메뉴 건너뛰기




Volumn 38, Issue 4, 2012, Pages 681-703

Folding of pig gastric mucin non-glycosylated domains: A discrete molecular dynamics study

Author keywords

DMD simulation; Free energy landscape; Mucin; Mucin gelation; PGM 2X; Pig gastric mucin; Protein folding; vWF C1

Indexed keywords

AMINO ACID; SOLVENT; STOMACH MUCIN; VON WILLEBRAND FACTOR;

EID: 84867893683     PISSN: 00920606     EISSN: 15730689     Source Type: Journal    
DOI: 10.1007/s10867-012-9280-x     Document Type: Article
Times cited : (18)

References (37)
  • 1
    • 33745001604 scopus 로고    scopus 로고
    • Mucin structure, aggregation, physiological functions and biomedical applications
    • 10.1016/j.cocis.2005.11.001
    • Bansil, R.; Turner, B.S.: Mucin structure, aggregation, physiological functions and biomedical applications. Curr. Opin. Colloid Interface Sci. 11, 164-170 (2006)
    • (2006) Curr. Opin. Colloid Interface Sci. , vol.11 , pp. 164-170
    • Bansil, R.1    Turner, B.S.2
  • 3
    • 0033527547 scopus 로고    scopus 로고
    • The structure and assembly of secreted mucins
    • 10.1074/jbc.274.45.31751
    • Perez-Vilar, J.; Hill, R.L.: The structure and assembly of secreted mucins. J. Biol. Chem. 274, 31751-31754 (1999)
    • (1999) J. Biol. Chem. , vol.274 , pp. 31751-31754
    • Perez-Vilar, J.1    Hill, R.L.2
  • 6
    • 0033022229 scopus 로고    scopus 로고
    • PH-dependent conformational change of gastric mucin leads to sol-gel transition
    • 10.1016/S0006-3495(99)77288-7
    • Cao, X.X.; Bansil, R.; Bhaskar, K.R.; Turner, B.S.; LaMont, J.T.; Niu, N.; Afdhal, N.H.: pH-dependent conformational change of gastric mucin leads to sol-gel transition. Biophys. J. 76, 1250-1258 (1999)
    • (1999) Biophys. J. , vol.76 , pp. 1250-1258
    • Cao, X.X.1    Bansil, R.2    Bhaskar, K.R.3    Turner, B.S.4    Lamont, J.T.5    Niu, N.6    Afdhal, N.H.7
  • 8
    • 84944661097 scopus 로고
    • The two-component mucous barrier; Its activity in protecting the gastroduodenal mucosa against peptic ulceration
    • 10.1001/archinte.1954.00240250117009
    • Hollander, F.: The two-component mucous barrier; its activity in protecting the gastroduodenal mucosa against peptic ulceration. AMA Arch. Intern. Med. 93, 107-120 (1954)
    • (1954) AMA Arch. Intern. Med. , vol.93 , pp. 107-120
    • Hollander, F.1
  • 13
    • 0035882559 scopus 로고    scopus 로고
    • α-helix formation: Discontinuous molecular dynamics on an intermediate-resolution protein model
    • 10.1002/prot.1100
    • Smith, A.V.; Hall, C.K.: α-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model. Protein Struct. Funct. Genet. 44, 344-360 (2001)
    • (2001) Protein Struct. Funct. Genet. , vol.44 , pp. 344-360
    • Smith, A.V.1    Hall, C.K.2
  • 15
    • 33749601705 scopus 로고    scopus 로고
    • Ab initio discrete molecular dynamics approach to protein folding and aggregation
    • 10.1016/S0076-6879(06)12019-4
    • Urbanc, B.; Borreguero, J.M.; Cruz, L.; Stanley, H.E.: Ab initio discrete molecular dynamics approach to protein folding and aggregation. Meth. Enzymol. 412, 314-338 (2006)
    • (2006) Meth. Enzymol. , vol.412 , pp. 314-338
    • Urbanc, B.1    Borreguero, J.M.2    Cruz, L.3    Stanley, H.E.4
  • 17
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • 10.1016/0022-2836(82)90515-0
    • Kyte, J.; Doolittle, R.F.: A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132 (1982)
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 18
    • 67849095816 scopus 로고    scopus 로고
    • Effects of the Arctic (E22->G) mutation on amyloid β-protein folding: Discrete molecular dynamics study
    • 10.1021/ja804984h
    • Lam, A.R.; Teplow, D.B.; Stanley, H.E.; Urbanc, B.: Effects of the Arctic (E22->G) mutation on amyloid β-protein folding: discrete molecular dynamics study. J. Am. Chem. Soc. 130, 17413-17422 (2008)
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 17413-17422
    • Lam, A.R.1    Teplow, D.B.2    Stanley, H.E.3    Urbanc, B.4
  • 19
    • 77950219248 scopus 로고    scopus 로고
    • Elucidation of amyloid β-protein oligomerization mechanisms: Discrete molecular dynamics study
    • 10.1021/ja9096303
    • Urbanc, B.; Betnel, M.; Cruz, L.; Bitan, G.; Teplow, D.B.: Elucidation of amyloid β-protein oligomerization mechanisms: discrete molecular dynamics study. J. Am. Chem. Soc. 132, 4266-4280 (2010)
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 4266-4280
    • Urbanc, B.1    Betnel, M.2    Cruz, L.3    Bitan, G.4    Teplow, D.B.5
  • 21
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics methods
    • 1984JChPh.81.511N 10.1063/1.447334
    • Nosé, S.: A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 81, 511 (1984)
    • (1984) J. Chem. Phys. , vol.81 , pp. 511
    • Nosé, S.1
  • 22
    • 0037880487 scopus 로고    scopus 로고
    • Revisited: Re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins
    • 10.1093/proeng/gzg024
    • Dani, V.S.; Ramakrishnan, C.; Varadarajan, R.: MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. Protein Eng. 16, 187-193 (2003)
    • (2003) Protein Eng. , vol.16 , pp. 187-193
    • Dani, V.S.1    Ramakrishnan, C.2    Varadarajan, R.3    Modip4
  • 23
    • 79958703402 scopus 로고    scopus 로고
    • Structural basis for Aβ1-42 toxicity inhibition by Aβ C-terminal fragments: Discrete molecular dynamics study
    • 10.1016/j.jmb.2011.05.021
    • Urbanc, B.; Betnel, M.; Cruz, L.; Li, H.; Fradinger, E.A.; Monien, B.H.; Bitan, G.: Structural basis for Aβ1-42 toxicity inhibition by Aβ C-terminal fragments: discrete molecular dynamics study. J. Mol. Biol. 410, 316-328 (2011)
    • (2011) J. Mol. Biol. , vol.410 , pp. 316-328
    • Urbanc, B.1    Betnel, M.2    Cruz, L.3    Li, H.4    Fradinger, E.A.5    Monien, B.H.6    Bitan, G.7
  • 24
    • 0037442915 scopus 로고    scopus 로고
    • Potentials of mean force between ionizable amino acid side chains in water
    • 10.1021/ja025521w
    • Masunov, A.; Lazaridis, T.: Potentials of mean force between ionizable amino acid side chains in water. J. Am. Chem. Soc. 125, 1722-1730 (2003)
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1722-1730
    • Masunov, A.1    Lazaridis, T.2
  • 25
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • 10.1016/0263-7855(96)00018-5
    • Humphrey, W.; Dalke, A.; Schulten, K.: VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-38 (1996)
    • (1996) J. Mol. Graph. , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 26
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • 10.1006/jmbi.1998.1645
    • Plaxco, K.W.; Simons, K.T.; Baker, D.: Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277, 985-994 (1998)
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 27
    • 0032852792 scopus 로고    scopus 로고
    • Cysteine-rich regions of pig gastric mucin contain von Willebrand factor and cystine knot domains at the carboxyl terminal
    • 10.1016/S0167-4781(99)00099-8
    • Turner, B.S.; Bhaskar, K.R.; Hadzopoulou-Cladaras, M.; LaMont, J.T.: Cysteine-rich regions of pig gastric mucin contain von Willebrand factor and cystine knot domains at the carboxyl terminal. Biochim. Biophys. Acta 1447, 77-92 (1999)
    • (1999) Biochim. Biophys. Acta , vol.1447 , pp. 77-92
    • Turner, B.S.1    Bhaskar, K.R.2    Hadzopoulou-Cladaras, M.3    Lamont, J.T.4
  • 28
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: A unified platform for automated protein structure and function prediction
    • 10.1038/nprot.2010.5
    • Roy, A.; Kucukural, A.; Zhang, Y.: I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 5, 725-738 (2010)
    • (2010) Nat. Protoc. , vol.5 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 29
    • 36749061828 scopus 로고    scopus 로고
    • Template-based modeling and free modeling by I-TASSER in CASP7
    • 10.1002/prot.21702
    • Zhang, Y.: Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 69(Suppl 8), 108-117 (2007)
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 108-117
    • Zhang, Y.1
  • 30
    • 34250326780 scopus 로고    scopus 로고
    • Role of electrostatic interactions in amyloid β-protein (Aβ) oligomer formation: A discrete molecular dynamics study
    • 2007BpJ.92.4064Y 10.1529/biophysj.106.097766
    • Yun, S.; Urbanc, B.; Cruz, L.; Bitan, G.; Teplow, D.B.; Stanley, H.E.: Role of electrostatic interactions in amyloid β-protein (Aβ) oligomer formation: a discrete molecular dynamics study. Biophys. J. 92, 4064-4077 (2007)
    • (2007) Biophys. J. , vol.92 , pp. 4064-4077
    • Yun, S.1    Urbanc, B.2    Cruz, L.3    Bitan, G.4    Teplow, D.B.5    Stanley, H.E.6
  • 31
    • 84859605341 scopus 로고    scopus 로고
    • Dimer formation enhances structural differences between amyloid β-protein (1-40) and (1-42): An explicit-solvent molecular dynamics study
    • 2012PLoSO.7E4345B 10.1371/journal.pone.0034345
    • Barz, B.; Urbanc, B.: Dimer formation enhances structural differences between amyloid β-protein (1-40) and (1-42): an explicit-solvent molecular dynamics study. PLoS ONE 7, e34345 (2012)
    • (2012) PLoS ONE , vol.7 , pp. 34345
    • Barz, B.1    Urbanc, B.2
  • 32
    • 78649843015 scopus 로고    scopus 로고
    • Coarse-grained Monte Carlo simulations of mucus: Structure, dynamics, and thermodynamics
    • 2010BpJ.99.3507G 10.1016/j.bpj.2010.09.047
    • Gniewek, P.; Kolinski, A.: Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamics. Biophys. J. 99, 3507-3516 (2010)
    • (2010) Biophys. J. , vol.99 , pp. 3507-3516
    • Gniewek, P.1    Kolinski, A.2
  • 33
    • 0031471111 scopus 로고    scopus 로고
    • Von Willebrand factor
    • Ruggeri, Z.M.: von Willebrand factor. J. Clin. Invest. 100, S41-S46 (1997)
    • (1997) J. Clin. Invest. , vol.100 , pp. 41-46
    • Ruggeri, Z.M.1
  • 34
    • 0034924908 scopus 로고    scopus 로고
    • Biosynthesis, processing and secretion of von Willebrand factor: Biological implications
    • 10.1053/beha.2001.0132
    • de Wit, T.R.; van Mourik, J.A.: Biosynthesis, processing and secretion of von Willebrand factor: biological implications. Best. Pract. Res. Cl. Ha. 14, 241-255 (2001)
    • (2001) Best. Pract. Res. Cl. Ha. , vol.14 , pp. 241-255
    • De Wit, T.R.1    Van Mourik, J.A.2
  • 36
    • 0029633168 scopus 로고
    • GROMACS: A message-passing parallel molecular dynamics implementation
    • 1995CoPhC.91.43B 10.1016/0010-4655(95)00042-E
    • Berendsen, H.J.C.; van der Spoel, D.; van Drunen, R.: GROMACS: a message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91, 43-56 (1995)
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    Van Der Spoel, D.2    Van Drunen, R.3
  • 37
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E.; Hess, B.; van der Spoel, D.: GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7, 306-317 (2001)
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.