scholarly journals Mapping transiently formed and sparsely populated conformations on a complex energy landscape

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Yong Wang ◽  
Elena Papaleo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Energy Landscape ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Internal Cavity ◽  
T4 Lysozyme ◽  
Enhanced Sampling ◽  
Exchange Processes ◽  
Dynamics Simulations ◽  
A Minor

Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult. Only in favourable cases is it possible to provide atomic-level descriptions of sparsely populated and transiently formed alternative conformations. Here we benchmark the ability of enhanced-sampling molecular dynamics simulations to determine the free energy landscape of the L99A cavity mutant of T4 lysozyme. We find that the simulations capture key properties previously measured by NMR relaxation dispersion methods including the structure of a minor conformation, the kinetics and thermodynamics of conformational exchange, and the effect of mutations. We discover a new tunnel that involves the transient exposure towards the solvent of an internal cavity, and show it to be relevant for ligand escape. Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally.

scholarly journals Structural ensembles based on NMR parameters suggest a complex pathway of ligand binding in human gastrotropin

2018 ◽  
Author(s):  
Zita Harmat ◽  
András L. Szabó ◽  
Orsolya Toke ◽  
Zoltán Gáspári
Keyword(s):  
Bile Salts ◽  
Conformational Exchange ◽  
Internal Cavity ◽  
Dynamic Nmr ◽  
Nmr Parameters ◽  
Exchange Processes ◽  
Second Mode ◽  
Structural Ensembles ◽  
Partial Unfolding ◽  
Dynamics Simulations

AbstractGastrotropin, the intracellular carrier of bile salts in the small intestine, binds two ligand molecules simultaneously in its internal cavity. The molecular rearrangements required for ligand entry are not yet fully clear. To improve our understanding of the binding process we combined molecular dynamics simulations with available structural and dynamic NMR parameters. The resulting ensembles reveal two distinct modes of barrel opening with one corresponding to the transition between the apo and holo states, whereas the other affecting different protein regions in both ligation states. Comparison of the calculated structures with NMR-derived parameters reporting on slow conformational exchange processes suggests that the protein undergoes partial unfolding along a path related to the second mode of the identified barrel opening motion.

scholarly journals Atomistic picture of conformational exchange in a T4 lysozyme cavity mutant: an experiment-guided molecular dynamics study

2016 ◽  
Vol 7 (6) ◽  
pp. 3602-3613 ◽  
Author(s):  
Pramodh Vallurupalli ◽  
Nilmadhab Chakrabarti ◽  
Régis Pomès ◽  
Lewis E. Kay
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
T4 Lysozyme ◽  
Nmr Techniques ◽  
Relaxation Dispersion Nmr ◽  
Dynamics Simulations

Relaxation-dispersion NMR techniques and molecular dynamics simulations have been used to understand how a cavity mutant of T4 lysozyme interconverts between two compact conformations.

scholarly journals Analysis of Artifacts Caused by Pulse Imperfections in CPMG Pulse Trains in NMR Relaxation Dispersion Experiments

2018 ◽  
Vol 4 (3) ◽  
pp. 33 ◽  
Author(s):  
Tsuyoshi Konuma ◽  
Aritaka Nagadoi ◽  
Jun-ichi Kurita ◽  
Takahisa Ikegami
Keyword(s):  
Dipolar Coupling ◽  
Residual Dipolar Coupling ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Resonance Effects ◽  
Pulse Trains ◽  
At Resonance ◽  
Selective Inversion ◽  
Resonance Relaxation

Nuclear magnetic resonance relaxation dispersion (rd) experiments provide kinetics and thermodynamics information of molecules undergoing conformational exchange. Rd experiments often use a Carr-Purcell-Meiboom-Gill (CPMG) pulse train equally separated by a spin-state selective inversion element (U-element). Even with measurement parameters carefully set, however, parts of 1H–15N correlations sometimes exhibit large artifacts that may hamper the subsequent analyses. We analyzed such artifacts with a combination of NMR measurements and simulation. We found that particularly the lowest CPMG frequency (νcpmg) can also introduce large artifacts into amide 1H–15N and aromatic 1H–13C correlations whose 15N/13C resonances are very close to the carrier frequencies. The simulation showed that the off-resonance effects and miscalibration of the CPMG π pulses generate artifact maxima at resonance offsets of even and odd multiples of νcpmg, respectively. We demonstrate that a method once introduced into the rd experiments for molecules having residual dipolar coupling significantly reduces artifacts. In the method the 15N/13C π pulse phase in the U-element is chosen between x and y. We show that the correctly adjusted sequence is tolerant to miscalibration of the CPMG π pulse power as large as ±10% for most amide 15N and aromatic 13C resonances of proteins.

Enhancing the Sensitivity of CPMG Relaxation Dispersion to Conformational Exchange Processes by Multiple-Quantum Spectroscopy

2016 ◽  
Vol 128 (38) ◽  
pp. 11662-11666 ◽  
Author(s):  
Tairan Yuwen ◽  
Pramodh Vallurupalli ◽  
Lewis E. Kay
Keyword(s):  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Multiple Quantum ◽  
Exchange Processes ◽  
Cpmg Relaxation Dispersion

scholarly journals Collagen I weakly interacts with the β-sheets of β2-microglobulin and enhances conformational exchange to induce amyloid formation

2019 ◽  
Author(s):  
Cody L. Hoop ◽  
Jie Zhu ◽  
Shibani Bhattacharya ◽  
Caitlyn A. Tobita ◽  
Sheena E. Radford ◽  
...  
Keyword(s):  
Protein Function ◽  
Weak Interactions ◽  
Nmr Relaxation ◽  
Conformational Exchange ◽  
Collagen I ◽  
Solution Nmr ◽  
Amyloid Formation ◽  
Relaxation Methods ◽  
A Minor

ABSTRACTAmyloidogenesis is significant in both protein function and pathology. Amyloid formation of folded, globular proteins is commonly initiated by partial unfolding. However, how this unfolding event is triggered for proteins that are otherwise stable in their native environments is not well understood. The accumulation of the immunoglobulin protein β2-microglobulin (β2m) into amyloid plaques in the joints of long-term hemodialysis patients is the hallmark of Dialysis Related Amyloidosis (DRA). While β2m does not form amyloid unassisted near neutral pH in vitro, the localization of β2m deposits to joint spaces suggests a role for the local extracellular matrix (ECM) proteins, specifically collagens, in promoting amyloid formation. Indeed, collagen and other ECM components have been observed to facilitate β2m amyloid formation, but the large size and anisotropy of the complex, combined with the low affinity of these interactions, has limited atomic-level elucidation of the amyloid-promoting mechanism by these molecules. Using solution NMR approaches that uniquely probe weak interactions and large complexes, we are able to derive binding interfaces for collagen I on β2m and detect collagen I-induced µs–ms timescale dynamics in the β2m backbone. By combining solution NMR relaxation methods and 15N-dark state exchange saturation transfer experiments, we propose a model in which weak, multimodal collagen I–β2m interactions promote exchange with a minor population of an amyloid-competent species to induce fibrillogenesis. The results portray the intimate role of the environment in switching an innocuous protein into an amyloid-competent state, rationalizing the localization of amyloid deposits in DRA.

Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data

2012 ◽  
Vol 134 (5) ◽  
pp. 2555-2562 ◽  
Author(s):  
Yi Xue ◽  
Joshua M. Ward ◽  
Tairan Yuwen ◽  
Ivan S. Podkorytov ◽  
Nikolai R. Skrynnikov
Keyword(s):  
Molecular Dynamics ◽  
Time Scale ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Dispersion Data ◽  
Molecular Dynamics Trajectory

Slow Internal Dynamics in Proteins:  Application of NMR Relaxation Dispersion Spectroscopy to Methyl Groups in a Cavity Mutant of T4 Lysozyme

2002 ◽  
Vol 124 (7) ◽  
pp. 1443-1451 ◽  
Author(s):  
Frans A. A. Mulder ◽  
Bin Hon ◽  
Anthony Mittermaier ◽  
Frederick W. Dahlquist ◽  
Lewis E. Kay
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Methyl Groups ◽  
T4 Lysozyme ◽  
Internal Dynamics

scholarly journals Analysis of Conformational Exchange Processes using Methyl-TROSY-Based Hahn Echo Measurements of Quadruple-Quantum Relaxation

2021 ◽  
Author(s):  
Christopher Andrew Waudby ◽  
John Christodoulou
Keyword(s):  
Chemical Shift ◽  
Chemical Exchange ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Parameter Estimates ◽  
Relaxation Rates ◽  
Exchange Processes ◽  
Methyl Trosy ◽  
Quantum Transitions ◽  
Order Of Magnitude

Abstract. Transverse nuclear spin relaxation is a sensitive probe of chemical exchange on timescales on the order of microseconds to milliseconds. Here we present an experiment for the simultaneous measurement of the relaxation rates of two quadruple-quantum transitions in 13CH3-labelled methyl groups. These coherences are protected against relaxation by intra-methyl dipolar interactions, and so have unexpectedly long lifetimes within perdeuterated biomacromolecules. However, these coherences also have an order of magnitude higher sensitivity to chemical exchange broadening than lower order coherences, and therefore provide ideal probes of dynamic processes. We show that analysis of the static magnetic field dependence of zero-, double- and quadruple-quantum Hahn echo relaxation rates provides a robust indication of chemical exchange, and can determine the signed relative magnitudes of proton and carbon chemical shift differences between ground and excited states. We also demonstrate that this analysis can be combined with established CPMG relaxation dispersion measurements, providing improved precision in parameter estimates, particularly in the determination of 1H chemical shift differences.

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