A distal regulatory strategy of enzymes: from local to global conformational dynamics

2021 ◽  
Vol 23 (39) ◽  
pp. 22451-22465
Author(s):  
Xue Peng ◽  
Chenlin Lu ◽  
Jian Pang ◽  
Zheng Liu ◽  
Diannan Lu
Keyword(s):  
Conformational Dynamics ◽  
Regulatory Strategy ◽  
Protein Ensembles

Modulating the distribution of various states in protein ensembles through distal sites may be promising in the evolution of enzymes in desired directions.

scholarly journals Markov State Models and NMR Uncover an Overlooked Allosteric Loop in p53

2020 ◽  
Author(s):  
Emilia P. Barros ◽  
Özlem Demir ◽  
Jenaro Soto ◽  
Melanie J. Cocco ◽  
Rommie E. Amaro
Keyword(s):  
Protein Function ◽  
Human Cancer ◽  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Markov State ◽  
Markov State Models ◽  
Distant Location ◽  
Protein Ensembles ◽  
State Models ◽  
Dynamics Simulations

ABSTRACTThe tumor suppressor p53 is the most frequently mutated gene in human cancer, and thus reactivation of mutated p53 is a promising avenue for cancer therapy. Analysis of wildtype p53 and the Y220C cancer mutant long-timescale molecular dynamics simulations with Markov state models and validation by NMR relaxation studies has uncovered the involvement of loop L6 in the slowest motions of the protein. Due to its distant location from the DNA-binding surface, the conformational dynamics of this loop has so far remained largely unexplored. We observe mutation-induced stabilization of alternate L6 conformations, distinct from all experimentally-determined structures, in which the loop is both extended and located further away from the DNA-interacting surface. Additionally, the effect of the L6-adjacent Y220C mutation on the conformational landscape of the functionally-important loop L1 suggests an allosteric role to this dynamic loop and the inactivation mechanism of the mutation. Finally, the simulations reveal a novel Y220C cryptic pocket that can be targeted for p53 rescue efforts. Our approach exemplifies the power of the MSM methodology for uncovering intrinsic dynamic and kinetic differences among distinct protein ensembles, such as for the investigation of mutation effects on protein function.

Idiographic Dynamics of Positive Affect in GAD

2020 ◽  
Vol 36 (3) ◽  
pp. 500-509
Author(s):  
Hannah G. Bosley ◽  
Devon B. Sandel ◽  
Aaron J. Fisher
Keyword(s):  
Positive Affect ◽  
Structural Equation ◽  
Alternative Hypothesis ◽  
Equation Model ◽  
Aggregated Data ◽  
Regulatory Strategy ◽  
Constant State ◽  
Automatic Search ◽  
Time Lagged ◽  
Exploratory Procedure

Abstract. Generalized anxiety disorder (GAD) is associated with worry and emotion regulation difficulties. The contrast-avoidance model suggests that individuals with GAD use worry to regulate emotion: by worrying, they maintain a constant state of negative affect (NA), avoiding a feared sudden shift into NA. We tested an extension of this model to positive affect (PA). During a week-long ecological momentary assessment (EMA) period, 96 undergraduates with a GAD analog provided four daily measurements of worry, dampening (i.e., PA suppression), and PA. We hypothesized a time-lagged mediation relationship in which higher worry predicts later dampening, and dampening predicts subsequently lower PA. A lag-2 structural equation model was fit to the group-aggregated data and to each individual time-series to test this hypothesis. Although worry and PA were negatively correlated in 87 participants, our model was not supported at the nomothetic level. However, idiographically, our model was well-fit for about a third (38.5%) of participants. We then used automatic search as an idiographic exploratory procedure to detect other time-lagged relationships between these constructs. While 46 individuals exhibited some cross-lagged relationships, no clear pattern emerged across participants. An alternative hypothesis about the speed of the relationship between variables is discussed using contemporaneous correlations of worry, dampening, and PA. Findings suggest heterogeneity in the function of worry as a regulatory strategy, and the importance of temporal scale for detection of time-lagged effects.

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue ◽  
Helen Zgurskaya ◽  
Wei Chen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Proton Release ◽  
Intrinsic Resistance ◽  
Constant Ph ◽  
Wide Range ◽  
Constant Ph Molecular Dynamics

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

Monitoring the Structural Dynamics of U2 snRNA Via Single-Molecule Förster Resonance Energy Transfer

2018 ◽  
Author(s):  
Alexander Carl DeHaven
Keyword(s):  
Energy Transfer ◽  
Structural Dynamics ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Förster Resonance Energy Transfer ◽  
U2 Snrna ◽  
Folding Dynamics ◽  
The Impact

This thesis contains four topic areas: a review of single-molecule microscropy methods and splicing, conformational dynamics of stem II of the U2 snRNA, the impact of post-transcriptional modifications on U2 snRNA folding dynamics, and preliminary findings on Mango aptamer folding dynamics.

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