메뉴 건너뛰기




Volumn 5, Issue 3, 2010, Pages

Oligomeric interfaces under the lens: Gemini

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

EID: 79952115911     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009897     Document Type: Article
Times cited : (4)

References (60)
  • 2
    • 0036708168 scopus 로고    scopus 로고
    • Paradigm shifts in Alzheimer's disease and other neurodegenerative disorders: The emerging role of oligomeric assemblies
    • Kirkitadze MD, Bitan G, Teplow DB (2002) Paradigm shifts in Alzheimer's disease and other neurodegenerative disorders: the emerging role of oligomeric assemblies. J Neurosci Res 69: 567-577.
    • (2002) J Neurosci Res , vol.69 , pp. 567-577
    • Kirkitadze, M.D.1    Bitan, G.2    Teplow, D.B.3
  • 4
    • 0023193446 scopus 로고
    • The accessible surface area and stability of oligomeric proteins
    • Miller S, Lesk AM, Janin J, Chothia C (1987) The accessible surface area and stability of oligomeric proteins. Nature 328: 834-836.
    • (1987) Nature , vol.328 , pp. 834-836
    • Miller, S.1    Lesk, A.M.2    Janin, J.3    Chothia, C.4
  • 5
    • 0029988383 scopus 로고    scopus 로고
    • Protein-protein interfaces: Architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences
    • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R (1996) Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Crit Rev Biochem Mol Biol 31: 127-152.
    • (1996) Crit Rev Biochem Mol Biol , vol.31 , pp. 127-152
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 6
  • 7
    • 5044235050 scopus 로고    scopus 로고
    • Ten thousand interactions for the molecular biologist
    • Aloy P, Russell RB (2004) Ten thousand interactions for the molecular biologist. Nat Biotechnol 22: 1317-1321.
    • (2004) Nat Biotechnol , vol.22 , pp. 1317-1321
    • Aloy, P.1    Russell, R.B.2
  • 9
    • 33749337098 scopus 로고    scopus 로고
    • The many faces of protein-protein interactions: A compendium of interface geometry
    • Kim WK, Henschel A, Winter C, Schroeder M (2006) The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput Biol 2: e124.
    • (2006) PLoS Comput Biol , vol.2
    • Kim, W.K.1    Henschel, A.2    Winter, C.3    Schroeder, M.4
  • 10
    • 52649130704 scopus 로고    scopus 로고
    • Protein-protein interaction and quaternary structure
    • Janin J, Bahadur RP, Chakrabarti P (2008) Protein-protein interaction and quaternary structure. Q Rev Biophys 41: 133-180.
    • (2008) Q Rev Biophys , vol.41 , pp. 133-180
    • Janin, J.1    Bahadur, R.P.2    Chakrabarti, P.3
  • 11
    • 49249109524 scopus 로고    scopus 로고
    • How proteins get in touch: Interface prediction in the study of biomolecular complexes
    • de Vries SJ, Bonvin AM (2008) How proteins get in touch: interface prediction in the study of biomolecular complexes. Curr Protein Pept Sci 9: 394-406.
    • (2008) Curr Protein Pept Sci , vol.9 , pp. 394-406
    • de Vries, S.J.1    Bonvin, A.M.2
  • 12
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • Henrick K, Thornton JM (1998) PQS: a protein quaternary structure file server. Trends Biochem Sci 23: 358-361.
    • (1998) Trends Biochem Sci , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 13
    • 0035853028 scopus 로고    scopus 로고
    • Identification of protein oligomerization states by analysis of interface conservation
    • Elcock AH, McCammon JA (2001) Identification of protein oligomerization states by analysis of interface conservation. Proc Natl Acad Sci U S A 98: 2990-2994.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 2990-2994
    • Elcock, A.H.1    McCammon, J.A.2
  • 14
    • 1042275583 scopus 로고    scopus 로고
    • A dissection of specific and non-specific protein-protein interfaces
    • Bahadur RP, Chakrabarti P, Rodier F, Janin J (2004) A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 336: 943-955.
    • (2004) J Mol Biol , vol.336 , pp. 943-955
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 15
  • 16
    • 0042594456 scopus 로고    scopus 로고
    • The binding interface database (BID): A compilation of amino acid hot spots in protein interfaces
    • Fischer TB, Arunachalam KV, Bailey D, Mangual V, Bakhru S, et al. (2003) The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces. Bioinformatics 19: 1453-1454.
    • (2003) Bioinformatics , vol.19 , pp. 1453-1454
    • Fischer, T.B.1    Arunachalam, K.V.2    Bailey, D.3    Mangual, V.4    Bakhru, S.5
  • 17
    • 44849127103 scopus 로고    scopus 로고
    • Alignment of noncovalent interactions at protein-protein interfaces
    • Zhu H, Sommer I, Lengauer T, Domingues FS (2008) Alignment of noncovalent interactions at protein-protein interfaces. PLoS One 3: e1926.
    • (2008) PLoS One , vol.3
    • Zhu, H.1    Sommer, I.2    Lengauer, T.3    Domingues, F.S.4
  • 18
    • 18744382508 scopus 로고    scopus 로고
    • PIBASE: A comprehensive database of structurally defined protein interfaces
    • Davis FP, Sali A (2005) PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21: 1901-1907.
    • (2005) Bioinformatics , vol.21 , pp. 1901-1907
    • Davis, F.P.1    Sali, A.2
  • 19
    • 0034572961 scopus 로고    scopus 로고
    • Genetic algorithms and protein folding
    • Schulze-Kremer S (2000) Genetic algorithms and protein folding. Methods Mol Biol 143: 175-222.
    • (2000) Methods Mol Biol , vol.143 , pp. 175-222
    • Schulze-Kremer, S.1
  • 20
    • 0346733329 scopus 로고    scopus 로고
    • Are proteinprotein interfaces more conserved in sequence than the rest of the protein surface?
    • Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES (2004) Are proteinprotein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13: 190-202.
    • (2004) Protein Sci , vol.13 , pp. 190-202
    • Caffrey, D.R.1    Somaroo, S.2    Hughes, J.D.3    Mintseris, J.4    Huang, E.S.5
  • 21
    • 2942644531 scopus 로고    scopus 로고
    • Probing the interface in a human co-chaperonin heptamer: Residues disrupting oligomeric unfolded state identified
    • Guidry JJ, Shewmaker F, Maskos K, Landry S, Wittung-Stafshede P (2003) Probing the interface in a human co-chaperonin heptamer: residues disrupting oligomeric unfolded state identified. BMC Biochem 4: 14.
    • (2003) BMC Biochem , vol.4 , pp. 14
    • Guidry, J.J.1    Shewmaker, F.2    Maskos, K.3    Landry, S.4    Wittung-Stafshede, P.5
  • 22
    • 0000920828 scopus 로고
    • The packing of alpha-helices: Simple coiled-coils
    • Crick FHC (1953) The packing of alpha-helices: simple coiled-coils. Acta Crystallogr 6: 689-697.
    • (1953) Acta Crystallogr , vol.6 , pp. 689-697
    • Crick, F.H.C.1
  • 23
    • 0344552313 scopus 로고    scopus 로고
    • Extended knobs-into-holes packing in classical and complex coiled-coil assemblies
    • Walshaw J, Woolfson DN (2003) Extended knobs-into-holes packing in classical and complex coiled-coil assemblies. J Struct Biol 144: 349-361.
    • (2003) J Struct Biol , vol.144 , pp. 349-361
    • Walshaw, J.1    Woolfson, D.N.2
  • 24
    • 0030271515 scopus 로고    scopus 로고
    • Coiled coils: New structures and new functions
    • Lupas A (1996) Coiled coils: new structures and new functions. Trends Biochem Sci 21: 375-382.
    • (1996) Trends Biochem Sci , vol.21 , pp. 375-382
    • Lupas, A.1
  • 25
    • 0033613385 scopus 로고    scopus 로고
    • A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein
    • van Raaij MJ, Mitraki A, Lavigne G, Cusack S (1999) A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein. Nature 401: 935-938.
    • (1999) Nature , vol.401 , pp. 935-938
    • van Raaij, M.J.1    Mitraki, A.2    Lavigne, G.3    Cusack, S.4
  • 27
    • 0032927791 scopus 로고    scopus 로고
    • Folding by association
    • Shakhnovich EI (1999) Folding by association. Nat Struct Biol 6: 99-102.
    • (1999) Nat Struct Biol , vol.6 , pp. 99-102
    • Shakhnovich, E.I.1
  • 29
    • 0034255123 scopus 로고    scopus 로고
    • Speeding molecular recognition by using the folding funnel: The fly-casting mechanism
    • Shoemaker BA, Portman JJ, Wolynes PG (2000) Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc Natl Acad Sci U S A 97: 8868-8873.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 8868-8873
    • Shoemaker, B.A.1    Portman, J.J.2    Wolynes, P.G.3
  • 30
    • 33749263567 scopus 로고    scopus 로고
    • Kinetic folding and assembly mechanisms differ for two homologous heptamers
    • Luke K, Perham M, Wittung-Stafshede P (2006) Kinetic folding and assembly mechanisms differ for two homologous heptamers. J Mol Biol 363: 729-742.
    • (2006) J Mol Biol , vol.363 , pp. 729-742
    • Luke, K.1    Perham, M.2    Wittung-Stafshede, P.3
  • 32
    • 23444436172 scopus 로고
    • Protein design by binary patterning of polar and nonpolar amino acids
    • Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH (1993) Protein design by binary patterning of polar and nonpolar amino acids. Science 262: 1680-1685.
    • (1993) Science , vol.262 , pp. 1680-1685
    • Kamtekar, S.1    Schiffer, J.M.2    Xiong, H.3    Babik, J.M.4    Hecht, M.H.5
  • 34
    • 0037022661 scopus 로고    scopus 로고
    • Rationally designed mutations convert de novo amyloid-like fibrils into monomeric beta-sheet proteins
    • Wang W, Hecht MH (2002) Rationally designed mutations convert de novo amyloid-like fibrils into monomeric beta-sheet proteins. Proc Natl Acad Sci U S A 99: 2760-2765.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 2760-2765
    • Wang, W.1    Hecht, M.H.2
  • 35
    • 37349043948 scopus 로고    scopus 로고
    • Amyloid toxicity is independent of polypeptide sequence, length and chirality
    • Pastor MT, Kummerer N, Schubert V, Esteras-Chopo A, Dotti CG, et al. (2008) Amyloid toxicity is independent of polypeptide sequence, length and chirality. J Mol Biol 375: 695-707.
    • (2008) J Mol Biol , vol.375 , pp. 695-707
    • Pastor, M.T.1    Kummerer, N.2    Schubert, V.3    Esteras-Chopo, A.4    Dotti, C.G.5
  • 36
    • 13844281391 scopus 로고    scopus 로고
    • Design of model systems for amyloid formation: Lessons for prediction and inhibition
    • Pastor MT, Esteras-Chopo A, Lopez de la Paz M (2005) Design of model systems for amyloid formation: lessons for prediction and inhibition. Curr Opin Struct Biol 15: 57-63.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 57-63
    • Pastor, M.T.1    Esteras-Chopo, A.2    de la Lopez Paz, M.3
  • 38
    • 40449091784 scopus 로고    scopus 로고
    • Geometric confinement governs the rupture strength of H-bond assemblies at a critical length scale
    • Keten S, Buehler MJ (2008) Geometric confinement governs the rupture strength of H-bond assemblies at a critical length scale. Nano Lett 8: 743-748.
    • (2008) Nano Lett , vol.8 , pp. 743-748
    • Keten, S.1    Buehler, M.J.2
  • 39
    • 20444363123 scopus 로고    scopus 로고
    • Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder
    • Tsai HH, Reches M, Tsai CJ, Gunasekaran K, Gazit E, et al. (2005) Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc Natl Acad Sci U S A 102: 8174-8179.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 8174-8179
    • Tsai, H.H.1    Reches, M.2    Tsai, C.J.3    Gunasekaran, K.4    Gazit, E.5
  • 40
    • 0036081257 scopus 로고    scopus 로고
    • Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant
    • Massi F, Klimov D, Thirumalai D, Straub JE (2002) Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. Protein Sci 11: 1639-1647.
    • (2002) Protein Sci , vol.11 , pp. 1639-1647
    • Massi, F.1    Klimov, D.2    Thirumalai, D.3    Straub, J.E.4
  • 41
    • 0037337271 scopus 로고    scopus 로고
    • Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets
    • Klimov DK, Thirumalai D (2003) Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets. Structure 11: 295-307.
    • (2003) Structure , vol.11 , pp. 295-307
    • Klimov, D.K.1    Thirumalai, D.2
  • 42
    • 0030891436 scopus 로고    scopus 로고
    • Simulation of the diffusional association of barnase and barstar
    • Gabdoulline RR, Wade RC (1997) Simulation of the diffusional association of barnase and barstar. Biophys J 72: 1917-1929.
    • (1997) Biophys J , vol.72 , pp. 1917-1929
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 43
    • 13044317297 scopus 로고    scopus 로고
    • Crystallization, x-ray diffraction and preliminary structure analysis of Mycobacterium tuberculosis chaperonin 10
    • Roberts MM, Coker AR, Fossati G, Mascagni P, Coates AR, et al. (1999) Crystallization, x-ray diffraction and preliminary structure analysis of Mycobacterium tuberculosis chaperonin 10. Acta Crystallogr D Biol Crystallogr 55: 910-914.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55 , pp. 910-914
    • Roberts, M.M.1    Coker, A.R.2    Fossati, G.3    Mascagni, P.4    Coates, A.R.5
  • 44
    • 20444453307 scopus 로고    scopus 로고
    • Protein length in eukaryotic and prokaryotic proteomes
    • Brocchieri L, Karlin S (2005) Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res 33: 3390-3400.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3390-3400
    • Brocchieri, L.1    Karlin, S.2
  • 45
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285: 2177-2198.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 46
    • 0034702177 scopus 로고    scopus 로고
    • Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export
    • Koronakis V, Sharff A, Koronakis E, Luisi B, Hughes C (2000) Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Nature 405: 914-919.
    • (2000) Nature , vol.405 , pp. 914-919
    • Koronakis, V.1    Sharff, A.2    Koronakis, E.3    Luisi, B.4    Hughes, C.5
  • 47
    • 0035910272 scopus 로고    scopus 로고
    • How to untwist an alpha-helix: Structural principles of an alpha-helical barrel
    • Calladine CR, Sharff A, Luisi B (2001) How to untwist an alpha-helix: structural principles of an alpha-helical barrel. J Mol Biol 305: 603-618.
    • (2001) J Mol Biol , vol.305 , pp. 603-618
    • Calladine, C.R.1    Sharff, A.2    Luisi, B.3
  • 48
    • 84873285167 scopus 로고    scopus 로고
    • Artificial Intelligence Research Laboratory
    • Honavar V, Dobbs D, Pathak J (2007) http://ppidb.cs.iastate.edu/ppidb/ ZDocumentation. Artificial Intelligence Research Laboratory.
    • (2007)
    • Honavar, V.1    Dobbs, D.2    Pathak, J.3
  • 49
    • 33646553913 scopus 로고    scopus 로고
    • SCOWLP: A web-based database for detailed characterization and visualization of protein interfaces
    • Teyra J, Doms A, Schroeder M, Pisabarro MT (2006) SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. BMC Bioinformatics 7: 104.
    • (2006) BMC Bioinformatics , vol.7 , pp. 104
    • Teyra, J.1    Doms, A.2    Schroeder, M.3    Pisabarro, M.T.4
  • 50
    • 49549094267 scopus 로고    scopus 로고
    • Structural specificity in coiled-coil interactions
    • Grigoryan G, Keating AE (2008) Structural specificity in coiled-coil interactions. Curr Opin Struct Biol 18: 477-483.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 477-483
    • Grigoryan, G.1    Keating, A.E.2
  • 52
    • 58149119313 scopus 로고    scopus 로고
    • A periodic table of coiled-coil protein structures
    • Moutevelis E, Woolfson DN (2009) A periodic table of coiled-coil protein structures. J Mol Biol 385: 726-732.
    • (2009) J Mol Biol , vol.385 , pp. 726-732
    • Moutevelis, E.1    Woolfson, D.N.2
  • 53
    • 1942473179 scopus 로고    scopus 로고
    • Monomer topology defines folding speed of heptamer
    • Bascos N, Guidry J, Wittung-Stafshede P (2004) Monomer topology defines folding speed of heptamer. Protein Sci 13: 1317-1321.
    • (2004) Protein Sci , vol.13 , pp. 1317-1321
    • Bascos, N.1    Guidry, J.2    Wittung-Stafshede, P.3
  • 54
    • 28444495078 scopus 로고    scopus 로고
    • Unfolding of heptameric co-chaperonin protein follows ''fly casting'' mechanism: Observation of transient nonnative heptamer
    • Perham M, Chen M, Ma J, Wittung-Stafshede P (2005) Unfolding of heptameric co-chaperonin protein follows ''fly casting'' mechanism: observation of transient nonnative heptamer. J Am Chem Soc 127: 16402-16403.
    • (2005) J Am Chem Soc , vol.127 , pp. 16402-16403
    • Perham, M.1    Chen, M.2    Ma, J.3    Wittung-Stafshede, P.4
  • 55
    • 0030031059 scopus 로고    scopus 로고
    • Structure of the heat shock protein chaperonin-10 of Mycobacterium leprae
    • Mande SC, Mehra V, Bloom BR, Hol WG (1996) Structure of the heat shock protein chaperonin-10 of Mycobacterium leprae. Science 271: 203-207.
    • (1996) Science , vol.271 , pp. 203-207
    • Mande, S.C.1    Mehra, V.2    Bloom, B.R.3    Hol, W.G.4
  • 56
    • 11344283815 scopus 로고    scopus 로고
    • Crystal structure of the Co-chaperonin Cpn10 from Thermus thermophilus HB8
    • Numoto N, Kita A, Miki K (2005) Crystal structure of the Co-chaperonin Cpn10 from Thermus thermophilus HB8. Proteins 58: 498-500.
    • (2005) Proteins , vol.58 , pp. 498-500
    • Numoto, N.1    Kita, A.2    Miki, K.3
  • 58
    • 0030792944 scopus 로고    scopus 로고
    • Structural adaptations in the specialized bacteriophage T4 co-chaperonin Gp31 expand the size of the Anfinsen cage
    • Hunt JF, van der Vies SM, Henry L, Deisenhofer J (1997) Structural adaptations in the specialized bacteriophage T4 co-chaperonin Gp31 expand the size of the Anfinsen cage. Cell(Cambridge, Mass) 90: 361-371.
    • (1997) Cell(Cambridge, Mass) , vol.90 , pp. 361-371
    • Hunt, J.F.1    van der Vies, S.M.2    Henry, L.3    Deisenhofer, J.4
  • 59
    • 34548141882 scopus 로고    scopus 로고
    • Secondary structure based analysis and classification of biological interfaces: Identification of binding motifs in proteinprotein interactions
    • Guharoy M, Chakrabarti P (2007) Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in proteinprotein interactions. Bioinformatics 23: 1909-1918.
    • (2007) Bioinformatics , vol.23 , pp. 1909-1918
    • Guharoy, M.1    Chakrabarti, P.2
  • 60
    • 38649087636 scopus 로고    scopus 로고
    • Spatial chemical conservation of hot spot interactions in protein-protein complexes
    • Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ (2007) Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol 5: 43.
    • (2007) BMC Biol , vol.5 , pp. 43
    • Shulman-Peleg, A.1    Shatsky, M.2    Nussinov, R.3    Wolfson, H.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.