메뉴 건너뛰기




Volumn 83, Issue 2, 2015, Pages 235-247

Exploring alternate states and oligomerization preferences of coiled-coils by de novo structure modeling

Author keywords

Asymmetric fold and dock; Free energy; Oligomeric state prediction; Rosetta; Structure prediction; Symmetry

Indexed keywords

ARTICLE; CALCULATION; CRYSTAL STRUCTURE; MATHEMATICAL MODEL; MOLECULAR DOCKING; MOLECULAR DYNAMICS; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN STRUCTURE; STOICHIOMETRY; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN MULTIMERIZATION; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

EID: 84924783388     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24729     Document Type: Article
Times cited : (20)

References (44)
  • 3
    • 0027756896 scopus 로고
    • A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants
    • Harbury PB, Zhang T, Kim PS, Alber T. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 1993;262:1401-1407.
    • (1993) Science , vol.262 , pp. 1401-1407
    • Harbury, P.B.1    Zhang, T.2    Kim, P.S.3    Alber, T.4
  • 4
    • 0036606751 scopus 로고    scopus 로고
    • Purification of the Escherichia coli ammonium transporter AmtB reveals a trimeric stoichiometry
    • Blakey D, Leech A, Thomas GH, Coutts G, Findlay K, Merrick M. Purification of the Escherichia coli ammonium transporter AmtB reveals a trimeric stoichiometry. Biochem J 2002;364:527-535.
    • (2002) Biochem J , vol.364 , pp. 527-535
    • Blakey, D.1    Leech, A.2    Thomas, G.H.3    Coutts, G.4    Findlay, K.5    Merrick, M.6
  • 6
    • 0032497322 scopus 로고    scopus 로고
    • A Buried Polar Interaction Can Direct the Relative Orientation of Helices in a Coiled Coil†
    • Oakley MG, Kim PS. A Buried Polar Interaction Can Direct the Relative Orientation of Helices in a Coiled Coil†. Biochemistry (Mosc) 1998;37:12603-12610.
    • (1998) Biochemistry (Mosc) , vol.37 , pp. 12603-12610
    • Oakley, M.G.1    Kim, P.S.2
  • 7
    • 0030983330 scopus 로고    scopus 로고
    • A single amino acid can switch the oligomerization state of the alpha-helical coiled-coil domain of cartilage matrix protein
    • Beck K, Gambee JE, Kamawal A, Bächinger HP. A single amino acid can switch the oligomerization state of the alpha-helical coiled-coil domain of cartilage matrix protein. EMBO J 1997;16:3767-3777.
    • (1997) EMBO J , vol.16 , pp. 3767-3777
    • Beck, K.1    Gambee, J.E.2    Kamawal, A.3    Bächinger, H.P.4
  • 8
    • 0032562663 scopus 로고    scopus 로고
    • Tenascin-C hexabrachion assembly is a sequential two-step process initiated by coiled-coil α-helices
    • Kammerer RA, Schulthess T, Landwehr R, Lustig A, Fischer D, Engel J. Tenascin-C hexabrachion assembly is a sequential two-step process initiated by coiled-coil α-helices. J Biol Chem 1998;273:10602-10608.
    • (1998) J Biol Chem , vol.273 , pp. 10602-10608
    • Kammerer, R.A.1    Schulthess, T.2    Landwehr, R.3    Lustig, A.4    Fischer, D.5    Engel, J.6
  • 9
    • 16944363590 scopus 로고    scopus 로고
    • Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism
    • Gonzalez L, Brown RA, Richardson D, Alber T. Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism. Nat Struct Mol Biol 1996;3:1002-1010.
    • (1996) Nat Struct Mol Biol , vol.3 , pp. 1002-1010
    • Gonzalez, L.1    Brown, R.A.2    Richardson, D.3    Alber, T.4
  • 10
    • 33645657331 scopus 로고    scopus 로고
    • Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution
    • Yadav MK, Leman LJ, Price DJ, Brooks CL, Stout CD, Ghadiri MR. Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Biochemistry (Mosc) 2006;45:4463-4473.
    • (2006) Biochemistry (Mosc) , vol.45 , pp. 4463-4473
    • Yadav, M.K.1    Leman, L.J.2    Price, D.J.3    Brooks, C.L.4    Stout, C.D.5    Ghadiri, M.R.6
  • 11
    • 49549094267 scopus 로고    scopus 로고
    • Structural specificity in coiled-coil interactions
    • Grigoryan G, Keating AE. Structural specificity in coiled-coil interactions. Curr Opin Struct Biol 2008;18:477-483.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 477-483
    • Grigoryan, G.1    Keating, A.E.2
  • 12
    • 84871757783 scopus 로고    scopus 로고
    • LOGICOIL-multi-state prediction of coiled-coil oligomeric state
    • Vincent TL, Green PJ, Woolfson DN. LOGICOIL-multi-state prediction of coiled-coil oligomeric state. Bioinformatics 2013;29:69-76.
    • (2013) Bioinformatics , vol.29 , pp. 69-76
    • Vincent, T.L.1    Green, P.J.2    Woolfson, D.N.3
  • 13
    • 33845293800 scopus 로고    scopus 로고
    • Energetic determinants of oligomeric state specificity in coiled coils
    • Ramos J, Lazaridis T. Energetic determinants of oligomeric state specificity in coiled coils. J Am Chem Soc 2006;128:15499-15510.
    • (2006) J Am Chem Soc , vol.128 , pp. 15499-15510
    • Ramos, J.1    Lazaridis, T.2
  • 14
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    • Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002;320:369-387.
    • (2002) J Mol Biol , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 15
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002;99:14116-14121.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 16
    • 0028360307 scopus 로고
    • The contribution of vibrational entropy to molecular association: the dimerization of insulin
    • Tidor B, Karplus M. The contribution of vibrational entropy to molecular association: the dimerization of insulin. J Mol Biol 1994;238:405-414.
    • (1994) J Mol Biol , vol.238 , pp. 405-414
    • Tidor, B.1    Karplus, M.2
  • 17
    • 34548232365 scopus 로고    scopus 로고
    • Inference of macromolecular assemblies from crystalline state
    • Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007;372:774-797.
    • (2007) J Mol Biol , vol.372 , pp. 774-797
    • Krissinel, E.1    Henrick, K.2
  • 19
    • 58149185130 scopus 로고    scopus 로고
    • CC+: a relational database of coiled-coil structures
    • Testa OD, Moutevelis E, Woolfson DN. CC+: a relational database of coiled-coil structures. Nucleic Acids Res 2009;37(Suppl 1):D315-D322.
    • (2009) Nucleic Acids Res , vol.37 , pp. D315-D322
    • Testa, O.D.1    Moutevelis, E.2    Woolfson, D.N.3
  • 20
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
    • (2003) J Mol Biol , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 28
    • 0031808074 scopus 로고    scopus 로고
    • A helix propensity scale based on experimental studies of peptides and proteins
    • Nick Pace C, Martin Scholtz J. A helix propensity scale based on experimental studies of peptides and proteins. Biophys J 1998;75:422-427.
    • (1998) Biophys J , vol.75 , pp. 422-427
    • Nick Pace, C.1    Martin Scholtz, J.2
  • 29
    • 0025222978 scopus 로고
    • A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids
    • O'Neil KT, DeGrado WF. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 1990;250:646-651.
    • (1990) Science , vol.250 , pp. 646-651
    • O'Neil, K.T.1    DeGrado, W.F.2
  • 33
    • 47349124555 scopus 로고    scopus 로고
    • Predicting helix orientation for coiled-coil dimers
    • Apgar JR, Gutwin KN, Keating AE. Predicting helix orientation for coiled-coil dimers. Proteins 2008;72:1048-1065.
    • (2008) Proteins , vol.72 , pp. 1048-1065
    • Apgar, J.R.1    Gutwin, K.N.2    Keating, A.E.3
  • 34
    • 38049069378 scopus 로고    scopus 로고
    • Core residue replacements cause coiled-coil orientation switching in vitro and in vivo: structure-function correlations for osmosensory transporter prop
    • Tsatskis Y, Kwok SC, Becker E, Gill C, Smith MN, Keates RAB, Hodges RS, Wood JM. Core residue replacements cause coiled-coil orientation switching in vitro and in vivo: structure-function correlations for osmosensory transporter prop. Biochemistry (Mosc) 2008;47:60-72.
    • (2008) Biochemistry (Mosc) , vol.47 , pp. 60-72
    • Tsatskis, Y.1    Kwok, S.C.2    Becker, E.3    Gill, C.4    Smith, M.N.5    Keates, R.A.B.6    Hodges, R.S.7    Wood, J.M.8
  • 35
    • 0007992814 scopus 로고    scopus 로고
    • Protein plasticity to the extreme: changing the topology of a 4-α-helical bundle with a single amino acid substitution
    • Glykos NM, Cesareni G, Kokkinidis M. Protein plasticity to the extreme: changing the topology of a 4-α-helical bundle with a single amino acid substitution. Structure 1999;7:597-603.
    • (1999) Structure , vol.7 , pp. 597-603
    • Glykos, N.M.1    Cesareni, G.2    Kokkinidis, M.3
  • 36
    • 80054723492 scopus 로고    scopus 로고
    • Computational analysis of residue contributions to coiled-coil topology
    • Ramos J, Lazaridis T. Computational analysis of residue contributions to coiled-coil topology. Protein Sci Publ Protein Soc 2011;20:1845-1855.
    • (2011) Protein Sci Publ Protein Soc , vol.20 , pp. 1845-1855
    • Ramos, J.1    Lazaridis, T.2
  • 37
    • 79551470095 scopus 로고    scopus 로고
    • Role of conformational sampling in computing mutation-induced changes in protein structure and stability
    • Kellogg EH, Leaver-Fay A, Baker D. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins Struct Funct Bioinform 2011;79:830-838.
    • (2011) Proteins Struct Funct Bioinform , vol.79 , pp. 830-838
    • Kellogg, E.H.1    Leaver-Fay, A.2    Baker, D.3
  • 38
    • 0035914479 scopus 로고    scopus 로고
    • Evaluation of the energetic contribution of interhelical coulombic interactions for coiled coil helix orientation specificity
    • McClain DL, Binfet JP, Oakley MG. Evaluation of the energetic contribution of interhelical coulombic interactions for coiled coil helix orientation specificity. J Mol Biol 2001;313:371-383.
    • (2001) J Mol Biol , vol.313 , pp. 371-383
    • McClain, D.L.1    Binfet, J.P.2    Oakley, M.G.3
  • 39
    • 0028330850 scopus 로고
    • Electrostatic interactions control the parallel and antiparallel orientation of.alpha.-helical chains in two-stranded alpha-helical coiled-coils
    • Monera OD, Kay CM, Hodges RS. Electrostatic interactions control the parallel and antiparallel orientation of.alpha.-helical chains in two-stranded alpha-helical coiled-coils. Biochemistry (Mosc) 1994;33:3862-3871.
    • (1994) Biochemistry (Mosc) , vol.33 , pp. 3862-3871
    • Monera, O.D.1    Kay, C.M.2    Hodges, R.S.3
  • 40
    • 1342304087 scopus 로고    scopus 로고
    • Structural insights into the interaction of ROCKI with the switch regions of rhoA
    • Dvorsky R, Blumenstein L, Vetter IR, Ahmadian MR. Structural insights into the interaction of ROCKI with the switch regions of rhoA. J Biol Chem 2004;279:7098-7104.
    • (2004) J Biol Chem , vol.279 , pp. 7098-7104
    • Dvorsky, R.1    Blumenstein, L.2    Vetter, I.R.3    Ahmadian, M.R.4
  • 41
    • 0030936995 scopus 로고    scopus 로고
    • Crystal structure of the nucleotide exchange factor grpe bound to the ATPase domain of the molecular chaperone DnaK
    • Harrison CJ, Hayer-Hartl M, Liberto MD, Hartl F-U, Kuriyan J. Crystal structure of the nucleotide exchange factor grpe bound to the ATPase domain of the molecular chaperone DnaK. Science 1997;276:431-435.
    • (1997) Science , vol.276 , pp. 431-435
    • Harrison, C.J.1    Hayer-Hartl, M.2    Liberto, M.D.3    Hartl, F.-U.4    Kuriyan, J.5
  • 42
    • 0037020082 scopus 로고    scopus 로고
    • Designing heterodimeric two-stranded alpha-helical coiled-coils. Effects of hydrophobicity and alpha-helical propensity on protein folding, stability, and specificity
    • Litowski JR, Hodges RS. Designing heterodimeric two-stranded alpha-helical coiled-coils. Effects of hydrophobicity and alpha-helical propensity on protein folding, stability, and specificity. J Biol Chem 2002;277:37272-37279.
    • (2002) J Biol Chem , vol.277 , pp. 37272-37279
    • Litowski, J.R.1    Hodges, R.S.2
  • 43
    • 0037634019 scopus 로고    scopus 로고
    • Unique stabilizing interactions identified in the two-stranded?-helical coiled-coil: crystal structure of a cortexillin I/GCN4 hybrid coiled-coil peptide
    • Lee DL, Ivaninskii S, Burkhard P, Hodges RS. Unique stabilizing interactions identified in the two-stranded?-helical coiled-coil: crystal structure of a cortexillin I/GCN4 hybrid coiled-coil peptide. Protein Sci Publ Protein Soc 2003;12:1395-1405.
    • (2003) Protein Sci Publ Protein Soc , vol.12 , pp. 1395-1405
    • Lee, D.L.1    Ivaninskii, S.2    Burkhard, P.3    Hodges, R.S.4
  • 44
    • 33745164260 scopus 로고    scopus 로고
    • Semirational design of Jun-Fos coiled coils with increased affinity: universal implications for leucine zipper prediction and design
    • Mason JM, Schmitz MA, Müller KM, Arndt KM. Semirational design of Jun-Fos coiled coils with increased affinity: universal implications for leucine zipper prediction and design. Proc Natl Acad Sci USA 2006;103:8989-8994.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 8989-8994
    • Mason, J.M.1    Schmitz, M.A.2    Müller, K.M.3    Arndt, K.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.