Hydrophobic collapse in multidomain protein folding - PubMed (original) (raw)
. 2004 Sep 10;305(5690):1605-9.
doi: 10.1126/science.1101176.
Affiliations
- PMID: 15361621
- DOI: 10.1126/science.1101176
Hydrophobic collapse in multidomain protein folding
Ruhong Zhou et al. Science. 2004.
Abstract
We performed molecular dynamics simulations of the collapse of a two-domain protein, the BphC enzyme, into a globular structure to examine how water molecules mediate hydrophobic collapse of proteins. In the interdomain region, liquid water persists with a density 10 to 15% lower than in the bulk, even at small domain separations. Water depletion and hydrophobic collapse occur on a nanosecond time scale, which is two orders of magnitude slower than that found in the collapse of idealized paraffin-like plates. When the electrostatic protein-water forces are turned off, a dewetting transition occurs in the interdomain region and the collapse speeds up by more than an order of magnitude. When attractive van der Waals forces are turned off as well, the dewetting in the interdomain region is more profound, and the collapse is even faster.
Similar articles
- Drying and hydrophobic collapse of paraffin plates.
Huang X, Zhou R, Berne BJ. Huang X, et al. J Phys Chem B. 2005 Mar 3;109(8):3546-52. doi: 10.1021/jp045520l. J Phys Chem B. 2005. PMID: 16851392 - Dynamics of water confined in the interdomain region of a multidomain protein.
Hua L, Huang X, Zhou R, Berne BJ. Hua L, et al. J Phys Chem B. 2006 Mar 2;110(8):3704-11. doi: 10.1021/jp055399y. J Phys Chem B. 2006. PMID: 16494427 - Observation of a dewetting transition in the collapse of the melittin tetramer.
Liu P, Huang X, Zhou R, Berne BJ. Liu P, et al. Nature. 2005 Sep 1;437(7055):159-62. doi: 10.1038/nature03926. Nature. 2005. PMID: 16136146 - Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations?
Hub JS, Grubmüller H, de Groot BL. Hub JS, et al. Handb Exp Pharmacol. 2009;(190):57-76. doi: 10.1007/978-3-540-79885-9_3. Handb Exp Pharmacol. 2009. PMID: 19096772 Review. - The model of hydrophobic attraction in the framework of classical DLVO forces.
Mishchuk NA. Mishchuk NA. Adv Colloid Interface Sci. 2011 Oct 14;168(1-2):149-66. doi: 10.1016/j.cis.2011.06.003. Epub 2011 Jun 23. Adv Colloid Interface Sci. 2011. PMID: 21752345 Review.
Cited by
- Electron videography of a lipid-protein tango.
Smith JW, Carnevale LN, Das A, Chen Q. Smith JW, et al. Sci Adv. 2024 Apr 19;10(16):eadk0217. doi: 10.1126/sciadv.adk0217. Epub 2024 Apr 17. Sci Adv. 2024. PMID: 38630809 Free PMC article. - Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder.
Villard J, Bircher MP, Rothlisberger U. Villard J, et al. Chem Sci. 2024 Feb 15;15(12):4434-4451. doi: 10.1039/d3sc05828j. eCollection 2024 Mar 20. Chem Sci. 2024. PMID: 38516095 Free PMC article. - Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment.
Bharmoria P, Tietze AA, Mondal D, Kang TS, Kumar A, Freire MG. Bharmoria P, et al. Chem Rev. 2024 Mar 27;124(6):3037-3084. doi: 10.1021/acs.chemrev.3c00551. Epub 2024 Mar 4. Chem Rev. 2024. PMID: 38437627 Free PMC article. Review. - APP-C31: An Intracellular Promoter of Both Metal-Free and Metal-Bound Amyloid-β40 Aggregation and Toxicity in Alzheimer's Disease.
Nam E, Lin Y, Park J, Do H, Han J, Jeong B, Park S, Lee DY, Kim M, Han J, Baik MH, Lee YH, Lim MH. Nam E, et al. Adv Sci (Weinh). 2024 Jan;11(4):e2307182. doi: 10.1002/advs.202307182. Epub 2023 Nov 10. Adv Sci (Weinh). 2024. PMID: 37949680 Free PMC article. - Solvation thermodynamics from cavity shapes of amino acids.
Azizi K, Laio A, Hassanali A. Azizi K, et al. PNAS Nexus. 2023 Jul 26;2(8):pgad239. doi: 10.1093/pnasnexus/pgad239. eCollection 2023 Aug. PNAS Nexus. 2023. PMID: 37545648 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources