A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins

The Journal of Chemical Physics
Lucas Sawle, Kingshuk Ghosh

Abstract

A general formalism to compute configurational properties of proteins and other heteropolymers with an arbitrary sequence of charges and non-uniform excluded volume interaction is presented. A variational approach is utilized to predict average distance between any two monomers in the chain. The presented analytical model, for the first time, explicitly incorporates the role of sequence charge distribution to determine relative sizes between two sequences that vary not only in total charge composition but also in charge decoration (even when charge composition is fixed). Furthermore, the formalism is general enough to allow variation in excluded volume interactions between two monomers. Model predictions are benchmarked against the all-atom Monte Carlo studies of Das and Pappu [Proc. Natl. Acad. Sci. U. S. A. 110, 13392 (2013)] for 30 different synthetic sequences of polyampholytes. These sequences possess an equal number of glutamic acid (E) and lysine (K) residues but differ in the patterning within the sequence. Without any fit parameter, the model captures the strong sequence dependence of the simulated values of the radius of gyration with a correlation coefficient of R(2) = 0.9. The model is then applied to real proteins ...Continue Reading

References

Jan 1, 1991·Annual Review of Biochemistry·K A Dill, D Shortle
Jul 20, 1973·Science·C B Anfinsen
Oct 1, 1995·Protein Science : a Publication of the Protein Society·J K MyersJ M Scholtz
Jan 1, 1996·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·D Shortle
Sep 15, 1992·Physical Review. a·B Y Ha, D Thirumalai
Nov 1, 1994·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·A M Gutin, E I Shakhnovich
Jun 13, 1994·Physical Review Letters·E I Shakhnovich
Jan 22, 2002·Journal of Molecular Biology·D Perl, F X Schmid
Sep 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Srebrenka RobicSusan Marqusee
Jul 23, 2004·The Journal of Chemical Physics·M Muthukumar
Aug 18, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jonathan E KohnKevin W Plaxco
Aug 25, 2004·Proteins·Brian N DominyCharles L Brooks
Sep 11, 2007·Journal of the American Chemical Society·Kingshuk GhoshKen A Dill
Jan 28, 2009·Journal of the American Chemical Society·Kingshuk Ghosh, K A Dill
Mar 12, 2010·Journal of the American Chemical Society·Vincent A VoelzVijay S Pande
Apr 21, 2010·Proceedings of the National Academy of Sciences of the United States of America·Albert H MaoRohit V Pappu
Jan 1, 2009·Annual Reports in Computational Chemistry·Andreas Vitalis, Rohit V Pappu
Jul 20, 2010·Proceedings of the National Academy of Sciences of the United States of America·Sonja Müller-SpäthBenjamin Schuler
Nov 6, 2010·Macromolecules·Arindam Kundagrami, M Muthukumar
Apr 20, 2011·The International Journal of Biochemistry & Cell Biology·Vladimir N Uversky
Apr 26, 2011·Current Opinion in Structural Biology·Peter Tompa
Jul 5, 2011·Biophysical Journal·Lucas Sawle, Kingshuk Ghosh
Feb 22, 2012·Journal of the American Chemical Society·Kresten Lindorff-LarsenDavid E Shaw
Sep 18, 2012·Proceedings of the National Academy of Sciences of the United States of America·Hagen HofmannBenjamin Schuler
Sep 20, 2012·Trends in Biochemical Sciences·Peter Tompa
Dec 5, 2012·The Journal of Chemical Physics·Mark Rustad, Kingshuk Ghosh
Aug 1, 2013·Proceedings of the National Academy of Sciences of the United States of America·Rahul K Das, Rohit V Pappu
Sep 10, 2013·Journal of the American Chemical Society·Mikayel AznauryanBenjamin Schuler
Oct 5, 2013·The Journal of Chemical Physics·A DasS S Plotkin
Jan 18, 2014·Journal of Chemical Theory and Computation·James C SweetJesús A Izaguirre

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Citations

May 6, 2016·Annual Review of Biophysics·Benjamin SchulerDaniel Nettels
Aug 12, 2016·The Journal of Physical Chemistry. B·Kingshuk GhoshKen A Dill
Oct 4, 2016·Journal of the American Chemical Society·Srivastav RanganathanRanjith Padinhateeri
Nov 7, 2017·Molecular Biology and Evolution·Sergey V Venev, Konstantin B Zeldovich
Jan 19, 2018·Annual Review of Biophysics·Alex S Holehouse, Rohit V Pappu
Sep 16, 2018·Proceedings of the National Academy of Sciences of the United States of America·Gregory L DignonJeetain Mittal
Oct 29, 2017·Proceedings of the National Academy of Sciences of the United States of America·Kathryn P SherryDoug Barrick
Nov 12, 2019·Journal of Biomolecular Structure & Dynamics·Jing YangYongqi Huang
Mar 7, 2020·Soft Matter·Charles E Sing, Sarah L Perry
Nov 16, 2016·Physical Biology·Toshiko Ichiye
Apr 2, 2018·The Journal of Chemical Physics·Taylor Firman, Kingshuk Ghosh
Jan 8, 2020·Nucleic Acids Research·Qian LiZhuqing Zhang
Apr 6, 2019·Proceedings of the National Academy of Sciences of the United States of America·Scott P O DanielsenGlenn H Fredrickson
Jan 25, 2018·PLoS Computational Biology·Gregory L DignonJeetain Mittal
Feb 24, 2020·The Journal of Chemical Physics·Antonia StattAthanassios Z Panagiotopoulos
Aug 4, 2019·Protein Engineering, Design & Selection : PEDS·Megan C CohanRohit V Pappu
May 13, 2020·Proceedings of the National Academy of Sciences of the United States of America·Benjamin S SchusterJeetain Mittal
Sep 2, 2020·International Journal of Molecular Sciences·Greta BianchiStefania Brocca
Oct 21, 2020·Emerging Topics in Life Sciences·Erik W Martin, Alex S Holehouse
Dec 6, 2019·Current Opinion in Structural Biology·Robert B Best
Feb 6, 2021·Current Opinion in Structural Biology·Joan-Emma SheaJeetain Mittal
Feb 15, 2021·Biophysical Journal·Theodora Myrto PerdikariJeetain Mittal
Mar 8, 2020·Archives of Biochemistry and Biophysics·Andrea Soranno
Jun 28, 2018·Journal of Molecular Biology·Kiersten M RuffRohit V Pappu
May 16, 2018·Journal of Molecular Biology·Anuradha MittalRohit V Pappu
Feb 23, 2021·Biophysical Journal·Luke K DavisAnton Zilman
Apr 9, 2021·Methods : a Companion to Methods in Enzymology·Jhullian J AlstonAlex S Holehouse
Dec 25, 2019·Current Opinion in Structural Biology·Benjamin SchulerAndrea Sottini
May 13, 2021·Scientific Reports·Sonia T NicolaouJim Warwicker
Jul 15, 2021·The Journal of Physical Chemistry Letters·Samuel WohlWenwei Zheng
Jul 11, 2021·Journal of Computational Chemistry·Nicolas Frazee, Blake Mertz
Jul 6, 2021·Journal of Molecular Biology·Roy NassarKen A Dill
Jul 9, 2021·Biophysical Journal·Mohaddeseh PeyroMohammad R K Mofrad

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