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

2008 ◽  
Vol 295 (4) ◽  
pp. H1439-H1450 ◽  
Author(s):  
Parag Pawar ◽  
Sameer Jadhav ◽  
Charles D. Eggleton ◽  
Konstantinos Konstantopoulos

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.


1998 ◽  
Vol 75 (3) ◽  
pp. 1553-1572 ◽  
Author(s):  
Scott E. Chesla ◽  
Periasamy Selvaraj ◽  
Cheng Zhu

2019 ◽  
Vol 15 (2) ◽  
pp. 139-153 ◽  
Author(s):  
Monica Bouzo-Lorenzo ◽  
Leigh A. Stoddart ◽  
Lizi Xia ◽  
Adriaan P. IJzerman ◽  
Laura H. Heitman ◽  
...  

1989 ◽  
Vol 259 (2) ◽  
pp. 443-452 ◽  
Author(s):  
D Kowlessur ◽  
M O'Driscoll ◽  
C M Topham ◽  
W Templeton ◽  
E W Thomas ◽  
...  

1. The pH-dependence of the second-order rate constant (k) for the reaction of actinidin (EC 3.4.22.14) with 2-(N'-acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide was determined and the contributions to k of various hydronic states were evaluated. 2. The data were used to assess the consequences for transition-state geometry of providing P2/S2 hydrophobic contacts in addition to hydrogen-bonding opportunities in the S1-S2 intersubsite region. 3. The P2/S2 contacts (a) substantially improve enzyme-ligand binding, (b) greatly enhance the contribution to reactivity of the hydronic state bounded by pKa 3 (the pKa characteristic of the formation of catalytic-site-S-/-ImH+ state) and pKa 5 (a relatively minor contributor in reactions that lack the P2/S2 contacts), such that the major rate optimum occurs at pH 4 instead of at pH 2.8-2.9, and (c) reveal the kinetic influence of a pKa approx. 6.3 not hitherto observed in reactions of actinidin. 4. Possibilities for the interplay of electrostatic effects and binding interactions in both actinidin and papain (EC 3.4.22.2) are discussed.


2014 ◽  
Vol 465 (1) ◽  
pp. 127-137 ◽  
Author(s):  
Penny Beckerson ◽  
Michael T. Wilson ◽  
Dimitri A. Svistunenko ◽  
Brandon J. Reeder

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.


2009 ◽  
Vol 62 (6) ◽  
pp. 528 ◽  
Author(s):  
Gideon J. Davies ◽  
Stephen G. Withers ◽  
David J. Vocadlo

Glycosidase inhibitors frequently reflect either the charge or the ‘flattened’ shape of the oxocarbenium-ion like transition state. Much of the impetus for such inhibitory strategies derives from historical studies on ligand binding to hen egg white lysozyme (HEWL); not least those suggesting that product complexes of the enzyme showed distortion of the pyranosides in the –1 subsite. Ironically, while distortion is undoubtedly a defining feature of glycosidases, product complexes themselves are rarely distorted. Here we show that the chitopentaose product complex of a mutant E35Q HEWL, solved at 1.8 Å resolution, is bound with all sugars in 4C1 conformation.


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