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Volumn 487, Issue C, 2011, Pages 575-593

Computational design of intermolecular stability and specificity in protein self-assembly

Author keywords

[No Author keywords available]

Indexed keywords

BIOMATERIAL; PROTEIN;

EID: 78650883017     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381270-4.00020-2     Document Type: Chapter
Times cited : (7)

References (46)
  • 1
    • 0027996196 scopus 로고
    • Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution
    • Bella, J., Eaton, M., et al. (1994). Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution. Science 266(5182), 75-81.
    • (1994) Science , vol.266 , Issue.5182 , pp. 75-81
    • Bella, J.1    Eaton, M.2
  • 2
    • 0029645406 scopus 로고
    • Hydration structure of a collagen peptide
    • Bella, J., Brodsky, B., et al. (1995). Hydration structure of a collagen peptide. Structure 3(9), 893-906.
    • (1995) Structure , vol.3 , Issue.9 , pp. 893-906
    • Bella, J.1    Brodsky, B.2
  • 3
    • 34047232678 scopus 로고    scopus 로고
    • Positive and negative design in stability and thermal adaptation of natural proteins
    • Berezovsky, I. N., Zeldovich, K. B., et al. (2007). Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput. Biol. 3(3), e52.
    • (2007) PLoS Comput. Biol. , vol.3 , Issue.3
    • Berezovsky, I.N.1    Zeldovich, K.B.2
  • 4
    • 61749104243 scopus 로고    scopus 로고
    • Designed alpha-helical tectons for constructing multicomponent synthetic biological systems
    • Bromley, E. H., Sessions, R. B., et al. (2009). Designed alpha-helical tectons for constructing multicomponent synthetic biological systems. J. Am. Chem. Soc. 131(3), 928-930.
    • (2009) J. Am. Chem. Soc. , vol.131 , Issue.3 , pp. 928-930
    • Bromley, E.H.1    Sessions, R.B.2
  • 5
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat, B. I., and Mayo, S. L. (1997). De novo protein design: Fully automated sequence selection. Science 278(5335), 82-87.
    • (1997) Science , vol.278 , Issue.5335 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 6
    • 0036303549 scopus 로고    scopus 로고
    • Structural properties of a collagenous heterotrimer that mimics the collagenase cleavage site of collagen type I
    • Fiori, S., Sacca, B., et al. (2002). Structural properties of a collagenous heterotrimer that mimics the collagenase cleavage site of collagen type I. J. Mol. Biol. 319(5), 1235-1242.
    • (2002) J. Mol. Biol. , vol.319 , Issue.5 , pp. 1235-1242
    • Fiori, S.1    Sacca, B.2
  • 7
    • 33847627484 scopus 로고    scopus 로고
    • Self-assembled heterotrimeric collagen triple helices directed through electrostatic interactions
    • Gauba, V., and Hartgerink, J. D. (2007a). Self-assembled heterotrimeric collagen triple helices directed through electrostatic interactions. J. Am. Chem. Soc. 129(9), 2683-2690.
    • (2007) J. Am. Chem. Soc. , vol.129 , Issue.9 , pp. 2683-2690
    • Gauba, V.1    Hartgerink, J.D.2
  • 8
    • 36849062200 scopus 로고    scopus 로고
    • Surprisingly high stability of collagen ABC heterotrimer: Evaluation of side chain charge pairs
    • Gauba, V., and Hartgerink, J. D. (2007b). Surprisingly high stability of collagen ABC heterotrimer: Evaluation of side chain charge pairs. J. Am. Chem. Soc. 129(48), 15034-15041.
    • (2007) J. Am. Chem. Soc. , vol.129 , Issue.48 , pp. 15034-15041
    • Gauba, V.1    Hartgerink, J.D.2
  • 9
    • 44949181913 scopus 로고    scopus 로고
    • Synthetic collagen heterotrimers: Structural mimics of wild-type and mutant collagen type I
    • Gauba, V., and Hartgerink, J. D. (2008). Synthetic collagen heterotrimers: Structural mimics of wild-type and mutant collagen type I. J. Am. Chem. Soc. 130(23), 7509-7515.
    • (2008) J. Am. Chem. Soc. , vol.130 , Issue.23 , pp. 7509-7515
    • Gauba, V.1    Hartgerink, J.D.2
  • 10
    • 65249171530 scopus 로고    scopus 로고
    • Design of protein-interaction specificity gives selective bZIP-binding peptides
    • Grigoryan, G., Reinke, A. W., et al. (2009). Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 458(7240), 859-864.
    • (2009) Nature , vol.458 , Issue.7240 , pp. 859-864
    • Grigoryan, G.1    Reinke, A.W.2
  • 11
    • 0035826571 scopus 로고    scopus 로고
    • Proof of principle in a de novo designed protein maquette: An allosterically regulated, charge-activated conformational switch in a tetraalpha- helix bundle
    • Grosset, A. M., Gibney, B. R., et al. (2001). Proof of principle in a de novo designed protein maquette: An allosterically regulated, charge-activated conformational switch in a tetraalpha- helix bundle. Biochemistry 40(18), 5474-5487.
    • (2001) Biochemistry , vol.40 , Issue.18 , pp. 5474-5487
    • Grosset, A.M.1    Gibney, B.R.2
  • 12
    • 0027756896 scopus 로고
    • A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants
    • Harbury, P. B., Zhang, T., et al. (1993). A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262(5138), 1401-1407.
    • (1993) Science , vol.262 , Issue.5138 , pp. 1401-1407
    • Harbury, P.B.1    Zhang, T.2
  • 13
    • 0032553587 scopus 로고    scopus 로고
    • High-resolution protein design with backbone freedom
    • Harbury, P. B., Plecs, J. J., et al. (1998). High-resolution protein design with backbone freedom. Science 282(5393), 1462-1467.
    • (1998) Science , vol.282 , Issue.5393 , pp. 1462-1467
    • Harbury, P.B.1    Plecs, J.J.2
  • 14
    • 0037217406 scopus 로고    scopus 로고
    • Automated design of specificity in molecular recognition
    • Havranek, J. J., and Harbury, P. B. (2003). Automated design of specificity in molecular recognition. Nat. Struct. Biol. 10(1), 45-52.
    • (2003) Nat. Struct. Biol. , vol.10 , Issue.1 , pp. 45-52
    • Havranek, J.J.1    Harbury, P.B.2
  • 15
    • 34948867738 scopus 로고    scopus 로고
    • The collagen family members as cell adhesion proteins
    • Heino, J. (2007). The collagen family members as cell adhesion proteins. Bioessays 29(10), 1001-1010.
    • (2007) Bioessays , vol.29 , Issue.10 , pp. 1001-1010
    • Heino, J.1
  • 16
    • 11244318120 scopus 로고    scopus 로고
    • Computational protein design is a challenge for implicit solvation models
    • Jaramillo, A., and Wodak, S. J. (2005). Computational protein design is a challenge for implicit solvation models. Biophys. J. 88(1), 156-171.
    • (2005) Biophys. J. , vol.88 , Issue.1 , pp. 156-171
    • Jaramillo, A.1    Wodak, S.J.2
  • 17
    • 40449116114 scopus 로고    scopus 로고
    • De novo computational design of retro-aldol enzymes
    • Jiang, L., Althoff, E. A., et al. (2008). De novo computational design of retro-aldol enzymes. Science 319(5868), 1387-1391.
    • (2008) Science , vol.319 , Issue.5868 , pp. 1387-1391
    • Jiang, L.1    Althoff, E.A.2
  • 18
    • 0029992496 scopus 로고    scopus 로고
    • Collagen fibril formation
    • Kadler, K. E., Holmes, D. F., et al. (1996). Collagen fibril formation. Biochem. J. 316(Pt 1), 1-11.
    • (1996) Biochem. J. , vol.316 , Issue.PART 1 , pp. 1-11
    • Kadler, K.E.1    Holmes, D.F.2
  • 19
    • 0037805549 scopus 로고    scopus 로고
    • Basement membranes: Structure, assembly and role in tumour angiogenesis
    • Kalluri, R. (2003). Basement membranes: Structure, assembly and role in tumour angiogenesis. Nat. Rev. Cancer 3(6), 422-433.
    • (2003) Nat. Rev. Cancer , vol.3 , Issue.6 , pp. 422-433
    • Kalluri, R.1
  • 20
    • 23444436172 scopus 로고
    • Protein design by binary patterning of polar and nonpolar amino-acids
    • Kamtekar, S., Schiffer, J. M., et al. (1993). Protein design by binary patterning of polar and nonpolar amino-acids. Science 262(5140), 1680-1685.
    • (1993) Science , vol.262 , Issue.5140 , pp. 1680-1685
    • Kamtekar, S.1    Schiffer, J.M.2
  • 22
    • 0345306764 scopus 로고    scopus 로고
    • Design of a novel globular protein fold with atomiclevel accuracy
    • Kuhlman, B., Dantas, G., et al. (2003). Design of a novel globular protein fold with atomiclevel accuracy. Science 302(5649), 1364-1368.
    • (2003) Science , vol.302 , Issue.5649 , pp. 1364-1368
    • Kuhlman, B.1    Dantas, G.2
  • 23
    • 0035910266 scopus 로고    scopus 로고
    • Achieving stability and conformational specificity in designed proteins via binary patterning
    • Marshall, S. A., and Mayo, S. L. (2001). Achieving stability and conformational specificity in designed proteins via binary patterning. J. Mol. Biol. 305(3), 619-631.
    • (2001) J. Mol. Biol. , vol.305 , Issue.3 , pp. 619-631
    • Marshall, S.A.1    Mayo, S.L.2
  • 24
    • 0029155380 scopus 로고
    • A designed heterotrimeric coiled coil
    • Nautiyal, S., Woolfson, D. N., et al. (1995). A designed heterotrimeric coiled coil. Biochemistry 34(37), 11645-11651.
    • (1995) Biochemistry , vol.34 , Issue.37 , pp. 11645-11651
    • Nautiyal, S.1    Woolfson, D.N.2
  • 25
    • 0030602223 scopus 로고    scopus 로고
    • Design and synthesis of heterotrimeric collagen peptides with a built-in cystine-knot. Models collagen catabolism by matrix metalloproteases
    • Ottl, J., Battistuta, R., et al. (1996). Design and synthesis of heterotrimeric collagen peptides with a built-in cystine-knot. Models collagen catabolism by matrix metalloproteases. FEBS Lett. 398(1), 31-36.
    • (1996) FEBS Lett. , vol.398 , Issue.1 , pp. 31-36
    • Ottl, J.1    Battistuta, R.2
  • 26
    • 1842559515 scopus 로고    scopus 로고
    • Equilibrium thermal transitions of collagen model peptides
    • Persikov, A. V., Xu, Y., et al. (2004). Equilibrium thermal transitions of collagen model peptides. Protein Sci. 13(4), 893-902.
    • (2004) Protein Sci , vol.13 , Issue.4 , pp. 893-902
    • Persikov, A.V.1    Xu, Y.2
  • 27
    • 13444292142 scopus 로고    scopus 로고
    • Electrostatic interactions involving lysine make major contributions to collagen triple-helix stability
    • Persikov, A. V., Ramshaw, J. A., et al. (2005). Electrostatic interactions involving lysine make major contributions to collagen triple-helix stability. Biochemistry 44(5), 1414-1422.
    • (2005) Biochemistry , vol.44 , Issue.5 , pp. 1414-1422
    • Persikov, A.V.1    Ramshaw, J.A.2
  • 28
    • 1842454839 scopus 로고    scopus 로고
    • Energy functions for protein design I: Efficient and accurate continuum electrostatics and solvation
    • Pokala, N., and Handel, T. M. (2004). Energy functions for protein design I: Efficient and accurate continuum electrostatics and solvation. Protein Sci. 13(4), 925-936.
    • (2004) Protein Sci , vol.13 , Issue.4 , pp. 925-936
    • Pokala, N.1    Handel, T.M.2
  • 29
    • 0000523565 scopus 로고
    • Structure of collagen
    • Ramachandran, G. N., and Kartha, G. (1955). Structure of collagen. Nature 176(4482), 593-595.
    • (1955) Nature , vol.176 , Issue.4482 , pp. 593-595
    • Ramachandran, G.N.1    Kartha, G.2
  • 30
    • 33845293800 scopus 로고    scopus 로고
    • Energetic determinants of oligomeric state specificity in coiled coils
    • Ramos, J., and Lazaridis, T. (2006). Energetic determinants of oligomeric state specificity in coiled coils. J. Am. Chem. Soc. 128(48), 15499-15510.
    • (2006) J. Am. Chem. Soc. , vol.128 , Issue.48 , pp. 15499-15510
    • Ramos, J.1    Lazaridis, T.2
  • 31
    • 77951685234 scopus 로고    scopus 로고
    • A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering
    • Reinke, A. W., Grant, R. A., et al. (2010). A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering. J. Am. Chem. Soc. 132(17), 6025-6031.
    • (2010) J. Am. Chem. Soc. , vol.132 , Issue.17 , pp. 6025-6031
    • Reinke, A.W.1    Grant, R.A.2
  • 32
    • 32444451050 scopus 로고
    • The molecular structure of collagen
    • Rich, A., and Crick, F. H. (1961). The molecular structure of collagen. J. Mol. Biol. 3, 483-506.
    • (1961) J. Mol. Biol. , vol.3 , pp. 483-506
    • Rich, A.1    Crick, F.H.2
  • 33
    • 0016669438 scopus 로고
    • Conformational implications of amino acid sequence regularities in collagen
    • Salem, G., and Traub, W. (1975). Conformational implications of amino acid sequence regularities in collagen. FEBS Lett. 51(1), 94-99.
    • (1975) FEBS Lett , vol.51 , Issue.1 , pp. 94-99
    • Salem, G.1    Traub, W.2
  • 34
    • 0020857308 scopus 로고
    • Design of immobile nucleic acid junctions
    • Seeman, N. C., and Kallenbach, N. R. (1983). Design of immobile nucleic acid junctions. Biophys. J. 44(2), 201-209.
    • (1983) Biophys. J. , vol.44 , Issue.2 , pp. 201-209
    • Seeman, N.C.1    Kallenbach, N.R.2
  • 35
    • 0027234766 scopus 로고
    • Engineering of stable and fast-folding sequences of model proteins
    • Shakhnovich, E. I., and Gutin, A. M. (1993a). Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. USA 90, 7195-7199.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 7195-7199
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 36
    • 0027438090 scopus 로고
    • A new approach to the design of stable proteins
    • Shakhnovich, E. I., and Gutin, A. M. (1993b). A new approach to the design of stable proteins. Protein Eng. 6(8), 793-800.
    • (1993) Protein Eng. , vol.6 , Issue.8 , pp. 793-800
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 37
    • 0035853042 scopus 로고    scopus 로고
    • Reverse engineering the (beta/alpha)8 barrel fold
    • Silverman, J. A., Balakrishnan, R., et al. (2001). Reverse engineering the (beta/alpha)8 barrel fold. Proc. Natl. Acad. Sci. USA 98(6), 3092-3097.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , Issue.6 , pp. 3092-3097
    • Silverman, J.A.1    Balakrishnan, R.2
  • 38
    • 0031659672 scopus 로고    scopus 로고
    • Effects of salt bridges on protein structure and design
    • Sindelar, C. V., Hendsch, Z. S., et al. (1998). Effects of salt bridges on protein structure and design. Protein Sci. 7(9), 1898-1914.
    • (1998) Protein Sci , vol.7 , Issue.9 , pp. 1898-1914
    • Sindelar, C.V.1    Hendsch, Z.S.2
  • 39
    • 0037305504 scopus 로고    scopus 로고
    • Computational design of a water-soluble analog of phospholamban
    • Slovic, A. M., Summa, C. M., et al. (2003). Computational design of a water-soluble analog of phospholamban. Protein Sci. 12(2), 337-348.
    • (2003) Protein Sci. , vol.12 , Issue.2 , pp. 337-348
    • Slovic, A.M.1    Summa, C.M.2
  • 40
    • 0036385840 scopus 로고    scopus 로고
    • Computational de novo design, and characterization of an A(2)B(2) diiron protein
    • Summa, C. M., Rosenblatt, M. M., et al. (2002). Computational de novo design, and characterization of an A(2)B(2) diiron protein. J. Mol. Biol. 321(5), 923-938.
    • (2002) J. Mol. Biol. , vol.321 , Issue.5 , pp. 923-938
    • Summa, C.M.1    Rosenblatt, M.M.2
  • 41
    • 0017103671 scopus 로고
    • Contribution of the A2 chain to the molecular stability of collagen
    • Traub, W., and Fietzek, P. P. (1976). Contribution of the A2 chain to the molecular stability of collagen. FEBS Lett. 68(2), 245-249.
    • (1976) FEBS Lett , vol.68 , Issue.2 , pp. 245-249
    • Traub, W.1    Fietzek, P.P.2
  • 42
    • 0028261035 scopus 로고
    • Electrostatic interactions in collagen-like triple-helical peptides
    • Venugopal, M. G., Ramshaw, J. A., et al. (1994). Electrostatic interactions in collagen-like triple-helical peptides. Biochemistry 33(25), 7948-7956.
    • (1994) Biochemistry , vol.33 , Issue.25 , pp. 7948-7956
    • Venugopal, M.G.1    Ramshaw, J.A.2
  • 43
    • 0027080909 scopus 로고
    • Atomic solvation parameters applied to molecular dynamics of proteins in solution
    • Wesson, L., and Eisenberg, D. (1992). Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1(2), 227-235.
    • (1992) Protein Sci , vol.1 , Issue.2 , pp. 227-235
    • Wesson, L.1    Eisenberg, D.2
  • 44
    • 0028846974 scopus 로고
    • Binary patterning of polar and nonpolar aminoacids in the sequences and structures of native proteins
    • West, M. W., and Hecht, M. H. (1995). Binary patterning of polar and nonpolar aminoacids in the sequences and structures of native proteins. Protein Sci. 4(10), 2032-2039.
    • (1995) Protein Sci , vol.4 , Issue.10 , pp. 2032-2039
    • West, M.W.1    Hecht, M.H.2
  • 45
    • 77949503842 scopus 로고    scopus 로고
    • De novo self-assembling collagen heterotrimers using explicit positive and negative design
    • Xu, F., Zhang, L., et al. (2010). De novo self-assembling collagen heterotrimers using explicit positive and negative design. Biochemistry 49(11), 2307-2316.
    • (2010) Biochemistry , vol.49 , Issue.11 , pp. 2307-2316
    • Xu, F.1    Zhang, L.2
  • 46
    • 0030670567 scopus 로고    scopus 로고
    • Gly-Pro-Arg confers stability similar to Gly-Pro-Hyp in the collagen triple-helix of host-guest peptides
    • Yang, W., Chan, V. C., et al. (1997). Gly-Pro-Arg confers stability similar to Gly-Pro-Hyp in the collagen triple-helix of host-guest peptides. J. Biol. Chem. 272(46), 28837-28840.
    • (1997) J. Biol. Chem. , vol.272 , Issue.46 , pp. 28837-28840
    • Yang, W.1    Chan, V.C.2


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