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Items: 1 to 20 of 26

1.

The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways.

Orevi T, Rahamim G, Hazan G, Amir D, Haas E.

Biophys Rev. 2013 Jun;5(2):85-98. doi: 10.1007/s12551-013-0113-3. Epub 2013 Apr 12. Review.

2.

Characterization of protein folding by a Φ-value calculation with a statistical-mechanical model.

Wako H, Abe H.

Biophys Physicobiol. 2016 Nov 18;13:263-279. doi: 10.2142/biophysico.13.0_263. eCollection 2016.

3.

Small Molecule-Induced Domain Swapping as a Mechanism for Controlling Protein Function and Assembly.

Karchin JM, Ha JH, Namitz KE, Cosgrove MS, Loh SN.

Sci Rep. 2017 Mar 13;7:44388. doi: 10.1038/srep44388.

4.

Structure-Based Prediction of Protein-Folding Transition Paths.

Jacobs WM, Shakhnovich EI.

Biophys J. 2016 Sep 6;111(5):925-36. doi: 10.1016/j.bpj.2016.06.031.

5.

Early steps in thermal unfolding of superoxide dismutase 1 are similar to the conformational changes associated with the ALS-associated A4V mutation.

Schmidlin T, Ploeger K, Jonsson AL, Daggett V.

Protein Eng Des Sel. 2013 Aug;26(8):503-13. doi: 10.1093/protein/gzt030. Epub 2013 Jun 19.

6.

A comparison of experimental and computational methods for mapping the interactions present in the transition state for folding of FKBP12.

Main ER, Fulton KF, Daggett V, Jackson SE.

J Biol Phys. 2001 Jun;27(2-3):99-117. doi: 10.1023/A:1013137924581.

7.

Golden triangle for folding rates of globular proteins.

Garbuzynskiy SO, Ivankov DN, Bogatyreva NS, Finkelstein AV.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):147-50. doi: 10.1073/pnas.1210180110. Epub 2012 Dec 18.

8.

Ligand-switchable substrates for a ubiquitin-proteasome system.

Egeler EL, Urner LM, Rakhit R, Liu CW, Wandless TJ.

J Biol Chem. 2011 Sep 9;286(36):31328-36. doi: 10.1074/jbc.M111.264101. Epub 2011 Jul 15.

9.

A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding.

Toofanny RD, Jonsson AL, Daggett V.

Biophys J. 2010 Jun 2;98(11):2671-81. doi: 10.1016/j.bpj.2010.02.048.

10.

Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation.

Yan C, Pattani V, Tunnell JW, Ren P.

J Mol Graph Model. 2010 Aug 24;29(1):2-12. doi: 10.1016/j.jmgm.2010.03.011. Epub 2010 Apr 4.

11.

Folding intermediate and folding nucleus for I-->N and U-->I-->N transitions in apomyoglobin: contributions by conserved and nonconserved residues.

Samatova EN, Melnik BS, Balobanov VA, Katina NS, Dolgikh DA, Semisotnov GV, Finkelstein AV, Bychkova VE.

Biophys J. 2010 Apr 21;98(8):1694-702. doi: 10.1016/j.bpj.2009.12.4326.

12.

Unfolding simulations reveal the mechanism of extreme unfolding cooperativity in the kinetically stable alpha-lytic protease.

Salimi NL, Ho B, Agard DA.

PLoS Comput Biol. 2010 Feb 26;6(2):e1000689. doi: 10.1371/journal.pcbi.1000689.

13.

Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds.

Jonsson AL, Scott KA, Daggett V.

Biophys J. 2009 Dec 2;97(11):2958-66. doi: 10.1016/j.bpj.2009.09.012.

14.
15.

Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis.

Faísca PF, Travasso RD, Ball RC, Shakhnovich EI.

J Chem Phys. 2008 Sep 7;129(9):095108. doi: 10.1063/1.2973624.

16.

Capillarity-like growth of protein folding nuclei.

Qi X, Portman JJ.

Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11164-9. doi: 10.1073/pnas.0711527105. Epub 2008 Aug 4.

17.

Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain.

McCully ME, Beck DA, Daggett V.

Biochemistry. 2008 Jul 8;47(27):7079-89. doi: 10.1021/bi800118b. Epub 2008 Jun 14.

18.

How general is the nucleation-condensation mechanism?

Nölting B, Agard DA.

Proteins. 2008 Nov 15;73(3):754-64. doi: 10.1002/prot.22099.

19.
20.

A directed approach for engineering conditional protein stability using biologically silent small molecules.

Maynard-Smith LA, Chen LC, Banaszynski LA, Ooi AG, Wandless TJ.

J Biol Chem. 2007 Aug 24;282(34):24866-72. Epub 2007 Jul 1.

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