Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy

Journal of the American Chemical Society
Tobias S UlmerA Bax

Abstract

NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besides the commonly used bicelle, poly(ethylene glycol), and filamentous phage liquid crystalline media, dipolar couplings were also measured when the protein was aligned inside either positively or negatively charged stretched acrylamide gels. Refinement of the GB3 crystal structure against the (13)C(alpha)-(13)C' and (13)C'-(15)N dipolar couplings improves the agreement between experimental and predicted (15)N-(1)H(N) as well as (13)C(alpha)-(1)H(alpha) dipolar couplings. Evaluation of the peptide bond N-H orientations shows a weak anticorrelation between the deviation of the peptide bond torsion angle omega from 180 degrees and the angle between the N-H vector and the C'-N-C(alpha) plane. The slope of this correlation is -1, indicating that, on average, pyramidalization of the peptide N contributes to small deviations from peptide bond planarity (<omega> = 179.3 +/- 3.1 degrees ) to the same degree as true twisting around the C'-N bond. Although hydrogens are commonly built onto cry...Continue Reading

References

Jan 1, 1989·Critical Reviews in Biochemistry and Molecular Biology·G M Clore, A M Gronenborn
Jul 14, 1971·Journal of Molecular Biology·F K Winkler, J D Dunitz
Sep 26, 1995·Proceedings of the National Academy of Sciences of the United States of America·J R TolmanJ H Prestegard
Nov 1, 1995·Journal of Biomolecular NMR·F DelaglioA Bax
Jul 1, 1996·Protein Science : a Publication of the Protein Society·P A Karplus
Dec 20, 1996·Journal of Molecular Biology·M W MacArthur, J M Thornton
Apr 1, 1997·Nature Structural Biology·J R TolmanJ H Prestegard
May 8, 1998·Journal of Magnetic Resonance·M OttigerA Bax
Jul 17, 1998·Nature Structural Biology·J H Prestegard
Dec 3, 1998·Journal of Biomolecular NMR·J A Losonczi, J H Prestegard
May 26, 1999·Journal of Magnetic Resonance·J A LosoncziJ H Prestegard
Mar 29, 2001·Journal of Magnetic Resonance·L G BarrientosA M Gronenborn
Jun 21, 2001·Journal of the American Chemical Society·J MeilerR Brüschweiler
Nov 17, 2001·Biomacromolecules·F HorkayP J Basser
May 16, 2002·Journal of the American Chemical Society·Wolfgang PetiChristian Griesinger
Aug 3, 2002·Journal of Biomolecular NMR·Markus Zweckstetter, Ad Bax

❮ Previous
Next ❯

Citations

Nov 1, 2005·Journal of Biomolecular NMR·Katya SimonNikolai R Skrynnikov
Oct 3, 2006·Journal of Biomolecular NMR·Tianzhi WangErik R P Zuiderweg
Dec 21, 2006·Journal of Biomolecular NMR·Myriam E VillegasHarold A Scheraga
Aug 19, 2007·Journal of Biomolecular NMR·Martti LouhivuoriArto Annila
Nov 27, 2008·Journal of Biomolecular NMR·Yang ShenAd Bax
Nov 12, 2009·Journal of Biomolecular NMR·Beat Vögeli, Roland Riek
Aug 10, 2010·Journal of Biomolecular NMR·Nicholas C Fitzkee, Ad Bax
Dec 25, 2010·Journal of Biomolecular NMR·Victoria A HigmanChristina Redfield
Jun 15, 2011·Journal of Biomolecular NMR·Paul ShealyHomayoun Valafar
Sep 29, 2011·Journal of Biomolecular NMR·Tairan YuwenNikolai R Skrynnikov
Jul 26, 2012·Journal of Biomolecular NMR·Joshua M Ward, Nikolai R Skrynnikov
May 21, 2013·Progress in Biophysics and Molecular Biology·Yury E Shapiro
Apr 23, 2011·Biochemistry·M Sameer Al-Abdul-WahidR Scott Prosser
Jun 17, 2010·Journal of the American Chemical Society·Konstantin BerlinDavid Fushman
Jun 8, 2010·Journal of the American Chemical Society·Jampani Nageswara RaoTobias S Ulmer
May 26, 2012·Journal of the American Chemical Society·Jae-Eun SukTobias S Ulmer
Dec 4, 2008·Journal of the American Chemical Society·Lishan YaoAd Bax
Feb 25, 2009·Journal of the American Chemical Society·Beat Vögeli, Lishan Yao
Dec 4, 2009·Journal of the American Chemical Society·Jianxi Xiao, Jean Baum
Dec 18, 2010·The Journal of Physical Chemistry. B·Eva MeirovitchJack H Freed
Jan 16, 2010·Nature·Andrew T UlijaszRichard D Vierstra
May 22, 2010·Nature Chemistry·Michael J PlevinJérôme Boisbouvier
Sep 4, 2012·Nature Structural & Molecular Biology·Beat VögeliRoland Riek
Apr 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Daniele GranataAlessandro Laio
Oct 13, 2011·The Journal of Biological Chemistry·Jampani N RaoTobias S Ulmer
Apr 18, 2008·The Journal of Biological Chemistry·Tong-Lay LauTobias S Ulmer
Jan 28, 2004·Nucleic Acids Research·Youxing QuYing Xu
Oct 9, 2013·BMC Bioinformatics·Chris SchmidtHomayoun Valafar
Sep 27, 2008·PLoS Computational Biology·Phineus R L MarkwickMichael Nilges

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.