메뉴 건너뛰기




Volumn 108, Issue 17, 2011, Pages 6963-6968

Minimum energy compact structures in force-quench polyubiquitin folding are domain swapped

Author keywords

Atomic force microscopy; Folding intermediates; Self organized polymer model; Three stage refolding; Unfolding kinetics

Indexed keywords

DIMER; POLYUBIQUITIN;

EID: 79955565416     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1018177108     Document Type: Article
Times cited : (15)

References (48)
  • 2
    • 16344371778 scopus 로고    scopus 로고
    • RNA and protein folding: Common themes and variations
    • DOI 10.1021/bi047314+
    • Thirumalai D, Hyeon C (2005) RNA and protein folding: Common themes and variations. Biochemistry 44:4957-4970. (Pubitemid 40471212)
    • (2005) Biochemistry , vol.44 , Issue.13 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 3
    • 33646931471 scopus 로고    scopus 로고
    • Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
    • Shakhnovich E (2006) Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chem Rev 106:1559-1588.
    • (2006) Chem Rev , vol.106 , pp. 1559-1588
    • Shakhnovich, E.1
  • 5
    • 39149087014 scopus 로고    scopus 로고
    • Protein folding studied by single-molecule FRET
    • Schuler B, Eaton WA (2008) Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 18:16-26.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 16-26
    • Schuler, B.1    Eaton, W.A.2
  • 8
    • 0041335634 scopus 로고    scopus 로고
    • Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments
    • Hyeon CB, Thirumalai D (2003) Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments. Proc Natl Acad Sci USA 100:10249-10253.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 10249-10253
    • Hyeon, C.B.1    Thirumalai, D.2
  • 9
  • 11
    • 1542513548 scopus 로고    scopus 로고
    • Force-Clamp Spectroscopy Monitors the Folding Trajectory of a Single Protein
    • DOI 10.1126/science.1092497
    • Fernández JM, Li H (2004) Force-clamp spectroscopy monitors the folding trajectory of a single protein. Science 303:1674-1678. (Pubitemid 38338326)
    • (2004) Science , vol.303 , Issue.5664 , pp. 1674-1678
    • Fernandez, J.M.1    Li, H.2
  • 12
    • 34848909232 scopus 로고    scopus 로고
    • Force-clamp spectroscopy of single-protein monomers reveals the individual unfolding and folding pathways of i27 and ubiquitin
    • DOI 10.1529/biophysj.107.104422
    • Garcia-Manyes S, Brujić J, Badilla CL, Fernández JM (2007) Force-clamp spectroscopy of single-protein monomers reveals the individual unfolding and folding pathways of I27 and ubiquitin. Biophys J 93:2436-2446. (Pubitemid 47511144)
    • (2007) Biophysical Journal , vol.93 , Issue.7 , pp. 2436-2446
    • Garcia-Manyes, S.1    Brujic, J.2    Badilla, C.L.3    Fernandez, J.M.4
  • 16
    • 33847217662 scopus 로고    scopus 로고
    • Fluctuations of primary ubiquitin folding intermediates in a force clamp
    • Gräter F, Grubmüller H (2007) Fluctuations of primary ubiquitin folding intermediates in a force clamp. J Struct Biol 157:557-569.
    • (2007) J Struct Biol , vol.157 , pp. 557-569
    • Gräter, F.1    Grubmüller, H.2
  • 17
    • 0031965674 scopus 로고    scopus 로고
    • Molecular dynamics simulations of hydrophobic collapse of ubiquitin
    • Alonso DOV, Daggett V (1998) Molecular dynamics simulations of hydrophobic collapse of ubiquitin. Protein Sci 7:860-874. (Pubitemid 28216528)
    • (1998) Protein Science , vol.7 , Issue.4 , pp. 860-874
    • Alonso, D.O.V.1    Daggett, V.2
  • 19
    • 2942623941 scopus 로고    scopus 로고
    • Multiple probes reveal a native-like intermediate during low-temperature refolding of ubiquitin
    • DOI 10.1016/j.jmb.2004.04.048, PII S0022283604004462
    • Larios E, Li JS, Schulten K, Kihara H, Gruebele M (2004) Multiple probes reveal a native-like intermediate during low-temperature refolding of ubiquitin. J Mol Biol 340:115-125. (Pubitemid 38739441)
    • (2004) Journal of Molecular Biology , vol.340 , Issue.1 , pp. 115-125
    • Larios, E.1    Li, J.S.2    Schulten, K.3    Kihara, H.4    Gruebele, M.5
  • 20
    • 4644357714 scopus 로고    scopus 로고
    • The folding pathway of ubiquitin from all-atom molecular dynamics simulations
    • DOI 10.1016/j.bpc.2004.05.009, PII S0301462204001231
    • Marianayagam NJ, Jackson SE (2004) The folding pathway of ubiquitin from all-atom molecular dynamics simulations. Biophys Chem 111:159-171. (Pubitemid 39277496)
    • (2004) Biophysical Chemistry , vol.111 , Issue.2 , pp. 159-171
    • Marianayagam, N.J.1    Jackson, S.E.2
  • 21
    • 44949091394 scopus 로고    scopus 로고
    • Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules
    • Best RB, Paci E, Hummer G, Dudko OK (2008) Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules. J Phys Chem B 112:5968-5976.
    • (2008) J Phys Chem B , vol.112 , pp. 5968-5976
    • Best, R.B.1    Paci, E.2    Hummer, G.3    Dudko, O.K.4
  • 22
    • 28844488857 scopus 로고    scopus 로고
    • Probing protein-protein interactions by dynamics force correlation spectroscopy
    • Barsegov V, Thirumalai D (2005) Probing protein-protein interactions by dynamics force correlation spectroscopy. Phys Rev Lett 95:168302.
    • (2005) Phys Rev Lett , vol.95 , pp. 168302
    • Barsegov, V.1    Thirumalai, D.2
  • 24
    • 67649774600 scopus 로고    scopus 로고
    • Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin
    • Garcia-Manyes S, Dougan L, Badilla CL, Brujić J, Fernández JM (2009) Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin. Proc Natl Acad Sci USA 106:10534-10539.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 10534-10539
    • Garcia-Manyes, S.1    Dougan, L.2    Badilla, C.L.3    Brujić, J.4    Fernández, J.M.5
  • 25
    • 0001510938 scopus 로고
    • Minimum energy compact structures of random sequences of heteropolymers
    • Camacho CJ, Thirumalai D (1993) Minimum energy compact structures of random sequences of heteropolymers. Phys Rev Lett 71:2505-2508.
    • (1993) Phys Rev Lett , vol.71 , pp. 2505-2508
    • Camacho, C.J.1    Thirumalai, D.2
  • 26
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 Å resolution
    • Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 Å resolution. J Mol Biol 194:531-544.
    • (1987) J Mol Biol , vol.194 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 28
    • 0037337270 scopus 로고    scopus 로고
    • The unfolding story of three-dimensional domain swapping
    • DOI 10.1016/S0969-2126(03)00029-7, PII S0969212603000297
    • Rousseau F, Schymkowitz JWH, Itzhaki LS (2003) The unfolding story of threedimensional domain swapping. Structure 11:243-251. (Pubitemid 36287689)
    • (2003) Structure , vol.11 , Issue.3 , pp. 243-251
    • Rousseau, F.1    Schymkowitz, J.W.H.2    Itzhaki, L.S.3
  • 29
    • 0028865843 scopus 로고
    • 3D domain swapping: A mechanism for oligomer assembly
    • Bennett MJ, Schlunegger MP, Eisenberg D (1995) 3D domain swapping: A mechanism for oligomer assembly. Protein Sci 4:2455-2468.
    • (1995) Protein Sci , vol.4 , pp. 2455-2468
    • Bennett, M.J.1    Schlunegger, M.P.2    Eisenberg, D.3
  • 30
    • 33646375442 scopus 로고    scopus 로고
    • Deposition Diseases and 3D Domain Swapping
    • DOI 10.1016/j.str.2006.03.011, PII S0969212606001791
    • Bennett MJ, Sawaya MR, Eisenberg D (2006) Deposition diseases and 3D domain swapping. Structure 14:811-824. (Pubitemid 43674098)
    • (2006) Structure , vol.14 , Issue.5 , pp. 811-824
    • Bennett, M.J.1    Sawaya, M.R.2    Eisenberg, D.3
  • 33
    • 33846460423 scopus 로고    scopus 로고
    • Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin
    • DOI 10.1529/biophysj.106.087684
    • Li MS, Kouza M, Hu CK (2007) Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin. Biophys J 92:547-561. (Pubitemid 46145788)
    • (2007) Biophysical Journal , vol.92 , Issue.2 , pp. 547-561
    • Mai, S.L.1    Kouza, M.2    Hu, C.-K.3
  • 34
    • 38849169933 scopus 로고    scopus 로고
    • New force replica exchange method and protein folding pathways probed by force-clamp technique
    • Kouza M, Hu C-K, Li MS (2008) New force replica exchange method and protein folding pathways probed by force-clamp technique. J Chem Phys 128:045103.
    • (2008) J Chem Phys , vol.128 , pp. 045103
    • Kouza, M.1    Hu, C.-K.2    Li, M.S.3
  • 36
    • 33645004171 scopus 로고    scopus 로고
    • Intrinsic rates and activation free energies from single-molecule pulling experiments
    • Dudko OK, Hummer G, Szabo A (2006) Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys Rev Lett 96:108101-108104.
    • (2006) Phys Rev Lett , vol.96 , pp. 108101-108104
    • Dudko, O.K.1    Hummer, G.2    Szabo, A.3
  • 37
    • 0000888684 scopus 로고
    • Escape-field distribution for escape from a metastable potential well subject to a steadily increasing bias field
    • Garg A (1995) Escape-field distribution for escape from a metastable potential well subject to a steadily increasing bias field. Phys Rev B 51:15592-15595.
    • (1995) Phys Rev B , vol.51 , pp. 15592-15595
    • Garg, A.1
  • 38
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • DOI 10.1006/jmbi.1998.1645
    • Plaxco KW, Simons KT, Baker D (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277:985-994. (Pubitemid 28195995)
    • (1998) Journal of Molecular Biology , vol.277 , Issue.4 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 40
    • 0030057477 scopus 로고    scopus 로고
    • Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues
    • Khorasanizadel S, Peters ID, Roder H (1996) Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nat Struct Biol 3:193-205.
    • (1996) Nat Struct Biol , vol.3 , pp. 193-205
    • Khorasanizadel, S.1    Peters, I.D.2    Roder, H.3
  • 41
    • 7044274259 scopus 로고    scopus 로고
    • Comment on force-clamp spectroscopy monitors the folding trajectory of a single protein
    • Sosnick TR (2004) Comment on force-clamp spectroscopy monitors the folding trajectory of a single protein. Science 306:411.
    • (2004) Science , vol.306 , pp. 411
    • Sosnick, T.R.1
  • 43
    • 0030601851 scopus 로고    scopus 로고
    • Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein
    • DOI 10.1006/jmbi.1996.0578
    • Guo Z, Thirumalai D (1996) Kinetics and thermodynamics of folding of a de Novo designed four-helix bundle protein. J Mol Biol 263:323-343. (Pubitemid 26363091)
    • (1996) Journal of Molecular Biology , vol.263 , Issue.2 , pp. 323-343
    • Guo, Z.1    Thirumalai, D.2
  • 44
    • 33846193288 scopus 로고    scopus 로고
    • Pathways and Kinetic Barriers in Mechanical Unfolding and Refolding of RNA and Proteins
    • DOI 10.1016/j.str.2006.09.002, PII S0969212606003881
    • Hyeon C, Dima RI, Thirumalai D (2006) Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure 14:1633-1645. (Pubitemid 46107269)
    • (2006) Structure , vol.14 , Issue.11 , pp. 1633-1645
    • Hyeon, C.1    Dima, R.I.2    Thirumalai, D.3
  • 45
    • 38049119865 scopus 로고    scopus 로고
    • Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations
    • Mickler M, et al. (2007) Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Proc Natl Acad Sci USA 104:20268-20273.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 20268-20273
    • Mickler, M.1
  • 46
    • 0022033183 scopus 로고
    • The human ubiquitin multigene family: Some genes contain multiple directly repeated ubiquitin coding sequences
    • Wiborg O, et al. (1985) The human ubiquitin multigene family: Some genes contain multiple directly repeated ubiquitin coding sequences. EMBO J 4:755-759.
    • (1985) EMBO J , vol.4 , pp. 755-759
    • Wiborg, O.1
  • 47
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermack DL, McCammon JA (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69:1352-1369.
    • (1978) J Chem Phys , vol.69 , pp. 1352-1369
    • Ermack, D.L.1    McCammon, J.A.2
  • 48
    • 0032424129 scopus 로고    scopus 로고
    • Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: Effect on stability, cooperativity and kinetics
    • Klimov DK, Betancourt MR, Thirumalai D (1998) Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: Effect on stability, cooperativity and kinetics. Fold Des 3:481-496.
    • (1998) Fold Des , vol.3 , pp. 481-496
    • Klimov, D.K.1    Betancourt, M.R.2    Thirumalai, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.