Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin

Protein Science : a Publication of the Protein Society
T LazaridisM Karplus

Abstract

Molecular dynamics simulations in solution are performed for a rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus (RdPf) and one from the mesophilic organism Desulfovibrio vulgaris (RdDv). The two proteins are simulated at four temperatures: 300 K, 373 K, 473 K (two sets), and 500 K; the various simulations extended from 200 ps to 1,020 ps. At room temperature, the two proteins are stable, remain close to the crystal structure, and exhibit similar dynamic behavior; the RMS residue fluctuations are slightly smaller in the hyperthermophilic protein. An analysis of the average energy contributions in the two proteins is made; the results suggest that the intraprotein energy stabilizes RdPf relative to RdDv. At 373 K, the mesophilic protein unfolds rapidly (it begins to unfold at 300 ps), whereas the hyperthermophilic does not unfold over the simulation of 600 ps. This is in accord with the expected stability of the two proteins. At 473 K, where both proteins are expected to be unstable, unfolding behavior is observed within 200 ps and the mesophilic protein unfolds faster than the hyperthermophilic one. At 500 K, both proteins unfold; the hyperthermophilic protein does so faster than the mesophilic protein. The unf...Continue Reading

References

Jul 5, 1979·Journal of Molecular Biology·K D WatenpaughL H Jensen
Dec 11, 1979·Biochemistry·P ArgosJ D Tratschin
Nov 1, 1992·Protein Science : a Publication of the Protein Society·P R BlakeM F Summers
Jun 5, 1992·Journal of Molecular Biology·E M MeieringA R Fersht
Feb 1, 1992·Acta Crystallographica. Section B, Structural Science·Z DauterK S Wilson
Dec 13, 1991·Science·H FrauenfelderP G Wolynes
Jan 20, 1991·Journal of Molecular Biology·E T AdmanL H Jensen
Feb 1, 1990·Biophysical Journal·G N Phillips
Aug 1, 1990·FEBS Letters·R Jaenicke, P Závodszky
Feb 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·J SmithM Karplus
Jan 1, 1989·Annual Review of Biochemistry·T Alber
Aug 1, 1986·Molecular & General Genetics : MGG·M MatsumuraS Aiba
Oct 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·B W MatthewsW J Becktel
Jul 1, 1965·Proceedings of the National Academy of Sciences of the United States of America·W Lovenberg, B E Sobel
Dec 1, 1982·The Biochemical Journal·R M DanielM P Curran
Aug 15, 1983·Journal of Molecular Biology·M DelepierreF M Poulsen
Jan 1, 1981·Annual Review of Biophysics and Bioengineering·R Jaenicke
Oct 1, 1980·Biophysical Journal·K WüthrichW Braun
Apr 15, 1980·Journal of Molecular Biology·K D WatenpaughL H Jensen
Dec 1, 1993·Protein Science : a Publication of the Protein Society·G I MakhatadzeP L Privalov
Oct 6, 1995·Journal of Molecular Biology·A Caflisch, M Karplus

❮ Previous
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Citations

Jun 14, 2005·Il Farmaco·Roberto ArtaliAntonio Del Pra
Apr 28, 2004·Biophysical Journal·Luca MaraglianoGiovanni Ciccotti
Mar 14, 2003·Journal of Molecular Biology·Patrick L WintrodeWilliam A Goddard
Feb 24, 2001·Trends in Biotechnology·G Carrea, G Colombo
Mar 21, 2003·Biophysical Chemistry·Themis Lazaridis, Martin Karplus
Jan 5, 2002·Journal of Molecular Graphics & Modelling·J GsponerA Caflisch
Feb 6, 2013·Physical Chemistry Chemical Physics : PCCP·O RahamanF Sterpone
Dec 26, 2001·Proceedings of the National Academy of Sciences of the United States of America·Dongping ZhongAhmed H Zewail
May 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·Linghao ZhongKara L Bren
Jan 20, 2010·Protein Engineering, Design & Selection : PEDS·Eric D MerkleyValerie Daggett
Apr 21, 1999·Protein Science : a Publication of the Protein Society·M A CerusoA Di Nola
Feb 24, 2001·Protein Science : a Publication of the Protein Society·F BonomiS Mazzini
Mar 10, 2001·Microbiology and Molecular Biology Reviews : MMBR·C Vieille, G J Zeikus
Jun 18, 2010·Journal of Bioinformatics and Computational Biology·Tatyana B MamonovaOxana V Galzitskaya
Feb 26, 2016·The Journal of Physical Chemistry. B·Marina KatavaFabio Sterpone
Jun 25, 2016·Langmuir : the ACS Journal of Surfaces and Colloids·Katarzyna M TychLorna Dougan
Jul 3, 1999·Journal of Molecular Biology·M J Thompson, D Eisenberg
May 26, 2017·Evolution; International Journal of Organic Evolution·Scott R Miller
Feb 7, 2017·International Journal of Biological Macromolecules·Maryam Rezaei ArjomandMassoud Amanlou
Nov 5, 2014·Protein Science : a Publication of the Protein Society·Vincent Frappier, Rafael Najmanovich
Feb 10, 2019·Applied and Environmental Microbiology·Luuk MestromPeter-Leon Hagedoorn
Oct 22, 2011·Extremophiles : Life Under Extreme Conditions·Yanrui DingBingqiang Zhao
Aug 13, 2015·Journal of Molecular Modeling·Yuliet MazolaAlexis Musacchio
Aug 14, 2020·Physical Chemistry Chemical Physics : PCCP·Irene MaffucciFabio Sterpone
Feb 19, 2000·Protein Engineering·S Parthasarathy, M R Murthy
Apr 27, 2004·Journal of Biomolecular Structure & Dynamics·S GarofoliA Desideri
Oct 7, 2011·Chemical Society Reviews·Fabio Sterpone, Simone Melchionna
Jul 25, 2007·Bioinformatics·Lydia TapiaNancy M Amato
Sep 7, 2011·Chemical Communications : Chem Comm·Hugo M Botelho, Cláudio M Gomes
Feb 9, 2002·Proteins·Alessandro GrottesiAlfredo Di Nola
Jan 20, 2007·Journal of Molecular Modeling·Vojtech SpiwokBlanka Králová
Nov 25, 2006·Protein Science : a Publication of the Protein Society·Vicky Doan-Nguyen, J Patrick Loria

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