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Volumn 15, Issue 9, 2006, Pages 2166-2177

The folding mechanism of collagen-like model peptides explored through detailed molecular simulations

Author keywords

Collagen; Molecular simulations; Osteogenesis imperfecta; Protein folding

Indexed keywords

COLLAGEN; GLYCINE; PEPTIDE; PROLINE; SERINE;

EID: 33748153236     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062124606     Document Type: Article
Times cited : (32)

References (38)
  • 1
    • 25444502378 scopus 로고    scopus 로고
    • Collagen triple-helix formation in all-trans chains proceeds by a nucleation/growth mechanism with a purely entropic barrier
    • Bachmann, A., Kiefhaber, T., Boudko, S., Jurgen Engel, J., and Bachinger, H.P. 2005. Collagen triple-helix formation in all-trans chains proceeds by a nucleation/growth mechanism with a purely entropic barrier. Proc. Natl. Acad. Sci. 102: 13897-13902.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 13897-13902
    • Bachmann, A.1    Kiefhaber, T.2    Boudko, S.3    Jurgen Engel, J.4    Bachinger, H.P.5
  • 2
    • 0026492532 scopus 로고
    • Characterization of three osteogenesis imperfecta collagen α1(I) glycine to serine mutations demonstrating a position-dependent gradient of phenotypic severity
    • Bateman, J.F., Moeller, I., Hannagan, M., Chan, D., and Cole, W.G. 1992. Characterization of three osteogenesis imperfecta collagen α1(I) glycine to serine mutations demonstrating a position-dependent gradient of phenotypic severity. Biochem. J. 288: 131-135.
    • (1992) Biochem. J. , vol.288 , pp. 131-135
    • Bateman, J.F.1    Moeller, I.2    Hannagan, M.3    Chan, D.4    Cole, W.G.5
  • 3
    • 0034636101 scopus 로고    scopus 로고
    • Destabilization of osteogenesis imperfecta collagen-like model peptides correlates with the identity of the residue replacing glycine
    • Beck, K., Chan, V.C., Shenoy, N., Kirkpatrick, A., Ramshaw, J.A.M., and Brodsky, B. 2000. Destabilization of osteogenesis imperfecta collagen-like model peptides correlates with the identity of the residue replacing glycine. Proc. Natl. Acad. Sci. 97: 4273-4278.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 4273-4278
    • Beck, K.1    Chan, V.C.2    Shenoy, N.3    Kirkpatrick, A.4    Ramshaw, J.A.M.5    Brodsky, B.6
  • 4
    • 0027996196 scopus 로고
    • Crystal and molecular streucture of a collagen-like peptide at 1.9 Å resolution
    • Bella, J., Eaton, M., Brodsky, B., and Berman, H.M. 1994. Crystal and molecular streucture of a collagen-like peptide at 1.9 Å resolution. Science 266: 75-81.
    • (1994) Science , vol.266 , pp. 75-81
    • Bella, J.1    Eaton, M.2    Brodsky, B.3    Berman, H.M.4
  • 7
    • 0036290657 scopus 로고    scopus 로고
    • Nucleation and propagation of the collagen triple helix in single-chain and trimerized peptides: Transition from third to first order kinetics
    • Boudko, S., Frank, S., Kammerer, R.A., Stetefeld, J., Schulthess, T., Landwehr, R., Lustig, A., Bachinger, H.P., and Engle, J. 2002. Nucleation and propagation of the collagen triple helix in single-chain and trimerized peptides: Transition from third to first order kinetics. J. Mol. Biol. 317: 459-470.
    • (2002) J. Mol. Biol. , vol.317 , pp. 459-470
    • Boudko, S.1    Frank, S.2    Kammerer, R.A.3    Stetefeld, J.4    Schulthess, T.5    Landwehr, R.6    Lustig, A.7    Bachinger, H.P.8    Engle, J.9
  • 8
    • 17444415358 scopus 로고    scopus 로고
    • Molecular structure of the collagen triple helix
    • Brodsky, B. and Persikov, A.V. 2005. Molecular structure of the collagen triple helix. Adv. Protein Chem. 70: 301-339.
    • (2005) Adv. Protein Chem. , vol.70 , pp. 301-339
    • Brodsky, B.1    Persikov, A.V.2
  • 9
    • 0024354001 scopus 로고
    • Solvent effects on protein motion and protein effects on solvent motion - Dynamics of the active-site region of lysozyme
    • Brooks, C. and Karplus, M. 1989. Solvent effects on protein motion and protein effects on solvent motion - Dynamics of the active-site region of lysozyme. J. Mol. Biol. 208: 159-181.
    • (1989) J. Mol. Biol. , vol.208 , pp. 159-181
    • Brooks, C.1    Karplus, M.2
  • 11
    • 0001031179 scopus 로고
    • Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
    • John Wiley, New York
    • Brooks, C.L., Karplus, M., and Pettitt, B.M. 1988. Proteins: A theoretical perspective of dynamics, structure, and thermodynamics. In Advances in chemical physics, Vol. 71. John Wiley, New York.
    • (1988) Advances in Chemical Physics , vol.71
    • Brooks, C.L.1    Karplus, M.2    Pettitt, B.M.3
  • 12
    • 0035961347 scopus 로고    scopus 로고
    • Nuclear magnetic resonance characterization of peptide models of collagen-folding diseases
    • Buevich, A. and Baum, J. 2001. Nuclear magnetic resonance characterization of peptide models of collagen-folding diseases. Philos. Trans. R. Soc. Lond. B Biol. Sci. 356: 159-168.
    • (2001) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.356 , pp. 159-168
    • Buevich, A.1    Baum, J.2
  • 13
    • 0034681942 scopus 로고    scopus 로고
    • Site-specific NMR monitoring of cis-trans isomerization in the folding of the proline-rich collagen triple helix
    • Buevich, A., Dai, Q., Liu, X., Brodsky, B., and Baum, J. 2000. Site-specific NMR monitoring of cis-trans isomerization in the folding of the proline-rich collagen triple helix. Biochemistry 39: 4299-4308.
    • (2000) Biochemistry , vol.39 , pp. 4299-4308
    • Buevich, A.1    Dai, Q.2    Liu, X.3    Brodsky, B.4    Baum, J.5
  • 14
    • 8744229956 scopus 로고    scopus 로고
    • Transformation of the mechanism of triple-helix peptide folding in the absence of a C-terminal nucleation domain and its implications for mutations in collagen disorders
    • Buevich, A., Silva, T., Brodsky, B., and Baum, J. 2004. Transformation of the mechanism of triple-helix peptide folding in the absence of a C-terminal nucleation domain and its implications for mutations in collagen disorders. J. Biol. Chem. 279: 46890-46895.
    • (2004) J. Biol. Chem. , vol.279 , pp. 46890-46895
    • Buevich, A.1    Silva, T.2    Brodsky, B.3    Baum, J.4
  • 16
    • 0027643044 scopus 로고
    • Conformational transitions using molecular-dynamics with minimum biasing
    • Harvey, S.C. and Gabb, H.A. 1993. Conformational transitions using molecular-dynamics with minimum biasing. Biopolymers 33: 1167-1172.
    • (1993) Biopolymers , vol.33 , pp. 1167-1172
    • Harvey, S.C.1    Gabb, H.A.2
  • 18
    • 8644234346 scopus 로고    scopus 로고
    • Water-mediated interaction at a protein-protein interface
    • Ikura, T., Urakubo, Y., and Ito, N. 2004. Water-mediated interaction at a protein-protein interface. Chem. Phys. 307: 111-119.
    • (2004) Chem. Phys. , vol.307 , pp. 111-119
    • Ikura, T.1    Urakubo, Y.2    Ito, N.3
  • 19
    • 0141956090 scopus 로고    scopus 로고
    • Generalized born model with a simple smoothing function
    • Im, W.P., Lee, M.S., and Brooks, C.L. 2003. Generalized born model with a simple smoothing function. J. Comput. Chem. 24: 1691-1702.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1691-1702
    • Im, W.P.1    Lee, M.S.2    Brooks, C.L.3
  • 20
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis, T. and Karplus, M. 1999. Effective energy function for proteins in solution. Proteins 35: 133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 21
    • 0021104755 scopus 로고
    • Molecular dynamics of native protein
    • Levitt, M. 1983. Molecular dynamics of native protein. J. Mol. Biol. 168: 621-657.
    • (1983) J. Mol. Biol. , vol.168 , pp. 621-657
    • Levitt, M.1
  • 22
    • 19644383795 scopus 로고    scopus 로고
    • Dissociation of an antiviral compound from the internal pocket of human rhinovirus 14 capsid
    • Li, Y., Zhou, A., and Post, C. 2005. Dissociation of an antiviral compound from the internal pocket of human rhinovirus 14 capsid. Proc. Natl. Acad. Sci. 102: 7529-7534.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 7529-7534
    • Li, Y.1    Zhou, A.2    Post, C.3
  • 23
    • 0001160648 scopus 로고    scopus 로고
    • Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems
    • Marchi, M. and Ballone, P. 1999. Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems. J. Chem. Phys. 110: 3697-3702.
    • (1999) J. Chem. Phys. , vol.110 , pp. 3697-3702
    • Marchi, M.1    Ballone, P.2
  • 24
    • 0035526029 scopus 로고    scopus 로고
    • Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K
    • Mark, P. and Nilsson, L. 2001. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. J. Phys. Chem. A 105: 9954-9960.
    • (2001) J. Phys. Chem. A , vol.105 , pp. 9954-9960
    • Mark, P.1    Nilsson, L.2
  • 25
    • 0242267532 scopus 로고    scopus 로고
    • Unfolding of the cold shock protein studied with biased molecular dynamics
    • Morra, G., Hodoscek, M., and Knapp, E. 2003. Unfolding of the cold shock protein studied with biased molecular dynamics. Proteins 53: 597-606.
    • (2003) Proteins , vol.53 , pp. 597-606
    • Morra, G.1    Hodoscek, M.2    Knapp, E.3
  • 26
    • 0033531973 scopus 로고    scopus 로고
    • Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
    • Paci, E. and Karplus, M. 1999. Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations. J. Mol. Biol. 288: 441-459.
    • (1999) J. Mol. Biol. , vol.288 , pp. 441-459
    • Paci, E.1    Karplus, M.2
  • 27
    • 0035976752 scopus 로고    scopus 로고
    • Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study
    • Paci, E., Caflisch, A., Pluckthun, A., and Karplus, M. 2001. Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. J. Mol. Biol. 314: 589-605.
    • (2001) J. Mol. Biol. , vol.314 , pp. 589-605
    • Paci, E.1    Caflisch, A.2    Pluckthun, A.3    Karplus, M.4
  • 28
    • 25444465414 scopus 로고    scopus 로고
    • Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach
    • Paci, E., Greene, L.H., Jones, R.M., and Smith, L.J. 2005. Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach. FEBS J. 272: 4826-4838.
    • (2005) FEBS J. , vol.272 , pp. 4826-4838
    • Paci, E.1    Greene, L.H.2    Jones, R.M.3    Smith, L.J.4
  • 29
    • 0000874777 scopus 로고    scopus 로고
    • Self-diffusion of supercooled water to 238 K using PGSE NMR diffusion measurements
    • Price, W.S., Ide, H., and Arata, Y.J. 1999. Self-diffusion of supercooled water to 238 K using PGSE NMR diffusion measurements. J. Phys. Chem. A 103: 448-450.
    • (1999) J. Phys. Chem. A , vol.103 , pp. 448-450
    • Price, W.S.1    Ide, H.2    Arata, Y.J.3
  • 30
    • 33748169127 scopus 로고    scopus 로고
    • Inherited disorders of connective tissue
    • eds. D.L. Kasper et al., McGraw-Hill Companies, New York
    • Prockop, D.L. and Ala-Kokko, L. 2004. Inherited disorders of connective tissue. In Harrison's principles of internal medicine (eds. D.L. Kasper et al.), pp. 2324-2331. McGraw-Hill Companies, New York.
    • (2004) Harrison's Principles of Internal Medicine , pp. 2324-2331
    • Prockop, D.L.1    Ala-Kokko, L.2
  • 31
    • 1942501149 scopus 로고    scopus 로고
    • Osteogenesis imperfecta
    • Rauch, F. and Glorieux, F.H. 2004. Osteogenesis imperfecta. Lancet 363: 1377-1385.
    • (2004) Lancet , vol.363 , pp. 1377-1385
    • Rauch, F.1    Glorieux, F.H.2
  • 33
    • 33646940952 scopus 로고
    • Numerical integration of cartesian equations of motion of a system with constraints: Molecular-dynamics of n-alkanes
    • Ryckaert, J.P., Ciccotti, G., and Berendsen, H.J.C. 1977. Numerical integration of cartesian equations of motion of a system with constraints: Molecular-dynamics of n-alkanes. J. Comput. Phys. 23: 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 34
    • 32944475390 scopus 로고    scopus 로고
    • Structure of a mutant T=1 capsid of Sesbania mosaic virus: Role of water molecules in capsid architecture and integrity
    • Sangita, V., Satheshkumar, P.S., Savithrib, H.S., and Murthy, M.R.N. 2005. Structure of a mutant T=1 capsid of Sesbania mosaic virus: Role of water molecules in capsid architecture and integrity. Acta Crystallogr. D Biol. Crystallogr. 61: 1406-1412.
    • (2005) Acta Crystallogr. D Biol. Crystallogr. , vol.61 , pp. 1406-1412
    • Sangita, V.1    Satheshkumar, P.S.2    Savithrib, H.S.3    Murthy, M.R.N.4
  • 36
    • 0004155427 scopus 로고
    • W.H. Freeman, New York
    • Stryer, L. 1988. Biochemistry. W.H. Freeman, New York.
    • (1988) Biochemistry
    • Stryer, L.1
  • 37
    • 0036300984 scopus 로고    scopus 로고
    • Localized unfolding of collagen explains collagenase cleavage near imino-poor sites
    • Stultz, C.M. 2002. Localized unfolding of collagen explains collagenase cleavage near imino-poor sites. J. Mol. Biol. 319: 997-1003.
    • (2002) J. Mol. Biol. , vol.319 , pp. 997-1003
    • Stultz, C.M.1
  • 38
    • 0025166689 scopus 로고
    • Mutations that substitute serine for glycine α1-598 and glycine α1-631 in type I procollagen
    • Westerhausen, A., Kishi, J., and Prockop, D.J. 1990. Mutations that substitute serine for glycine α1-598 and glycine α1-631 in type I procollagen. J. Biol. Chem. 265: 13995-14000.
    • (1990) J. Biol. Chem. , vol.265 , pp. 13995-14000
    • Westerhausen, A.1    Kishi, J.2    Prockop, D.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.