Kinetics of divalent cation induced fusion of phosphatidylserine vesicles: correlation between fusogenic capacities and binding affinities

Biochemistry ◽  
1983 ◽  
Vol 22 (14) ◽  
pp. 3320-3330 ◽  
Author(s):  
Joe Bentz ◽  
Nejat Duzgune ◽  
Shlomo Nir
Keyword(s):  
Divalent Cation ◽  
Binding Affinities ◽  
Kinetics Of

INFLUENCE OF THE STATE OF AGGREGATION OF DIVALENT CATION IMPURITIES ON THE F-COLORING KINETICS OF NaCl

1976 ◽  
Vol 37 (C7) ◽  
pp. C7-87-C7-88
Author(s):  
J. L. PASCUAL ◽  
F. J. LÓPEZ ◽  
F. JAQUE ◽  
F. AGULLÓ-LÓPEZ
Keyword(s):  
Divalent Cation ◽  
The State ◽  
Kinetics Of

scholarly journals Recognition of hydrogen isotopomers by an open-cage fullerene

2013 ◽  
Vol 371 (1998) ◽  
pp. 20110629 ◽  
Author(s):  
Yasujiro Murata ◽  
Shih-Ching Chuang ◽  
Fumiyuki Tanabe ◽  
Michihisa Murata ◽  
Koichi Komatsu
Keyword(s):  
Equilibrium Constants ◽  
Equilibrium Mixture ◽  
Size Difference ◽  
Binding Affinities ◽  
Kinetic Isotope ◽  
Molecular Sizes ◽  
Lower Temperature ◽  
Kinetics Of ◽  
Pressure Hydrogen

We present our study on the recognition of hydrogen isotopes by an open-cage fullerene through determination of binding affinity of isotopes H 2 /HD/D 2 with the open-cage fullerene and comparison of their relative molecular sizes through kinetic-isotope-release experiments. We took advantage of isotope H 2 /D 2 exchange that generated an equilibrium mixture of H 2 /HD/D 2 in a stainless steel autoclave to conduct high-pressure hydrogen insertion into an open-cage fullerene. The equilibrium constants of three isotopes with the open-cage fullerene were determined at various pressures and temperatures. Our results show a higher equilibrium constant for HD into open-cage fullerene than the other two isotopomers, which is consistent with its dipolar nature. D 2 molecule generally binds stronger than H 2 because of its heavier mass; however, the affinity for H 2 becomes larger than D 2 at lower temperature, when size effect becomes dominant. We further investigated the kinetics of H 2 /HD/D 2 release from open-cage fullerene, proving their relative escaping rates. D 2 was found to be the smallest and H 2 the largest molecule. This notion has not only supported the observed inversion of relative binding affinities between H 2 and D 2 , but also demonstrated that comparison of size difference of single molecules through non-convalent kinetic-isotope effect was applicable.

Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids

1999 ◽  
Vol 55 (11) ◽  
pp. 1850-1857 ◽  
Author(s):  
Barnali Neel Chaudhuri ◽  
Gerard J. Kleywegt ◽  
Isabelle Broutin-L'Hermite ◽  
Terese Bergfors ◽  
Hans Senn ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Binding Proteins ◽  
Specific Protein ◽  
Binding Affinities ◽  
Cellular Processes ◽  
Crabp I ◽  
Retinoid Binding Proteins ◽  
Retinoic Acid Binding Proteins ◽  
Crabp Ii ◽  
Kinetics Of

Retinoids play important roles in diverse cellular processes including growth, cell differentiation and vision. Many natural and synthetic retinoids are used as drugs in dermatology and oncology. A large amount of data has been accumulated on the cellular activity of different synthetic retinoids. They are stabilized and transported inside the cell cytoplasm by binding and transport proteins, such as cellular retinol-binding proteins and cellular retinoic acid binding proteins (CRABPs). The structures of human CRABP II in complex with two different synthetic retinoids, Ro13-6307 and Ro12-7310 (at 2.1 and 2.0 Å resolution, respectively) and of bovine CRABP I in complex with a retinobenzoic acid, Am80 (at 2.8 Å resolution) are described. The binding affinities of human CRABP I and II for the retinoids studied here have been determined. All these compounds have comparable binding affinities (nanomolar range) for both CRABPs. Apart from the particular interactions of the carboxylate group of the retinoids with specific protein groups, each structure reveals characteristic interactions. Studying the atomic details of the interaction of retinoids with retinoid-binding proteins facilitates the understanding of the kinetics of retinoid trafficking inside the cytoplasm.

scholarly journals Estimation of Binding Rates and Affinities from Multiensemble Markov Models and Ligand Decoupling

2021 ◽  
Author(s):  
Yunhui Ge ◽  
Vincent Voelz
Keyword(s):  
Ligand Binding ◽  
Markov Models ◽  
Time Correlation ◽  
Test System ◽  
Binding Affinities ◽  
Limited Data ◽  
Markov State Model ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Kinetics Of

Accurate and efficient simulation of the thermodynamics and kinetics of protein-ligand interactions is crucial for computational drug discovery. Multiensemble Markov Model (MEMM) estimators can provide estimates of both binding rates and affinities from collections of short trajectories, but have not been systematically explored for situations when a ligand is decoupled through scaling of non-bonded interactions. In this work, we compare the performance of two MEMM approaches for estimating ligand binding affinities and rates: (1) the transition-based reweighting analysis method (TRAM) and (2) a Maximum Caliber (MaxCal) based method. As a test system, we construct a small host-guest system where the ligand is a single uncharged Lennard-Jones (LJ) particle, and the receptor is an 11-particle icosahedral pocket made from the same atom type. To realistically mimic a protein-ligand binding system, the LJ ε parameter was tuned, and the system placed in a periodic box with 860 TIP3P water molecules. A benchmark was performed using over 80 μs of unbiased simulation, and an 18-state Markov state model used to estimate reference binding affinities and rates. We then tested the performance of TRAM and MaxCal when challenged with limited data. Both TRAM and MaxCal approaches perform better than conventional MSMs, with TRAM showing better convergence and accuracy. We find that subsampling of trajectories to remove time correlation improves the accuracy of both TRAM and MaxCal, and that in most cases only a single biased ensemble to enhance sampled transitions is required to make accurate estimates.

KINETICS OF HEPARIN CO-FACTOR II (HCII):THROMBIN AND ANTITHROMBIN III (ATIII):THROMBIN INTERACTION. MOLECULAR WEIGHT DEPENDENCY

1987 ◽  
Author(s):  
V E Ellis ◽  
M F Scully ◽  
V V Kakkar
Keyword(s):  
Unfractionated Heparin ◽  
Antithrombin Iii ◽  
Binding Affinities ◽  
Peak Acceleration ◽  
First Order ◽  
High Affinity ◽  
Heparin Concentration ◽  
Factor Ii ◽  
Kinetics Of ◽  
Stimulation Of

The influence of increasing concentrations of heparin of different molecular mass (Mr) has been compared in potentiation of the rate of HCII:thrombin interaction and of ATIII:thrombin interaction under pseudo first order conditions. Unfractionated and fractionated heparin showed a concentration dependent ascending and descending limb of stimulation of the rate which was closely similar for both inhibitors. Unfractionated heparin and fractions of 16.5 KDa or less showed a peak acceleration of the rate of interaction of thrombin with both inhibitors at 0.3×10−6 heparin although the observed maximum rate at this peak decreased with fall in Mr. For both inhibitors two high Mr fractions (22KDa and 32KDa) showed peak stimulation at a lower heparin concentration (0.3×10−7M) and 1.5 to 2 fold greater increase in rate than that observed with unfractionated heparin. Under these conditions it could be calculated that the potency of a 32KDa fraction was 1200iu/mg with respect to UF heparin (150iu/mg). Three further pools were prepared and ATIII .high affinity fraction prepared by chromatography. Acceleration of rate of interaction was measured according to concentration and inverse plots gave values for apparent Kd amd maximal rate.These results suggest that differences in the profiles of stimulation by high Mr fractions to those of lower Mr are related to higher binding affinities for the inhibitor permitting maximal binding of heparin before the descending part of the slope due to saturation of thrombin (according to the template hypothesis). Although close similarity was found between heparin stimulation of HCII and ATIII, potentiation of HCII inhibitory activity differed in that it was reversed by lower ionic strength and was not reversed by a heparin pentasaccharide with high affinity for ATIII.

Bindings of NO, CO, and O2 to multifunctional globin type dehaloperoxidase follow the ‘sliding scale rule’

2017 ◽  
Vol 474 (20) ◽  
pp. 3485-3498 ◽  
Author(s):  
Gang Wu ◽  
Jing Zhao ◽  
Stefan Franzen ◽  
Ah-Lim Tsai
Keyword(s):  
Oxygen Carrier ◽  
Sperm Whale ◽  
Dissociation Rate ◽  
Heme Iron ◽  
Binding Affinities ◽  
Ligand Selectivity ◽  
Sliding Scale ◽  
One Step ◽  
Sensor Proteins ◽  
Kinetics Of

Dehaloperoxidase–hemoglobin (DHP), a multifunctional globin protein, not only functions as an oxygen carrier as typical globins such as myoglobin and hemoglobin, but also as a peroxidase, a mono- and dioxygenase, peroxygenase, and an oxidase. Kinetics of DHP binding to NO, CO, and O2 were characterized for wild-type DHP A and B and the H55D and H55V DHP A mutants using stopped-flow methods. All three gaseous ligands bind to DHP significantly more weakly than sperm whale myoglobin (SWMb). Both CO and NO bind to DHP in a one-step process to form a stable six-coordinate complex. Multiple-step NO binding is not observed in DHP, which is similar to observations in SWMb, but in contrast with many heme sensor proteins. The weak affinity of DHP for O2 is mainly due to a fast O2 dissociation rate, in accordance with a longer εN–Fe distance between the heme iron and distal histidine in DHP than that in Mb, and an open-distal pocket that permits ligand escape. Binding affinities in DHP show the same 3–4 orders separation between the pairs NO/CO and CO/O2, consistent with the ‘sliding scale rule’ hypothesis. Strong gaseous ligand discrimination by DHP is very different from that observed in typical peroxidases, which show poor gaseous ligand selectivity, correlating with a neutral proximal imidazole ligand rather than an imidazolate. The present study provides useful insights into the rationale for DHP to function both as mono-oxygenase and oxidase, and is the first example of a globin peroxidase shown to follow the ‘sliding scale rule’ hypothesis in gaseous ligand discrimination.

Single-Molecule Kinetics of Two-Step Divalent Cation Chelation

2010 ◽  
Vol 49 (30) ◽  
pp. 5085-5090 ◽  
Author(s):  
Anne F. Hammerstein ◽  
Seong-Ho Shin ◽  
Hagan Bayley
Keyword(s):  
Single Molecule ◽  
Divalent Cation ◽  
Kinetics Of

scholarly journals Nebulin binding impedes mutant desmin filament assembly

2013 ◽  
Vol 24 (12) ◽  
pp. 1918-1932 ◽  
Author(s):  
Laura K. Baker ◽  
David C. Gillis ◽  
Sarika Sharma ◽  
Andy Ambrus ◽  
Harald Herrmann ◽  
...  
Keyword(s):  
Striated Muscle ◽  
Actin Binding ◽  
Binding Affinities ◽  
Wild Type ◽  
Filament Assembly ◽  
Assembly Kinetics ◽  
Molecular Etiology ◽  
Filament Protein ◽  
Kinetics Of

Desmin intermediate filaments (DIFs) form an intricate meshwork that organizes myofibers within striated muscle cells. The mechanisms that regulate the association of desmin to sarcomeres and their role in desminopathy are incompletely understood. Here we compare the effect nebulin binding has on the assembly kinetics of desmin and three desminopathy-causing mutant desmin variants carrying mutations in the head, rod, or tail domains of desmin (S46F, E245D, and T453I). These mutants were chosen because the mutated residues are located within the nebulin-binding regions of desmin. We discovered that, although nebulin M160–164 bound to both desmin tetrameric complexes and mature filaments, all three mutants exhibited significantly delayed filament assembly kinetics when bound to nebulin. Correspondingly, all three mutants displayed enhanced binding affinities and capacities for nebulin relative to wild-type desmin. Electron micrographs showed that nebulin associates with elongated normal and mutant DIFs assembled in vitro. Moreover, we measured significantly delayed dynamics for the mutant desmin E245D relative to wild-type desmin in fluorescence recovery after photobleaching in live-cell imaging experiments. We propose a mechanism by which mutant desmin slows desmin remodeling in myocytes by retaining nebulin near the Z-discs. On the basis of these data, we suggest that for some filament-forming desmin mutants, the molecular etiology of desminopathy results from subtle deficiencies in their association with nebulin, a major actin-binding filament protein of striated muscle.

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