scholarly journals Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Nuria Plattner ◽  
Frank Noé
Keyword(s):  
Ligand Binding ◽  
Markov Models ◽  
Binding Kinetics ◽  
Atomistic Simulations ◽  
Conformational Plasticity ◽  
Complex Ligand

Statistical comparison of ligand-binding kinetics

1989 ◽  
Vol 8 (7) ◽  
pp. 871-881
Author(s):  
John B. Cologne ◽  
Paul M. Mendelman ◽  
Donald O. Chaffin
Keyword(s):  
Ligand Binding ◽  
Binding Kinetics ◽  
Statistical Comparison

scholarly journals Roles of cell and microvillus deformation and receptor-ligand binding kinetics in cell rolling

2008 ◽  
Vol 295 (4) ◽  
pp. H1439-H1450 ◽  
Author(s):  
Parag Pawar ◽  
Sameer Jadhav ◽  
Charles D. Eggleton ◽  
Konstantinos Konstantopoulos
Keyword(s):  
Ligand Binding ◽  
Three Dimensional ◽  
Theoretical Models ◽  
Binding Kinetics ◽  
Cell Deformation ◽  
Receptor Ligand ◽  
Length Scales ◽  
Bond Behavior ◽  
Cell Rolling ◽  
Threshold Phenomenon

Polymorphonuclear leukocyte (PMN) recruitment to sites of inflammation is initiated by selectin-mediated PMN tethering and rolling on activated endothelium under flow. Cell rolling is modulated by bulk cell deformation (mesoscale), microvillus deformability (microscale), and receptor-ligand binding kinetics (nanoscale). Selectin-ligand bonds exhibit a catch-slip bond behavior, and their dissociation is governed not only by the force but also by the force history. Whereas previous theoretical models have studied the significance of these three “length scales” in isolation, how their interplay affects cell rolling has yet to be resolved. We therefore developed a three-dimensional computational model that integrates the aforementioned length scales to delineate their relative contributions to PMN rolling. Our simulations predict that the catch-slip bond behavior and to a lesser extent bulk cell deformation are responsible for the shear threshold phenomenon. Cells bearing deformable rather than rigid microvilli roll slower only at high P-selectin site densities and elevated levels of shear (≥400 s−1). The more compliant cells (membrance stiffness = 1.2 dyn/cm) rolled slower than cells with a membrane stiffness of 3.0 dyn/cm at shear rates >50 s−1. In summary, our model demonstrates that cell rolling over a ligand-coated surface is a highly coordinated process characterized by a complex interplay between forces acting on three distinct length scales.

scholarly journals Measuring Two-Dimensional Receptor-Ligand Binding Kinetics by Micropipette

1998 ◽  
Vol 75 (3) ◽  
pp. 1553-1572 ◽  
Author(s):  
Scott E. Chesla ◽  
Periasamy Selvaraj ◽  
Cheng Zhu
Keyword(s):  
Ligand Binding ◽  
Binding Kinetics ◽  
Two Dimensional ◽  
Receptor Ligand

scholarly journals A live cell NanoBRET binding assay allows the study of ligand-binding kinetics to the adenosine A3 receptor

2019 ◽  
Vol 15 (2) ◽  
pp. 139-153 ◽  
Author(s):  
Monica Bouzo-Lorenzo ◽  
Leigh A. Stoddart ◽  
Lizi Xia ◽  
Adriaan P. IJzerman ◽  
Laura H. Heitman ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Assay ◽  
Live Cell ◽  
Binding Kinetics ◽  
Adenosine A3 Receptor

Cytoglobin ligand binding regulated by changing haem-co-ordination in response to intramolecular disulfide bond formation and lipid interaction

2014 ◽  
Vol 465 (1) ◽  
pp. 127-137 ◽  
Author(s):  
Penny Beckerson ◽  
Michael T. Wilson ◽  
Dimitri A. Svistunenko ◽  
Brandon J. Reeder
Keyword(s):  
Ligand Binding ◽  
Redox State ◽  
Structural Changes ◽  
Bond Formation ◽  
Lipid Binding ◽  
Binding Kinetics ◽  
Disulfide Bond Formation ◽  
Physiological Properties ◽  
Intramolecular Disulfide Bond ◽  
Lipid Interaction

The redox state of the two-surface exposed cysteine residues in cytoglobin (Cygb) regulates the biochemical and potential physiological properties of the protein. Significant changes to ligand-binding kinetics, peroxidase activity and lipid-binding-induced structural changes are observed.

scholarly journals Impact of protein–ligand solvation and desolvation on transition state thermodynamic properties of adenosine A2A ligand binding kinetics

2017 ◽  
Vol 5 (1) ◽  
Author(s):  
Giuseppe Deganutti ◽  
Andrei Zhukov ◽  
Francesca Deflorian ◽  
Stephanie Federico ◽  
Giampiero Spalluto ◽  
...  
Keyword(s):  
Thermodynamic Properties ◽  
Ligand Binding ◽  
Transition State ◽  
Binding Kinetics ◽  
Adenosine A2a

scholarly journals Spectroscopic analyses of the binding kinetics of 15d-PGJ2 to the PPARγ ligand-binding domain by multi-wavelength global fitting

2006 ◽  
Vol 393 (3) ◽  
pp. 749-755 ◽  
Author(s):  
Takuma Shiraki ◽  
Takashi S. Kodama ◽  
Sayaka Shiki ◽  
Tatsuo Nakagawa ◽  
Hisato Jingami
Keyword(s):  
Ligand Binding ◽  
Intermediate State ◽  
Covalent Binding ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Binding Kinetics ◽  
Multi Wavelength ◽  
Lipid Metabolites ◽  
Kinetics Of ◽  
Global Fitting

PPARγ (peroxisome proliferator-activated receptor γ) is a nuclear receptor that is activated by natural lipid metabolites, including 15d-PGJ2 (15-deoxy-Δ12,14-prostaglandin J2). We previously reported that several oxidized lipid metabolites covalently bind to PPARγ through a Michael-addition to activate transcription. To separate the ligand-entering (dock) and covalent-binding (lock) steps in PPARγ activation, we investigated the binding kinetics of 15d-PGJ2 to the PPARγ LBD (ligand-binding domain) by stopped-flow spectroscopy. We analysed the spectral changes of 15d-PGJ2 by multi-wavelength global fitting based on a two-step chemical reaction model, in which an intermediate state represents the 15d-PGJ2–PPARγ complex without covalent binding. The extracted spectrum of the intermediate state in wild-type PPARγ was quite similar to the observed spectrum of 15d-PGJ2 in the C285S mutant, which cannot be activated by 15d-PGJ2, indicating that the complex remains in the inactive, intermediate state in the mutant. Thus ‘lock’ rather than ‘dock’ is one of the critical steps in PPARγ activation by 15d-PGJ2.

scholarly journals Conformational Plasticity and Ligand Binding of Bacterial Monoacylglycerol Lipase

2013 ◽  
Vol 288 (43) ◽  
pp. 31093-31104 ◽  
Author(s):  
Srinivasan Rengachari ◽  
Philipp Aschauer ◽  
Matthias Schittmayer ◽  
Nicole Mayer ◽  
Karl Gruber ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Monoacylglycerol Lipase ◽  
Conformational Plasticity
Sign in / Sign up

Export Citation Format

Share Document