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Folding nucleus: specific or multiple? Insights from lattice models and experiments.

作者信息

Shakhnovich E I

机构信息

Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA 02138, USA.

出版信息

Fold Des. 1998;3(6):R108-11; discussion R107. doi: 10.1016/s1359-0278(98)00056-x.

DOI:10.1016/s1359-0278(98)00056-x

PMID:9889170

Abstract

摘要

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Folding nucleus: specific or multiple? Insights from lattice models and experiments.

作者信息

Shakhnovich E I

机构信息

Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA 02138, USA.

出版信息

Fold Des. 1998;3(6):R108-11; discussion R107. doi: 10.1016/s1359-0278(98)00056-x.

DOI:10.1016/s1359-0278(98)00056-x

PMID:9889170

Abstract

摘要

相似文献

Folding nucleus: specific or multiple? Insights from lattice models and experiments.

Fold Des. 1998;3(6):R108-11; discussion R107. doi: 10.1016/s1359-0278(98)00056-x.

Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models.

Curr Opin Struct Biol. 1999 Apr;9(2):197-207. doi: 10.1016/S0959-440X(99)80028-1.

The folding of knotted proteins: insights from lattice simulations.

Phys Biol. 2010 Feb 3;7(1):16009. doi: 10.1088/1478-3975/7/1/016009.

Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism.

J Mol Biol. 1998 Sep 18;282(2):471-92. doi: 10.1006/jmbi.1998.1997.

Identifying the protein folding nucleus using molecular dynamics.

J Mol Biol. 2000 Mar 10;296(5):1183-8. doi: 10.1006/jmbi.1999.3534.

Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus.

Nat Struct Biol. 2000 Apr;7(4):336-42. doi: 10.1038/74111.

The importance of hydration for the kinetics and thermodynamics of protein folding: simplified lattice models.

Fold Des. 1998;3(6):523-34. doi: 10.1016/S1359-0278(98)00068-6.

Hydrodynamic description of protein folding.

Phys Rev Lett. 2008 Jan 11;100(1):018107. doi: 10.1103/PhysRevLett.100.018107.

Cooperativity in protein folding: from lattice models with sidechains to real proteins.

Fold Des. 1998;3(2):127-39. doi: 10.1016/s1359-0278(98)00018-2.

Effect of the ordered water on protein folding: an off-lattice Gō-like model study.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Mar;79(3 Pt 1):031925. doi: 10.1103/PhysRevE.79.031925. Epub 2009 Mar 31.

引用本文的文献

Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming β-propeller.

Nat Commun. 2024 Jan 2;15(1):155. doi: 10.1038/s41467-023-44479-2.

Investigating the Effect of Chain Connectivity on the Folding of a Beta-Sheet Protein On and Off the Ribosome.

J Mol Biol. 2018 Dec 7;430(24):5207-5216. doi: 10.1016/j.jmb.2018.10.011. Epub 2018 Oct 23.

Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

J R Soc Interface. 2015 Nov 6;12(112). doi: 10.1098/rsif.2015.0876.

Take home lessons from studies of related proteins.

Curr Opin Struct Biol. 2013 Feb;23(1):66-74. doi: 10.1016/j.sbi.2012.11.009. Epub 2012 Dec 20.

A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable.

Protein Sci. 2012 Jun;21(6):819-27. doi: 10.1002/pro.2065. Epub 2012 Apr 23.

Computational exploration of the network of sequence flow between protein structures.

Proteins. 2010 Mar;78(4):985-1003. doi: 10.1002/prot.22622.

Protein unfolding transitions in an intrinsically unstable annexin domain: molecular dynamics simulation and comparison with nuclear magnetic resonance data.

Biophys J. 2002 Aug;83(2):681-98. doi: 10.1016/S0006-3495(02)75200-4.

NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: implications for protein folding initiation.

Protein Sci. 2001 Jun;10(6):1100-12. doi: 10.1110/ps.52701.

Long-range order in the src SH3 folding transition state.

Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7084-9. doi: 10.1073/pnas.97.13.7084.

From snapshot to movie: phi analysis of protein folding transition states taken one step further.

Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):14854-9. doi: 10.1073/pnas.96.26.14854.