scholarly journals Systematic Approach to Find the Global Minimum of Relaxation Dispersion Data for Protein-Induced B–Z Transition of DNA

2021 ◽  
Vol 22 (7) ◽  
pp. 3517
Author(s):  
Kwang-Im Oh ◽  
Ae-Ree Lee ◽  
Seo-Ree Choi ◽  
Youyeon Go ◽  
Kyoung-Seok Ryu ◽  
...  
Keyword(s):  
Protein Binding ◽  
Conformational Changes ◽  
Global Minimum ◽  
Global Search ◽  
Relaxation Dispersion ◽  
State Transitions ◽  
Oscillatory Regime ◽  
Cpmg Relaxation Dispersion ◽  
Search Approach ◽  
Dna Complex

Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion spectroscopy is commonly used for quantifying conformational changes of protein in μs-to-ms timescale transitions. To elucidate the dynamics and mechanism of protein binding, parameters implementing CPMG relaxation dispersion results must be appropriately determined. Building an analytical model for multi-state transitions is particularly complex. In this study, we developed a new global search algorithm that incorporates a random search approach combined with a field-dependent global parameterization method. The robust inter-dependence of the parameters carrying out the global search for individual residues (GSIR) or the global search for total residues (GSTR) provides information on the global minimum of the conformational transition process of the Zα domain of human ADAR1 (hZαADAR1)–DNA complex. The global search results indicated that a α-helical segment of hZαADAR1 provided the main contribution to the three-state conformational changes of a hZαADAR1—DNA complex with a slow B–Z exchange process. The two global exchange rate constants, kex and kZB, were found to be 844 and 9.8 s−1, respectively, in agreement with two regimes of residue-dependent chemical shift differences—the “dominant oscillatory regime” and “semi-oscillatory regime”. We anticipate that our global search approach will lead to the development of quantification methods for conformational changes not only in Z-DNA binding protein (ZBP) binding interactions but also in various protein binding processes.

NMR studies of the post-activated neocarzinostatin chromophore-DNA complex. Conformational changes induced in drug and DNA

1995 ◽  
Vol 3 (6) ◽  
pp. 795-809 ◽  
Author(s):  
Xiaolian Gao ◽  
Adonis Stassinopoulos ◽  
Juan Gu ◽  
Irving H. Goldberg
Keyword(s):  
Conformational Changes ◽  
Nmr Studies ◽  
Dna Complex

scholarly journals Using single-molecule FRET to probe the nucleotide-dependent conformational landscape of polymerase β-DNA complexes

2020 ◽  
Vol 295 (27) ◽  
pp. 9012-9020
Author(s):  
Carel Fijen ◽  
Mariam M. Mahmoud ◽  
Meike Kronenberg ◽  
Rebecca Kaup ◽  
Mattia Fontana ◽  
...  
Keyword(s):  
Dna Repair ◽  
Single Molecule ◽  
Conformational Changes ◽  
Dna Complexes ◽  
Single Molecule Fret ◽  
Nucleotide Incorporation ◽  
Eukaryotic Dna ◽  
Cellular Dna ◽  
Dna Complex ◽  
Gapped Dna

Eukaryotic DNA polymerase β (Pol β) plays an important role in cellular DNA repair, as it fills short gaps in dsDNA that result from removal of damaged bases. Since defects in DNA repair may lead to cancer and genetic instabilities, Pol β has been extensively studied, especially its mechanisms for substrate binding and a fidelity-related conformational change referred to as “fingers closing.” Here, we applied single-molecule FRET to measure distance changes associated with DNA binding and prechemistry fingers movement of human Pol β. First, using a doubly labeled DNA construct, we show that Pol β bends the gapped DNA substrate less than indicated by previously reported crystal structures. Second, using acceptor-labeled Pol β and donor-labeled DNA, we visualized dynamic fingers closing in single Pol β-DNA complexes upon addition of complementary nucleotides and derived rates of conformational changes. We further found that, while incorrect nucleotides are quickly rejected, they nonetheless stabilize the polymerase-DNA complex, suggesting that Pol β, when bound to a lesion, has a strong commitment to nucleotide incorporation and thus repair. In summary, the observation and quantification of fingers movement in human Pol β reported here provide new insights into the delicate mechanisms of prechemistry nucleotide selection.

scholarly journals Probing RNA dynamics via longitudinal exchange and CPMG relaxation dispersion NMR spectroscopy using a sensitive 13C-methyl label

2011 ◽  
Vol 39 (10) ◽  
pp. 4340-4351 ◽  
Author(s):  
Karin Kloiber ◽  
Romana Spitzer ◽  
Martin Tollinger ◽  
Robert Konrat ◽  
Christoph Kreutz
Keyword(s):  
Nmr Spectroscopy ◽  
Relaxation Dispersion ◽  
Rna Dynamics ◽  
Cpmg Relaxation Dispersion ◽  
Relaxation Dispersion Nmr

scholarly journals Exploring chromosomal structural heterogeneity across multiple cell lines

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Ryan R Cheng ◽  
Vinicius G Contessoto ◽  
Erez Lieberman Aiden ◽  
Peter G Wolynes ◽  
Michele Di Pierro ◽  
...  
Keyword(s):  
Cell Lines ◽  
Conformational Changes ◽  
Human Cell ◽  
Structural Heterogeneity ◽  
State Transitions ◽  
Human Cell Lines ◽  
Hydrophobic Collapse ◽  
Chromosomal Territories ◽  
Multiple Cell ◽  
Inactive Chromatin

Using computer simulations, we generate cell-specific 3D chromosomal structures and compare them to recently published chromatin structures obtained through microscopy. We demonstrate using machine learning and polymer physics simulations that epigenetic information can be used to predict the structural ensembles of multiple human cell lines. Theory predicts that chromosome structures are fluid and can only be described by an ensemble, which is consistent with the observation that chromosomes exhibit no unique fold. Nevertheless, our analysis of both structures from simulation and microscopy reveals that short segments of chromatin make two-state transitions between closed conformations and open dumbbell conformations. Finally, we study the conformational changes associated with the switching of genomic compartments observed in human cell lines. The formation of genomic compartments resembles hydrophobic collapse in protein folding, with the aggregation of denser and predominantly inactive chromatin driving the positioning of active chromatin toward the surface of individual chromosomal territories.

The coupling mechanism of mammalian respiratory complex I

Science ◽  
2020 ◽  
Vol 370 (6516) ◽  
pp. eabc4209 ◽  
Author(s):  
Domen Kampjut ◽  
Leonid A. Sazanov
Keyword(s):  
Conformational Changes ◽  
Complex I ◽  
Electrostatic Interactions ◽  
Proton Translocation ◽  
Proton Pumping ◽  
State Transitions ◽  
Coupling Mechanism ◽  
Cryo Electron Microscopy ◽  
Open Conformation ◽  
Respiratory Complex I

Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo–electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.

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