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132
Section VI
Cited literature
133
Section VI
Cited literature
134
A
Almeida MS, Cabral KM, Kurtenbach E, Almeida FC and Valente AP 2002
Solution structure of Pisum sativum defensin 1 by high resolution NMR: plant
defensins, identical backbone with different mechanisms of action. J Mol Biol.
315:749-757.
Altschul SF, Gish W, Miller W, Myers EW. and Lipman DJ 1990
Basic local alignment search tool. J Mol Biol. 215:403-410.
Arnold K, Bordoli L, Kopp J and Schwede T 2006 The SWISS-MODEL
Workspace: A web-based environment for protein structure homology
modelling. Bioinformatics 22:195-201.
Aumelas A, Mangoni M, Roumestand C, Chiche L, Despaux E, Grassy G, Calas
B and Chavanieu A. 1996 Eur J Biochem. 237:575-583.
B
Bala P, Kumar J and Kumar VB 2008 Study on the effectiveness of a new
antimicrobial peptide. OL. J. Mod. Biol. 01 (02):12-14.
Bayer AS, Prasad R, Chandra J, Koul A, Smriti M, Varma A, Skurray RA, Firth
N, Brown MH, Koo SP and Yeaman MR 2000 In vitro resistance of
Staphylococcus aureus to thrombin induced platelet microbial protein is
associated with alteration in cytoplasmic membrane fluidity. Infect Immun.
68:3548-3553.
Bellamy W, Takase M, Yamauchi K, Wakabayashi H, Kawase K, and Tomita
M 1992 Identification of the bactericidal domain of lactoferrin. Biochim
Biophys Acta. 1121:130-136.
Bellamy W, Wakabayashi H, Takase M, Kawase K, Shimamura S and Tomita
M 1993 Killing of Candida albicans by lactoferricin B, a potent antimicrobial
peptide derived from the N-terminal region of bovine lactoferrin. Med
Microbiol Immunol. 182:97-105.
135
Bello J, Bello HR and Grandos E 1982 conformation and aggregation of
melittin dependence on pH and concentration. Biochemistry. 21:461-465.
Bensch KW, Raida M, Magert HJ, Schulz-Knappe P and Forssmann WG 1995
The HBD-1: a novel beta-defensin from human plasma. FEBS Lett. 368:331-5.
Bessalle R, Gorea A, Shalit I, Metzger JW, Dass C and Desiderio DM 1993
Structure-function studies of amphiphilic antibacterial peptides. J. Med. Chem.
36:1203–1209.
Beven L, Hellluin O, Molle G, Ducloheir H and Wroblewski H. 1999
Correlation between antibacterial activity and pore-sizes of two classes of
voltage-dependent channel-forming peptides. Biochim Biophys Acta. 1462:89-
108.
Bloch C Jr, Patel SU, Baud F, Zvelebil MJ, Carr M.D, Sadler PJ and Thornton
J.M 1998 1H NMR structure of an antifungal gamma-thionin protein SI alpha1:
similarity to scorpion toxins. Proteins. 32:334-349.
Blondelle SE, Lohner K and Aguilar M. 1999 Lipid-induced conformation and
lipid-binding properties of cytolytic and antimicrobial peptides: determination
and biological specificity. Biochem Biophysics Acta. 1462:89-108.
Boman HG, Agerberth B, and Boman A 1993 Mechanisms of action on
Escherichia coli of cecropin P1 and PR-39, two antibacterial peptides from pig
intestine. Infect Immun. 61:2978-2984.
Boman HG, Wade D, Boman IA, Wahlin B, and Merrifield RB 1989
Antibacterial and antimalarial properties of peptides that are cecropinA-melittin.
hybrids. FEBS Lett. 259:103–106.
Borukhov S, Sagitov V and Goldfarb A 1993 Transcript cleavage factors from
E. coli. Cell 72:459-66.
136
Bowdish DM, Davidson DJ and Hancock RE 2005 A re-evaluation of the role
of host defence peptides in mammalian immunity. Curr Protein Pept Sci. 6:35-
51.
Breukink E and Kruijjff BD 1999 The lantibiotic nisin, a special case or not?
BBA. 1462:223-34.
Brewer D, Hunter H, and Lajoie G 1998 NMR studies of the antimicrobial
salivary peptides histatin 3 and histatin 5 in aqueous and nonaqueous solutions.
Biochem Cell Biol. 76:247-256.
Bruix M, Jimenez MA, Santoro J, Gonzalez C, Colilla FJ, Mendez E and Rico
M 1993 Solution structure of gamma 1-H and gamma 1-P thionins from barley
and wheat endosperm determined by 1H-NMR: a structural motif common to
toxic arthropod proteins. Biochemistry. 32:715-724.
Brumfitt W, Salton MR and Hamilton–Miller JM 2002 Nisin, alone and
combined with peptidoglycan-modulating antibiotics: activity against
methillicin-resistant Staphylococcus aureus and Vancomycin resistant
enterococci. J. Antimicrob Chemother. 50:731-734.
Brümmer J, Thole H and Kloppstech K 1994 Eur J Biochem. 219:425-433.
Bu X, Wu X, Xie G, and Guo Z 2002 Synthesis of Tyrocidine A and Its
Analogues by Spontaneous Cyclization in Aqueous Solution. Org Lett. 4:2893-
2895.
Bulet P, Charlet M and Hetru C 2003 In Innate Immunity, (Ezekowitz, RAB
and Hoffmann JA, Eds.) pp. 89-107. Humana Press. Totowa, NJ.
Bulet P, Hetru C, Dimarcq J and Hoffmann D. 1999 Antimicrobial peptides
from insects: structure and function. Dev Comp Immunol. 23:329-44.
C
137
Cabiaux V, Agerberth B, Johansson J, Homblé F, Goormaghtigh E, and
Ruysschaert JM 1994 Secondary structure and membrane interaction of PR-39,
a Pro+ Arg-rich antibacterial peptide. Eur J Biochem. 224:1019-1027.
Cai W, Shao X and Maigret B 2002 Protein-ligand recognition using spherical
harmonic molecular surfaces: towards a fast and efficient filter for large virtual
throughput screening". J. Mol. Graph. Model. 20(4): 313–28.
Chatterjee A, Cui Y and Chatterjee AK 2009 RsmC of Erwinia carotovora
subsp. carotovora negatively controls motility, extracellular protein production,
and virulence by binding FlhD and modulating transcriptional activity of the
master regulator, FlhDC. J Bacteriol. 191(14):4582-93.
Chen R and Weng Z 2002 Docking unbound proteins using shape
complementarity, desolvation, and electrostatics. Proteins: Struct. Func. Genet.
47:281-294.
computational approaches to estimate solubility and permeability in drug
discovery and development settings. Adv.Drug Del.Rev.46: 3-26.
Cotter PD, Hill C and Ross RP 2005 Bacteriocin: developing innate immunity
for food. Nat Rev Microbiol. 3:777.
D
Dathe M and Wieprechet T 1999 Structural features of helical antimicrobial
peptide: their potential to modulate activity on model membranes and biological
cells. Biochim Biophys Acta. 1462:71-87.
De Kruijff B 1997 Biomembranes - Lipids beyond the bilayer. Nature. 386:
129-130.
del Castillo FJ, del Castillo I and Moreno F 2001 Construction and characteriza-
tion of mutations at codon 751 of the Escherichia coli gyrB gene that confers
resistance to the antimicrobial peptide microcin B17 and alter the activity of
DNA gyrase. J Bacteriol. 183:2137-2140.
138
Devaux PF 1991 Static and dynamic asymmetry in cell membranes.
Biochemistry. 30:1163-1173.
Ding L, Yang L, Weiss TM, Waring AJ, Lehrer RI and Huang HW 2003
Interaction of antimicrobial peptides with lipopolysaccharides.
Biochemistry.42:12251-12259.
Dolis D, Moreau C, Zachowski C and Devaux PF 1997 Aminophospholipid
translocase and proteins involved in transmembrane phospholipid traffic.
Biophys Chem. 68:221-231.
Dowhan W 1997 Molecular basis for membrane phospholipid diversity: why
are there so many lipids? Ann Rev Biochem. 66:199-232.
Duclohier H and Wroblewski H 2001 Voltage-dependent pore formation and
antimicrobial activity by alamethicin and analogues. J Membr Biol. 184:1-12.
E
Ehrenstein G and Lecar H 1997 Elecrically-gated ionic channels in lipid bilayer.
Q Rev Biophys. 10:1-34.
Eisenberg D, Schwarz E, Komaromy M and Wall R 1984 Analysis of
membrane and surface protein sequences with the hydrophobic moment plot. J
Mol Biol. 179:125-142.
Epand RM and Vogel HJ 1999 Diversity of antimicrobial peptides and their
mechanisms of action. Biochim Biophys Acta. 1462:11-28.
F
Fahrner RL, Dieckmann T, Harwig SS, Lehrer RI, Eisenberg D and Feigon J
1996 Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide
from porcine leukocytes. Chem Biol. 3:543-550.
Fant F, Vranken W, Broekaert W and Borremans F 1998 Determination of the
three-dimensional solution structure of Raphanus sativus antifungal protein 1 by
1HNMR. J Mol Biol. 279:257-270.
139
Fearon D and Locksley R 1996 The instructive role of innate immunity in
aquired immune response. Science. 272:50-4.
Fehlbaum P, Bulet P, Chernysh S, Briand JP, Roussel JP, Letellier L, Hetru C
and Hoffmann JA 1996 Structure-activity analysis of thanatin, a 21-residue
inducible insect defense peptide with sequence homology to frog skin
antimicrobial peptides. Proc Natl Acad Sci USA. 93:1221-1225.
Feig M, Onufriev A, Lee MS, Im W, Case DA and Brooks CL 2004
Performance comparison of generalized born and Poisson methods in the
calculation of electrostatic solvation energies for protein structures. Journal of
Computational Chemistry 25 (2): 265–84.
Florin-Christensen J, Suarez C.E, Florin-Christensen M, Waniszelbaum M,
Brown WC, McElwin TF and Palmer G.H 2001 A unique phospholipids
organization in bovine erythrocyte membrane. Proc Natl Acd Sci USA. 98:7736-
7741.
G
Gabb HA, Jackson RM and Sternberg MJE 1997 Modelling protein docking
using shape complementarity, electrostatics and biochemical information. J.
Mol. Biol. 272(1):106-120.
Ganz T and Lehrer RI 1998 Antimicrobial peptides of vertebrates. Curr Opin
Immunol. 10:41-4.
Ganz T, Selsted ME, Szklarek D, Harwig SS, Daher K and Bainton DF 1985
Defensins: natural peptide antibiotics of human neutrophils. J Clin Invest.
76:1427-35.
Ganz T 2003 Defensin: Antimicrobial of innate immunity. Nature Rev Immunol.
3: 710-720.
140
Garcia JR, Krause A, Schulz S, Rodriguez-Jimenez FJ, Kluver E and Adermann
K 2001 Human beta-defensin 4: a novel inducible peptide with a specific salt-
sensitive spectrum of antimicrobial activity. FASEB J. 15:1819-21.
García-Olmedo F, Carbonero P, Hernandez-Lucas C, Paz-Ares J, Ponz F,
Vicente O and Sierra JM 1983 Inhibition of eucaryotic cell free protein
synthesis by thionins from wheat endosperm. Biochim Biophys Acta. 740:52-56.
Gibson TJ, Chenna R, Sugawara H, Koike T, Lopez R, Higgins DG and
Thompson JD 2003 Multiple sequence alignment with the clustal series of
programs. Nucleic Acids Res. 31(13): 3497-3500.
Goffin C and Ghuysen JM 1998 Multimodular penicillin-binding proteins: An
enigmatic family of orthologs and paralogs. Microbiol Mol Biol Rev 62:1079–
1093.
Grant JA and Pickup BT 1995 A Gaussian description of molecular shape. J.
Phys. Chem. 99:3503-3510.
H
Hancock R.E.W. 2001 Cationic peptide: effectors in innate immunity and novel
antimicrobials. Lancet Infect Dis. 1:156-164.
Hancock REW and Chapple DS 1999 Peptide Antibiotics. Antimicrobial agents
and chemotherapy 43 (6):1317–1323.
Hara T, Kodama H, Kondo M, Wakamatsu K, Takeda A, Tachi T and
Matsuzaki K 2001 Effects of peptide dimerization on pore formation:
Antiparalle disulfide dimerized magainin-2 analogue. Biopolymers. 58:437-446.
Harder J, Bartels J, Christopher E and Schroeder JM 1997 A peptide antibiotic
from human skin. Nature. 387:861-862.
Harwig SS, Swiderek KM, Lee TD, and Lehrer RI 1995 Determination of
disulphide bridges in PG-2, an antimicrobial peptide from porcine leukocytes. J
Pept Sci. 1:207-215.
141
Helmerhorst EJ, Breeuwer P, van't Hof W, Walgreen-Weterings E, Oomen LC,
Veerman EC, Amerongen AV and Abee T 1999 The cellular target of histatin 5
on Candida albicans is the energized mitochondrion. J Biol Chem. 274:7286-
7291.
Hetru C, Hoffmann JA and Hancock REW 2002 In Peptide Antibiotics, (Dutton
CJ, Haxell MA, McArthur HII and Wax RG Eds.) pp. 117-144. Marcel Dekker
Inc., New York and Basel.
Hill CP, Yee J, Selsted ME, and Eisenberg D 1991 Crystal structure of defensin
HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization.
Science. 251:1481-1485.
Holtje JV 1998 Growth of the stress-bearing and shape-maintaining murein
sacculus of Escherichia coli.Microbiol Mol Biol Rev 62:181–203.
Hudson BP, Quispe J, González SL, Kim Y, Berman HM, Arnold E, Ebright
RH and Lawson CL 2009 Three-dimensional EM structure of an intact
activator-dependent transcription initiation complex. Proc Natl Acad
Sci 106:19830-19835.
J
Jacob L. and Zasloff M 1994 Potential therapeutic applications of magainins
and other antimicrobial agents of animal origin. Antimicrobial Peptides. Wiley,
Chichester (Ciba Foundation Symposium 186), 197-223.
Jia HP, Schutte BC, Schudy A, Linzmeier R, Guthmiller JM and Johnson GK
2001Discovery of new human beta-defensins using a genomics-based approach.
Gene. 263:211-8.
Jones DE and Bevins CL 1992 Paneth cells of the human small intestine express
an antimicrobial peptide gene. J Biol Chem. 267:23216-25
142
Jones DE and Bevins CL 1993 Defensin-6 mRNA in human Paneth cells:
implications for antimicrobial peptides in host defense of the human bowel.
FEBS Lett. 315:187-92.
Jones DT 1999 Protein secondary structure prediction based on position-specific
scoring matrices. J. Mol. Biol. 292:195-202.
Jones DT, Taylor WR and Thornton JM 1994 Biochemistry 33:3038-3049.
Jones EM, Smart A, Bloomberg G, Burgess L and Miller MR 1994
Lactoferricin a new antimicrobial peptide. The Journal of Applied Bacteriology.
77(2):208-214.
Juretic D, Chen HC, Brown JH, Morell JL, Hendler RW and Westerhoff HV
1989 Magainin 2 amide and analogues. Antimicrobial activity, membrane
depolariza-tion and susceptibility to proteolysis. FEBS Lett. 249:219-223.
K
Kahraman A, Morris RJ, Laskowski RA and Thornton JM 2007 Shape variation
in protein binding pockets and their ligands. J. Mol. Biol. 368 (1): 283–301.
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA and Aflalo C 1992
Molecular surface recognition: Determination of geometric fit between proteins
and their ligands by correlation techniques. Proc. Natl. Acad. Sci. 89:2195-
2199.
Kawano K, Yoneya T, Miyata T, Yoshikawa K, Tokunaga F, Terada Y and
Iwanaga S 1990 Antimicrobial peptide, Tachyplesin I, isolated from hemocytes
of the horseshoe crab (Tachypleus tridentatus). J Biol Chem. 265:15365-15367.
Kelly JA and Kuzin AP 1995 The refined cryatallographic structure of a DD-
peptidase penicillin – target enzyme at 1.6 A resolution. J. Mol. Biol. 254:223-
236.
Ketchem R, Hu W and Cross TA 1993 High-resolution conformation of
gramicidin A in a lipid bilayer by solid-state NMR. Science. 261:1457-1460.
143
Kiefer F, Arnold K, Künzli M, Bordoli L and Schwede T 2009 The SWISS-
MODEL Repository and associated resources. Nucleic Acids Research.
37:D387-D392.
Kikukawa T and Araiso T 2002 Changes in lipid mobility associated with
alamethicin incorporation into membranes. Arch Biochem Biophys. 405:214-
222.
Kinnunen PKJ 1991 On the principles of functional ordering in biological
membranes. Chem Phys Lipids. 57:375-399.
Kitchen DB, Decornez H, Furr JR and Bajorath J 2004 Docking and scoring in
virtual screening for drug discovery: methods and applications. Nature reviews.
Drug discovery 3 (11): 935–49.
Kol MA, de Kroon AI, Rijkers DT, Killian JA and de Kruijiff B 2001
Membrane spanning peptides induce phospholipid flop: a model for
phospholipids translocation across the inner membrane of E.coli. Biochemistry.
40: 10500-10506.
Kragol G, Lovas S, Varadi G, Condie BA, Hoffmann R and Otvos L Jr. 2001
The antibacterial peptide pyrrhocoricin inhibits the ATPase actions of DnaK
and prevents chaperone-assisted protein folding. Biochemistry 40:3016-3026.
L
Ladkokhin AS, Selested ME, White SH 1997 Sizing membrane pores in lipids
vesicles by leakage of co-encapsulated markers pore formation by melittin.
Biophysics J. 72:1762-1766.
Laederach A, Andreotti A and Fulton D 2002 Solution and micelle- bound
structures of tachyplesin I and its active aromatic linear derivatives.
Biochemistry 41:12359-12368.
144
Lambert C, Leonard N, De Bolle X and Depiereux E. 2002
ESyPred3D: Prediction of proteins 3D structures. Bioinformatics 18(9):1250-
1256.
Lasch P, Schultz CP, and Naumann D 1998 The influence of poly-(L-lysine) an
porin on the domain structure of mixed vesicles composed of lipopolysaccharid
and phospholipid: an infrared spectroscopic study. Biophys J. 75:840-852.
Latal A, Degovics G, Epand RF, Epand RM and Lohner K 1997 Structural
aspects of the interaction of peptidyl-glycylleucine-carboxyamide, a highly
potent antimicrobial peptide from frog skin, with lipids. Eur J Biochem. 248:
938-946.
Lee DG, Kim HN, Park Y, Kim HK, Choi BH, Choi C and Hahm K 2002
Design of novel analog peptides with potent antibiotic activity based on the
antimicrobial peptide, HP (2-20), derived from N-terminus of Helicobacter
pylori ribosomal protein L1. Biochemica et Biophysica Acta 1598 (1-2):185-
194.
Lee W, McDonough, Kotra L, Li ZH, Silvaggi NR, Takeda Y, Kelly JA and
Mobashery S 2001 A 1.2 – A snapshot of the final step of bacterial cell wall
biosynthesis. Proc. Natl. Acad. Sc. USA 98:1427-1431.
Lehrer RI, Barton A, Daher KA, Harwig SS, Ganz T, and Selsted ME 1989
Interaction of human defensins with Escherichia coli - Mechanism of
bactericidal activity. J Clin Invest. 84:553–561.
Leippe M 1999 Antimicrobial and cytolytic polypeptides of amoeboid protozoa-
effector molecules of primitive phagocytes. Dev Comp Immunol. 23:267-79.
Lengauer T and Rarey M 1996 Computational methods for biomolecular
docking. Curr. Opin. Struct. Biol. 6 (3): 402–6.
Lien S and Lowman HB 2003 Therapeutic peptides. Trends in Biotechnology
21:556-562.
145
Linde CMA, Hoffner SE, Refai E and Andersson M 2001 In vitro activity of
PR-39, a proline-arginine-rich peptide, against susceptible and multi-drug-
resistant Mycobacterium tuberculosis. J Antimicrob Chemother. 47:575-580.
Lipinski CA, Lombardo F, Dominy BW and Feeney PJ 2001 Experimental and
computational approaches to estimate solubility and permeability in drug
discovery and development settings. Adv.Drug Del.Rev.46: 3-26.
Lohner K 2001 The role of membrane lipid composition in cell targeting of
antimicrobial peptides. In: Lohner, K. (ed.), Development of novle antimicrobial
agents: emerging strategies. Horizon Scientific Press pp.149-165.
Lohner K and Prenner EJ 1999 Differential scanning calorimetry and X-ray
diffraction studies of the specificity of the interaction of antimicrobial peptides
with membrane-mimic systems. Biochim Biophys Acta. 1462:141-156.
M
Maloy WL and Kari UP 1995 Structure-activity studies on magainins and other
host defense peptides. Biopolymers 37:105-122.
Matsuzaki K, Harada M, Funakoshi S, Fujii N and Miyajima M 1991
Physicochemical determinants for the interactions of magainins 1 and 2 with
acidic lipid bilayers. Biochim Biophys Acta 1063:162-170.
Matsuzaki K, Murase O and Miyajima M 1995 Kinetics of pore formation by an
antimicrobial peptide, magainin 2, in phospholipid bilayers. Biochemistry 34:
12553-12559.
Matsuzaki K, Sugishita K, Fujii N and Miyajima K 1995 Molecular basis for
membrane selectivity of an antimicrobial peptide, magainin 2. Biochemistry 34:
3423-3429.
Matsuzaki K, Yoneyama S, Fujii N, Miyajima K, Yamada K, Kirino Y and
Anzai K 1997 Membrane permeabilization mechanisms of a cyclic
146
antimicrobial peptide, tachyplesin I, and its linear analog. Biochemistry 36:
9799-9806.
Matsuzaki K 1998 Magainins as paradigm for the mode of action of pore
forming polypeptides. Biochim Biophys Acta. 1376:391-400.
Matsuzaki K 1999 Why and how are peptide-lipid interactions utilized for self-
defense? Magainins and tachyplesins as archetypes. Biochim Biophys Acta.
1462:1-10.
McIntosh T.J, Lin H, Li S, Huang C 2001 The effect of ethanol on the phase
transition temperature and the phase structure of mono unsaturated
phosphatidylcholines. Biochem Biophys Acta. 1510:219-230.
Meng EC, Shoichet BK, Kuntz ID 2004 Automated docking with grid-based
energy evaluation. Journal of Computational Chemistry 13 (4): 505–524.
Merrifield RB 1963 Solid Phase Peptide Synthesis. I. The Synthesis of a
Tetrapeptide. J. Am. Chem. Soc. 85 (14): 2149–2154.
Miyata T, Tokunaga F, Yoneya T, Yoshikawa K, Iwanaga S, Niwa M, Takao T
and Shimonishi Y 1989 Antimicrobial peptides, isolated from horseshoe crab
hemocytes, tachyplesin II, and polyphemusins I and II: chemical structures and
biological activity. J Biochem. 106:663-668.
Moreno M, Segura A, Garcia-Olmedo F 1994 Pseudothionin-St1, a potato
peptide active against potato pathogens. Eur J Biochem. 223:135-139.
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK and
Olson AJ 1998 Automated docking using a Lamarckian genetic algorithm and
an empirical binding free energy function. Journal of Computational
Chemistry 19 (14): 1639–1662.
Morris RJ, Najmanovich RJ, Kahraman A and Thornton JM 2005 Real spherical
harmonic expansion coefficients as 3D shape descriptors for protein binding
pocket and ligand comparisons. Bioinformatics 21(10): 2347–55.
147
Morvan A, Iwanaga S, Comps M and Bachere E 1997 In vitro activity of the
Limulus antimicrobial peptide tachyplesin I on marine bivalve pathogens. J
Invertebr Pathol. 69:177-182.
O
Ohta M, Ito H, Masuda K, Tanaka S, Arakawa Y, Wacharotayankun R and Kato
N 1992 Mechanisms of antibacterial action of tachyplesins and polyphemusins,
a group of antimicrobial peptides isolated from horseshoe crab hemocytes.
Antimicrob Agents Chemother. 36:1460-1465.
Opalka N, Chlenov M, Chacon P, Rice WJ, Wriggers W and Darst SA 2003
Structure and function of the transcription elongation factor GreB bound to
bacterial RNA polymerase. Cell 114:335-45.
Oren Z, Lerman JC, Gudmundsson GH, Agerberth B, and Shai Y 1999
Structure and organization of the human antimicrobial peptide LL-37 in
phospholipid mem-branes: relevance to the molecular basis for its non-cell-
selective activity. Biochem J. 341:501-513.
Osborn RW, De Samblanx GW, Thevissen K, Goderis I, Torrekens S, Van
Leuven F, Attenborough S, Rees SB and Broekaert WF 1995 Isolation and
characterisation of plant defensins from seeds of Asteraceae, Fabaceae,
Hippocastanaceae and Saxifragaceae. FEBS Lett. 368:257-262.
Otvos L. Jr. 2000 Antibacterial peptides isolated from insects. J Pept Sci. 6:497-
511.
P
Park CB, Kim HS, and Kim SC 1998 Mechanism of action of the antimicrobial
peptide buforin II: buforin II kills microorganisms by penetrating the cell
membrane and inhibiting cellular functions. Biochem Biophys Res Commun.
244:253-257.
148
Pattery T, Hernalsteens JP, De Greve H 1999 Identification and molecular
characterization of a novel Salmonella enteritidis pathogenicity islet encoding
an ABC transporter. Mol Microbiol. 33(4):791-805.
Pedretti A, Villa L and Vistoli G 2004 Vega - an open platform to develop
chemo-bio-informatics applications, using plug-in architecture and script
programming. J.C.A.M.D. 18:167-173.
Peitsch MC 1995 Protein modeling by E-mail. BioTechnology 13: 658-660.
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenbalt DM, Meng EC
and Ferrin TE 2004 UCSF Chimera – a visualization system for exploratory
research and analysis. J. Comput chem. 25(13):1605-1612.
Prenner E.J, Lewis RN, and McElhaney RN 1999 The interaction of the
antimicrobial peptide gramicidin S with lipid bilayer model and biological
membranes. Biochim Biophys Acta. 1462:201-221.
R
Rana FR, Macias EA, Sultany CM, Modzrakowski MC and Blazyk J 1991
Interactions between magainin 2 and Salmonella typhimurium outer
membranes: effect of lipopolysaccharide structure. Biochemistry. 30:5858-5866.
Rao AG 1999 Conformation and antimicrobial activity of linear derivatives of
tachyplesin lacking disulfide bonds. Arch Biochem Biophys. 361:127-134.
Rawlings ND and Barrett AJ 1994 Families of serine peptidases.
Meth. Enzymol. 244:19-61.
Rice JJ, Schohn A, Bessette PH, Boulware KT and Daugherty PS 2006
Bacterial display using circularly permuted outer membrane protein OmpX
yields high affinity peptide ligands. Protein Sci. 15(4):825-36.
Richon AB 1994 An Introduction to Molecular modeling. Mathematech. 1:83-
100.
149
Ritchie DW 2008 Recent progress and future directions in protein-protein
docking. Curr Prot Pept Sci. 9(1):1-15.
Ritchie DW and Kemp GJL 2000 Protein docking using spherical polar Fourier
correlations. Proteins: Struct. Func. Genet. 39(2):178-194.
Rodriguez-Jimenez F.J, Krause A, Schulz S, Forssmann WG, Conejo-Garcia
JR, Schreeb R 2003 Distribution of new human beta-defensin genes clustered
on chromosome 20 in functionally different segments of epididymis. Genomics.
81:175-83.
S
Sali A and Overrington J 1994 Protein Sci. 3:1582-1596.
Sali A and Blundell TL 1993 Comparative protein modelling by satisfaction of
spatial restraints. J Mol Biol. 234(3):779-815.
Sali A and Fisher A 2003 Modeller: generation and refinement of homology-
based protein structure models. Meth Enzymol. 374:461-91.
Sansom MS 1991 The biophysics of peptide models of ion channels. Prog
Biophys Mol Biol. 55:139-235.
Scocchi M, Wang S and Zanetti M 1997 FEBS Lett. 417:311-315.
Scott MG, Davidson DJ, Gold MR, Bowdish D and Hancock R.E. 2002 J
Immunol. 169:3883-3891.
Segura A, Moreno M, Molina A and Garcia-Olmedo F 1998 Novel defensin
subfamily from spinach (Spinacia oleracea). FEBS Lett. 435:159-162.
Selsted ME, Harwig SS, Ganz T, Schilling JW and Lehrer RI 1985 Primary
structures of three human neutrophil defensins. J Clin Invest.76:1436-9.
Selsted ME, Novotny MJ, Morris WL, Tang YQ, Smith W and Cullen JS 1992
Indolicidin, a novel bactericidal tridecapeptide amide from neutrophils. J Biol
Chem. 267:4292-4295.
150
Silvestro L, Gupta K, Weiser JN and Axelsen PH 1997 The concentration-
dependent membrane activity of cecropin A. Biochemistyry. 36:11452-11460.
Simmaco M, Mignogna G, Canofeni S, Miele R, Mangoni ML and Barra D
1996 Temporins, antimicrobial peptides from the European red frog Rana
temporaria. Eur J Biochem. 242:788-792.
Singh A, Bateman A, Zhu QZ, Shimasaki S, Esch F and Solomon S 1988
Structure of a novel human granulocyte peptide withanti-ACTH activity.
Biochem Biophys Res Commun. 155:524-9.
Singh SK, Maithal K, Balaram H and Balaram P 2001 Synthetic peptides as
inactivators of multimeric enzymes: inhibition of Plasmodium falciparum triose
phosphate isomerase by interface peptides. FEBS letters 501:19-23.
Sitaram N and Nagaraj R 1999 Interaction of antimicrobial peptide with
biological and model membrane:structural and charge requirement for activity.
Biochem Biophys Acta. 1462:29-54.
Sosunova V, Kozlov M, Nikiforov V, Goldfarb A, and Arkady Mustaev A 2003
Donation of catalytic residues to RNA polymerase active center by transcription
factor Gre. PNAS 100 (26):15469 –15474.
Stebbins CE, Borukhov S, Orlova M, Polyakov A, Goldfarb A and Darst SA
1995 Crystal structure of the GreA transcript cleavage factor from Escherichia
coli. Nature 373:636-40.
Steiner H, Hultmark D, Engström A, Bennich H and Boman HG 1981 Nature.
292:246-248.
Subbalakshmi C, Krishnakumari V, Nagaraj R and Sitaram N 1996
Requirements for antibacterial and hemolytic activities in the bovine neutrophil
derived 13-residue peptide indolicidin. FEBS Lett. 395:48-52.
Subbalakshmi C and Sitaram N 1998 Mechanism of antimicrobial action of
indolicidin. FEMS Microbiol Lett. 160:91-96.
151
Sung MT, Lai YT, Huang CY, Chou LY, Shih HW, Cheng WC, Wong
CH and Ma C 2009 Crystal structure of the membrane-bound bifunctional
transglycosylase PBP1b from Escherichia coli. PNAS 106 (22): 8824-8829.
Symersky J, Perederina A, Vassylyeva MN, Svetlov V, Artsimovitch I and
Vassylyev DG 2006 Regulation through the RNA polymerase secondary
channel. Structural and functional variability of the coiled-coil transcription
factors. J. Biol. Chem. 281:1309-12.
T
Tack BF, Sawai MV, Kearney WR, Robertson A.D, Sherman MA, Wang W,
Hong T, Boo LM Wu H, Waring AJ and Lehrer RI 2002 Eur J Biochem.
269:1181-1189.
Tam JP, Wu C and Yang JL 2000 Membranolytic selectivity of cysteine
stabilized cyclic protegrins. Eur J Biochem. 267:3289-3300.
Tamamura H, Waki M, Imai M, Otaka A, Ibuka T, Waki K, Miyamoto K,
Matsumoto A, Murakami T, Nakashima H, Yamamoto N, and Fujii N 1998
Downsizing of an HIV-cell fusion inhibitor, T22 (Tyr5,12, Lys7-polyphemusin
II), with the maintenance of anti-HIV activity and solution structure. Bioorganic
Med Chem. 6:473-479.
Thompson M 2004 ArgusLab 4.0.1 (http//www.planaria-software.com).
Tomasinsig L, Zanetti M 2005 The cathelicidin- structure, function and
evolution. Curr Protein Pept Sci. 6:23-34.
Tsai H and Bobek LA 1998 Human salivary histatins:promising anti-fungal
therapeutic agents. Critical Reviews in Oral Biology and Medicine. 9(4):480-
497.
Turner J, Cho Y, Dinh NN, Waning A.J, Lehrer RI 1998 Activities of LL-37 a
cathelicidin associated antimicrobial peptide of human neutrophils. Antimicrob
Agents Chemother. 42:2206-2214.
152
Tytler EM, Ananthramaiah GM, Walker DE, Mishra VK, Palgunachaari MN
and Segrest JP 1995 Molecular basis for prokaryotic specificity of magainin-
induced lysis. Biochemistry. 34:4393-4401.
U
Uematsu H and Matsuzaki K 2000 Polar angle as a determinant of amphipathic
α-helix lipid interaction: a model peptide study. Biophys J. 79:2075-2083.
Unger T, Oren Z, Shai Y. 2001 The effect of cycliclization of magainin 2 and
melittin analogs on structure, function and model membrane interactions:
implications to their mode of action. Biochemistry. 40:6388-6397.
V
van't Hof W, Veerman ECI, Helmerhorst EJ and Amerongen AVN 2001
Antimicrobial peptides: properties and applicability. Biol Chem. 382:597-619.
Verkleij AJ, Post JA 2000 Membrane phopholipid asymmertry and signal
transduction. J Member Biol. 178:1-10.
Vogt TCB and Bechinger B 1999 The interactions of histidine-containing
amphipathic helical peptide antibiotics with lipid bilayers. The effects of
charges and pH. J Biol Chem. 274:29115-29121.
Vogt TCB and Schulz GE 1999 The structure of the outer membrane protein
OmpX from Escherichia coli reveals possible mechanisms of virulence.
Structure Fold. Res. 7:1301-1309.
W
Wang S, Fleming RT, Westbrook EM, Matsumara P and McKay DB 2006
Structure of the Escherichia coli FIhDC complex, a prokaryotic heteromeric
regulator of transcription. J. Mol. Biol. 355:798-808.
Wang W, Smith D.K, Moulding K and Chen HM 1998 The dependence of
membrane permeability by the antimicrobial peptide cecropin B and its analogs,
153
CB-1 and CB-3, on liposomes of different composition. J Biol chem.
273:27438-27448.
Wang Z and Wang G 2004 APD: The Antimicrobial Peptide Database. Nucleic
Acids Research. 32:D590-592.
Wei BL, Brun-Zinkernagel AM, Simecka JW, Prüss BM, Babitzke P and
Romeo T 2001 Positive regulation of motility and flhDC expression by the
RNA-binding protein CsrA of Escherichia coli. Mol Microbiol. 40(1):245-56.
Wei BQ, Weaver LH, Ferrari AM, Matthews BW and Shoichet BK 2004
Testing a flexible-receptor docking algorithm in a model binding site. J. Mol.
Biol. 337 (5): 1161–82.
Wieprecht T, Dathe M, Krause E, Beyermann M, Maloy WL, MacDonald DL
and Bienert M 1997 Modulation of membrane activity of amphipathic
antimicrobial peptides by slight modulations of the hydrophobic mement. FEBS
Lett. 417:135-140.
Wiese A, Gutsmann T and Seydel U 2003 J Endotoxin Res. 9:67-84.
Wilde CG, Griffith JE, Marra MN, Snable JL and Scott RW 1989 Purification
and characterization of human neutrophil peptide 4, a new member of the
defensin family. J Biol Chem. 264:11200-3.
Williams T and Kelley C 1986-2009 Gnuplot: An Interactive Plotting Program.
V4.4 Copyright 1986-1993, 1998, 2004 Thomas Williams, Colin Kelley;
Copyright 2004-2009 various authors; http://sourceforge.net/projects/gnuplot.
Y
Yamaguchi Y, Nagase T, Makita R, Fukuhara S, Tomita T, Tominaga T 2002
Identification of multiple novel epididymis-specific beta-defensin isoforms in
the humans and mice. J Immunol. 169:2516-23.
Yang D, Biragyn A, Kwak LW and Oppenheim JJ 2002 Mammalian defensins
in immunity: more than just microbiocidal. Trends Immunol. 23:291-296.
154
Yang L, Harron TA, Weisss TM, Ding L, Huang HW 2001 Barrel-stave model
or torroidal model? A case study on melittin pores. Biophys J. 81:1475-1485.
Yonezawa A, Kuwahara J, Fujii N and Sugiura Y 1992 Binding of tachyplesin I
to DNA revealed by footprinting analysis: significant contribution of secondary
structure to DNA binding and implication for biological action. Biochemistry.
31:2998-3004.
Z
Zaltash S, Palmblad M, Curstedt T, Johansson J, and Persson B 2000
Pulmonary surfactant protein B: a structural model and a functional analogue.
Biochim Biophys Acta. 1466:179-186.
Zasloff M 1987 Magainin, a class of antimicrobial peptides from Xenopus skin:
Isolation characterization of two active forms and partial cDNA sequence of a
precursor. Proc Natl Acad Sci USA. 84(9):5449-5453.
Zdobnov EM and Apweiler R 2001 InterProScan - an integration platform for
the signature-recognition methods in InterPro. Bioinformatics 17:847-848.
Zhang XL, Selsted M.E and Pardi A 1992 NMR studies of defensin
antimicrobial peptides. 1. Resonance assignment and secondary structure
determination of rabbit NP-2 and human HNP-1. Biochemistry. 31:11348-
11356.
Zhao C, Ganz T, and Lehrer RI 1995 Structures of genes for two cathelin-
associated antimicrobial peptides: prophenin-2 and PR-39. FEBS Lett. 376:130-
134.
Zhao H, Mattila JP, Holopainen JM and Kinnunen PK 2001 Composition of the
membrane association of two antimicrobial peptides, magainin 2 and
indolicidin. Biophys J. 81:2979-2991.
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