Hydrodynamic study of flexibility in immunoglobulin igG1 using Brownian dynamics and the Monte Carlo simulations of a simple model

Díaz, Francisco Antonio González; Iniesta, A.; Torre, José Garcı́a de la

doi:10.1002/bip.360300507

Cited by 15 publications

(14 citation statements)

References 25 publications

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“…The Brownian dynamics simulation of segmentally flexible macromolecules has been used previously by our group. [44][45][46][47][48] We use a simulation procedure based on the algorithm of Ermak and McCammon, 49 with a modification proposed by Iniesta and García de la Torre. 50 Each step is taken twice in a predictor-corrector manner and the position of the beads after the time step is obtained from the previous position.…”

Section: Model and Methodsmentioning

confidence: 99%

Influence of Field Strength and Flexibility on the Transient Electric Birefringence of Segmentally Flexible Macromolecules

2002

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The influence of field strength and flexibility on the transient electric birefringence (TEB) of segmentally flexible macromolecules is studied using a trumbbell with induced and permanent dipoles as a model. According to TEB experiments, the birefringence reaches a steady state after the application of an electric field, a situation which is simulated using a Monte Carlo method. Once the field is removed, relaxation is studied by simulating the Brownian dynamics of the system. Special care has been taken in the statistical quality of the data and the procedure for multiexponential fitting of the decay profiles to obtain the amplitudes and relaxation times. The results are compared with different treatments with occasional agreement and disagreement. The range of applicability of the method proposed by Allison and Nambi (Macromolecules 1992, 25, 759) is discussed. We found that for bent molecules relaxation decay depends on the averaged conformation, flexibility, orientation mechanism, and field intensity. In addition, we show that TEB experiments could be sufficient to characterize the averaged angle of a segmentally flexible macromolecule and its dispersion, mainly if the information concerning amplitudes and faster relaxation times is used.

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Section: Model and Methodsmentioning

confidence: 99%

Influence of Field Strength and Flexibility on the Transient Electric Birefringence of Segmentally Flexible Macromolecules

2002

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“…On the contrary, binding of clusters' I-V epitopes to their respective mAb was affected only when neighboring overlapping epitopes were occupied first. Two remarkable exclusions were detected: IG-6 and IG- 16 antibodies were able to inhibit binding of the two ( 2) a) Reactivity for native IgG was considered to be 100% SpA -> findings seem to demonstrate the flexibility of entire Fc region and will be discussed in details later. The flexibility of some Fc epitopes was confirmed by sandwich assay data.…”

Section: Conformational Changes Of Igg Fc Region Epitopesmentioning

confidence: 97%

“…The antigens were diluted in 50 mM NaHC03 pH 9.5 to 10 ¿¿g/ml and pipetted into 96 well microtiter plates, 0.1 ml per well. Following [16][17][18] h at 4°C wells were blocked with 1% BSA-PBS (0.15 ml/well, 0.5 h, room temperature). 0.1 ml of culture media, containing mAb or purified mAb (10 ,ug/ml) were incubated with each antigen for 1 h at room temperature.…”

Section: Specificity Analysesmentioning

confidence: 99%

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Immunochemical Study of Human Immunoglobulin G Fc Region

Girkontaitė¹,

Leckiene²,

Mauricas³

1996

Cancer Biotherapy and Radiopharmaceuticals

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Fifteen murine monoclonal antibodies (mAb) were produced that reacted with conformational epitopes present on the Fc portion of all human IgG subclasses (PAN-Fc). Inhibition and sandwich ELISA were used to elucidate overlapping and distinct epitopes. The epitopes were aligned to form a continuous "chain" of overlapping determinants from the CH2-CH3 interface to the direction of hinge. The five more hinge-proximal epitopes demonstrated high lability both in competitive and sandwich assays, being completely or partially destroyed when any of these 15 other mAb bound the IgG first. Heat-inactivation of IgG caused full disruption of these epitopes. In contrast, epitopes situated at the opposite distal of the "chain" were more stable and mAb binding could only be affected by occupying an overlapping epitope. Under heat-inactivation these epitopes were affected, but not completely destroyed. Human IgG class anti-DNA autoantibodies were bound to insolubilized dsDNA and their reaction with PAN-Fc mAb was studied. mAb titration plots on IgG and dsDNA-IgG were compared. Five epitopes proved to be altered by antigen (dsDNA) binding. Two of these were the labile hinge-proximal epitopes and the other three were situated near the CH2-CH3 interface. Cross-reactivity of mAb with xenogeneic IgG was also studied. An "epitope map" of the crystallographic model of human IgG Fc portion drawn was based on these experimental data and printed matter, concerning the location of subclass-specific amino acids and homology regions of human and animal IgG.

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“…58,[60][61][62][63][64] We use a simulation procedure based on Ermak and McCammon's algorithm, 65 with a modification proposed by Iniesta and García de la Torre. 58,[60][61][62][63][64] We use a simulation procedure based on Ermak and McCammon's algorithm, 65 with a modification proposed by Iniesta and García de la Torre.…”

Section: B Brownian Dynamics Simulationmentioning

confidence: 99%

Transient electric birefringence of wormlike macromolecules in electric fields of arbitrary strength: A computer simulation study

Pérez‐Sánchez¹,

Torre²,

Baños³

2005

The Journal of Chemical Physics

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We have studied the birefringence decay of linear models of macromolecules for two different types of flexibility, the broken-rod chain and the wormlike chain, using a computer simulation of a transient electric birefringence experiment. We have paid particular attention to the influence of the intensity of the orienting field, including two orienting mechanisms, the induced dipole, and the permanent dipole. We have compared wormlike and broken-rod models of the same radius of gyration, finding that they present a different decay curve under the influence of the same intensity of the field. We have seen that these differences are due to the faster relaxation times (smaller in the wormlike chain model) and amplitudes, because, regardless of the type of flexibility, the overall size of a molecule (measured by the radius of gyration) essentially determines the longest relaxation time. We have also analyzed how the relaxation process is affected by the degree of flexibility, the orientation mechanisms, and the intensity of the field. Studying a different aspect, we have paid attention to the deformation of a molecule in a transient electric birefringence experiment as a source of information. In this work we have developed equations to characterize this deformation in terms of one of the components of the gyration tensor, if a dynamic light scattering experiment under the influence of an electric field could be performed. To develop this work we have simulated the Brownian dynamics of the different models, relaxing after the removal of an orienting external electric field of arbitrary strength. A comparison with other methods such a the rigid body treatment or the correlation analysis of Brownian trajectories has also been included. We have seen that differences between the two Brownian dynamics methods are small and that the rigid-body treatment is only an acceptable approximation to obtain the longest relaxation time.

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Hydrodynamic study of flexibility in immunoglobulin igG1 using Brownian dynamics and the Monte Carlo simulations of a simple model

Cited by 15 publications

References 25 publications

Influence of Field Strength and Flexibility on the Transient Electric Birefringence of Segmentally Flexible Macromolecules

Influence of Field Strength and Flexibility on the Transient Electric Birefringence of Segmentally Flexible Macromolecules

Immunochemical Study of Human Immunoglobulin G Fc Region

Transient electric birefringence of wormlike macromolecules in electric fields of arbitrary strength: A computer simulation study

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