Bibliography

References next up previous contents
Next: About this document ... Up: Structural and evolutionary studies Previous: Summary and Common Themes

References

1
M. Trabi and D.J. Craik.
Circular proteins-no end in sight.
Trends Biochem. Sci., 27(3):132-138, 2002.

2
M.L. Colgrave and D.J. Craik.
Thermal, chemical, and enzymatic stability of the cyclotide kalata B1: the importance of the cyclic cystine knot.
Biochemistry, 43(20):5965-5975, 2004.

3
R.L. Juliano, A. Astriab-Fisher, and D. Falke.
Macromolecular therapeutics: emerging strategies for drug discovery in the postgenome era.
Mol. Interv., 1(1):40-53, 2001.

4
M.J. Valler and D. Green.
Diversity screening versus focussed screening in drug discovery.
Drug Discov. Today, 5(7):286-293, 2000.

5
E.H. Ohlstein, R.R. Ruffolo, and J.D. Elliott.
Drug discovery in the next millennium.
Annu. Rev. Pharmacol. Toxicol., 40:177-191, 2000.

6
H.X. Zhou.
Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins.
Acc. Chem. Res., 37(2):123-130, 2004.

7
M.E. Felizmenio-Quimio, N.L. Daly, and D.J. Craik.
Circular proteins in plants - solution structure of a novel macrocyclic trypsin inhibitor from Momordica cochinchinensis.
J. Biol. Chem., 276(25):22875-22882, 2001.

8
M.L. Korsinczky, H.J. Schirra, K.J. Rosengren, J. West, B.A. Condie, L. Otvos, M.A. Anderson, and D.J. Craik.
Solution structures by 1H NMR of the novel cyclic trypsin inhibitor SFTI-1 from sunflower seeds and an acyclic permutant.
J. Mol. Biol, 311(3):579-91, 2001.

9
S. Luckett, R.S. Garcia, J.J. Barker, A.V. Konarev, P.R. Shewry, A.R. Clarke, and R.L. Brady.
High-resolution structure of a potent, cyclic proteinase inhibitor from sunflower seeds.
J. Mol. Biol, 290(2):525-533, 1999.

10
J.A. Camarero and T.W. Muir.
Chemoselective backbone cyclization of unprotected peptides.
Chem. Commun. (Camb), 15:1369-1370, 1997.

11
S. Deechongkit and J.W. Kelly.
The effect of backbone cyclization on the thermodynamics of beta-sheet unfolding: stability optimization of the PIN WW domain.
J. Am. Chem. Soc., 124(18):4980-4986, 2002.

12
H. Iwai and A. Plückthun.
Circular beta-lactamase: stability enhancement by cyclizing the backbone.
FEBS Letters, 459(2):166-172, 1999.

13
N.K. Williams, P. Prosselkov, E. Liepinsh, I. Line, A. Sharipo, D.R. Littler, P.M. Curmi, G. Otting, and N.E. Dixon.
In vivo protein cyclization promoted by a circularly permuted Synechocystis sp. PCC6803 DnaB mini-intein.
J. Biol. Chem., 277(10):7790-7798, 2002.

14
L. Gran.
An oxytocic principle found in oldenlandia affinis dc. An indigenous, congolese drug ``Kalata-Kalata'' used to accelerate delivery.
Medd. Nor. Farm. Selsk., 12:173-180, 1970.

15
L. Gran.
Isolation of oxytocic peptides from Oldenlandia affinis by solvent extraction of tetraphenylborate complexes and chromatography on sephadex LH-20.
Lloydia, 36:207-208, 1973.

16
L. Gran.
On the effect of a polypeptide isolated from "Kalata-Kalata" (Oldenlandia affinis DC) on the oestrogen dominated uterus.
Acta Pharmacol. Toxicol., 33:400-408, 1973.

17
L. Gran.
Oxytocic principles of oldenlandia affinis.
Lloydia, 36:174-178, 1973.

18
L. Gran, F. Sandberg, and K. Sletten.
Oldenlandia affinis (R&S) DC. A plant containing uteroactive peptides used in african traditional medicine.
J. Ethnopharmacol., 70(3):197-203, 2000.

19
O. Saether, D.J. Craik, I.D. Campbell, K. Sletten, J. Juul, and D.G. Norman.
Elucidation of the primary and three-dimensional structure of the utertonic polypeptide kalata B1.
Biochemistry, 34:4147-4158, 1995.

20
U. Göransson and D.J. Craik.
Disulfide mapping of the cyclotide kalata B1. Chemical proof of the cystic cystine knot motif.
J. Biol. Chem., 278:48188-48196, 2003.

21
T. Schöpke, M.I. Hasan Agha, R. Kraft, A. Otto, and K. Hiller.
Hämolytisch aktive komponenten aus Viola tricolor l. und Viola arvensis.
Murray. Sci. Pharm., 61:145-153, 1993.

22
K.R. Gustafson, R.C. Sowder, L.E. Henderson, I.C. Parsons I.C., Y. Kashman Y., J.H. Cardellina, J.B. McMahon, R.W. Buckheit Jr. R.W., L.K. Pannell, and M.R. Boyd.
Circulins A and B: Novel HIV-inhibitory macrocyclic peptides from the tropical tree Chassalia parvifolia.
J. Am. Chem. Soc., 116:9337-9338, 1994.

23
K.M. Witherup, M.J. Bogusky, P.S. Anderson, H. Ramjit, R.W. Ransom, T. Wood, and Sardana M.
Cyclopsychotride A, a biologically active, 31-residue cyclic peptide isolated from Psychotria Longipes.
J. Nat. Prod., 57:1619-1625, 1994.

24
H.R. Bokesch, L.K. Pannell, P.K. Cochran, R.C. Sowder, T.C. McKee, and M.R. Boyd.
A novel anti-HIV macrocyclic peptide from Palicourea condensata.
J. Nat. Prod., 64:249-250, 2001.

25
A.M. Broussalis, U. Goransson, J.D. Coussio, G. Ferraro, V. Martino, and P. Claeson.
First cyclotide from Hybanthus (Violaceae).
Phytochemistry, 58:47-51, 2001.

26
D.J. Craik, N.L. Daly, T. Bond, and C. Waine.
Plant cyclotides: A unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif.
J. Mol. Biol, 294:1327-1336, 1999.

27
U. Göransson, T. Luijendijk, S. Johansson, L. Bohlin, and P. Claeson.
Seven novel macrocyclic polypeptides from Viola arvensis.
J. Nat. Prod., 62:283-286, 1999.

28
K.R. Gustafson, L.K. Walton, R.C. Sowder D.G. Johnson L.K. Pannell, J.H. Cardellina, and M.R. Boyd.
New circulin macrocyclic polypeptides from Chassalia parvifolia.
J. Nat. Prod., 63:176-178, 2000.

29
Y.F. Hallock, R.C.I. Sowder, L.K. Pannell, C.B. Hughes, D.G. Johnson, R. Gulakowski, J.H.I. Cardellina, and M.R. Boyd.
Cycloviolins A-D, anti-HIV macrocyclic peptides from Leonia cymosa.
J. Org. Chem., 65:124-128, 2000.

30
J.F. Hernandez, J. Gagnon, L. Chiche, T.M. Nguyen, J.P. Andrieu, A. Heitz, T. Trinh Hong, T.T. Pham, and D. Le Nguyen.
Squash trypsin inhibitors from Momordica cochinchinensis exhibit an atypical macrocyclic structure.
Biochemistry, 39:5722-5730, 2000.

31
D.J. Craik, N.L. Daly, J. Mulvenna, M.R. Plan, and M. Trabi.
Discovery, structure and biological activities of the cyclotides.
Curr. Protein. Pept. Sci., 5:297-315, 2004.

32
K.J. Rosengren, N.L. Daly, M.R. Plan, C. Waine, and D.J. Craik.
Twists, knots, and rings in proteins. Structural definition of the cyclotide framework.
J. Biol. Chem., 278(10):8606-8616, 2003.

33
G.E. Crooks, G. Hon, J.-M. Chandonia, and S.E. Brenner.
Weblogo: a sequence logo generator.
Genome Res., 14:1188-1190, 2004.

34
N.L. Daly, A. Koltay, K.R. Gustafson, M.R. Boyd, J.R. Casas-Finet, and D.J. Craik.
Solution structure by NMR of circulin A: a macrocyclic knotted peptide having anti-HIV activity.
J. Mol. Biol, 285(1):333-345, 1999.

35
M. Trabi and D.J. Craik.
Tissue-specific expression of head-to-tail cyclized miniproteins in violaceae and structure determination of the root cyclotide Viola hederacea root cyclotide1.
Plant Cell, 16:2204-2216, 2004.

36
D.G. Barry, N.L. Daly, H.R. Bokesch, K.R. Gustafson, and D.J. Craik.
Solution structure of the cyclotide palicourein: implications for the development of a pharmaceutical framework.
Structure, 12(1):85-94, 2004.

37
R. Koradi, M. Billeter, and K. Wüthrich.
MOLMOL: a program for display and analysis of macromolecular structures.
14(1):51-55, 1996.

38
NQ. McDonald and WA. Hendrickson.
A structural superfamily of growth factors containing a cystine knot motif.
Cell, 73:421-424, 1993.

39
D. Le Nguyen, A. Heitz, L. Chiche, B. Castro, R.A. Boigegrain, A. Favel, and M.A. Coletti-Previero.
Molecular recognition between serine proteases and new bioactive microproteins with a knotted structure.
Biochimie, 72:431-435, 1990.

40
NW. Isaacs.
Cystine knots.
Curr. Opin. Struc. Biol., 5:391-395, 1995.

41
P.K. Pallaghy, K.J. Nielsen, D.J. Craik, and R.S. Norton.
A common structural motif incorporating a cystine knot and a triple-stranded beta-sheet in toxic and inhibitory polypeptides.
Protein Sci., 3(10):1833-1839, 1994.

42
D.G. Barry, N.L. Daly, R.J. Clark, L. Sando, and D.J. Craik.
Linearization of a naturally occurring circular protein maintains structure but eliminates hemolytic activity.
Biochemistry, 42(22):6688-6695, 2003.

43
W.L. DeLano.
The PyMOL Molecular Graphics System, 2002.

44
R.M. Kohli and C.T. Walsh.
Enzymology of acyl chain macrocyclization in natural product biosynthesis.
Chem. Commun. (Camb), (3):297-307, 2003.

45
J.A. Camarero and T.W. Muir.
Biosynthesis of a head-to-tail cyclized protein with improved biological activity.
J. Am. Chem. Soc., 121:5597-5598, 1999.

46
C. Jennings, J. West, C. Waine, D. Craik, and M. Anderson.
Biosynthesis and insecticidal properties of plant cyclotides: the cyclic knotted proteins from Oldenlandia affinis.
Proc. Natl. Acad. Sci. U. S. A., 98:10614-10619, 2001.

47
J.L. Dutton, R.F. Renda, C. Waine, R.J. Clark, N.L. Daly, C.V. Jennings, M.A. Anderson, and D.J. Craik.
Conserved structural and sequence elements implicated in the processing of gene-encoded circular proteins.
J. Biol. Chem., 279:46858-46867.

48
I. Hara-Hishimura, Y. Takeuchi, K. Inoue, and M. Nishimura.
Vesicle transport and processing of the precursor to 2s albumin in pumpkin.
Plant J., 4(5):793-800, 1993.

49
M.P. Scott, R. Jung, K. Muntz, and N.C. Nielsen.
A protease responsible for post-translational cleavage of a conserved Asn-Gly linkage in glycinin, the major seed storage protein of soybean.
Proc. Natl. Acad. Sci. U. S. A., 89(2):658-62, 1992.

50
O. Takeda, Y. Miura, M. Mitta, H. Matsushita, I. Kato, Y. Abe, H. Yokosawa, and S. Ishii.
Isolation and analysis of cDNA encoding a precursor of Canavalia ensiformis asparaginyl endopeptidase (legumain).
J. Biochem. (Tokyo), 116:541-546, 1994.

51
S. Ishii.
Legumain: asparaginyl endopeptidase.
Methods Enzymol., 244:604-615, 1994.

52
K. Muntz, F.R. Blattner, and A.D. Shutov.
Legumains - a family of asparagine-specific cysteine endopeptidases involved in propolypeptide processing and protein breakdown in plants.
Journal of Plant Physiology, 159:1281-1293, 2002.

53
T.C. Evans, J. Benner, and M.Q. Xu.
The cyclization and polymerization of bacterially expressed proteins using modified self-splicing inteins.
J. Biol. Chem., 274:18359-18363, 1999.

54
C.P. Scott, E. Abel-Santos, M. Wall, D.C. Wahnon, and S.J. Benkovic.
Production of cyclic peptides and proteins in vivo.
Proc. Natl. Acad. Sci. U. S. A., 96(24):13638-13643, 1999.

55
N.L. Daly, S. Love, P.F. Alewood, and D.J. Craik.
Chemical synthesis and folding pathways of large cyclic polypeptides: studies of the cystine knot polypeptide kalata B1.
Biochemistry, 38(32):10606-10614, 1999.

56
J.P. Tam, Y.-A. Lu, and Q. Yu.
Thia zip reaction for synthesis of large cyclic peptides: Mechanisms and applications.
J. Am. Chem. Soc., 121:4316-4324, 1999.

57
P. Lindholm, U. Göransson, S. Johansson, P. Claeson, J. Gullbo, R. Larsson, L. Bohlin, and A. Backlund.
Cyclotides: a novel type of cytotoxic agents.
Mol. Cancer. Ther., 1(6):365-369, 2002.

58
J P Tam, Y A Lu, J L Yang, and K W Chiu.
An unusual structural motif of antimicrobial peptides containing end-to-end macrocycle and cystine-knot disulfides.
Proc. Natl. Acad. Sci. U. S. A., 96(16):8913-8918, 1999.

59
A.M.R Gatehouse and J.A. Gatehouse.
Identifying proteins with insecticidal activity: use of encoding genes to produce insect-resistant transgenic crops.
Pestic. Sci., 52:165-175, 1998.

60
L. Jouanin, M. Bonadé-Bottino, C. Girard, G. Morrot, and M. Giband.
Transgenic plants for insect resistance.
Plant Sci., 131:1-11, 1998.

61
K.J. Nielsen, R.L. Heath, M.A. Anderson, and D.J. Craik.
The three-dimensional solution structure by 1H NMR of a 6-kDa proteinase inhibitor isolated from the stigma of Nicotiana alata.
J. Mol. Biol, 242:231-243, 1994.

62
K.J. Nielsen, R.L. Heath, M.A. Anderson, and D.J. Craik.
Structures of a series of 6-kDa trypsin inhibitors isolated from the stigma of Nicotiana alata.
Biochemistry, 34:14304-14311, 1995.

63
M. Trabi, E. Svangard, A. Herrmann, U. Göransson, P. Claeson, D.J. Craik, and L. Bohlin.
Variations in cyclotide expression in viola species.
J. Nat. Prod., 67(5):806-810, 2004.

64
S. Rivas and C.M. Thomas.
Recent advances in the study of tomato Cf resistance genes.
Mol. plant Pathol., 3:277-282, 2002.

65
A.R. Lopes, M.A. Juliano, L. Juliano, and W.R. Terra.
Coevolution of insect trypsins and inhibitors.
Arch. Insect Biochem. Physiol., 55:140-152, 2004.

66
D.E. Soltis, P.S. Soltis, M.W.Chase, M.E.Mort, D.C. Albach, . Zanis, V. Savolainen, W.H. Hahn, S.B. Hoot, M.F. Fay, M. Axtell, S.M. Swensen, L.M. Prince, W.J. Kress, K.C. Nixon, and J.S. Farris.
Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences.
Bot. J. Linn. Soc., 133:381-461, 2000.

67
Keith D Allen.
Assaying gene content in Arabidopsis.
Proc. Natl. Acad. Sci. U. S. A., 99(14):9568-9572, 2002.

68
M Lynch and J.S. Conery.
The evolutionary fate and consequences of duplicate genes.
Science, 290:1151-1155, 2000.

69
U. Bergthorsson, K.L. Adams, B. Thomason, and J.D. Palmer.
Widespread horizontal transfer of mitochondrial genes in flowering plants.
Nature, 424:197-201, 2003.

70
R. Matthew and P.J. Keeling.
Lateral transfer and recompartmentalization of calvin cycle enzymes of plants and algae.
J. Mol. Evol., pages 367-375, 2003.

71
H. Won and S.S. Renner.
Horizontal gene transfer from flowering plants to Gnetum.
Proc. Natl. Acad. Sci. U. S. A., 100:10824-10829, 2003.

72
A. Heitz, D. Le-Nguyen, and L. Chiche.
Min-21 and min-23, the smallest peptides that fold like a cystine-stabilized $ \beta$-sheet motif: design, solution structure, and thermal stability.
Biochemistry, 38:10615-10625, 1999.

73
A. Heitz, L. Chiche, D. Le-Nguyen, and B. Castro.
Folding of the squash trypsin inhibitor EETI II. Evidence of native and non-native local structural preferences in a linear analogue.
Eur. J. Biochem., 233:837-846, 1995.

74
A. Heitz, D. Le-Nguyen, B. Castro, and L. Chiche.
Conformational study of a native monodisulfide bridge analogue of EETI II.
Lett. Pept. Sci., 4:245-249, 1997.

75
D. Le-Nguyen, A. Heitz, L. Chiche, M. el Hajji, and B. Castro.
Characterization and 2D NMR study of the stable [9-21, 15-27] 2 disulfide intermediate in the folding of the 3 disulfide trypsin inhibitor EETI II.
Protein Sci., 2:165-174, 1993.

76
S. Zhu, H. Darbon, K. Dyason, F. Verdonck, and J. Tytgat.
Evolutionary origin of inhibitor cystine knot peptides.
FASEB J., 17(12):1765-1767, 2003.

77
Y. Birk.
The Bowman-Birk inhibitor. Trypsin- and chymotrypsin-inhibitor from soybeans.
Int. J. Pept. Protein Res., 25:113-131, 1985.

78
B. Prakash, S. Selvaraj, M.R. Murthy, Y.N. Sreerama, D.R. Rao, and L.R. Gowda.
Analysis of the amino acid sequences of plant Bowman-Birk inhibitors.
J. Mol. Evol., 42:560-569, 1996.

79
J.D. McBride, E.M. Watson, A.B. Brauer, A.M. Jaulent, and R.J. Leatherbarrow.
Peptide mimics of the Bowman-Birk inhibitor reactive site loop.
Biopolymers, 66:79-92, 2002.

80
H.K. Song, Y.S. Kim, J.K. Yang, J. Moon, J.Y. Lee, and S.W. Suh.
Crystal structure of a 16 kDa Double-headed Bowman- Birk trypsin inhibitor from barley seeds at 1.9 $ \AA$ resolution.
J. Mol. Biol, 293:1133-1144, 1999.

81
A.V. Konarev, I.N. Anisimova, V.A. Gavrilova, and P.R. Shewry.
Dontknow.
In G.T.S. Mugnozza, E. Porceddu, and M.A. Pagnotta, editors, Genetics and Breeding for Crop quality and Resistance, pages 135-144, Dordrecht, 1999. Kluwer Academic Publishers.

82
T. Gariani and R.J. Leatherbarrow.
Stability of protease inhibitors based on the Bowman-Birk reactive site loop to hydrolysis by proteases.
J. Pept. Res., 49:467-475, 1997.

83
D.L. Maeder, M. Sunde, and D.P. Botes.
Design and inhibitory properties of synthetic Bowman-Birk loops.
Int. J. Pept. Protein Res., 40:97-102, 1992.

84
N. Nishino, H. Aoyagi, T. Kato, and N. Izumiya.
Synthesis and activity of nonapeptide fragments of soybean Bowman-Birk inhibitor.
Experientia, 31:410-412, 1975.

85
N. Nishino, H. Aoyagi, T. Kato, and N. Izumiya.
Studies on the synthesis of proteinase inhibitors. I. Synthesis and activity of nonapeptide fragments of soybean Bowman-Birk inhibitor.
J. Biochem. (Tokyo), 82:901-909, 1977.

86
I. Schechter and A. Berger.
On the size of the active site in proteases. i. papain.
Biochem. Biophys. Res. Commun., 27:157-162, 1967.

87
A. Descours, K. Moehle, A. Renard, and J.A. Robinson.
A new family of $ \beta$-hairpin mimetics based on a trypsin inhibitor from sunflower seeds.
Chembiochem, 3:318-323, 2002.

88
S. Ando, A. Yasutake, M. Waki, N. Nishino, T. Kato, and N. Izumiya.
Anti-chymotrypsin and anti-elastase activities of a synthetic bicyclic fragment containing a chymotrypsin-reactive site of soybean Bowman-Birk inhibitor.
Biochim. Biophys. Acta, 916:527-531, 1987.

89
G.J. Domingo, R.J. Leatherbarrow, N. Freeman, S. Patel, and M. Weir.
Synthesis of a mixture of cyclic peptides based on the Bowman-Birk reactive site loop to screen for serine protease inhibitors.
Int. J. Pept. Protein Res., 46:79-87, 1995.

90
S. Terada, K. Sato, T. Kato, and N. Izumiya.
Inhibitory properties of nonapeptide loop structures related to reactive sites of soybean Bowman-Birk inhibitor.
FEBS Letters, 90:89-92, 1978.

91
T. Gariani, J.D. McBride, and R.J. Leatherbarrow.
The role of the P2' position of Bowman-Birk proteinase inhibitor in the inhibition of trypsin. studies on P2' variation in cyclic peptides encompassing the reactive site loop.
Biochim. Biophys. Acta, 1431:232-237, 1999.

92
J.D. McBride, A.B. Brauer, M. Nievo, and R.J. Leatherbarrow.
The role of threonine in the P2 position of Bowman-Birk proteinase inhibitors: studies on P2 variation in cyclic peptides encompassing the reactive site loop.
J. Mol. Biol, 282:447-458, 1998.

93
I. Li de la Sierra, L. Quillien, P. Flecker, J. Gueguen, and S. Brunie.
Dimeric crystal structure of a Bowman-Birk protease inhibitor from pea seeds.
J. Mol. Biol, 285:1195-1207, 1999.

94
R.H. Voss, U. Ermler, L.O. Essen, G. Wenzl, Y.M. Kim, and P. Flecker.
Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28-nm resolution. Structural peculiarities in a folded protein conformation.
Eur. J. Biochem., 242:122-131, 1996.

95
J. Koepke, U. Ermler, E. Warkentin, G. Wenzl, and P. Flecker.
Crystal structure of cancer chemopreventive Bowman-Birk inhibitor in ternary complex with bovine trypsin at 2.3 $ \AA$ resolution. Structural basis of Janus-faced serine protease inhibitor specificity.
J. Mol. Biol, 298:477-491, 2000.

96
Y. Li, Q. Huang, S. Zhang, S. Liu, C. Chi, and Y. Tang.
Studies on an artificial trypsin inhibitor peptide derived from the mung bean trypsin inhibitor: chemical synthesis, refolding, and crystallographic analysis of its complex with trypsin.
J. Biochem. (Tokyo), 116:18-25, 1994.

97
Y. Tsunogae, I. Tanaka, T. Yamane, J. Kikkawa, T. Ashida, C. Ishikawa, K. Watanabe, S. Nakamura, and K. Takahashi.
Structure of the trypsin-binding domain of Bowman-Birk type protease inhibitor and its interaction with trypsin.
J. Biochem. (Tokyo), 100:1637-1646, 1986.

98
M.H. Werner and D.E. Wemmer.
Three-dimensional structure of soybean trypsin/chymotrypsin Bowman-Birk inhibitor in solution.
Biochemistry, 31:999-1010, 1992.

99
A.B. Brauer, G. Kelly, S.J. Matthews, and R.J. Leatherbarrow.
The $ ^1$H-NMR solution structure of the antitryptic core peptide of Bowman-Birk inhibitor proteins: a minimal canonical loop.
J. Biomol. Struct. Dyn., 20:59-70, 2002.

100
M.L.J. Korsinczky, H.J. Schirra, and D.J. Craik.
Sunflower Trypsin Inhibitor-1.
Curr. Protein. Pept. Sci., 5:351-364, 2004.

101
F. Lipmann, W. Gevers, H. Kleinkauf, and R. Roskoski.
Polypeptide synthesis on protein templates: the enzymatic synthesis of gramicidin S and tyrocidine.
Adv. Enzymol. Relat. Areas. Mol. Biol., 35:1-34, 1971.

102
A. Lawen and R. Zocher.
Cyclosporin synthetase. The most complex peptide synthesizing multienzyme polypeptide so far described.
J. Biol. Chem., 265:11355-11360, 1990.

103
H. Kleinkauf and H. von Dohren.
Biosynthesis of peptide antibiotics.
Annu. Rev. Microbiol., 41:259-289, 1987.

104
K. Kurahashi.
Biosynthesis of small peptides.
Annu. Rev. Biochem., 43:445-459, 1974.

105
U.C. Marx, M.L. Korsinczky, H.J. Schirra, A. Jones, B. Condie, L. Otvos, and D.J. Craik.
Enzymatic cyclization of a potent Bowman-Birk protease inhibitor, sunflower trypsin inhibitor-1, and solution structure of an acyclic precursor peptide.
J. Biol. Chem., 278:21782-21789, 2003.

106
A. Fliess, B. Motro, and R. Unger.
Swaps in protein sequences.
Proteins, 48:377-387, 2002.

107
S.J. de Souza, M. Long, R.J. Klein, S. Roy, S. Lin, and W. Gilbert.
Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins.
Proc. Natl. Acad. Sci. U. S. A., 95:5094-5099, 1998.

108
A. Stoltzfus, D.F. Spencer, M. Zuker, J.M. Logsdon, and W.F. Doolittle.
Testing the exon theory of genes: the evidence from protein structure.
Science, 265:202-207, 1994.

109
S. Odani, T. Koide, and T. Ono.
Wheat germ trypsin inhibitors. Isolation and structural characterization of single-headed and double-headed inhibitors of the Bowman-Birk type.
J. Biochem. (Tokyo), 100:975-983, 1986.

110
W. Ardelt and M. Laskowski.
Turkey ovomucoid third domain inhibits eight different serine proteinases of varied specificity on the same ...leu18-glu19 ... reactive site.
Biochemistry, 24:5313-5320, 1985.

111
J. Otlewski, T. Zbyryt, M. Dryja, G. Bulaj, and T. Wilusz.
Single peptide bond hydrolysis/resynthesis in squash inhibitors of serine proteinases. 2. Limited proteolysis of Curcurbita maxima trypsin inhibitor I by pepsin.
Biochemistry, 33:208-213, 1994.

112
A.V. Konarev, I.N. Anisimova, V.A. Gavrilova, T.E. Vachrusheva, G.Y. Konechnaya, M. Lewis, and P.R. Shewry.
Serine proteinase inhibitors in the Compositae: distribution, polymorphism and properties.
Phytochemistry, 59:279-291, 2002.

113
M.O. Mello, A.S. Tanaka, and M.C. Silva-Filho.
Molecular evolution of Bowman-Birk type proteinase inhibitors in flowering plants.
Mol. Phylogenet. Evol., 27:103-112, 2003.

114
A. Polanowski, T. Wilusz, B. Nienartowicz, E. Cieslar, A. Slominska, and K. Nowak.
Isolation and partial amino acid sequence of the trypsin inhibitor from the seeds of Cucurbita maxima.
Acta Biochim. Pol., 27:371-382, 1980.

115
J. Otlewski and D. Krowarsch.
Squash inhibitor family of serine proteinases.
Acta Biochim. Pol., 43:431-444, 1996.

116
A. Favel, H. Mattras, M.A. Coletti-Previero, R. Zwilling, E.A. Robinson, and B. Castro.
Protease inhibitors from Ecballium elaterium seeds.
Int. J. Pept. Protein Res., 33:202-208, 1989.

117
M. Wieczorek, J. Otlewski, J. Cook, K. Parks, J. Leluk, A. Wilimowska-Pelc, A. Polanowski, T. Wilusz, and M. Laskowski.
The squash family of serine proteinase inhibitors. Amino acid sequences and association equilibrium constants of inhibitors from squash, summer squash, zucchini, and cucumber seeds.
Biochem. Biophys. Res. Commun., 126:646-652, 1985.

118
M.H. Ling, H.Y. Qi, and C.W. Chi.
Protein, cDNA, and genomic DNA sequences of the towel gourd trypsin inhibitor. A squash family inhibitor.
J. Biol. Chem., 268:810-814, 1993.

119
A. Heitz, J.F. Hernandez, J. Gagnon, T.T. Hong, T.T. Pham, T.M. Nguyen, D. Le-Nguyen, and L. Chiche.
Solution structure of the squash trypsin inhibitor MCoTI-II. A new family for cyclic knottins.
Biochemistry, 40:7973-7983, 2001.

120
L. Chiche, C. Gaboriaud, A. Heitz, J.P. Mornon, B. Castro, and P.A. Kollman.
Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II.
Proteins, 6:405-417, 1989.

121
A. Heitz, L. Chiche, D. Le-Nguyen, and B. Castro.
1H 2D NMR and distance geometry study of the folding of Ecballium elaterium trypsin inhibitor, a member of the squash inhibitors family.
Biochemistry, 28:2392-2398, 1989.

122
W. Bode, H.J. Greyling, R. Huber, J. Otlewski, and T. Wilusz.
The refined 2.0 $ \AA$ X-ray crystal structure of the complex formed between bovine $ \beta$-trypsin and CMTI-I, a trypsin inhibitor from squash seeds (Cucurbita maxima). Topological similarity of the squash seed inhibitors with the carboxypeptidase A inhibitor from potatoes.
FEBS Letters, 242:285-292, 1989.

123
R. Helland, G.I. Berglund, J. Otlewski, W. Apostoluk, O.A. Andersen, N.P. Willassen, and A.O. Smalås.
High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes.
Acta Crystallogr. D. Biol. Crystallogr., 55:139-148, 1999.

124
J.M. Thornton and B.L. Sibanda.
Amino and carboxy-terminal regions in globular proteins.
J. Mol. Biol, 167:443-460, 1983.

125
M. Maqueda, A. Galvez, M.M. Bueno, M.J.o.s.e. Sanchez-Barrena, C. Gonzalez, A. Albert, M. Rico, and E. Valdivia.
Peptide AS-48: Prototype of a new class of cyclic bacteriocins.
Curr. Protein. Pept. Sci., pages 399-416, 2004.

126
A. Gálvez, E. Valdivia, M. Maqueda, and E. Montoya.
Production of bacteriocin-like substances by group D streptococci of human origin.
Microbios., 43:223-232, 1985.

127
B. Samyn, M. Martínez-Bueno, B. Devreese, M. Maqueda, A. Gálvez, E. Valdivia, J. Coyette, and J. Van Beeumen.
The cyclic structure of the enterococcal peptide antibiotic AS-48.
FEBS Letters, 352:87-90, 1994.

128
Y. Kawai, T. Saito, H. Kitazawa, and T. Itoh.
Gassericin A; an uncommon cyclic bacteriocin produced by lactobacillus gasseri LA39 linked at N- and C-terminal ends.
Biosci. Biotechnol. Biochem., 62:2438-2440, 1998.

129
Y. Kawai, T. Saito, T. Toba, S.K. Samant, and T. Itoh.
Isolation and characterization of a highly hydrophobic new bacteriocin (gassericin A) from Lactobacillus gasseri LA39.
Biosci. Biotechnol. Biochem., 58:1218-1221, 1994.

130
R. Kemperman, M. Jonker, A. Nauta, O.P. Kuipers, and J. Kok.
Functional analysis of the gene cluster involved in production of the bacteriocin circularin A by Clostridium beijerinckii ATCC 25752.
Appl. Environ. Microbiol., 69:5839-5848, 2003.

131
R. Kemperman, A. Kuipers, H. Karsens, A. Nauta, O. Kuipers, and J. Kok.
Identification and characterization of two novel clostridial bacteriocins, circularin A and closticin 574.
Appl. Environ. Microbiol., 69:1589-1597, 2003.

132
A. Gálvez, E. Valdivia, M. Mart, and M. Maqueda.
Bactericidal action of peptide antibiotic AS-48 against Escherichia coli K-12.
Can. J. Microbiol., 35:318-321, 1989.

133
C. Gonz, G.M. Langdon, M. Bruix, A. Gálvez, E. Valdivia, M. Maqueda, and M. Rico.
Bacteriocin AS-48, a microbial cyclic polypeptide structurally and functionally related to mammalian NK-lysin.
Proc. Natl. Acad. Sci. U. S. A., 97:11221-11226, 2000.

134
E. Sánchez-Cobos, V.V. Filimonov, A. Gálvez, M. Maqueda, E. Valdivia, J.C. Mart, and P.L. Mateo.
AS-48: a circular protein with an extremely stable globular structure.
FEBS Letters, 505:379-382, 2001.

135
H.M. Joosten, M. Nunez, B. Devreese, J. Van Beeumen, and J.D. Marugg.
Purification and characterization of enterocin 4, a bacteriocin produced by Enterococcus faecalis INIA 4.
Appl. Environ. Microbiol., 62:4220-4223, 1996.

136
Y. Kawai, K. Arakawa, A. Itoh, B. Saitoh, Y. Ishii, J. Nishimura, H. Kitazawa, T. Itoh, and T. Saito.
Heterologous expression of gassericin A, a bacteriocin produced by Lactobacillus gasseri LA39.
Animal Sci. J., 74:45-51, 2003.

137
A. Gálvez, M. Maqueda, E. Valdivia, A. Quesada, and E. Montoya.
Characterization and partial purification of a broad spectrum antibiotic AS-48 produced by Streptococcus faecalis.
Can. J. Microbiol., 32:765-771, 1986.

138
Y. Kawai, T. Saito, M. Suzuki, and T. Itoh.
Sequence analysis by cloning of the structural gene of gassericin a, a hydrophobic bacteriocin produced by Lactobacillus gasseri LA39.
Biosci. Biotechnol. Biochem., 62:887-892, 1998.

139
M. Martínez-Bueno, M. Maqueda, A. Gálvez, B. Samyn, J. Van Beeumen, J. Coyette, and E. Valdivia.
Determination of the gene sequence and the molecular structure of the enterococcal peptide antibiotic AS-48.
J. Bacteriol., 176:6334-6339, 1994.

140
M. Díaz, E. Valdivia, M. Martínez-Bueno, M. Fernández, A.S. Soler-González, H. Ramírez-Rodrigo, and M. Maqueda.
Characterization of a new operon, as-48EFGH, from the as-48 gene cluster involved in immunity to enterocin AS-48.
Appl. Environ. Microbiol., 69:1229-1236, 2003.

141
M. Martínez-Bueno, E. Valdivia, A. Gálvez, J. Coyette, and M. Maqueda.
Analysis of the gene cluster involved in production and immunity of the peptide antibiotic AS-48 in Enterococcus faecalis.
Mol. Microbiol., 27:347-358, 1998.

142
D. Destoumieux-Garzón, J. Peduzzi, and S. Rebuffat.
Focus on modified microcins: structural features and mechanisms of action.
Biochimie, 84:511-519, 2002.

143
F. Moreno, J.E. Gónzalez-Pastor, M-R. Baquero, and D. Bravo.
The regulation of microcin B, C and J operons.
Biochimie, 84:521-529, 2002.

144
A-M. Pons, I. Lanneluc, G. Cottenceau, and S. Sable.
New developments in non-post translationally modified microcins.
Biochimie, 84:531-537, 2002.

145
R.A. Salomón and R.N. Farías.
Microcin 25, a novel antimicrobial peptide produced by Escherichia coli.
J. Bacteriol., 174:7428-7435, 1992.

146
A. Blond, M. Cheminant, I. Ségalas-Milazzo, J. Péduzzi, M. Barthélémy, C. Goulard, R. Salomón, F. Moreno, R. Farías, and S. Rebuffat.
Solution structure of microcin J25, the single macrocyclic antimicrobial peptide from Escherichia coli.
Eur. J. Biochem., 268:2124-2133, 2001.

147
M.J. Bayro, J. Mukhopadhyay, G.V. Swapna, J.Y. Huang, L.C. Ma, E. Sineva, P.E. Dawson, G.T. Montelione, and R.H. Ebright.
Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot.
J. Am. Chem. Soc., 125:12382-12383, 2003.

148
K.J. Rosengren, R.J. Clark, N.L. Daly, U. Göransson, A. Jones, and D.J. Craik.
Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone.
J. Am. Chem. Soc., 125:12464-12474, 2003.

149
K.A. Wilson, M. Kalkum, J. Ottesen, J. Yuzenkova, B.T. Chait, R. Landick, T. Muir, K. Severinov, and S.A. Darst.
Structure of microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail.
J. Am. Chem. Soc., 125:12475-12483, 2003.

150
N. Datta, R.W. Hedges, E.J. Shaw, R.B. Sykes, and M.H. Richmond.
Properties of an r factor from Pseudomonas aeruginosa.
J. Bacteriol., 108:1244-1249, 1971.

151
E.J. Lowbury, H.A. Lilly, A. Kidson, G.A. Ayliffe, and R.J. Jones.
Sensitivity of Pseudomonas aeruginosa to antibiotics: emergence of strains highly resistant to carbenicillin.
Lancet, 2:448-452, 1969.

152
W. Pansegrau, E. Lanka, P.T. Barth, D.H. Figurski, D.G. Guiney, D. Haas, D.R. Helinski, H. Schwab, V.A. Stanisich, and C.M. Thomas.
Complete nucleotide sequence of birmingham IncP alpha plasmids. Compilation and comparative analysis.
J. Mol. Biol, 239:623-663, 1994.

153
R. Eisenbrandt, M. Kalkum, E.M. Lai, R. Lurz, C.I. Kado, and E. Lanka.
Conjugative pili of IncP plasmids, and the Ti plasmid T pilus are composed of cyclic subunits.
J. Biol. Chem., 274:22548-22555, 1999.

154
J. Haase and E. Lanka.
A specific protease encoded by the conjugative DNA transfer systems of IncP and Ti plasmids is essential for pilus synthesis.
J. Bacteriol., 179:5728-5735, 1997.

155
M. Kalkum, R. Eisenbrandt, R. Lurz, and E. Lanka.
Tying rings for sex.
Trends Microbiol., 10:382-387, 2002.

156
R. Eisenbrandt, M. Kalkum, R. Lurz, and E. Lanka.
Maturation of IncP pilin precursors resembles the catalytic Dyad-like mechanism of leader peptidases.
J. Bacteriol., 182:6751-6761, 2000.

157
A.A. Weiss, F.D. Johnson, and D.L. Burns.
Molecular characterization of an operon required for pertussis toxin secretion.
Proc. Natl. Acad. Sci. U. S. A., 90:2970-2974, 1993.

158
D. O'Callaghan, C. Cazevieille, A. Allardet-Servent, M.L. Boschiroli, G. Bourg, V. Foulongne, P. Frutos, Y. Kulakov, and M. Ramuz.
A homologue of the Agrobacterium tumefaciens VirB and Bordetella pertussis Ptl type IV secretion systems is essential for intracellular survival of Brucella suis.
Mol. Microbiol., 33:1210-1220, 1999.

159
R. Sieira, D.J. Comerci, D.O. Sánchez, and R.A. Ugalde.
A homologue of an operon required for DNA transfer in Agrobacterium is required in Brucella abortus for virulence and intracellular multiplication.
J. Bacteriol., 182:4849-4855, 2000.

160
H.G. Boman.
Antibacterial peptides: basic facts and emerging concepts.
J. Intern. Med. 254:197-215, 2003.

161
J.A. Hoffmann, F.C. Kafatos, C.A. Janeway, and R.A. Ezekowitz.
Phylogenetic perspectives in innate immunity.
Science, 284:1313-1318, 1999.

162
G.R. Zimmermann, P. Legault, M.E. Selsted, and A. Pardi.
Solution structure of bovine neutrophil $ \beta$-defensin-12: the peptide fold of the $ \beta$-defensins is identical to that of the classical defensins.
Biochemistry, 34:13663-13671, 1995.

163
YQ. Tang, J. Yuan, G. Osapay, K. Osapay, D. Tran, CJ. Miller, AJ. Ouellette, and ME. Selsted.
A cyclic antimicrobial peptide produced in primate leukocytes by the ligation of two truncated $ \alpha$-defensins.
Science, 286:498-502, 1999.

164
M. Trabi, H.J. Schirra, and D.J. Craik.
Three-dimensional structure of RTD-1, a cyclic antimicrobial defensin from Rhesus macaque leukocytes.
Biochemistry, 40:4211-4221, 2001.

165
T.M. Weiss, L. Yang, L. Ding, A.J. Waring, R.I. Lehrer, and H.W. Huang.
Two states of cyclic antimicrobial peptide RTD-1 in lipid bilayers.
Biochemistry, 41:10070-10076, 2002.

166
M.E. Selsted.
$ \theta $-defensins: Cyclic antimicrobial peptides produced by binary ligation of truncated $ \alpha$-defensins.
Curr. Protein. Pept. Sci., 5:365-371, 2004.

167
A.M. Cole, T. Hong, L.M. Boo, T. Nguyen, C. Zhao, G. Bristol, J.A. Zack, A.J. Waring, O.O. Yang, and R.I. Lehrer.
Retrocyclin: a primate peptide that protects cells from infection by T- and M-tropic strains of HIV-1.
Proc. Natl. Acad. Sci. U. S. A., 99:1813-1828, 2002.

168
L. Leonova, V.N. Kokryakov, G. Aleshina, T. Hong, T. Nguyen, C. Zhao, A.J. Waring, and R.I. Lehrer.
Circular minidefensins and posttranslational generation of molecular diversity.
J. Leukoc. Biol., 70:461-464, 2001.

169
D. Tran, P.A. Tran, Y.Q. Tang, J. Yuan, T. Cole, and M.E. Selsted.
Homodimeric $ \theta $-defensins from rhesus macaque leukocytes: isolation, synthesis, antimicrobial activities, and bacterial binding properties of the cyclic peptides.
J. Biol. Chem., 277:3079-3084, 2002.


Jason Mulvenna
2005-04-24