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2012 5
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Crowding within synaptic junctions influences the degradation of nucleotides by CD39 and CD73 ectonucleotidases.
Rahmaninejad H, Pace T, Chun BJ, Kekenes-Huskey PM. Rahmaninejad H, et al. Among authors: kekenes huskey pm. Biophys J. 2022 Jan 18;121(2):309-318. doi: 10.1016/j.bpj.2021.12.013. Epub 2021 Dec 16. Biophys J. 2022. PMID: 34922916 Free PMC article.
Specifically, we developed a spatially explicit, reaction-diffusion model for the coupled conversion of ATP AMP and AMP adenosine in a model synaptic junction with crowders that is solved via the finite element method. ...
Specifically, we developed a spatially explicit, reaction-diffusion model for the coupled conversion of ATP AMP and AMP adenosine in …
Homogenization of Continuum-Scale Transport Properties from Molecular Dynamics Simulations: An Application to Aqueous-Phase Methane Diffusion in Silicate Channels.
Pace T, Rahmaninejad H, Sun B, Kekenes-Huskey PM. Pace T, et al. Among authors: kekenes huskey pm. J Phys Chem B. 2021 Oct 21;125(41):11520-11533. doi: 10.1021/acs.jpcb.1c07062. Epub 2021 Oct 7. J Phys Chem B. 2021. PMID: 34618464
The molecular dynamics simulations indicate that methane diffusivity at the silica surface is lower than the bulk-like rates observed at the center of channels of sufficient width. However, potentials of mean force generally evidence attractive methane/silica interactions …
The molecular dynamics simulations indicate that methane diffusivity at the silica surface is lower than the bulk-like rates observed …
Assessing the Role of Calmodulin's Linker Flexibility in Target Binding.
Sun B, Kekenes-Huskey PM. Sun B, et al. Among authors: kekenes huskey pm. Int J Mol Sci. 2021 May 8;22(9):4990. doi: 10.3390/ijms22094990. Int J Mol Sci. 2021. PMID: 34066691 Free PMC article.
By calculating the mean-first-passage-time for these simulations, we estimated the association rate to be ka= 8.7 108 M-1 s-1, which is similar to the diffusion-limited, experimentally-determined rate of 2.2 108 M-1 s-1. Furthermore, our simulations recapitulated its well- …
By calculating the mean-first-passage-time for these simulations, we estimated the association rate to be ka= 8.7 108 M-1 s-1, which is simi …
Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions.
Rahmaninejad H, Pace T, Bhatt S, Sun B, Kekenes-Huskey P. Rahmaninejad H, et al. Among authors: kekenes huskey p. PLoS Comput Biol. 2020 Jun 25;16(6):e1007903. doi: 10.1371/journal.pcbi.1007903. eCollection 2020 Jun. PLoS Comput Biol. 2020. PMID: 32584811 Free PMC article.
While the contributions of electrostatic and steric interactions within such nanodomains are known to shape diffusion-limited reaction rates, less is understood about how these factors control the kinetics of nucleotidase activity. To quantify these factors, we utilized re …
While the contributions of electrostatic and steric interactions within such nanodomains are known to shape diffusion-limited reactio …
Electrostatic control of calcineurin's intrinsically-disordered regulatory domain binding to calmodulin.
Sun B, Cook EC, Creamer TP, Kekenes-Huskey PM. Sun B, et al. Among authors: kekenes huskey pm. Biochim Biophys Acta Gen Subj. 2018 Dec;1862(12):2651-2659. doi: 10.1016/j.bbagen.2018.07.027. Epub 2018 Jul 31. Biochim Biophys Acta Gen Subj. 2018. PMID: 30071273 Free PMC article.
Specifically, we examined several RD constructs that contain the CaM binding region (CAMBR) to characterize the roles of electrostatics versus conformational diversity in controlling diffusion-limited association rates, via microsecond-scale molecular dynamics (MD) and Bro …
Specifically, we examined several RD constructs that contain the CaM binding region (CAMBR) to characterize the roles of electrostatics vers …
Myofilament Calcium Sensitivity: Consequences of the Effective Concentration of Troponin I.
Siddiqui JK, Tikunova SB, Walton SD, Liu B, Meyer M, de Tombe PP, Neilson N, Kekenes-Huskey PM, Salhi HE, Janssen PM, Biesiadecki BJ, Davis JP. Siddiqui JK, et al. Among authors: kekenes huskey pm. Front Physiol. 2016 Dec 21;7:632. doi: 10.3389/fphys.2016.00632. eCollection 2016. Front Physiol. 2016. PMID: 28066265 Free PMC article.
Considering TnI is essentially tethered to TnC and cannot diffuse away in the absence of calcium, we suggest that the apparent calcium binding properties of TnC are highly dependent upon an "effective concentration" of TnI available to bind TnC. ...
Considering TnI is essentially tethered to TnC and cannot diffuse away in the absence of calcium, we suggest that the apparent calciu …
Quantifying the Influence of the Crowded Cytoplasm on Small Molecule Diffusion.
Kekenes-Huskey PM, Scott CE, Atalay S. Kekenes-Huskey PM, et al. J Phys Chem B. 2016 Aug 25;120(33):8696-706. doi: 10.1021/acs.jpcb.6b03887. Epub 2016 Jul 7. J Phys Chem B. 2016. PMID: 27327486 Free PMC article.
Most significantly, proteins and nucleic acid crowders reduce the accessible volume fraction, , available to a diffusing substrate, thereby reducing its effective diffusion rate, Deff, relative to its rate in bulk solution. ...More generally, the quantitative agreem …
Most significantly, proteins and nucleic acid crowders reduce the accessible volume fraction, , available to a diffusing substrate, t …
Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling.
Kekenes-Huskey PM, Eun C, McCammon JA. Kekenes-Huskey PM, et al. J Chem Phys. 2015 Sep 7;143(9):094103. doi: 10.1063/1.4929528. J Chem Phys. 2015. PMID: 26342355 Free PMC article.
For diffusion-influenced reactions, the spatial organization of diffusion barriers arising from intracellular structures, non-specific crowders, and specific-binders (buffers) strongly controls the temporal and spatial reaction kinetics. ...We find that diffusion …
For diffusion-influenced reactions, the spatial organization of diffusion barriers arising from intracellular structures, non- …
Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation.
Kekenes-Huskey PM, Gillette AK, McCammon JA. Kekenes-Huskey PM, et al. J Chem Phys. 2014 May 7;140(17):174106. doi: 10.1063/1.4873382. J Chem Phys. 2014. PMID: 24811624 Free PMC article.
The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. ...J. 105, 2130 (2013)] using homogenization theory that the configurat …
The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and ( …
17 results