "51",
pages = "227--233",
journal = "Journal of Biomolecular NMR",
issn = "0925-2738",
publisher = "Springer Netherlands",
number = "3",

}

TY - JOUR

T1 - High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data

AU - Tang, Ming

AU - Sperling, Lindsay J.

AU - Berthold, Deborah A.

AU - Schwieters, Charles D.

AU - Nesbitt, Anna E.

AU - Nieuwkoop, Andrew J.

AU - Gennis, Robert B.

AU - Rienstra, Chad M.

PY - 2011/11/1

Y1 - 2011/11/1

N2 - X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.

AB - X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.

KW - High resolution

KW - Joint calculation

KW - Membrane protein

KW - Solid-state NMR

KW - X-ray reflections

UR - http://www.scopus.com/inward/record.url?scp=80755190085&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80755190085&partnerID=8YFLogxK

U2 - 10.1007/s10858-011-9565-6

DO - 10.1007/s10858-011-9565-6

M3 - Article

C2 - 21938394

AN - SCOPUS:80755190085

VL - 51

SP - 227

EP - 233

JO - Journal of Biomolecular NMR

JF - Journal of Biomolecular NMR

SN - 0925-2738

IS - 3

ER -