scholarly journals Catalysis by a rigid enzyme

2019 ◽  
Author(s):  
F. Ben Bdira ◽  
C. A. Waudby ◽  
A. N. Volkov ◽  
S. P. Schröder ◽  
E. AB ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Nmr Spectroscopy ◽  
Complex Formation ◽  
Crystal Structures ◽  
Structural Changes ◽  
Substrate Binding ◽  
Protein Matrix ◽  
Catalytic Intermediates ◽  
Multiple Conformations ◽  
Rigid Matrix

AbstractMany enzymes are dynamic entities, sampling conformational states that are relevant for catalytic activity. Crystal structures of catalytic intermediates suggest, however, that not all enzymes require structural changes for activity. The single-domain enzyme xylanase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose. We demonstrate that BCX in solution undergoes minimal structural changes during catalysis. NMR spectroscopy results show that the rigid protein matrix provides a frame for fast substrate binding in multiple conformations, accompanied by slow, enzyme induced substrate distortion. Therefore, we propose a model in which the rigid enzyme takes advantage of substrate flexibility to induce a conformation that facilitates catalysis.One Sentence SummaryThe rigid matrix of BCX uses substrate flexibility in Michaelis complex formation.

scholarly journals Dynamic Aha1 Co-Chaperone Binding to Human Hsp90

2019 ◽  
Author(s):  
Javier Oroz ◽  
Laura J. Blair ◽  
Markus Zweckstetter
Keyword(s):  
Nmr Spectroscopy ◽  
Atpase Activity ◽  
Binding Site ◽  
Solution Structure ◽  
Structural Changes ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
Binding Mechanism ◽  
Chaperone Binding ◽  
Multiple Conformations

AbstractHsp90 is an essential chaperone that requires large allosteric changes to determine its ATPase activity and client binding. Because of the inherent low ATPase activity of human Hsp90, the co-chaperone Aha1, which is the only known ATPase stimulator in eukaryotes, is important for regulation of Hsp90’s allosteric timing. Little is known, however, about the structure of the Hsp90/Aha1 full-length complex. Here, we characterize the solution structure of unmodified human Hsp90 in complex with Aha1 using NMR spectroscopy. We show that the 214 kDa complex adopts multiple conformations in the absence of nucleotide. Interaction with Aha1 induces structural changes near the nucleotide-binding site in Hsp90’s N-terminal domain, providing a basis for its ATPase-enhancing activity. Moreover, the E67K mutation in Aha1 strongly diminishes the interaction, supporting a two-step binding mechanism. Our data reveal important aspects of this pivotal chaperone/co-chaperone interaction and emphasize the relevance of characterizing dynamic chaperone structures in solution.

scholarly journals Analysis of β2AR-Gs and β2AR-Gi complex formation by NMR spectroscopy

2020 ◽  
Vol 117 (37) ◽  
pp. 23096-23105 ◽  
Author(s):  
Xiuyan Ma ◽  
Yunfei Hu ◽  
Hossein Batebi ◽  
Jie Heng ◽  
Jun Xu ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Complex Formation ◽  
G Protein ◽  
Conformational Changes ◽  
Structural Changes ◽  
Protein G ◽  
G Protein Coupling ◽  
Protein Coupling ◽  
G Protein Coupled ◽  
Camp Formation

The β2-adrenergic receptor (β2AR) is a prototypical G protein-coupled receptor (GPCR) that preferentially couples to the stimulatory G protein Gs and stimulates cAMP formation. Functional studies have shown that the β2AR also couples to inhibitory G protein Gi, activation of which inhibits cAMP formation [R. P. Xiao, Sci. STKE 2001, re15 (2001)]. A crystal structure of the β2AR-Gs complex revealed the interaction interface of β2AR-Gs and structural changes upon complex formation [S. G. Rasmussen et al., Nature 477, 549–555 (2011)], yet, the dynamic process of the β2AR signaling through Gs and its preferential coupling to Gs over Gi is still not fully understood. Here, we utilize solution nuclear magnetic resonance (NMR) spectroscopy and supporting molecular dynamics (MD) simulations to monitor the conformational changes in the G protein coupling interface of the β2AR in response to the full agonist BI-167107 and Gs and Gi1. These results show that BI-167107 stabilizes conformational changes in four transmembrane segments (TM4, TM5, TM6, and TM7) prior to coupling to a G protein, and that the agonist-bound receptor conformation is different from the G protein coupled state. While most of the conformational changes observed in the β2AR are qualitatively the same for Gs and Gi1, we detected distinct differences between the β2AR-Gs and the β2AR-Gi1 complex in intracellular loop 2 (ICL2). Interactions with ICL2 are essential for activation of Gs. These differences between the β2AR-Gs and β2AR-Gi1 complexes in ICL2 may be key determinants for G protein coupling selectivity.

The crystal structures of 4-methoxybenzoate bound CYP199A2 and CYP199A4: structural changes on substrate binding and the identification of an anion binding site

2012 ◽  
Vol 41 (28) ◽  
pp. 8703 ◽  
Author(s):  
Stephen G. Bell ◽  
Wen Yang ◽  
Adrian B. H. Tan ◽  
Ruimin Zhou ◽  
Eachan O. D. Johnson ◽  
...  
Keyword(s):  
Binding Site ◽  
Crystal Structures ◽  
Structural Changes ◽  
Substrate Binding ◽  
Anion Binding

Catalytic activity of rhodium(I) complexes containing (ω-trimethylsilylalkyl)diphenylphosphines

1980 ◽  
Vol 45 (8) ◽  
pp. 2219-2223 ◽  
Author(s):  
Marie Jakoubková ◽  
Martin Čapka
Keyword(s):  
Catalytic Activity ◽  
Nmr Spectroscopy ◽  
Ir Spectroscopy ◽  
Electron Density ◽  
Phosphorus Atom ◽  
Proton Acceptor ◽  
Trimethylsilyl Group ◽  
Kinetics Of

Kinetics of homogenous hydrogenation of 1-heptene catalysed by rhodium(I) complexes prepared in situ from μ,μ'-dichloro-bis(cyclooctenerhodium) and phosphines of the type RP(C6H5)2 (R = -CH3, -(CH2)nSi(CH3)3; n = 1-4) have been studied. The substitution of the ligands by the trimethylsilyl group was found to increase significantly the catalytic activity of the complexes. The results are discussed in relation to the electron density on the phosphorus atom determined by 31P NMR spectroscopy and to its proton acceptor ability determined by IR spectroscopy.

Unravelling the dissolution mechanism of polyphosphate glasses by 31P NMR spectroscopy: ligand competition and reactivity of intermediate complexes

2021 ◽  
Author(s):  
Dahiana Andrea Avila Salazar ◽  
Peter Bellstedt ◽  
Atsuhiro Miura ◽  
Yuki Oi ◽  
Toshihiro Kasuga ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Solid State ◽  
Nmr Spectroscopy ◽  
Biomedical Applications ◽  
Structural Changes ◽  
31P Nmr ◽  
Dissolution Mechanism ◽  
31P Nmr Spectroscopy ◽  
Glass Dissolution ◽  
Polyphosphate Glasses

Phosphate glass dissolution can be tailored via compositional and subsequent structural changes, which is of interest for biomedical applications such as therapeutic ion delivery. Here, solid-state 31P nuclear magnetic resonance...

scholarly journals Crystal structures of an E1–E2–ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lingmin Yuan ◽  
Zongyang Lv ◽  
Melanie J. Adams ◽  
Shaun K. Olsen
Keyword(s):  
Complex Formation ◽  
Crystal Structures ◽  
Molecular Mechanisms ◽  
Conformational State ◽  
Biochemical Data ◽  
Conformational States ◽  
Product Release ◽  
Closed Conformation ◽  
Open Conformation ◽  
Conjugating Enzymes

AbstractE1 enzymes function as gatekeepers of ubiquitin (Ub) signaling by catalyzing activation and transfer of Ub to tens of cognate E2 conjugating enzymes in a process called E1–E2 transthioesterification. The molecular mechanisms of transthioesterification and the overall architecture of the E1–E2–Ub complex during catalysis are unknown. Here, we determine the structure of a covalently trapped E1–E2–ubiquitin thioester mimetic. Two distinct architectures of the complex are observed, one in which the Ub thioester (Ub(t)) contacts E1 in an open conformation and another in which Ub(t) instead contacts E2 in a drastically different, closed conformation. Altogether our structural and biochemical data suggest that these two conformational states represent snapshots of the E1–E2–Ub complex pre- and post-thioester transfer, and are consistent with a model in which catalysis is enhanced by a Ub(t)-mediated affinity switch that drives the reaction forward by promoting productive complex formation or product release depending on the conformational state.

Crystal structures of nickel(II) and copper(Il)-Schiff-bases complexes with tetramic and tetronic acid subunits

1994 ◽  
Vol 209 (12) ◽  
Author(s):  
G. Reck ◽  
B. Schulz ◽  
A. Zschunke ◽  
O. Tietze ◽  
J. Haferkorn
Keyword(s):  
Complex Formation ◽  
Water Molecule ◽  
Crystal Structures ◽  
Schiff Bases ◽  
Water Molecules ◽  
Ligand Molecule ◽  
Tetragonal Pyramid ◽  
Space Group ◽  
Tetronic Acid ◽  
Oxygen Ligand

AbstractN,N′-ethylene-bis-(tetronic-acid-3-formiminato)-copper(II)/K1 crystallizes in space groupN,N′-ethylene-bis-(tetronic-acid-3-formiminato)-nikkel(II)/K2 crystallizes in space groupN,N′-ethylene-bis-(1,5,5-trimethyltetramic-acid-3-formiminato)-copper(II)/K3 crystallizes in space groupIn K1 and K3 copper is coordinated by two nitrogen and two oxygen atoms of the ligand molecule as well as by one water molecule on top of a tetragonal pyramid. In K2 two water molecules are included in the complex formation. These and two nitrogen as well as two oxygen ligand atoms form a nearly regular octahedron.

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