SEARCH

SEARCH BY CITATION

References

  • 1
    Giraldo R ( 2003) Common domains in the initiators of DNA replication in Bacteria, Archaea, and Eukarya: combined structural, functional and phylogenetic perspectives. FEMS Microbiol Rev 26: 533554.
  • 2
    Cunningham EL, Berger JM ( 2005) Unraveling the early steps of prokaryotic replication. Curr Opin Struct Biol 15: 6876.
  • 3
    Kornacki JA, West AH, Firshein W ( 1984) Proteins encoded by the trans-acting replication and maintenance regions of broad host range plasmid RK2. Plasmid 11: 4857.
  • 4
    Shingler V, Thomas CM ( 1984) Analysis of the trfA region of broad host-range plasmid RK2 by transposon mutagenesis and identification of polypeptide products. J Mol Biol 175: 229249.
  • 5
    Perri S, Helinski DR, Toukdarian A ( 1991) Interactions of plasmid-encoded replication initiation proteins with the origin of DNA replication in the broad host range plasmid RK2. J Biol Chem 266: 1253612543.
  • 6
    Lin J, Helinski DR ( 1992) Analysis of mutations in trfA, the replication initiation gene of the broad-host-range plasmid RK2. J Bacteriol 174: 41104119.
  • 7
    Cereghino JL, Helinski DR ( 1993) Essentiality of the three carboxyl-terminal amino acids of the plasmid RK2 replication initiation protein TrfA for DNA binding and replication activity in gram-negative bacteria. J Biol Chem 268: 2492624932.
  • 8
    Konieczny I, Doran KS, Helinski DR, Blasina A ( 1997) Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication of the broad host range plasmid RK2. J Biol Chem 272: 2017320178.
  • 9
    Konieczny I, Helinski DR ( 1997a) Helicase delivery and activation by DnaA and TrfA proteins during the initiation of replication of the broad host range plasmid RK2. J Biol Chem 272: 3331233318.
  • 10
    Konieczny I, Liberek K ( 2002) Cooperative action of Escherichia coli ClpB protein and DnaK chaperone in the activation of a replication initiation protein. J Biol Chem 277: 1848318488.
  • 11
    Kawasaki Y, Wada C, Yura T ( 1990) Roles of Escherichia coli heat shock proteins DnaK, DnaJ, and GrpE in mini-F plasmid replication. Mol Gen Genet 220: 277282.
  • 12
    Wickner S, Skowyra D, Hoskins J, McKenney K ( 1992) DnaJ, DnaK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization step. Proc Natl Acad Sci USA 89: 1034510349.
  • 13
    Dasgupta S, Mukhopadhyay G, Papp PP, Lewis MS, Chattoraj DK ( 1993) Activation of DNA binding by the monomeric form of the P1 replication initiator RepA by heat shock proteins DnaJ and DnaK. J Mol Biol 232: 2334.
  • 14
    Wickner S, Gottesman S, Skowyra D, Hoskins J, McKenney K, Maurizi MR ( 1994) A molecular chaperone, ClpA, functions like DnaK and DnaJ. Proc Natl Acad Sci USA 91: 1221812222.
  • 15
    Wawrzynow A, Wojtkowiak D, Marszalek J, Banecki B, Jonsen M, Graves B, Georgopoulos C, Zylicz M ( 1995) The ClpX heat-shock protein of Escherichia coli, the ATP-dependent substrate specificity component of the ClpP-ClpX protease, is a novel molecular chaperone. EMBO J 14: 18671877.
  • 16
    Konieczny I, Helinski DR ( 1997b) The replication initiation protein of the broad-host-range plasmid RK2 is activated by the ClpX chaperone. Proc Natl Acad Sci USA 94: 1437814382.
  • 17
    Gottesman S ( 2003) Proteolysis in bacterial regulatory circuits. Annu Rev Cell Dev Biol 19: 565587.
  • 18
    Ortega J, Lee HS, Maurizi MR, Steven AC ( 2004) ClpA and ClpX ATPases bind simultaneously to opposite ends of ClpP peptidase to form active hybrid complexes. J Struct Biol 146: 217226.
  • 19
    Beuron F, Maurizi MR, Belnap DM, Kocsis E, Booy FP, Kessel M, Steven AC ( 1998) At sixes and sevens: characterization of the symmetry mismatch of the ClpAP chaperone-assisted protease. J Struct Biol 123: 248259.
  • 20
    Thompson MW, Maurizi MR ( 1994) Activity and specificity of Escherichia coli ClpAP protease in cleaving model peptide substrates. J Biol Chem 269: 1820118208.
  • 21
    Thompson MW, Singh SK, Maurizi MR ( 1994) Processive degradation of proteins by the ATP-dependent Clp protease from Escherichia coli. Requirement for the multiple array of active sites in ClpP but not ATP hydrolysis. J Biol Chem 269: 1820918215.
  • 22
    Kim YI, Burton RE, Burton BM, Sauer RT, Baker TA ( 2000) Dynamics of substrate denaturation and translocation by the ClpXP degradation machine. Mol Cell 5: 639648.
  • 23
    Kenniston JA, Burton RE, Siddiqui SM, Baker TA, Sauer RT ( 2004) Effects of local protein stability and the geometric position of the substrate degradation tag on the efficiency of ClpXP denaturation and degradation. J Struct Biol 146: 130140.
  • 24
    Sauer RT, Bolon DN, Burton BM, Burton RE, Flynn JM, Grant RA, Hersch GL, Joshi SA, Kenniston JA, Levchenko I, Neher SB, Oakes ES, Siddiqui SM, Wah DA, Baker TA ( 2004) Sculpting the proteome with AAA(+) proteases and disassembly machines. Cell 119: 918.
  • 25
    Flynn JM, Neher SB, Kim YI, Sauer RT, Baker TA ( 2003) Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol Cell 11: 671683.
  • 26
    Keiler KC, Sauer RT ( 1996) Sequence determinants of C-terminal substrate recognition by the Tsp protease. J Biol Chem 271: 25892593.
  • 27
    Laachouch JE, Desmet L, Geuskens V, Grimaud R, Toussaint A ( 1996) Bacteriophage Mu repressor as a target for the Escherichia coli ATP-dependent Clp Protease. EMBO J 15: 437444.
  • 28
    Levchenko I, Smith CK, Walsh NP, Sauer RT, Baker TA ( 1997) PDZ-like domains mediate binding specificity in the Clp/Hsp100 family of chaperones and protease regulatory subunits. Cell 91: 939947.
  • 29
    Gonciarz-Swiatek M, Wawrzynow A, Um SJ, Learn BA, McMacken R, Kelley WL, Georgopoulos C, Sliekers O, Zylicz M ( 1999) Recognition, targeting, and hydrolysis of the lambda O replication protein by the ClpP/ClpX protease. J Biol Chem 274: 1399914005.
  • 30
    Gonzalez M, Rasulova F, Maurizi MR, Woodgate R ( 2000) Subunit-specific degradation of the UmuD/D' heterodimer by the ClpXP protease: the role of trans recognition in UmuD' stability. EMBO J 19: 52515258.
  • 31
    Hoskins JR, Kim SY, Wickner S ( 2000) Substrate recognition by the ClpA chaperone component of ClpAP protease. J Biol Chem 275: 3536135367.
  • 33
    Blasina A, Kittell BL, Toukdarian AE, Helinski DR ( 1996) Copy-up mutants of the plasmid RK2 replication initiation protein are defective in coupling RK2 replication origins. Proc Natl Acad Sci USA 93: 35593564.
  • 34
    Toukdarian AE, Helinski DR ( 1998) TrfA dimers play a role in copy-number control of RK2 replication. Gene 223: 205211.
  • 34
    Toukdarian AE, Helinski DR, Perri S ( 1996) The plasmid RK2 initiation protein binds to the origin of replication as a monomer. J Biol Chem 271: 70727078.
  • 35
    Moult J ( 2006) Rigorous performance evaluation in protein structure modeling and implications for computational biology. Philosophical transactions of the Royal Society of London 361: 453458.
  • 36
    Sharma S, Sathyanarayana BK, Bird JG, Hoskins JR, Lee B, Wickner S ( 2004) Plasmid P1 RepA is homologous to the F plasmid RepE class of initiators. J Biol Chem 279: 60276034.
  • 37
    Kurowski MA, Bujnicki JM ( 2003) GeneSilico protein structure prediction meta-server. Nucleic Acids Res 31: 33053307.
  • 38
    Kissinger CR, Parge HE, Knighton DR, Lewis CT, Pelletier LA, Tempczyk A, Kalish VJ, Tucker KD, Showalter RE, Moomaw EWGastinel LN, Habuka N, Chen X, Maldonado F, Barker JE, Bacquet R, Villafranca JE ( 1995) Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex. Nature 378: 641644.
  • 39
    Iakoucheva LM, Kimzey AL, Masselon CD, Bruce JE, Garner EC, Brown CJ, Dunker AK, Smith RD, Ackerman EJ ( 2001) Identification of intrinsic order and disorder in the DNA repair protein XPA. Protein Sci 10: 560571.
  • 40
    Gall C, Xu H, Brickenden A, Ai X, Choy WY ( 2007) The intrinsically disordered TC-1 interacts with Chibby via regions with high helical propensity. Protein Sci 16: 25102518.
  • 41
    Komori H, Matsunaga F, Higuchi Y, Ishiai M, Wada C, Miki K ( 1999) Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution. EMBO J 18: 45974607.
  • 42
    Swan MK, Bastia D, Davies C ( 2006) Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication. Proc Natl Acad Sci USA 103: 1848118486.
  • 43
    Giraldo R, Fernandez-Tornero C, Evans PR, Diaz-Orejas R, Romero A ( 2003) A conformational switch between transcriptional repression and replication initiation in the RepA dimerization domain. Nat Struct Biol 10: 565571.
  • 44
    Wallner B, Elofsson A ( 2003) Can correct protein models be identified? Protein Sci 12: 10731086.
  • 45
    Nakamura A, Komori H, Kobayashi G, Kita A, Wada C, Miki K ( 2004) The N-terminal domain of the replication initiator protein RepE is a dimerization domain forming a stable dimer. Biochem Biophys Res Commun 315: 1015.
  • 46
    Bowie JU, Sauer RT ( 1989) Identification of C-terminal extensions that protect proteins from intracellular proteolysis. J Biol Chem 264: 75967602.
  • 47
    Parsell DA, Silber KR, Sauer RT ( 1990) Carboxy-terminal determinants of intracellular protein degradation. Genes Dev 4: 277286.
  • 48
    Dalrymple BP, Kongsuwan K, Wijffels G ( 2007) Identification of putative DnaN-binding motifs in plasmid replication initiation proteins. Plasmid 57: 8288.
  • 49
    Kenniston JA, Baker TA, Fernandez JM, Sauer RT ( 2003) Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell 114: 511520.
  • 50
    Kenniston JA, Baker TA, Sauer RT ( 2005) Partitioning between unfolding and release of native domains during ClpXP degradation determines substrate selectivity and partial processing. Proc Natl Acad Sci USA 102: 13901395.
  • 51
    Caspi R, Pacek M, Consiglieri G, Helinski DR, Toukdarian A, Konieczny I ( 2001) A broad host range replicon with different requirements for replication initiation in three bacterial species. EMBO J 20: 32623271.
  • 52
    Jiang Y, Pacek M, Helinski DR, Konieczny I, Toukdarian A ( 2003) A multifunctional plasmid-encoded replication initiation protein both recruits and positions an active helicase at the replication origin. Proc Natl Acad Sci USA 100: 86928697.
  • 53
    Kruger R, Konieczny I, Filutowicz M ( 2001) Monomer/dimer ratios of replication protein modulate the DNA strand-opening in a replication origin. J Mol Biol 306: 945955.
  • 54
    Diaz-Lopez T, Lages-Gonzalo M, Serrano-Lopez A, Alfonso C, Rivas G, Diaz-Orejas R, Giraldo R ( 2003) Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA. J Biol Chem 278: 1860618616.
  • 55
    Giraldo R, Andreu JM, Diaz-Orejas R ( 1998) Protein domains and conformational changes in the activation of RepA, a DNA replication initiator. EMBO J 17: 45114526.
  • 56
    Marshall-Batty KR, Nakai H ( 2008) Activation of a dormant ClpX recognition motif of bacteriophage Mu repressor by inducing high local flexibility. J Biol Chem 283: 90609070.
  • 57
    Gottesman S, Clark WP, de Crecy-Lagard V, Maurizi MR ( 1993) ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli. Sequence and in vivo activities. J Biol Chem 268: 2261822626.
  • 58
    Wojtkowiak D, Georgopoulos C, Zylicz M ( 1993) Isolation and characterization of ClpX, a new ATP-dependent specificity component of the Clp protease of Escherichia coli. J Biol Chem 268: 2260922617.
  • 59
    Doran KS, Konieczny I, Helinski DR ( 1998) Replication origin of the broad host range plasmid RK2. Positioning of various motifs is critical for initiation of replication. J Biol Chem 273: 84478453.
  • 60
    Sreerama N, Woody RW ( 2000) Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal Biochem 287: 252260.
  • 61
    Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A ( 2001) Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 10: 23542362.
  • 62
    Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK, Obradovic Z ( 2005) Optimizing long intrinsic disorder predictors with protein evolutionary information. J Bioinform Comput Biol 3: 3560.
  • 63
    Jones DT, Ward JJ ( 2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins 53 ( Suppl 6): 573578.
  • 64
    Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, Boniecki M, Obarska A, Papaj G, Sroczynska-Obuchowicz P, Tkaczuk KL, Sniezynska P, Sasin JM, Augustyn A, Bujnicki JM, Feder M ( 2005) FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6. Proteins 61 ( Suppl 7): 106113.
  • 65
    Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM ( 2008) MetaMQAP: a meta-server for the quality assessment of protein models. BMC bioinformatics 9: 403.