Simulation of diffusion time of small molecules in protein crystals

Structure
Silvano GeremiaLouise N Johnson

Abstract

A simple model for evaluation of diffusion times of small molecule into protein crystals has been developed, which takes into account the physical and chemical properties both of protein crystal and the diffusing molecules. The model also includes consideration of binding and the binding affinity of a ligand to the protein. The model has been validated by simulation of experimental set-ups of several examples found in the literature. These experiments cover a wide range of situations: from small to relatively large diffusing molecules, crystals having low, medium, or high protein density, and different size. The reproduced experiments include ligand exchange in protein crystals by soaking techniques. Despite the simplifying assumptions of the model, theoretical and experimental data are in agreement with available data, with experimental diffusion times ranging from a few seconds to several hours. The method has been used successfully for planning intermediate cryotrapping experiments in maltodextrin phosphorylase crystals.

References

Jan 1, 1976·Advances in Enzyme Regulation·F H BatzoldP Talalay
Jan 1, 1977·Annual Review of Biophysics and Bioengineering·M W Makinen, A L Fink
Mar 1, 1992·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·L N Johnson
May 17, 1973·Biochimica Et Biophysica Acta·J J BeintemaM Gruber
Feb 11, 1969·Biochimica Et Biophysica Acta·L A Sluyterman, M J de Graaf
Aug 1, 1994·Biophysical Journal·J Garcia de la TorreJ J Lopez Cascales
Sep 10, 2002·Journal of Molecular Biology·S GeremiaL N Johnson
Sep 1, 1994·Acta Crystallographica. Section D, Biological Crystallography·UNKNOWN Collaborative Computational Project, Number 4
Nov 13, 2004·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Kourosh MalekMarc-Olivier Coppens
Jan 20, 1997·Biotechnology and Bioengineering·D de BeerZ Lewandowski

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Citations

Dec 3, 2008·The Journal of Chemical Physics·Zhongqiao HuStanley I Sandler
Dec 6, 2014·Proceedings of the National Academy of Sciences of the United States of America·Wei Xia, Timothy A Springer
Jun 14, 2008·Biochemical and Biophysical Research Communications·Takayoshi KinoshitaIsao Nakanishi
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·Thomas Alcorn, Douglas H Juers
Jan 1, 2008·Archives of Biochemistry and Biophysics·Mara CampagnoloSilvano Geremia
Feb 11, 2015·Acta Crystallographica. Section D, Biological Crystallography·Takashi KawamuraNobuhisa Watanabe
Nov 4, 2016·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Folasade M OlajuyigbeSilvano Geremia
Jul 22, 2014·Scientific Reports·Ryuta MizutaniYoshio Suzuki
Jan 23, 2018·Journal of Physics D: Applied Physics·Vukica Šrajer, Marius Schmidt
Jul 30, 2018·Protein Science : a Publication of the Protein Society·Renee J AriasDouglas C Rees
Dec 4, 2015·The Journal of Biological Chemistry·Fu-Yang LinTimothy A Springer
Jan 30, 2018·Structural Dynamics·Rafael AbelaLuc Patthey
May 30, 2009·Journal of Computational Chemistry·Zhongqiao Hu, Jianwen Jiang
Jun 1, 2018·BMC Biology·Allen M Orville
Jan 14, 2017·Structural Dynamics·Christopher KupitzMarius Schmidt
Oct 3, 2020·Structure·Michael W Martynowycz, Tamir Gonen
Feb 13, 2021·International Journal of Molecular Sciences·Ilona Turek, Helen Irving
Apr 8, 2021·Acta Crystallographica. Section D, Structural Biology·Janina SprengerLeila Lo Leggio
Jan 18, 2008·The Journal of Physical Chemistry. B·Kourosh Malek, Marc-Olivier Coppens
Mar 6, 2008·Langmuir : the ACS Journal of Surfaces and Colloids·Zhongqiao Hu, Jianwen Jiang
Jun 22, 2021·Annual Review of Biochemistry·Xuelang MuTamir Gonen
Oct 24, 2018·The Journal of Physical Chemistry. B·Kazuo Mori, Bernd Kuhn

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