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Volumn 10, Issue 1, 2016, Pages 317-323

Nanomechanics of protein unfolding outside a generic nanopore

Author keywords

Nanomechanics; Protease; Protein unfolding

Indexed keywords

ATOMIC FORCE MICROSCOPY; FRACTURE; NANOMECHANICS; NANOPORES;

EID: 84989260767     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/acsnano.5b04557     Document Type: Article
Times cited : (27)

References (42)
  • 2
    • 0028500779 scopus 로고
    • A short linear peptide that folds into a native stable β-hairpin in aqueous solution
    • Blanco, F. J.; Rivas, G.; Serrano, L. A Short Linear Peptide That Folds into a Native Stable β-Hairpin in Aqueous Solution. Nat. Struct. Biol. 1994, 1, 584-590.
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 584-590
    • Blanco, F.J.1    Rivas, G.2    Serrano, L.3
  • 3
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of β-hairpin formation
    • Munoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A. Folding Dynamics and Mechanism of β-Hairpin Formation. Nature 1997, 390, 196-199.
    • (1997) Nature , vol.390 , pp. 196-199
    • Munoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 5
    • 0035909921 scopus 로고    scopus 로고
    • The energy landscape for β Hairpin folding in explicit water
    • Zhou, R.; Berne, B. J.; Germain, R. The Energy Landscape for β Hairpin Folding in Explicit Water. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 14931-14936.
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , pp. 14931-14936
    • Zhou, R.1    Berne, B.J.2    Germain, R.3
  • 7
    • 78650617915 scopus 로고    scopus 로고
    • Water's role in the force-induced unfolding of ubiquitin
    • Li, J.; Fernandez, J. M.; Berne, B. Water's Role in the Force-Induced Unfolding of Ubiquitin. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 19284-19289.
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 19284-19289
    • Li, J.1    Fernandez, J.M.2    Berne, B.3
  • 8
    • 2442448427 scopus 로고    scopus 로고
    • The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques
    • Schlierf, M.; Li, H.; Fernandez, J. M. The Unfolding Kinetics of Ubiquitin Captured with Single-Molecule Force-Clamp Techniques. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 7299-7304.
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 7299-7304
    • Schlierf, M.1    Li, H.2    Fernandez, J.M.3
  • 10
    • 79959389010 scopus 로고    scopus 로고
    • AAA+ proteases: ATP-fueled machines of Protein destruction
    • Sauer, R. T.; Baker, T. A. AAA+ Proteases: ATP-Fueled Machines of Protein Destruction. Annu. Rev. Biochem. 2011, 80, 587-612.
    • (2011) Annu. Rev. Biochem. , vol.80 , pp. 587-612
    • Sauer, R.T.1    Baker, T.A.2
  • 11
    • 84855195754 scopus 로고    scopus 로고
    • ClpXP, an ATP-powered unfolding and protein-degradation machine
    • Baker, T. A.; Sauer, R. T. ClpXP, an ATP-Powered Unfolding and Protein-Degradation Machine. Biochim. Biophys. Acta, Mol. Cell Res. 2012, 1823, 15-28.
    • (2012) Biochim. Biophys. Acta, Mol. Cell Res. , vol.1823 , pp. 15-28
    • Baker, T.A.1    Sauer, R.T.2
  • 12
    • 13444306170 scopus 로고    scopus 로고
    • Partitioning between unfolding and release of native domains during ClpXP degradation determines substrate selectivity and partial processing
    • Kenniston, J. A.; Baker, T. A.; Sauer, R. T. Partitioning Between Unfolding and Release of Native Domains During ClpXP Degradation Determines Substrate Selectivity and Partial Processing. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 1390-1395.
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 1390-1395
    • Kenniston, J.A.1    Baker, T.A.2    Sauer, R.T.3
  • 14
    • 0344824655 scopus 로고    scopus 로고
    • Proteolysis in bacterial regulatory circuits
    • Gottesman, S. Proteolysis in Bacterial Regulatory Circuits. Annu. Rev. Cell Dev. Biol. 2003, 19, 565-587.
    • (2003) Annu. Rev. Cell Dev. Biol. , vol.19 , pp. 565-587
    • Gottesman, S.1
  • 15
    • 79953888421 scopus 로고    scopus 로고
    • Single-molecule Protein unfolding and translocation by an ATP-fueled proteolytic machine
    • Aubin-Tam, M.-E.; Olivares, A. O.; Sauer, R. T.; Baker, T. A.; Lang, M. J. Single-Molecule Protein Unfolding and Translocation by an ATP-Fueled Proteolytic Machine. Cell 2011, 145, 257-267.
    • (2011) Cell , vol.145 , pp. 257-267
    • Aubin-Tam, M.-E.1    Olivares, A.O.2    Sauer, R.T.3    Baker, T.A.4    Lang, M.J.5
  • 17
  • 18
    • 70350772363 scopus 로고    scopus 로고
    • Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine
    • Glynn, S. E.; Martin, A.; Nager, A. R.; Baker, T. A.; Sauer, R. T. Structures of Asymmetric ClpX Hexamers Reveal Nucleotide-Dependent Motions in a AAA+ Protein-Unfolding Machine. Cell 2009, 139, 744-756.
    • (2009) Cell , vol.139 , pp. 744-756
    • Glynn, S.E.1    Martin, A.2    Nager, A.R.3    Baker, T.A.4    Sauer, R.T.5
  • 19
    • 79952293131 scopus 로고    scopus 로고
    • Unfolding and translocation pathway of substrate Protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase
    • Kravats, A.; Jayasinghe, M.; Stan, G. Unfolding and Translocation Pathway of Substrate Protein Controlled by Structure in Repetitive Allosteric Cycles of the ClpY ATPase. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 2234-2239.
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , pp. 2234-2239
    • Kravats, A.1    Jayasinghe, M.2    Stan, G.3
  • 20
    • 84885448973 scopus 로고    scopus 로고
    • Asymmetric processing of a substrate Protein in sequential allosteric cycles of AAA+ nanomachines
    • Kravats, A. N.; Tonddast-Navaei, S.; Bucher, R. J.; Stan, G. Asymmetric Processing of a Substrate Protein in Sequential Allosteric Cycles of AAA+ Nanomachines. J. Chem. Phys. 2013, 139, 121921.
    • (2013) J. Chem. Phys. , vol.139 , pp. 121921
    • Kravats, A.N.1    Tonddast-Navaei, S.2    Bucher, R.J.3    Stan, G.4
  • 21
    • 70849108762 scopus 로고    scopus 로고
    • Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations
    • Koga, N.; Kameda, T.; Okazaki, K.-I.; Takada, S. Paddling Mechanism for the Substrate Translocation by AAA+ Motor Revealed by Multiscale Molecular Simulations. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 18237-18242.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 18237-18242
    • Koga, N.1    Kameda, T.2    Okazaki, K.-I.3    Takada, S.4
  • 22
    • 84885112814 scopus 로고    scopus 로고
    • Mechanism of transient binding and release of substrate Protein during the allosteric cycle of the p97 nanomachine
    • Tonddast-Navaei, S.; Stan, G. Mechanism of Transient Binding and Release of Substrate Protein During the Allosteric Cycle of the P97 Nanomachine. J. Am. Chem. Soc. 2013, 135, 14627-14636.
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 14627-14636
    • Tonddast-Navaei, S.1    Stan, G.2
  • 23
    • 26044464483 scopus 로고    scopus 로고
    • Computer simulations of the translocation and unfolding of a Protein pulled mechanically through a pore
    • Huang, L.; Kirmizialtin, S.; Makarov, D. E. Computer Simulations of the Translocation and Unfolding of a Protein Pulled Mechanically Through a Pore. J. Chem. Phys. 2005, 123, 124903.
    • (2005) J. Chem. Phys. , vol.123 , pp. 124903
    • Huang, L.1    Kirmizialtin, S.2    Makarov, D.E.3
  • 24
    • 33748442341 scopus 로고    scopus 로고
    • Prediction of the translocation kinetics of a Protein from its mechanical properties
    • West, D. K.; Brockwell, D. J.; Paci, E. Prediction of the Translocation Kinetics of a Protein from Its Mechanical Properties. Biophys. J. 2006, 91, L51-L53.
    • (2006) Biophys. J. , vol.91 , pp. L51-L53
    • West, D.K.1    Brockwell, D.J.2    Paci, E.3
  • 25
    • 84932092986 scopus 로고    scopus 로고
    • Protein unfolding by biological unfoldases: Insights from modeling
    • Wojciechowski, M.; Szymczak, P.; Carrion-Vazquez, M.; Cieplak, M. Protein Unfolding by Biological Unfoldases: Insights from Modeling. Biophys. J. 2014, 107, 1661-1668.
    • (2014) Biophys. J. , vol.107 , pp. 1661-1668
    • Wojciechowski, M.1    Szymczak, P.2    Carrion-Vazquez, M.3    Cieplak, M.4
  • 29
    • 84907157675 scopus 로고    scopus 로고
    • Controlled transport of DNA through a Y-shaped carbon nanotube in a solid membrane
    • Luan, B.; Zhou, B.; Huynh, T.; Zhou, R. Controlled Transport of DNa Through a Y-Shaped Carbon Nanotube in a Solid Membrane. Nanoscale 2014, 6, 11479-11483.
    • (2014) Nanoscale , vol.6 , pp. 11479-11483
    • Luan, B.1    Zhou, B.2    Huynh, T.3    Zhou, R.4
  • 30
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • Isralewitz, B.; Gao, M.; Schulten, K. Steered Molecular Dynamics and Mechanical Functions of Proteins. Curr. Opin. Struct. Biol. 2001, 11, 224-230.
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 31
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell, A., Jr.; et al. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
    • MacKerell, A.1
  • 32
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
    • Beglov, D.; Roux, B. Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations. J. Chem. Phys. 1994, 100, 9050-9063.
    • (1994) J. Chem. Phys. , vol.100 , pp. 9050-9063
    • Beglov, D.1    Roux, B.2
  • 34
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria, E.; Fischer, S.; Karplus, M. Simulation of Activation Free Energies in Molecular Systems. J. Chem. Phys. 1996, 105, 1902.
    • (1996) J. Chem. Phys. , vol.105 , pp. 1902
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 37
    • 21244462347 scopus 로고    scopus 로고
    • The breakdown of continuum models for mechanical contacts
    • Luan, B.; Robbins, M. O. The Breakdown of Continuum Models for Mechanical Contacts. Nature 2005, 435, 929-932.
    • (2005) Nature , vol.435 , pp. 929-932
    • Luan, B.1    Robbins, M.O.2
  • 39
    • 0018101150 scopus 로고
    • Models for the specific adhesion of cells to cells
    • Bell, G. I. Models for the Specific Adhesion of Cells to Cells. Science 1978, 200, 618-627.
    • (1978) Science , vol.200 , pp. 618-627
    • Bell, G.I.1
  • 42
    • 36449003554 scopus 로고
    • Constant pressure molecular dynamics algorithms
    • Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant Pressure Molecular Dynamics Algorithms. J. Chem. Phys. 1994, 101, 4177-4189.
    • (1994) J. Chem. Phys. , vol.101 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.