scholarly journals Identification of productive and futile encounters in an electron transfer protein complex

2017 ◽  
Vol 114 (10) ◽  
pp. E1840-E1847 ◽  
Author(s):  
Witold Andrałojć ◽  
Yoshitaka Hiruma ◽  
Wei-Min Liu ◽  
Enrico Ravera ◽  
Masaki Nojiri ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Paramagnetic Nmr ◽  
Conformational Ensemble ◽  
X Ray Diffraction ◽  
Cytochrome P450cam ◽  
Transfer Protein ◽  
Nmr Data ◽  
Electron Transfer Protein ◽  
Potential Map ◽  
Positively Charged

Well-defined, stereospecific states in protein complexes are often in exchange with an ensemble of more dynamic orientations: the encounter states. The structure of the stereospecific complex between cytochrome P450cam and putidaredoxin was solved recently by X-ray diffraction as well as paramagnetic NMR spectroscopy. Other than the stereospecific complex, the NMR data clearly show the presence of additional states in the complex in solution. In these encounter states, populated for a small percentage of the time, putidaredoxin assumes multiple orientations and samples a large part of the surface of cytochrome P450cam. To characterize the nature of the encounter states, an extensive paramagnetic NMR dataset has been analyzed using the Maximum Occurrence of Regions methodology. The analysis reveals the location and maximal spatial extent of the additional states needed to fully explain the NMR data. Under the assumption of sparsity of the size of the conformational ensemble, several minor states can be located quite precisely. The distribution of these minor states correlates with the electrostatic potential map around cytochrome P450cam. Whereas some minor states are on isolated positively charged patches, others are connected to the stereospecific site via positively charged paths. The existence of electrostatically favorable pathways between the stereospecific interaction site and the different minor states or lack thereof suggests a means to discriminate between productive and futile encounter states.

scholarly journals Dynamics in electron transfer protein complexes

FEBS Journal ◽  
2011 ◽  
Vol 278 (9) ◽  
pp. 1391-1400 ◽  
Author(s):  
Qamar Bashir ◽  
Sandra Scanu ◽  
Marcellus Ubbink
Keyword(s):  
Electron Transfer ◽  
Protein Complexes ◽  
Transfer Protein ◽  
Electron Transfer Protein

scholarly journals Electron transfer protein complexes in the thylakoid membranes of heterocysts from the cyanobacterium Nostoc punctiforme

2009 ◽  
Vol 1787 (4) ◽  
pp. 252-263 ◽  
Author(s):  
Tanai Cardona ◽  
Natalia Battchikova ◽  
Pengpeng Zhang ◽  
Karin Stensjö ◽  
Eva-Mari Aro ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Protein Complexes ◽  
Thylakoid Membranes ◽  
Nostoc Punctiforme ◽  
Transfer Protein ◽  
Electron Transfer Protein

1,2-Hydroboration of Alkyn-1-yldichlorosilanes using Triethylborane

2008 ◽  
Vol 63 (11) ◽  
pp. 1267-1275 ◽  
Author(s):  
Bernd Wrackmeyer ◽  
Ezzat Khan ◽  
Wolfgang Milius
Keyword(s):  
Molecular Structure ◽  
Single Crystal ◽  
Hydrogen Transfer ◽  
X Ray Diffraction ◽  
X Ray ◽  
Ethyl Group ◽  
Nmr Data

Abstract Triethylborane, BEt3, can act as a 1,2-hydroborating reagent towards alkyn-1-ylsilanes, depending on the nature of the silane. A mechanism is proposed invoking hydrogen transfer from the β -carbon of one ethyl group, quite different from the 1,2-hydroboration mechanism using tri-n-propylborane, BnPr3. The structure of the products has been confirmed by comparison with that obtained using 9-borabicyclo[3.3.1]nonane, 9-BBN, as a well established 1,2-hydroborating reagent. All products have been characterized by a consistent set of NMR data (1H, 11B, 13C and 29Si NMR). The molecular structure of (Z)-1-dichlorosilyl-1-[9-(9-borabicyclo[3.3.1]nonyl)]-2-phenylethene has been determined by single crystal X-ray diffraction.

scholarly journals Combined XRD-paramagnetic 13C NMR spectroscopy of 1,2,3-triazoles for revealing copper traces in a Huisgen click-chemistry cycloaddition. A model case

2019 ◽  
Vol 25 (1) ◽  
pp. 98-106
Author(s):  
Daniel Canseco-González ◽  
José Luis Rodríguez de la O ◽  
José Enrique Herbert-Pucheta
Keyword(s):  
Click Chemistry ◽  
13C Nmr Spectroscopy ◽  
Model Systems ◽  
Paramagnetic Nmr ◽  
Resonance Spectroscopy ◽  
X Ray Diffraction ◽  
Model Case ◽  
Purification Methods ◽  
Paramagnetic Metal ◽  
Torsional Angles

AbstractCopper-catalyzed Alkyne-Azide Cycloaddition (CuAAC) click chemistry robustness has been demonstrated over recent years to produce 1,2,3-triazoles with excellent yields at mild conditions with simple purification methods. However, the consequences of having copper paramagnetic traces in final products, which complicate spectroscopic assignments and can produce inaccurate conclusions, has been scarcely discussed. Herein we present a strategy that combines X-Ray Diffraction (XRD) with 13C- paramagnetic Nuclear Magnetic Resonance spectroscopy, in order to demonstrate the presence of paramagnetic metal traces at standard Huisgen synthesis and purification conditions. We also demonstrate that the derivatization of 1,4-disubstituted-1,2,3-triazoles to produce 1,3,4,-trisubstituted-1,2,3.triazolium salts, promotes an efficient removal of Cu(II/I) moieties. Evidence of paramagnetic metal moieties is given using XRD structural analysis of abnormalities in torsional angles between substituents and the 1,2,3-triazole center, in parallel to 13C- paramagnetic NMR chemical shift and line width analysis. As model systems to demonstrate the importance of characterizing paramagnetic traces, we present the synthesis of novel 1-((3s,5s,7s)-adamantan-1-yl)-4-cyclopropyl-1H-1,2,3-triazole and its derivatized 1-((3s,5s,7s)-adamantan-1-yl)-4-cyclopropyl-3-methyl-1H-[1,2,3]-triazol-3-ium triflate salt.

First (3 + 2)-dimensional superspace approach to the structure of levyclaudite-(Sb), a member of the cylindrite-type minerals

2006 ◽  
Vol 62 (5) ◽  
pp. 775-789 ◽  
Author(s):  
Michel Evain ◽  
Vaclav Petricek ◽  
Yves Moëlo ◽  
Colette Maurel
Keyword(s):  
Energy Minimization ◽  
Inorganic Compounds ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Layer Compound ◽  
X Ray ◽  
Density Modulation ◽  
Wavelength Control ◽  
A Charge ◽  
Positively Charged

The structure of synthetic levyclaudite-(Sb), approximately (Pb1 − y Sb y S)1.357[Sn1 − x (Cu2) x S2], has been determined by single-crystal X-ray diffraction on the basis of the (3 + 2)-dimensional superspace approach. This misfit-layer compound, of the cylindrite type, results from the combination of two heavily modulated triclinic Q and H subsystems with a common q wavevector and only one shared reciprocal axis (stacking direction). The Q pseudo-tetragonal layer, ∼(Pb0.70Sb0.30S), derived from the NaCl archetype, is positively charged; the H pseudo-hexagonal layer, ∼(Sn0.85Cu0.30S2), derived from the CdI2 archetype, is negatively charged, owing to the replacement of Sn4+ in an octahedral coordination by Cu+ pairs in an opposite triangular coordination. The analysis shows a strong transverse displacive modulation of the two layers, referred to as a `mondulation', correlated to a maximal Sb site occupation factor in the concavity of the Q layer undulation. The wavelength control of the `mondulation' obeys the vernier principle (14cQ ≅ 13cH ), which would correspond to an energy minimization through a charge transfer density modulation wave, common to all two-dimensional misfit-layer inorganic compounds.

scholarly journals Unexpected Specificity within Dynamic Transcriptional Protein-Protein Complexes

2020 ◽  
Author(s):  
Matthew J. Henley ◽  
Brian M. Linhares ◽  
Brittany S. Morgan ◽  
Tomasz Cierpicki ◽  
Carol A. Fierke ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Electrostatic Interactions ◽  
Protein Complexes ◽  
Critical Role ◽  
Gene Activation ◽  
Disordered Proteins ◽  
Conformational Ensemble ◽  
Regulation Of Transcription ◽  
Protein Protein Interaction ◽  
Eukaryotic Gene

AbstractA key functional event in eukaryotic gene activation is the formation of dynamic protein-protein interaction networks between transcriptional activators and transcriptional coactivators. Seemingly incongruent with the tight regulation of transcription, many biochemical and biophysical studies suggest that activators use nonspecific hydrophobic and/or electrostatic interactions to bind to coactivators, with few if any specific contacts. Here a mechanistic dissection of a set of representative dynamic activator•coactivator complexes, comprised of the ETV/PEA3 family of activators and the coactivator Med25, reveals a different molecular recognition model. The data demonstrate that small sequence variations within an activator family significantly redistribute the conformational ensemble of the complex while not affecting overall affinity, and distal residues within the activator—not often considered as contributing to binding—play a key role in mediating conformational redistribution. The ETV/PEA3•Med25 ensembles are directed by specific contacts between the disordered activator and the Med25 interface, which is facilitated by structural shifts of the coactivator binding surface. Taken together, these data highlight the critical role coactivator plasticity plays in recognition of disordered activators, and indicates that molecular recognition models of disordered proteins must consider the ability of the binding partners to mediate specificity.

scholarly journals Atomic-level characterization of protein–protein association

2019 ◽  
Vol 116 (10) ◽  
pp. 4244-4249 ◽  
Author(s):  
Albert C. Pan ◽  
Daniel Jacobson ◽  
Konstantin Yatsenko ◽  
Duluxan Sritharan ◽  
Thomas M. Weinreich ◽  
...  
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Md Simulations ◽  
Atomic Level ◽  
Conformational Ensemble ◽  
Native State ◽  
Protein Interfaces ◽  
Study Association ◽  
Functionally Diverse

Despite the biological importance of protein–protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein–protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)–based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual reassociation near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein–protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.

scholarly journals Braiding topology and the energy landscape of chromosome organization proteins

2019 ◽  
Vol 117 (3) ◽  
pp. 1468-1477 ◽  
Author(s):  
Dana Krepel ◽  
Aram Davtyan ◽  
Nicholas P. Schafer ◽  
Peter G. Wolynes ◽  
José N. Onuchic
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Energy Landscape ◽  
Critical Role ◽  
Coiled Coil ◽  
Structural Data ◽  
Atomic Scale ◽  
Integrative Approach ◽  
Chromosome Organization ◽  
Conformational Ensemble

Assemblies of structural maintenance of chromosomes (SMC) proteins and kleisin subunits are essential to chromosome organization and segregation across all kingdoms of life. While structural data exist for parts of the SMC−kleisin complexes, complete structures of the entire complexes have yet to be determined, making mechanistic studies difficult. Using an integrative approach that combines crystallographic structural information about the globular subdomains, along with coevolutionary information and an energy landscape optimized force field (AWSEM), we predict atomic-scale structures for several tripartite SMC−kleisin complexes, including prokaryotic condensin, eukaryotic cohesin, and eukaryotic condensin. The molecular dynamics simulations of the SMC−kleisin protein complexes suggest that these complexes exist as a broad conformational ensemble that is made up of different topological isomers. The simulations suggest a critical role for the SMC coiled-coil regions, where the coils intertwine with various linking numbers. The twist and writhe of these braided coils are coupled with the motion of the SMC head domains, suggesting that the complexes may function as topological motors. Opening, closing, and translation along the DNA of the SMC−kleisin protein complexes would allow these motors to couple to the topology of DNA when DNA is entwined with the braided coils.

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