Polarizability and Kerr constant of proteins by boundary element methods

Aragón, Sergio R.; Hahn, David K.

doi:10.1016/j.colsurfb.2006.11.027

Cited by 5 publications

(3 citation statements)

References 21 publications

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“…These two tensors were computed via precise boundary element methods given for the molecular structures of TEGDE in dilute water and in the neat liquid. The program POL was used to compute the classical polarizability tensor for a dielectric constant of 2.054, which corresponds to the optical index of refraction of 1.4332. POL solves the surface integral equation formulation of the electrostatic problem as given by Senior using a surface triangulation of TEGDE produced by Connolly’s program MSROLL.…”

Section: Resultsmentioning

confidence: 99%

Orientational and Translational Dynamics of Polyether/Water Solutions

et al. 2010

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Optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments and pulsed field-gradient spin-echo NMR (PFGSE-NMR) experiments were performed to measure the rotational and translational diffusion constants of a polyether, tetraethylene glycol dimethyl ether (TEGDE), in binary mixtures with water over concentrations ranging from pure TEGDE to approaching infinite dilution. In addition, hydrodynamic calculations of the rotational and translational diffusion constants for several rigid TEGDE conformations in the neat liquid and in the infinitely dilute solution were performed to supplement the experimental data. The rotational relaxation data follow the Debye-Stokes-Einstein (DSE) equation within experimental error over the entire water concentration range. The agreement with the DSE equation indicates that there is no significant structural change of the polyether as the water content is changed. In contrast to the rotational dynamics, the translational diffusion data show a distinct deviation from Stokes-Einstein (SE) behavior. As the water content of the mixture is reduced, the translational diffusion rate decreases less rapidly than the increase in viscosity alone predicts until the water/TEGDE mole ratio of 7:1 is reached. Upon further reduction of water content, the translational diffusion tracks the viscosity. Comparison of the translational data with the rotational data and the hydrodynamic computations shows that the translational dynamics cannot be explained by a molecular shape change and that the low water fraction solutions are the ones that deviate from hydrodynamic behavior. A conjecture is presented as a possible explanation for the different behaviors of the rotational and translational dynamics.

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Section: Resultsmentioning

confidence: 99%

Orientational and Translational Dynamics of Polyether/Water Solutions

et al. 2010

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“…At first glance it may seem that the two values imply a range of experimental error but theoretically the value measured by fluorescence [53], which samples all the eigenvalues of the diffusion tensor, may be different from the depolarized dynamic light scattering value [54]. If the rotational diffusion tensor is diagonalized in the same principal axes system as the polarizability of lysozyme, then the birefringence value will not depend on the faster “axial” eigenvalue, called Dr 2 in Table V.. Aragon [55] has also implemented a very accurate BE method (POL) for the solution of the electrostatics equations for the determination of classical polarizabilities. Using the program POL, with the identical triangulation input file used for the hydrodynamics, it can be shown that both the polarizability and rotational diffusion tensor are diagonalized in essentially the same principal axes – despite its irregular shape, lysozyme is optically a symmetric top!…”

Section: Combination Of Molecular Dynamics Simulation and Hydrodynmentioning

confidence: 99%

Recent advances in macromolecular hydrodynamic modeling

Aragón¹

2011

Methods

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The modern implementation of the boundary element method (S.R. Aragon, J. Comput. Chem. 25(2004)1191–12055) has ushered unprecedented accuracy and precision for the solution of the Stokes equations of hydrodynamics with stick boundary conditions. This article begins by reviewing computations with the program BEST of smooth surface objects such as ellipsoids, the dumbbell, and cylinders that demonstrate that the numerical solution of the integral equation formulation of hydrodynamics yields very high precision and accuracy. When BEST is used for macromolecular computations, the limiting factor becomes the definition of the molecular hydrodynamic surface and the implied effective solvation of the molecular surface. Studies on 49 different proteins, ranging in molecular weight from 9 to over 400 kDa, have shown that a model using a 1.1 A thick hydration layer describes all protein transport properties very well for the overwhelming majority of them. In addition, this data implies that the crystal structure is an excellent representation of the average solution structure for most of them. In order to investigate the origin of a handful of significant discrepancies in some multimeric proteins (over −20% observed in the intrinsic viscosity), the technique of Molecular Dynamics simulation (MD) has been incorporated into the research program. A preliminary study of dimeric α-chymotrypsin using approximate implicit water MD is presented. In addition I describe the successful validation of modern protein force fields, ff03 and ff99SB, for the accurate computation of solution structure in explicit water simulation by comparison of trajectory ensemble average computed transport properties with experimental measurements. This work includes small proteins such as lysozyme, ribonuclease and ubiquitin using trajectories around 10 ns duration. We have also studied a 150 kDa flexible monoclonal IgG antibody, trastuzumab, with multiple independent trajectories encompassing over 320 ns of simulation. The close agreement within experimental error of the computed and measured properties allows us to conclude that MD does produce structures typical of those in solution, and that flexible molecules can be properly described using the method of ensemble averaging over a trajectory. We review similar work on the study of a transfer RNA molecule and DNA oligomers that demonstrate that within 3% a simple uniform hydration model 1.1 A thick provides agreement with experiment for these nucleic acids. In the case of linear oligomers, the precision can be improved close to 1% by a non-uniform hydration model that hydrates mainly in the DNA grooves, in agreement with high resolution x-ray diffraction. We conclude with a vista on planned improvements for the BEST program to decrease its memory requirements and increase its speed without sacrificing accuracy.

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“…Physiological pH is around 7.4. The refractive index of proteins has been suggested to be around 1.45, but it is known to be dependent size, shape, and environment . Proteins also have chiral properties that may be exploited in enantioselective trapping and manipulation. , …”

Section: Physical Considerationsmentioning

confidence: 99%

Future Prospects for Biomolecular Trapping with Nanostructured Metals

Gordon

2022

ACS Photonics

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Optical trapping with nanostructured metals has allowed for label-free tether-free analysis of single proteins (and other biomolecules) and their interactions with detector-limited time resolution and a duration extending to hours. This Perspective will provide a brief historical introduction, discuss recent advances to augment the technique with other approaches, and discuss the potential for improved performance and widescale adoption in a range of applications from biologics and drug discovery to fundamental biophysical studies.

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Polarizability and Kerr constant of proteins by boundary element methods

Cited by 5 publications

References 21 publications

Orientational and Translational Dynamics of Polyether/Water Solutions

Orientational and Translational Dynamics of Polyether/Water Solutions

Recent advances in macromolecular hydrodynamic modeling

Future Prospects for Biomolecular Trapping with Nanostructured Metals

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