메뉴 건너뛰기




Volumn 11, Issue 95, 2014, Pages

A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure

Author keywords

Evolvability; Genotype phenotype map; Polyomino; Protein quaternary structure; Robustness; Self assembly

Indexed keywords

BIOLOGY; COMPLEX NETWORKS; REDUNDANCY; ROBUSTNESS (CONTROL SYSTEMS); SELF ASSEMBLY;

EID: 84901436725     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2014.0249     Document Type: Article
Times cited : (59)

References (58)
  • 1
    • 0025941171 scopus 로고
    • From genes to phenotype: Dynamical systems and evolvability
    • doi:10.1007/BF00123979
    • Alberch P. 1991 From genes to phenotype: dynamical systems and evolvability. Genetica 84, 5-11. (doi:10.1007/BF00123979)
    • (1991) Genetica , vol.84 , pp. 5-11
    • Alberch, P.1
  • 4
    • 76749127527 scopus 로고    scopus 로고
    • Genotype-phenotype mapping and the end of the 'genes as blueprint' metaphor
    • doi:10.1098/rstb.2009.0241
    • Pigliucci M. 2010 Genotype-phenotype mapping and the end of the 'genes as blueprint' metaphor. Phil. Trans. R. Soc. B 365, 557-566. (doi:10.1098/rstb. 2009.0241)
    • (2010) Phil. Trans. R. Soc. B , vol.365 , pp. 557-566
    • Pigliucci, M.1
  • 6
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • doi:10.1016/0022-5193(69)90015-0
    • Kauffman SA. 1969 Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22, 437-467. (doi:10.1016/0022- 5193(69)90015-0)
    • (1969) J. Theor. Biol. , vol.22 , pp. 437-467
    • Kauffman, S.A.1
  • 7
    • 1842687878 scopus 로고    scopus 로고
    • The yeast cell-cycle network is robustly designed
    • doi:10.1073/pnas.0305937101
    • Li F, Long T, Lu Y, Ouyang Q, Tang C. 2004 The yeast cell-cycle network is robustly designed. Proc. Natl Acad. Sci. USA 101, 4781-4786. (doi:10.1073/pnas.0305937101)
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 4781-4786
    • Li, F.1    Long, T.2    Lu, Y.3    Ouyang, Q.4    Tang, C.5
  • 9
    • 0028196714 scopus 로고
    • From sequences to shapes and back: A case study in RNA secondary structures
    • doi:10.1098/rspb.1994.0040
    • Schuster P, Fontana W, Stadler PF, Hofacker IL. 1994 From sequences to shapes and back: a case study in RNA secondary structures. Proc. R. Soc. Lond. B 255, 279-284. (doi:10.1098/rspb.1994.0040)
    • (1994) Proc. R. Soc. Lond. B , vol.255 , pp. 279-284
    • Schuster, P.1    Fontana, W.2    Stadler, P.F.3    Hofacker, I.L.4
  • 10
    • 37749000336 scopus 로고    scopus 로고
    • How mutational networks shape evolution: Lessons from RNA models
    • doi:10.1146/annurev.ecolsys.38.091206.095507
    • Cowperthwaite MC, Meyers LA. 2007 How mutational networks shape evolution: lessons from RNA models. Annu. Rev. Ecol. Evol. Syst. 38, 203-230. (doi:10.1146/annurev.ecolsys.38.091206.095507)
    • (2007) Annu. Rev. Ecol. Evol. Syst. , vol.38 , pp. 203-230
    • Cowperthwaite, M.C.1    Meyers, L.A.2
  • 11
    • 0022423920 scopus 로고
    • Theory for the folding and stability of globular proteins
    • doi:10.1021/bi00327a032
    • Dill KA. 1985 Theory for the folding and stability of globular proteins. Biochemistry 240, 1501-1509. (doi:10.1021/bi00327a032)
    • (1985) Biochemistry , vol.240 , pp. 1501-1509
    • Dill, K.A.1
  • 12
    • 0029772552 scopus 로고    scopus 로고
    • Emergence of preferred structures in a simple model of protein folding
    • doi:10.1126/science.273.5275.666
    • Li H, Helling R, Tang C, Wingreen N. 1996 Emergence of preferred structures in a simple model of protein folding. Science 273, 666-669. (doi:10.1126/science.273.5275.666)
    • (1996) Science , vol.273 , pp. 666-669
    • Li, H.1    Helling, R.2    Tang, C.3    Wingreen, N.4
  • 13
    • 0030782481 scopus 로고    scopus 로고
    • How are model protein structures distributed in sequence space?
    • doi:10.1016/S0006-3495(97)78268-7
    • Bornberg-Bauer E. 1997 How are model protein structures distributed in sequence space? Biophys. J. 73, 2393-2403. (doi:10.1016/S0006-3495(97)78268-7)
    • (1997) Biophys. J. , vol.73 , pp. 2393-2403
    • Bornberg-Bauer, E.1
  • 14
    • 77956118094 scopus 로고    scopus 로고
    • Self-assembly, modularity, and physical complexity
    • doi:10.1103/PhysRevE.82.026117
    • Ahnert SE, Johnston IG, Fink TMA, Doye JPK, Louis AA. 2010 Self-assembly, modularity, and physical complexity. Phys. Rev. E. 82, 026117. (doi:10.1103/PhysRevE.82.026117)
    • (2010) Phys. Rev. E. , vol.82 , pp. 026117
    • Ahnert, S.E.1    Johnston, I.G.2    Fink, T.M.A.3    Doye, J.P.K.4    Louis, A.A.5
  • 15
    • 79961067755 scopus 로고    scopus 로고
    • Evolutionary dynamics in a simple model of self-assembly
    • doi:10.1103/PhysRevE.83.066105
    • Johnston IG, Ahnert SE, Doye JPK, Louis AA. 2011 Evolutionary dynamics in a simple model of self-assembly. Phys. Rev. E. 83, 066105. (doi:10.1103/ PhysRevE.83.066105)
    • (2011) Phys. Rev. E. , vol.83 , pp. 066105
    • Johnston, I.G.1    Ahnert, S.E.2    Doye, J.P.K.3    Louis, A.A.4
  • 16
    • 33751415854 scopus 로고    scopus 로고
    • 3D complex: A structural classification of protein complexes
    • doi:10.1371/journal.pcbi.0020155
    • Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA. 2006 3D complex: a structural classification of protein complexes. PLoS Comput. Biol. 2, e155. (doi:10.1371/journal.pcbi.0020155)
    • (2006) PLoS Comput. Biol. , vol.2
    • Levy, E.D.1    Pereira-Leal, J.B.2    Chothia, C.3    Teichmann, S.A.4
  • 17
    • 84861511557 scopus 로고    scopus 로고
    • The emergence of protein complexes: Quaternary structure, dynamics and allostery
    • doi:10.1042/BST20120056
    • Perica T, Marsh J, Sousa F, Natan E, Colwell L, Ahnert S, Teichmann S. 2012 The emergence of protein complexes: quaternary structure, dynamics and allostery. Biochem. Soc. Trans. 40, 475. (doi:10.1042/BST20120056)
    • (2012) Biochem. Soc. Trans. , vol.40 , pp. 475
    • Perica, T.1    Marsh, J.2    Sousa, F.3    Natan, E.4    Colwell, L.5    Ahnert, S.6    Teichmann, S.7
  • 19
    • 46249083761 scopus 로고    scopus 로고
    • Assembly reflects evolution of protein complexes
    • doi:10.1038/nature06942
    • Levy ED, Erba EB, Robinson CV, Teichmann SA. 2008 Assembly reflects evolution of protein complexes. Nature 453, 1262-1265. (doi:10.1038/nature06942)
    • (2008) Nature , vol.453 , pp. 1262-1265
    • Levy, E.D.1    Erba, E.B.2    Robinson, C.V.3    Teichmann, S.A.4
  • 21
    • 0027973506 scopus 로고
    • A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements
    • doi:10.1126/science.7973630
    • Tuschl T, Gohlke C, Jovin TM, Westhof E, Eckstein F. 1994 A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements. Science 266, 785-789. (doi:10.1126/science.7973630)
    • (1994) Science , vol.266 , pp. 785-789
    • Tuschl, T.1    Gohlke, C.2    Jovin, T.M.3    Westhof, E.4    Eckstein, F.5
  • 22
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • doi:10.1093/nar/gkg599
    • Hofacker IL. 2003 Vienna RNA secondary structure server. Nucleic Acids Res. 31, 3429-3431. (doi:10.1093/nar/gkg599)
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 23
    • 0026620720 scopus 로고
    • Conformational changes in cubic insulin crystals in the pH range 7-11
    • doi:10.1016/S0006-3495(92)81697-1
    • Gursky O, Badger J, Li Y, Caspar DL. 1992 Conformational changes in cubic insulin crystals in the pH range 7-11. Biophys. J. 63, 1210-1220. (doi:10.1016/S0006-3495(92)81697-1)
    • (1992) Biophys. J. , vol.63 , pp. 1210-1220
    • Gursky, O.1    Badger, J.2    Li, Y.3    Caspar, D.L.4
  • 24
    • 0032560850 scopus 로고    scopus 로고
    • The structural basis of the activation of RAS by SOS
    • doi:10.1038/28548
    • Boriack-Sjodin PA, Margarit SM, Bar-Sagi D, Kuriyan J. 1998 The structural basis of the activation of RAS by SOS. Nature 394, 337-343. (doi:10.1038/28548)
    • (1998) Nature , vol.394 , pp. 337-343
    • Boriack-Sjodin, P.A.1    Margarit, S.M.2    Bar-Sagi, D.3    Kuriyan, J.4
  • 25
    • 0030000410 scopus 로고    scopus 로고
    • Crystal structure of T state haemoglobin with oxygen bound at all four haems
    • doi:10.1006/jmbi.1996.0124
    • Paoli M, Liddington R, Tame J, Wilkinson A, Dodson G. 1996 Crystal structure of T state haemoglobin with oxygen bound at all four haems. J. Mol. Biol. 256, 775-792. (doi:10.1006/jmbi.1996.0124)
    • (1996) J. Mol. Biol. , vol.256 , pp. 775-792
    • Paoli, M.1    Liddington, R.2    Tame, J.3    Wilkinson, A.4    Dodson, G.5
  • 26
    • 0031587292 scopus 로고    scopus 로고
    • The high resolution crystal structure of deoxyhemoglobin S
    • doi:10.1006/jmbi.1997.1253
    • Harrington DJ, Adachi K, Royer Jr WE. 1997 The high resolution crystal structure of deoxyhemoglobin S. J. Mol. Biol. 272, 398-407. (doi:10.1006/jmbi. 1997.1253)
    • (1997) J. Mol. Biol. , vol.272 , pp. 398-407
    • Harrington, D.J.1    Adachi, K.2    Royer Jr., W.E.3
  • 27
    • 0016743236 scopus 로고
    • Crystal structure of sickle-cell deoxyhemoglobin at 5 Å resolution
    • doi:10.1016/S0022-2836(75)80108-2
    • Wishner BC, Ward KB, Lattman EE, Love WE. 1975 Crystal structure of sickle-cell deoxyhemoglobin at 5 Å resolution. J. Mol. Biol. 98, 179-194. (doi:10.1016/S0022-2836(75)80108-2)
    • (1975) J. Mol. Biol. , vol.98 , pp. 179-194
    • Wishner, B.C.1    Ward, K.B.2    Lattman, E.E.3    Love, W.E.4
  • 28
    • 14044251445 scopus 로고    scopus 로고
    • Algorithmic self-assembly of DNA Sierpinski triangles
    • doi:10.1371/journal.pbio.0020424
    • Rothemund PWK, Papadakis N, Winfree E. 2004 Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2, e424. (doi:10.1371/journal.pbio.0020424)
    • (2004) PLoS Biol. , vol.2
    • Rothemund, P.W.K.1    Papadakis, N.2    Winfree, E.3
  • 29
    • 84859919548 scopus 로고    scopus 로고
    • A comparison of genotype-phenotype maps for RNA and proteins
    • doi:10.1016/j.bpj.2012.01.047
    • Ferrada E, Wagner A. 2012 A comparison of genotype-phenotype maps for RNA and proteins. Biophys. J. 102, 1916-1925. (doi:10.1016/j.bpj.2012.01.047)
    • (2012) Biophys. J. , vol.102 , pp. 1916-1925
    • Ferrada, E.1    Wagner, A.2
  • 30
    • 36348992094 scopus 로고    scopus 로고
    • Robustness and evolvability: A paradox resolved
    • doi:10.1098/rspb.2007.1137
    • Wagner A. 2008 Robustness and evolvability: a paradox resolved. Proc. R. Soc. B 275, 91-100. (doi:10.1098/rspb.2007.1137)
    • (2008) Proc. R. Soc. B , vol.275 , pp. 91-100
    • Wagner, A.1
  • 31
    • 84944488797 scopus 로고
    • Proving theorems by pattern recognition - II
    • doi:10.1002/j.1538-7305.1961.tb03975.x
    • Wang H. 1961 Proving theorems by pattern recognition - II. Bell Syst. Tech. J. 40, 1-41. (doi:10.1002/j.1538-7305.1961.tb03975.x)
    • (1961) Bell Syst. Tech. J. , vol.40 , pp. 1-41
    • Wang, H.1
  • 32
    • 0000223418 scopus 로고    scopus 로고
    • Universal computation via self-assembly of DNA: Some theory and experiments
    • Winfree E, Yang X, Seeman NC. 1996 Universal computation via self-assembly of DNA: some theory and experiments. DNA Based Comp. Two 44, 191-213.
    • (1996) DNA Based Comp. Two , vol.44 , pp. 191-213
    • Winfree, E.1    Yang, X.2    Seeman, N.C.3
  • 34
    • 34948823969 scopus 로고    scopus 로고
    • Complexity of self-assembled shapes
    • doi:10.1137/S0097539704446712
    • Soloveichik D, Winfree E. 2007 Complexity of self-assembled shapes. SIAM J. Comput. 36, 1544-1569. (doi:10.1137/S0097539704446712)
    • (2007) SIAM J. Comput. , vol.36 , pp. 1544-1569
    • Soloveichik, D.1    Winfree, E.2
  • 35
    • 44449168461 scopus 로고    scopus 로고
    • On the structural repertoire of pools of short, random RNA sequences
    • doi:10.1016/j.jtbi.2008.02.018
    • Stich M, Briones C, Manrubia SC. 2008 On the structural repertoire of pools of short, random RNA sequences. J. Theor. Biol. 252, 750-763. (doi:10.1016/j.jtbi.2008.02.018)
    • (2008) J. Theor. Biol. , vol.252 , pp. 750-763
    • Stich, M.1    Briones, C.2    Manrubia, S.C.3
  • 36
    • 0036345270 scopus 로고    scopus 로고
    • Enumerating designing sequences in the HP model
    • doi:10.1023/A:1016225010659
    • Irbäck A, Troein C. 2002 Enumerating designing sequences in the HP model. J. Biol. Phys. 28, 1-15. (doi:10.1023/A:1016225010659)
    • (2002) J. Biol. Phys. , vol.28 , pp. 1-15
    • Irbäck, A.1    Troein, C.2
  • 38
    • 0020373863 scopus 로고
    • The molecular clock hypothesis: Biochemical evolution, genetic differentiation and systematics
    • doi:10.1146/annurev.es.13.110182.001035
    • Thorpe JP. 1982 The molecular clock hypothesis: biochemical evolution, genetic differentiation and systematics. Annu. Rev. Ecol. Syst. 13, 139-168. (doi:10.1146/annurev.es.13.110182.001035)
    • (1982) Annu. Rev. Ecol. Syst. , vol.13 , pp. 139-168
    • Thorpe, J.P.1
  • 39
    • 33847268619 scopus 로고    scopus 로고
    • Robustness can evolve gradually in complex regulatory gene networks with varying topology
    • doi:10.1371/journal.pcbi.0030015
    • Ciliberti S, Martin OC, Wagner A. 2007 Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Comput. Biol. 3, e15. (doi:10.1371/journal.pcbi.0030015)
    • (2007) PLoS Comput. Biol. , vol.3
    • Ciliberti, S.1    Martin, O.C.2    Wagner, A.3
  • 40
    • 33846867274 scopus 로고    scopus 로고
    • Neutral fitness landscapes in signalling networks
    • doi:10.1098/rsif.2006.0152
    • Fernández P, Solé RV. 2007 Neutral fitness landscapes in signalling networks. J. R. Soc. Interface 4, 41-47. (doi:10.1098/rsif.2006.0152)
    • (2007) J. R. Soc. Interface , vol.4 , pp. 41-47
    • Fernández, P.1    Solé, R.V.2
  • 42
    • 60749114979 scopus 로고    scopus 로고
    • Neutral network sizes of biological RNA molecules can be computed and are not atypically small
    • doi:10.1186/1471-2105-9-464
    • Jörg T, Martin O, Wagner A. 2008 Neutral network sizes of biological RNA molecules can be computed and are not atypically small. BMC Bioinform. 9, 464. (doi:10.1186/1471-2105-9-464)
    • (2008) BMC Bioinform. , vol.9 , pp. 464
    • Jörg, T.1    Martin, O.2    Wagner, A.3
  • 43
    • 80054765283 scopus 로고    scopus 로고
    • Topological structure of the space of phenotypes: The case of RNA neutral networks
    • doi:10.1371/journal.pone.0026324
    • Aguirre J, Buldú JM, Stich M, Manrubia SC. 2011 Topological structure of the space of phenotypes: the case of RNA neutral networks. PLoS ONE 6, e263241. (doi:10.1371/journal.pone.0026324)
    • (2011) PLoS ONE , vol.6
    • Aguirre, J.1    Buldú, J.M.2    Stich, M.3    Manrubia, S.C.4
  • 44
    • 84858778369 scopus 로고    scopus 로고
    • Epistasis can lead to fragmented neutral spaces and contingency in evolution
    • doi:10.1098/rspb.2011.2183
    • Schaper S, Johnston IG, Louis AA. 2012 Epistasis can lead to fragmented neutral spaces and contingency in evolution. Proc. R. Soc. B 279, 1777-1783. (doi:10.1098/rspb.2011.2183)
    • (2012) Proc. R. Soc. B , vol.279 , pp. 1777-1783
    • Schaper, S.1    Johnston, I.G.2    Louis, A.A.3
  • 45
    • 0023647382 scopus 로고
    • Towards a general theory of adaptive walks on rugged landscapes
    • doi:10.1016/S0022-5193(87)80029-2
    • Kauffman S, Levin S. 1987 Towards a general theory of adaptive walks on rugged landscapes. J. Theor. Biol. 128, 11-45. (doi:10.1016/S0022-5193(87)80029- 2)
    • (1987) J. Theor. Biol. , vol.128 , pp. 11-45
    • Kauffman, S.1    Levin, S.2
  • 46
    • 34548706596 scopus 로고    scopus 로고
    • Percolation on fitness landscapes: Effects of correlation, phenotype, and incompatibilities
    • doi:10.1016/j.jtbi.2007.07.009
    • Gravner J, Pitman D, Gavrilets S. 2007 Percolation on fitness landscapes: effects of correlation, phenotype, and incompatibilities. J. Theor. Biol. 248, 627-645. (doi:10.1016/j.jtbi.2007.07.009)
    • (2007) J. Theor. Biol. , vol.248 , pp. 627-645
    • Gravner, J.1    Pitman, D.2    Gavrilets, S.3
  • 47
    • 0018567632 scopus 로고
    • Theoretical studies of clonal selection: Minimal antibody repertoire size and reliability of self-non-self discrimination
    • doi:10.1016/0022-5193(79)90275-3
    • Perelson AS, Oster GF. 1979 Theoretical studies of clonal selection: minimal antibody repertoire size and reliability of self-non-self discrimination. J. Theor. Biol. 81, 645-670. (doi:10.1016/0022-5193(79)90275-3)
    • (1979) J. Theor. Biol. , vol.81 , pp. 645-670
    • Perelson, A.S.1    Oster, G.F.2
  • 48
  • 49
    • 34447537179 scopus 로고    scopus 로고
    • Evolution favors protein mutational robustness in sufficiently large populations
    • doi:10.1186/1741-7007-5-29
    • Bloom J, Lu Z, Chen D, Raval A, Venturelli O, Arnold F. 2007 Evolution favors protein mutational robustness in sufficiently large populations. BMC Biol. 5, 29. (doi:10.1186/1741-7007-5-29)
    • (2007) BMC Biol. , vol.5 , pp. 29
    • Bloom, J.1    Lu, Z.2    Chen, D.3    Raval, A.4    Venturelli, O.5    Arnold, F.6
  • 51
    • 77955844575 scopus 로고    scopus 로고
    • Robustness and evolvability
    • doi:10.1016/j.tig.2010.06.002
    • Masel J, Trotter MV. 2010 Robustness and evolvability. Trends Genet. 26, 406-414. (doi:10.1016/j.tig.2010.06.002)
    • (2010) Trends Genet. , vol.26 , pp. 406-414
    • Masel, J.1    Trotter, M.V.2
  • 53
    • 75149186552 scopus 로고    scopus 로고
    • Mutational robustness can facilitate adaptation
    • doi:10.1038/nature08694
    • Draghi JA, Parsons TL, Wagner GP, Plotkin JB. 2010 Mutational robustness can facilitate adaptation. Nature 463, 353-355. (doi:10.1038/nature08694)
    • (2010) Nature , vol.463 , pp. 353-355
    • Draghi, J.A.1    Parsons, T.L.2    Wagner, G.P.3    Plotkin, J.B.4
  • 54
    • 78650804058 scopus 로고    scopus 로고
    • The evolvability of programmable hardware
    • doi:10.1098/rsif.2010.0212
    • Raman K, Wagner A. 2011 The evolvability of programmable hardware. J. R. Soc. Interface 8, 269-281. (doi:10.1098/rsif.2010.0212)
    • (2011) J. R. Soc. Interface , vol.8 , pp. 269-281
    • Raman, K.1    Wagner, A.2
  • 55
    • 55449093810 scopus 로고    scopus 로고
    • An end to endless forms: Epistasis, phenotype distribution bias, and nonuniform evolution
    • doi:10.1371/journal.pcbi.1000202
    • Borenstein E, Krakauer DC. 2008 An end to endless forms: epistasis, phenotype distribution bias, and nonuniform evolution. PLoS Comput. Biol. 4, e1000202. (doi:10.1371/journal.pcbi.1000202)
    • (2008) PLoS Comput. Biol. , vol.4
    • Borenstein, E.1    Krakauer, D.C.2
  • 56
    • 78149283618 scopus 로고    scopus 로고
    • Regulatory networks and connected components of the neutral space
    • doi:10.1140/epjb/e2010-00176-4
    • Boldhaus G, Klemm K. 2010 Regulatory networks and connected components of the neutral space. Eur. Phys. J. B 77, 233-237. (doi:10.1140/epjb/e2010-00176- 4)
    • (2010) Eur. Phys. J. B , vol.77 , pp. 233-237
    • Boldhaus, G.1    Klemm, K.2
  • 58
    • 0000686163 scopus 로고    scopus 로고
    • Computer generation and enumeration of compact self-avoiding walks within simple geometries on lattices
    • doi:10.1016/S1089-3156(97)00022-6
    • Kloczkowski A, Jernigan RL. 1997 Computer generation and enumeration of compact self-avoiding walks within simple geometries on lattices. Comput. Theor. Polymer Sci. 7, 163-173. (doi:10.1016/S1089-3156(97)00022-6)
    • (1997) Comput. Theor. Polymer Sci. , vol.7 , pp. 163-173
    • Kloczkowski, A.1    Jernigan, R.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.