Measurement of Active Site Ionization Equilibria in the 670 kDa Proteasome Core Particle Using Methyl-TROSY NMR

2013 ◽  
Vol 135 (25) ◽  
pp. 9259-9262 ◽  
Author(s):  
Algirdas Velyvis ◽  
Lewis E. Kay
Keyword(s):  
Active Site ◽  
Core Particle ◽  
Methyl Trosy ◽  
Ionization Equilibria ◽  
Methyl Trosy Nmr

scholarly journals A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle

2020 ◽  
Vol 117 (23) ◽  
pp. 12836-12846 ◽  
Author(s):  
Gili Abramov ◽  
Algirdas Velyvis ◽  
Enrico Rennella ◽  
Leo E. Wong ◽  
Lewis E. Kay
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Methyl Groups ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Nmr Studies ◽  
High Molecular Weight Dna ◽  
Nucleosome Core ◽  
Structure And Dynamics ◽  
Methyl Trosy

The development of methyl-transverse relaxation-optimized spectroscopy (methyl-TROSY)–based NMR methods, in concert with robust strategies for incorporation of methyl-group probes of structure and dynamics into the protein of interest, has facilitated quantitative studies of high-molecular-weight protein complexes. Here we develop a one-pot in vitro reaction for producing NMR quantities of methyl-labeled DNA at the C5 and N6 positions of cytosine (5mC) and adenine (6mA) nucleobases, respectively, enabling the study of high-molecular-weight DNA molecules using TROSY approaches originally developed for protein applications. Our biosynthetic strategy exploits the large number of naturally available methyltransferases to specifically methylate DNA at a desired number of sites that serve as probes of structure and dynamics. We illustrate the methodology with studies of the 153-base pair Widom DNA molecule that is simultaneously methyl-labeled at five sites, showing that high-quality13C-1H spectra can be recorded on 100 μM samples in a few minutes. NMR spin relaxation studies of labeled methyl groups in both DNA and the H2B histone protein component of the 200-kDa nucleosome core particle (NCP) establish that methyl groups at 5mC and 6mA positions are, in general, more rigid than Ile, Leu, and Val methyl probes in protein side chains. Studies focusing on histone H2B of NCPs wrapped with either wild-type DNA or DNA methylated at all 26 CpG sites highlight the utility of NMR in investigating the structural dynamics of the NCP and how its histone core is affected through DNA methylation, an important regulator of transcription.

Application of Methyl-TROSY NMR to Test Allosteric Models Describing Effects of Nucleotide Binding to Aspartate Transcarbamoylase

2009 ◽  
Vol 387 (3) ◽  
pp. 540-547 ◽  
Author(s):  
Algirdas Velyvis ◽  
Howard K. Schachman ◽  
Lewis E. Kay
Keyword(s):  
Nucleotide Binding ◽  
Aspartate Transcarbamoylase ◽  
Methyl Trosy ◽  
Methyl Trosy Nmr

Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY NMR

2018 ◽  
Vol 140 (14) ◽  
pp. 4774-4777 ◽  
Author(s):  
Julianne L. Kitevski-LeBlanc ◽  
Tairan Yuwen ◽  
Pamela N. Dyer ◽  
Johannes Rudolph ◽  
Karolin Luger ◽  
...  
Keyword(s):  
Methyl Trosy ◽  
Methyl Trosy Nmr

scholarly journals Exploring long-range cooperativity in the 20S proteasome core particle from Thermoplasma acidophilum using methyl-TROSY–based NMR

2020 ◽  
Vol 117 (10) ◽  
pp. 5298-5309
Author(s):  
Enrico Rennella ◽  
Rui Huang ◽  
Zanlin Yu ◽  
Lewis E. Kay
Keyword(s):  
Molecular Machines ◽  
Molecular Assembly ◽  
20S Proteasome ◽  
Core Particle ◽  
Thermoplasma Acidophilum ◽  
Transverse Relaxation ◽  
Catalytic Sites ◽  
Methyl Trosy ◽  
Transverse Relaxation Optimized Spectroscopy ◽  
Allosteric Pathway

The 20S core particle (CP) proteasome is a molecular assembly catalyzing the degradation of misfolded proteins or proteins no longer required for function. It is composed of four stacked heptameric rings that form a barrel-like structure, sequestering proteolytic sites inside its lumen. Proteasome function is regulated by gates derived from the termini of α-rings and through binding of regulatory particles (RPs) to one or both ends of the barrel. The CP is dynamic, with an extensive allosteric pathway extending from one end of the molecule to catalytic sites in its center. Here, using methyl-transverse relaxation optimized spectroscopy (TROSY)-based NMR optimized for studies of high–molecular-weight complexes, we evaluate whether the pathway extends over the entire 150-Å length of the molecule. By exploiting a number of different labeling schemes, the two halves of the molecule can be distinguished, so that the effects of 11S RP binding, or the introduction of gate or allosteric pathway mutations at one end of the barrel can be evaluated at the distal end. Our results establish that while 11S binding and the introduction of key mutations affect each half of the CP allosterically, they do not further couple opposite ends of the molecule. This may have implications for the function of so-called “hybrid” proteasomes where each end of the CP is bound with a different regulator, allowing the CP to be responsive to both RPs simultaneously. The methodology presented introduces a general NMR strategy for dissecting pathways of communication in homo-oligomeric molecular machines.

scholarly journals High Quality Methyl-TROSY NMR Studies of the Interactions Between the Small GTPase ARF1 and Its ArfGAP ASAP1 at the Membrane Surface

2020 ◽  
Vol 118 (3) ◽  
pp. 17a
Author(s):  
Yue Zhang ◽  
Olivier Soubias ◽  
Andrew Byrd
Keyword(s):  
Membrane Surface ◽  
Small Gtpase ◽  
Nmr Studies ◽  
High Quality ◽  
Methyl Trosy ◽  
Methyl Trosy Nmr

Probing Slow Dynamics in High Molecular Weight Proteins by Methyl-TROSY NMR Spectroscopy:  Application to a 723-Residue Enzyme

2004 ◽  
Vol 126 (12) ◽  
pp. 3964-3973 ◽  
Author(s):  
Dmitry M. Korzhnev ◽  
Karin Kloiber ◽  
Voula Kanelis ◽  
Vitali Tugarinov ◽  
Lewis E. Kay
Keyword(s):  
Molecular Weight ◽  
Nmr Spectroscopy ◽  
High Molecular Weight ◽  
Slow Dynamics ◽  
Methyl Trosy ◽  
High Molecular Weight Proteins ◽  
Methyl Trosy Nmr

scholarly journals Oligomeric assembly regulating mitochondrial HtrA2 function as examined by methyl-TROSY NMR

2021 ◽  
Vol 118 (11) ◽  
pp. e2025022118
Author(s):  
Yuki Toyama ◽  
Robert W. Harkness ◽  
Tim Y. T. Lee ◽  
Jason T. Maynes ◽  
Lewis E. Kay
Keyword(s):  
Active Sites ◽  
Transverse Relaxation ◽  
Catalytic Center ◽  
Protective Enzyme ◽  
Biochemical Assays ◽  
Methyl Trosy ◽  
Oligomeric Assembly ◽  
Domain Reorientation ◽  
Methyl Trosy Nmr ◽  
Trimeric Structure

Human High temperature requirement A2 (HtrA2) is a mitochondrial protease chaperone that plays an important role in cellular proteostasis and in regulating cell-signaling events, with aberrant HtrA2 function leading to neurodegeneration and parkinsonian phenotypes. Structural studies of the enzyme have established a trimeric architecture, comprising three identical protomers in which the active sites of each protease domain are sequestered to form a catalytically inactive complex. The mechanism by which enzyme function is regulated is not well understood. Using methyl transverse relaxation optimized spectroscopy (TROSY)-based solution NMR in concert with biochemical assays, a functional HtrA2 oligomerization/binding cycle has been established. In the absence of substrates, HtrA2 exchanges between a heretofore unobserved hexameric conformation and the canonical trimeric structure, with the hexamer showing much weaker affinity toward substrates. Both structures are substrate inaccessible, explaining their low basal activity in the absence of the binding of activator peptide. The binding of the activator peptide to each of the protomers of the trimer occurs with positive cooperativity and induces intrasubunit domain reorientations to expose the catalytic center, leading to increased proteolytic activity. Our data paint a picture of HtrA2 as a finely tuned, stress-protective enzyme whose activity can be modulated both by oligomerization and domain reorientation, with basal levels of catalysis kept low to avoid proteolysis of nontarget proteins.

Bringing Dynamic Molecular Machines into Focus by Methyl-TROSY NMR

2014 ◽  
Vol 83 (1) ◽  
pp. 291-315 ◽  
Author(s):  
Rina Rosenzweig ◽  
Lewis E. Kay
Keyword(s):  
Molecular Machines ◽  
Methyl Trosy ◽  
Methyl Trosy Nmr

Proteasome β-type subunits: unequal roles of propeptides in core particle maturation and a hierarchy of active site function

1999 ◽  
Vol 291 (4) ◽  
pp. 997-1013 ◽  
Author(s):  
Sibylle Jäger ◽  
Michael Groll ◽  
Robert Huber ◽  
Dieter H Wolf ◽  
Wolfgang Heinemeyer
Keyword(s):  
Active Site ◽  
Core Particle ◽  
Site Function

scholarly journals Ligand modulation of sidechain dynamics in a wild-type human GPCR

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Lindsay D Clark ◽  
Igor Dikiy ◽  
Karen Chapman ◽  
Karin EJ Rödström ◽  
James Aramini ◽  
...  
Keyword(s):  
Human Physiology ◽  
Structural Changes ◽  
Inverse Agonist ◽  
Methyl Groups ◽  
Signaling Proteins ◽  
Wild Type ◽  
Biophysical Studies ◽  
Methyl Trosy ◽  
Conformational Regulation ◽  
Methyl Trosy Nmr

GPCRs regulate all aspects of human physiology, and biophysical studies have deepened our understanding of GPCR conformational regulation by different ligands. Yet there is no experimental evidence for how sidechain dynamics control allosteric transitions between GPCR conformations. To address this deficit, we generated samples of a wild-type GPCR (A2AR) that are deuterated apart from 1H/13C NMR probes at isoleucine δ1 methyl groups, which facilitated 1H/13C methyl TROSY NMR measurements with opposing ligands. Our data indicate that low [Na+] is required to allow large agonist-induced structural changes in A2AR, and that patterns of sidechain dynamics substantially differ between agonist (NECA) and inverse agonist (ZM241385) bound receptors, with the inverse agonist suppressing fast ps-ns timescale motions at the G protein binding site. Our approach to GPCR NMR creates a framework for exploring how different regions of a receptor respond to different ligands or signaling proteins through modulation of fast ps-ns sidechain dynamics.

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