scholarly journals Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins

2012 ◽  
Vol 219 ◽  
pp. 75-82 ◽  
Author(s):  
Nathaniel J. Traaseth ◽  
Fa-An Chao ◽  
Larry R. Masterson ◽  
Silvia Mangia ◽  
Michael Garwood ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Conformational Dynamics ◽  
Relaxation Dispersion

scholarly journals Searching for Correlated Conformational Dynamics: Analysis of the NMR Relaxation Dispersions with Akaike's Information Theory and Hierarchical Clustering

2017 ◽  
Author(s):  
Evgenii L. Kovrigin
Keyword(s):  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Hierarchical Cluster ◽  
Information Criteria ◽  
Relaxation Dispersion ◽  
Spin Groups ◽  
Dispersion Data ◽  
Poorly Soluble ◽  
The Difference ◽  
Best Fit

ABSTRACT:In this manuscript, I am proposing an approach for identification of correlated exchange in proteins via analysis of the NMR relaxation dispersion data. For a set of spins experiencing exchange, every relaxation dispersion datasets is fit individually and then—globally while paired with every other dataset. The corrected Akaike’ s Information Criteria (AICc) for individual and global fits are used to evaluate the likelihood of two spins to report on the same dynamic event. Application of hierarchical cluster analysis reveals correlated spin groups using the difference in AICcs as a measure of similarity within the pairs. This approach to detection of correlated dynamics is independent of accuracy of best-fit parameters rendering it less sensitive to experimental noise. High throughput and the absence of the operator bias might make it applicable to a relatively lower quality NMR relaxation dispersion data from large and poorly soluble systems.

scholarly journals Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses

2020 ◽  
Vol 117 (12) ◽  
pp. 6550-6558 ◽  
Author(s):  
Jae-Hyun Cho ◽  
Baoyu Zhao ◽  
Jie Shi ◽  
Nowlan Savage ◽  
Qingliang Shen ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Influenza A ◽  
Nonstructural Protein ◽  
Conformational Dynamics ◽  
Relaxation Dispersion ◽  
Binding Kinetics ◽  
Host Protein ◽  
Dynamics Simulation ◽  
Nonstructural Protein 1 ◽  
Strain Dependent

The 1918 influenza A virus (IAV) caused the most severe flu pandemic in recorded human history. Nonstructural protein 1 (NS1) is an important virulence factor of the 1918 IAV. NS1 antagonizes host defense mechanisms through interactions with multiple host factors. One pathway by which NS1 increases virulence is through the activation of phosphoinositide 3-kinase (PI3K) by binding to its p85β subunit. Here we present the mechanism underlying the molecular recognition of the p85β subunit by 1918 NS1. Using X-ray crystallography, we determine the structure of 1918 NS1 complexed with p85β of human PI3K. We find that the 1918 NS1 effector domain (1918 NS1ED) undergoes a conformational change to bind p85β. Using NMR relaxation dispersion and molecular dynamics simulation, we identify that free 1918 NS1EDexists in a dynamic equilibrium between p85β-binding–competent and –incompetent conformations in the submillisecond timescale. Moreover, we discover that NS1EDproteins of 1918 (H1N1) and Udorn (H3N2) strains exhibit drastically different conformational dynamics and binding kinetics to p85β. These results provide evidence of strain-dependent conformational dynamics of NS1. Using kinetic modeling based on the experimental data, we demonstrate that 1918 NS1EDcan result in the faster hijacking of p85β compared to Ud NS1ED, although the former has a lower affinity to p85β than the latter. Our results suggest that the difference in binding kinetics may impact the competition with cellular antiviral responses for the activation of PI3K. We anticipate that our findings will increase the understanding of the strain-dependent behaviors of influenza NS1 proteins.

scholarly journals Binding kinetics and substrate selectivity in HIV-1 protease−Gag interactions probed at atomic resolution by chemical exchange NMR

2017 ◽  
Vol 114 (46) ◽  
pp. E9855-E9862 ◽  
Author(s):  
Lalit Deshmukh ◽  
Vitali Tugarinov ◽  
John M. Louis ◽  
G. Marius Clore
Keyword(s):  
Chemical Exchange ◽  
Conformational Dynamics ◽  
Specific Antigen ◽  
Relaxation Dispersion ◽  
Chemical Exchange Saturation Transfer ◽  
Cleavage Sites ◽  
Gag Polyprotein ◽  
Intrinsically Disordered ◽  
Catalytic Cleft ◽  
Hiv 1

The conversion of immature noninfectious HIV-1 particles to infectious virions is dependent upon the sequential cleavage of the precursor group-specific antigen (Gag) polyprotein by HIV-1 protease. The precise mechanism whereby protease recognizes distinct Gag cleavage sites, located in the intrinsically disordered linkers connecting the globular domains of Gag, remains unclear. Here, we probe the dynamics of the interaction of large fragments of Gag and various variants of protease (including a drug resistant construct) using Carr−Purcell−Meiboom−Gill relaxation dispersion and chemical exchange saturation transfer NMR experiments. We show that the conformational dynamics within the flaps of HIV-1 protease that form the lid over the catalytic cleft play a significant role in substrate specificity and ordered Gag processing. Rapid interconversion between closed and open protease flap conformations facilitates the formation of a transient, sparsely populated productive complex between protease and Gag substrates. Flap closure traps the Gag cleavage sites within the catalytic cleft of protease. Modulation of flap opening through protease−Gag interactions fine-tunes the lifetime of the productive complex and hence the likelihood of Gag proteolysis. A productive complex can also be formed in the presence of a noncognate substrate but is short-lived owing to lack of optimal complementarity between the active site cleft of protease and the substrate, resulting in rapid flap opening and substrate release, thereby allowing protease to differentiate between cognate and noncognate substrates.

scholarly journals The Picornavirus Precursor 3CD Has Different Conformational Dynamics Compared to 3Cpro and 3Dpol in Functionally Relevant Regions

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 442
Author(s):  
Dennis S. Winston ◽  
David D. Boehr
Keyword(s):  
Active Sites ◽  
Conformational Dynamics ◽  
Genetic Material ◽  
Lipid Binding ◽  
Relaxation Dispersion ◽  
Chemical Exchange Saturation Transfer ◽  
Resonance Spectroscopy ◽  
Conformational Ensemble ◽  
Multiple Quantum ◽  
Functional Differences

Viruses have evolved numerous strategies to maximize the use of their limited genetic material, including proteolytic cleavage of polyproteins to yield products with different functions. The poliovirus polyprotein 3CD is involved in important protein-protein, protein-RNA and protein-lipid interactions in viral replication and infection. It is a precursor to the 3C protease and 3D RNA-dependent RNA polymerase, but has different protease specificity, is not an active polymerase, and participates in other interactions differently than its processed products. These functional differences are poorly explained by the known X-ray crystal structures. It has been proposed that functional differences might be due to differences in conformational dynamics between 3C, 3D and 3CD. To address this possibility, we conducted nuclear magnetic resonance spectroscopy experiments, including multiple quantum relaxation dispersion, chemical exchange saturation transfer and methyl spin-spin relaxation, to probe conformational dynamics across multiple timescales. Indeed, these studies identified differences in conformational dynamics in functionally important regions, including enzyme active sites, and RNA and lipid binding sites. Expansion of the conformational ensemble available to 3CD may allow it to perform additional functions not observed in 3C and 3D alone despite having nearly identical lowest-energy structures.

scholarly journals Probing transient excited states of the bacterial cell division regulator MinE by relaxation dispersion NMR spectroscopy

2019 ◽  
Vol 116 (51) ◽  
pp. 25446-25455 ◽  
Author(s):  
Mengli Cai ◽  
Ying Huang ◽  
Yang Shen ◽  
Min Li ◽  
Michiyo Mizuuchi ◽  
...  
Keyword(s):  
Cell Division ◽  
Excited States ◽  
Resting State ◽  
Conformational Dynamics ◽  
Quantitative Information ◽  
Full Length ◽  
Relaxation Dispersion ◽  
Dimer Interface ◽  
Relaxation Dispersion Nmr ◽  
Β Sheet

Bacterial MinD and MinE form a standing oscillatory wave which positions the cell division inhibitor MinC, that binds MinD, everywhere on the membrane except at the midpoint of the cell, ensuring midcell positioning of the cytokinetic septum. During this process MinE undergoes fold switching as it interacts with different partners. We explore the exchange dynamics between major and excited states of the MinE dimer in 3 forms using15N relaxation dispersion NMR: the full-length protein (6-stranded β-sheet sandwiched between 4 helices) representing the resting state; a 10-residue N-terminal deletion (Δ10) mimicking the membrane-binding competent state where the N-terminal helix is detached to interact with membrane; and N-terminal deletions of either 30 (Δ30) or 10 residues with an I24N mutation (Δ10/I24N), in which the β1-strands at the dimer interface are extruded and available to bind MinD, leaving behind a 4-stranded β-sheet. Full-length MinE samples 2 “excited” states: The first is similar to a full-length/Δ10 heterodimer; the second, also sampled by Δ10, is either similar to or well along the pathway toward the 4-stranded β-sheet form. Both Δ30 and Δ10/I24N sample 2 excited species: The first may involve destabilization of the β3- and β3′-strands at the dimer interface; changes in the second are more extensive, involving further disruption of secondary structure, possibly representing an ensemble of states on the pathway toward restoration of the resting state. The quantitative information on MinE conformational dynamics involving these excited states is crucial for understanding the oscillation pattern self-organization by MinD–MinE interaction dynamics on the membrane.

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