Effects of macromolecular crowding agents on protein folding in vitro and in silico

Biophysics Reviews
Alexander ChristiansenPernilla Wittung-Stafshede

Abstract

Proteins fold and function inside cells which are environments very different from that of dilute buffer solutions most often used in traditional experiments. The crowded milieu results in excluded-volume effects, increased bulk viscosity and amplified chances for inter-molecular interactions. These environmental factors have not been accounted for in most mechanistic studies of protein folding executed during the last decades. The question thus arises as to how these effects-present when polypeptides normally fold in vivo-modulate protein biophysics. To address excluded volume effects, we use synthetic macromolecular crowding agents, which take up significant volume but do not interact with proteins, in combination with strategically selected proteins and a range of equilibrium and time-resolved biophysical (spectroscopic and computational) methods. In this review, we describe key observations on macromolecular crowding effects on protein stability, folding and structure drawn from combined in vitro and in silico studies. As expected based on Minton's early predictions, many proteins (apoflavodoxin, VlsE, cytochrome c, and S16) became more thermodynamically stable (magnitude depends inversely on protein stability in buffer) an...Continue Reading

References

Oct 15, 1991·Physical Review. a·M R Shaw, D Thirumalai
Jun 8, 2001·Annual Review of Biochemistry·J Frydman
Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Matthew M DedmonGary J Pielak
Nov 7, 2002·Advances in Protein Chemistry·Ian S MillettKevin W Plaxco
Dec 19, 2002·Biophysical Chemistry·Youxing Qu, D W Bolen
Feb 19, 2003·Journal of Molecular Biology·Kenji SasaharaAllen P Minton
Dec 24, 2003·Protein Science : a Publication of the Protein Society·Nobuhiko TokurikiTetsuya Yomo
Jan 8, 2004·EMBO Reports·Germán RivasJudith Herzfeld
Mar 23, 2005·Proceedings of the National Academy of Sciences of the United States of America·Margaret S CheungD Thirumalai
Mar 23, 2006·Journal of the American Chemical Society·Xuanjun AiWing-Yiu Choy
Apr 14, 2006·European Biophysics Journal : EBJ·Daniel LavaletteAntonie J Visser
Jun 15, 2007·Archives of Biochemistry and Biophysics·Svetlana LutsenkoUjwal Shinde
Jun 15, 2007·Nucleic Acids Research·Yoshiharu SasakiNaoki Sugimoto
Oct 9, 2007·FEBS Letters·Michael PerhamPernilla Wittung-Stafshede
Nov 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Loren StaggPernilla Wittung-Stafshede
Jun 25, 2008·Annual Review of Biophysics·Huan-Xiang ZhouAllen P Minton
Aug 14, 2008·Proceedings of the National Academy of Sciences of the United States of America·Dirar HomouzPernilla Wittung-Stafshede
Jan 15, 2009·Journal of the American Chemical Society·Conggang Li, Gary J Pielak
Jan 27, 2009·Biophysical Journal·Dirar HomouzMargaret S Cheung
Apr 1, 2009·International Journal of Molecular Sciences·Antonios SamiotakisMargaret S Cheung
Apr 11, 2009·Langmuir : the ACS Journal of Surfaces and Colloids·S Rajendra KulothunganRaghavan Varadarajan
May 2, 2009·Proteins·Jyotica BatraHuan-Xiang Zhou
Jul 7, 2009·Journal of Molecular Biology·Dirar HomouzMargaret S Cheung
Aug 18, 2009·Journal of Molecular Biology·Smita MukherjeeFeng Gai
Nov 17, 2009·Journal of Molecular Biology·Loren StaggPernilla Wittung-Stafshede
Nov 26, 2009·Biochimica Et Biophysica Acta·Irina Pozdnyakova, Pernilla Wittung-Stafshede
Mar 12, 2010·PLoS Computational Biology·Sean R McGuffee, Adrian H Elcock
Jun 22, 2010·Journal of the American Chemical Society·Yaqiang WangGary J Pielak
Jul 29, 2010·Journal of the American Chemical Society·Jiang Hong, Lila M Gierasch
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·C Le CoeurS Longeville
Oct 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Apratim DharMargaret S Cheung
Dec 24, 2010·Journal of the American Chemical Society·Loren StaggPernilla Wittung-Stafshede
Mar 8, 2011·Biochemistry·Ximena AguilarPernilla Wittung-Stafshede

❮ Previous
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Citations

Aug 16, 2017·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Mimi GaoRoland Winter
Aug 2, 2018·Cellular and Molecular Life Sciences : CMLS·Alexander V FoninVladimir N Uversky
Aug 30, 2019·European Biophysics Journal : EBJ·Ksenia MaximovaJoanna Trylska
Sep 12, 2020·Organic & Biomolecular Chemistry·Saurja DasGupta
Aug 28, 2019·International Journal of Molecular Sciences·Lorea VelascoArturo Muga
May 14, 2020·European Biophysics Journal : EBJ·Sanjib K MukherjeePramit K Chowdhury
Oct 8, 2016·RNA Biology·Iain A SawyerMiroslav Dundr
Jan 1, 2018·Quarterly Reviews of Biophysics·Candan Ariöz, Pernilla Wittung-Stafshede
Feb 5, 2014·FEBS Letters·Alexander Christiansen, Pernilla Wittung-Stafshede
Feb 9, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Alexander V FoninKonstantin K Turoverov
Feb 9, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Pedro P González-PérezSalomón J Alas
Jul 30, 2016·PLoS Computational Biology·Michela Candotti, Modesto Orozco
Jun 4, 2020·Proceedings of the National Academy of Sciences of the United States of America·Franziska ZoselBenjamin Schuler
Oct 2, 2019·Frontiers in Molecular Biosciences·Natalia OstrowskaJoanna Trylska
Feb 21, 2018·Journal of Materials Chemistry. B, Materials for Biology and Medicine·J Madeira do OG Mantovani
Feb 10, 2019·Applied Biochemistry and Biotechnology·Sumra ShahidAsimul Islam
Nov 20, 2018·Biomaterials·Valeria GraceffaDimitrios I Zeugolis
Nov 15, 2020·Nature Communications·Birgit Köhn, Michael Kovermann
Nov 11, 2020·The Journal of Chemical Physics·Mark P TaylorRyogo Suzuki
Jul 18, 2020·International Journal of Biological Macromolecules·Andrea De PieriDimitrios I Zeugolis
Apr 17, 2021·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Shawn Yoshida, Lydia Kisley
May 1, 2021·Cells·Sergio Garnica-GalvezDimitrios I Zeugolis
Jun 23, 2021·Journal of Fluorescence·Gufran Ahmed Siddiqui, Aabgeena Naeem
Jul 24, 2021·Biochimica Et Biophysica Acta. Proteins and Proteomics·Harshita Rastogi, Pramit K Chowdhury
Nov 26, 2019·The Journal of Physical Chemistry Letters·David GomezStefan Klumpp
Jun 22, 2013·The Journal of Physical Chemistry. B·Luca Larini, Joan-Emma Shea
Mar 29, 2014·Biochemistry·Jörgen Adén, Pernilla Wittung-Stafshede
Feb 5, 2019·Biochemistry·Shuntaro TakahashiNaoki Sugimoto
Aug 13, 2015·The Journal of Physical Chemistry Letters·Mary Rose HilaireFeng Gai
Nov 14, 2020·ACS Synthetic Biology·Bhanu P JagilinkiVikas Nanda
Aug 31, 2021·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Subhasree GhoshN Prakash Prabhu
Dec 17, 2021·Journal of Materials Chemistry. B, Materials for Biology and Medicine·Manish GorePrajakta Dandekar

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