ArticleBiophysical journal2006
Precise boundary element computation of protein transport properties: Diffusion tensors, specific volume, and hydration.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed.
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- Computational simulations of bispecific T cell engagers by a multiscale model.Biophysical journal · 2024Article
- Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.Nature communications · 2023Article
- How does the same ligand activate signaling of different receptors in TNFR superfamily: a computational study.Journal of cell communication and signaling · 2023Article
- Revisiting macromolecular hydration with HullRadSAS.European biophysics journal : EBJ · 2023Article
- Dissecting the general mechanisms of protein cage self-assembly by coarse-grained simulations.Protein science : a publication of the Protein Society · 2023Article
- Understanding the functional role of membrane confinements in TNF-mediated signaling by multiscale simulations.Communications biology · 2022Article
- Multiphysics Modeling and Simulation of Subcutaneous Injection and Absorption of Biotherapeutics: Model Development.Pharmaceutical research · 2021Article
- A multiscale study on the mechanisms of spatial organization in ligand-receptor interactions on cell surfaces.Computational and structural biotechnology journal · 2021Article
- Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association.Biomolecules · 2020Article
- GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules.Biophysical journal · 2018Article
- HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties.Biophysical journal · 2018Article
- A Multiscale Computational Model for Simulating the Kinetics of Protein Complex Assembly.Methods in molecular biology (Clifton, N.J.) · 2018Article
- General principles of binding between cell surface receptors and multi-specific ligands: A computational study.PLoS computational biology · 2017Article
- Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.Scientific reports · 2017Article
- The unusual internal motion of the villin headpiece subdomain.Protein science : a publication of the Protein Society · 2016Article
- Linking 3D and 2D binding kinetics of membrane proteins by multiscale simulations.Protein science : a publication of the Protein Society · 2014Article
- Hard sphere-like glass transition in eye lens α-crystallin solutions.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Elucidating molecular motion through structural and dynamic filters of energy-minimized conformer ensembles.The journal of physical chemistry. B · 2014Article
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2 authors.
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Abstract
A precise boundary element method for the computation of hydrodynamic properties has been applied to the study of a large suite of 41 soluble proteins ranging from 6.5 to 377 kDa in molecular mass. A hydrodynamic model consisting of a rigid protein excluded volume, obtained from crystallographic coordinates, surrounded by a uniform hydration thickness has been found to yield properties in excellent agreement with experiment. The hydration thickness was determined to be delta = 1.1 +/- 0.1 A. Using this value, standard deviations from experimental measurements are: 2% for the specific volume; 2% for the translational diffusion coefficient, and 6% for the rotational diffusion coefficient. These deviations are comparable to experimental errors in these properties. The precision of the boundary element method allows the unified description of all of these properties with a single hydration parameter, thus far not achieved with other methods. An approximate method for computing transport properties with a statistical precision of 1% or better (compared to 0.1-0.2% for the full computation) is also presented. We have also estimated the total amount of hydration water with a typical -9% deviation from experiment in the case of monomeric proteins. Both the water of hydration and the more precise translational diffusion data hint that some multimeric proteins may not have the same solution structure as that in the crystal because the deviations are systematic and larger than in the monomeric case. On the other hand, the data for monomeric proteins conclusively show that there is no difference in the protein structure going from the crystal into solution.
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