-
1
-
-
0030198873
-
Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes
-
Fahrner, R.L.; Dieckmann, T.; Harwig, S.S.; Lehrer, R.I.; Eisenberg, D.; Feigon, J. Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes. Chem. Biol. 1996, 3, 543-550.
-
(1996)
Chem. Biol.
, vol.3
, pp. 543-550
-
-
Fahrner, R.L.1
Dieckmann, T.2
Harwig, S.S.3
Lehrer, R.I.4
Eisenberg, D.5
Feigon, J.6
-
2
-
-
33746532309
-
Peptide antimicrobial agents
-
Jenssen, H.; Hammil, P.; Hancock, R.E. Peptide antimicrobial agents. Clin. Microbiol. Rev. 2006, 19, 491-511.
-
(2006)
Clin. Microbiol. Rev.
, vol.19
, pp. 491-511
-
-
Jenssen, H.1
Hammil, P.2
Hancock, R.E.3
-
3
-
-
33745855891
-
Membrane-bound dimer structure of a beta-hairpin antimicrobial peptide from rotational-echo double-resonance solid state NMR
-
Mani, R.; Tang, M.; Wu, X.; Buffy, I.J.; Waring, A.J.; Sherman, M.A.; Hong, M. Membrane-bound dimer structure of a beta-hairpin antimicrobial peptide from rotational-echo double-resonance solid state NMR. Biochemistry 2006, 45, 8341-8349.
-
(2006)
Biochemistry
, vol.45
, pp. 8341-8349
-
-
Mani, R.1
Tang, M.2
Wu, X.3
Buffy, I.J.4
Waring, A.J.5
Sherman, M.A.6
Hong, M.7
-
4
-
-
41549125949
-
On the nature of antimicrobial activity: A model for protegrin-1 pores
-
Langham, A.A.; Sayyed-Ahmad, A.; Kaznessis, Y.N. On the nature of antimicrobial activity: A model for protegrin-1 pores. J. Am. Chem. Soc. 2008, 130, 4338-4346.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 4338-4346
-
-
Langham, A.A.1
Sayyed-Ahmad, A.2
Kaznessis, Y.N.3
-
5
-
-
59149103015
-
Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore
-
Bolintineanu, D.; Sayyed-Ahmad, A.; Davis, H.T.; Kaznessis, Y.N. Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore. PLoS Comput. Biol. 2009, 5, e1000277.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Bolintineanu, D.1
Sayyed-Ahmad, A.2
Davis, H.T.3
Kaznessis, Y.N.4
-
6
-
-
72749105356
-
Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli
-
Bolintineanu, D.; Hazrati, E.; Davis, H.T.; Lahrer, R.I.; Kaznessis, Y.N. Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli. Peptides 2009, 31, 1-8.
-
(2009)
Peptides
, vol.31
, pp. 1-8
-
-
Bolintineanu, D.1
Hazrati, E.2
Davis, H.T.3
Lahrer, R.I.4
Kaznessis, Y.N.5
-
7
-
-
0032536098
-
Oligomerization of protegrin-1 in the presence of DPC micells
-
Roumestand, C.; Louis, V.; Aumelas, A.; Grasi, G.; Calas, B.; Chavanieu, A. Oligomerization of protegrin-1 in the presence of DPC micells. A proton high-resolution NMR study. FEBS Lett. 1998, 421, 263-267.
-
(1998)
A proton high-resolution NMR study. FEBS Lett.
, vol.421
, pp. 263-267
-
-
Roumestand, C.1
Louis, V.2
Aumelas, A.3
Grasi, G.4
Calas, B.5
Chavanieu, A.6
-
8
-
-
11144242839
-
Protegrin structure activity relationships: Using homology models of synthetic sequences to determine structural characteristics important for activity
-
Ostberg, N.; Khandelia, H.; Kaznessis, Y.N. Protegrin structure activity relationships: Using homology models of synthetic sequences to determine structural characteristics important for activity. Peptides 2005, 26, 297-306.
-
(2005)
Peptides
, vol.26
, pp. 297-306
-
-
Ostberg, N.1
Khandelia, H.2
Kaznessis, Y.N.3
-
9
-
-
33645751940
-
How can protegrin-1 be both a potent antimicrobial and harmfully toxic? Molecular dynamics simulations of a beta-sheet antimicrobial peptide in micelles
-
Langham, A.A.; Khandelia, H.; Kaznessis, Y.N. How can protegrin-1 be both a potent antimicrobial and harmfully toxic? Molecular dynamics simulations of a beta-sheet antimicrobial peptide in micelles. Biopolymers: Peptide Sci. 2006, 84, 219-231.
-
(2006)
Biopolymers: Peptide Sci.
, vol.84
, pp. 219-231
-
-
Langham, A.A.1
Khandelia, H.2
Kaznessis, Y.N.3
-
10
-
-
34548316598
-
Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data
-
Langham, A.A.; Waring, A.J.; Kaznessis, Y.N. Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data. BMC Biochem. 2007, 8, 11.
-
(2007)
BMC Biochem.
, vol.8
, pp. 11
-
-
Langham, A.A.1
Waring, A.J.2
Kaznessis, Y.N.3
-
11
-
-
33746651219
-
Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions
-
Khandelia, H.; Langham, A.A.; Kaznessis, Y.N. Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions. BBA 2006, 1758, 1224-1234.
-
(2006)
BBA
, vol.1758
, pp. 1224-1234
-
-
Khandelia, H.1
Langham, A.A.2
Kaznessis, Y.N.3
-
12
-
-
33847078068
-
Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation
-
Khandelia, H.; Kaznessis, Y.N. Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation. BBA Biomembr. 2007, 1768, 509-520.
-
(2007)
BBA Biomembr.
, vol.1768
, pp. 509-520
-
-
Khandelia, H.1
Kaznessis, Y.N.2
-
13
-
-
58149311146
-
Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels
-
Jang, H.; Ma, B.; Lal, R.; Nussinov, R. Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. Biophys. J. 2008, 95, 4631-4642.
-
(2008)
Biophys. J.
, vol.95
, pp. 4631-4642
-
-
Jang, H.1
Ma, B.2
Lal, R.3
Nussinov, R.4
-
14
-
-
66449133930
-
Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance
-
Lee, J.; Im, W. Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance. J. Comput. Chem. 2009, 30, 1334-1343.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1334-1343
-
-
Lee, J.1
Im, W.2
-
15
-
-
77749304229
-
Free energy profile of the interaction between a monomer or a dimer of protegrin-1 in a specific binding orientation and a model lipid bilayer
-
Vivcharuk, V.; Kaznessis, Y. Free energy profile of the interaction between a monomer or a dimer of protegrin-1 in a specific binding orientation and a model lipid bilayer. J. Phys. Chem. B 2010, 114, 2790-2797.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 2790-2797
-
-
Vivcharuk, V.1
Kaznessis, Y.2
-
16
-
-
62849091215
-
Determining the orientation of protegrin-1 in DLPC bilayers using an implicit solvent-membrane model
-
Sayyed-Ahmad, A.; Kaznessis, Y.N. Determining the orientation of protegrin-1 in DLPC bilayers using an implicit solvent-membrane model. PLoS One 2009, 4, e4799.
-
(2009)
PLoS One
, vol.4
-
-
Sayyed-Ahmad, A.1
Kaznessis, Y.N.2
-
17
-
-
47149096704
-
CHARMM-GUI: A web-based graphical user interface for CHARMM
-
Jo, S.; Kim, T.; Iyer, V.G.; Im, W. CHARMM-GUI: A web-based graphical user interface for CHARMM. J. Comput. Chem. 2008, 29, 1859-1865.
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1859-1865
-
-
Jo, S.1
Kim, T.2
Iyer, V.G.3
Im, W.4
-
18
-
-
84986512474
-
A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B.R.; Brucolleri, R.E.; Olafsoan, B.D.; States, D.J.; Swaminathan, S.; Karplus, M. A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 1983, 4, 187-217.
-
(1983)
J. Comp. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Brucolleri, R.E.2
Olafsoan, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
19
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A.D.; Bashford, D.; Bellot, M.; Dunbrack, R.L.; Evanseek, J.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellot, M.3
Dunbrack, R.L.4
Evanseek, J.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
20
-
-
1642576012
-
Improved treatment of the protein backbone in empirical force fields
-
MacKerell, A.D.; Feig, M.; Brooks, C.L. Improved treatment of the protein backbone in empirical force fields. J. Chem. Soc. 2004, 126, 698-699.
-
(2004)
J. Chem. Soc.
, vol.126
, pp. 698-699
-
-
MacKerell, A.D.1
Feig, M.2
Brooks, C.L.3
-
21
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J.C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.D.; Kalle, L.; Schulten, K. Scalable molecular dynamics with NAMD. J. Comp. Chem. 2005, 26, 1781-1802.
-
(2005)
J. Comp. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalle, L.9
Schulten, K.10
-
22
-
-
36449003554
-
Constant pressure molecular dynamics algorithms
-
Martyna, G.J.; Tobias, D.J.; Klein, M.L. Constant pressure molecular dynamics algorithms. J. Chem. Phys. 1994, 101, 4177-4189.
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
23
-
-
36449007836
-
Constant pressure molecular dynamics simulation: The Langevin piston method
-
Feller, S.E.; Zhang, Y.; Pastor, R.W.; Brooks, B.R. Constant pressure molecular dynamics simulation: The Langevin piston method. J. Chem. Phys. 1995, 103, 4613-4621.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.2
Pastor, R.W.3
Brooks, B.R.4
-
24
-
-
49249088676
-
Arginine dynamics in a membrane-bound cationic beta-hairpin peptide from solid-state NMR
-
Tang, M.; Waring, J.; Hong, M. Arginine dynamics in a membrane-bound cationic beta-hairpin peptide from solid-state NMR. ChemBioChem 2008, 9, 1487-1482.
-
(2008)
ChemBioChem
, vol.9
, pp. 1487-1482
-
-
Tang, M.1
Waring, J.2
Hong, M.3
-
25
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen,W.L.; Chandrasekhar, J.; Madura, J.D.; Impey, R.W.; Klein, M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
26
-
-
0033104039
-
New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations
-
Darden, T.; Perera, L.; Li, L.; Pedersen, L. New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure 1999, 7, R55-R60.
-
(1999)
Structure
, vol.7
-
-
Darden, T.1
Perera, L.2
Li, L.3
Pedersen, L.4
-
27
-
-
36549102647
-
Error-estimates on averages of correlated data
-
Flyvbjerg, H.; Petersen, H.G. Error-estimates on averages of correlated data. J. Chem. Phys. 1989, 91, 461-466.
-
(1989)
J. Chem. Phys.
, vol.91
, pp. 461-466
-
-
Flyvbjerg, H.1
Petersen, H.G.2
-
28
-
-
41149175486
-
Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane
-
Vivcharuk, V.; Tomberli, B.; Tolokh, I.S.; Gray, C.G. Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane. Phys. Rev. E 2008, 77, 031913.
-
(2008)
Phys. Rev. E
, vol.77
, pp. 031913
-
-
Vivcharuk, V.1
Tomberli, B.2
Tolokh, I.S.3
Gray, C.G.4
-
30
-
-
0001087856
-
Calculation of free energy surfaces using the methods of thermodynamic perturbation theory
-
Tobias, D.J.; Brooks, C.L., III Calculation of free energy surfaces using the methods of thermodynamic perturbation theory. Chem. Phys. Lett. 1987, 142, 472-476.
-
(1987)
Chem. Phys. Lett.
, vol.142
, pp. 472-476
-
-
Tobias, D.J.1
Brooks III., C.L.2
-
31
-
-
0025882246
-
Ion transport in a gramicidin-like channel: Structure and thermodynamics
-
Roux, B.; Karplus, M. Ion transport in a gramicidin-like channel: Structure and thermodynamics. Biophys. J. 1991, 59, 961-981.
-
(1991)
Biophys. J.
, vol.59
, pp. 961-981
-
-
Roux, B.1
Karplus, M.2
-
32
-
-
0347929642
-
Constrained molecular dynamics and the mean potential for an ion pair in a polar solvent
-
Ciccotti, G.; Ferrario, M.; Hynes, J.T.; Kapral, R. Constrained molecular dynamics and the mean potential for an ion pair in a polar solvent. Chem. Phys. 1989, 129, 241-251.
-
(1989)
Chem. Phys.
, vol.129
, pp. 241-251
-
-
Ciccotti, G.1
Ferrario, M.2
Hynes, J.T.3
Kapral, R.4
-
33
-
-
0037223889
-
A reexamination of mean force potentials for the methane pair and the constituent ion pairs of NaCl in water
-
Shinto, H.; Morisada, S.; Miyahara, M.; Higashitani, K. A reexamination of mean force potentials for the methane pair and the constituent ion pairs of NaCl in water. J. Chem. Eng. Jap. 2003, 36, 57-65.
-
(2003)
J. Chem. Eng. Jap.
, vol.36
, pp. 57-65
-
-
Shinto, H.1
Morisada, S.2
Miyahara, M.3
Higashitani, K.4
-
34
-
-
34548680131
-
-
Chipot, C., Pohorille, A., Eds.; Springer: Berlin, Germany
-
Darve, E. In Free Energy Calculations; Chipot, C., Pohorille, A., Eds.; Springer: Berlin, Germany, 2007; p. 119.
-
(2007)
In Free Energy Calculations
, pp. 119
-
-
Darve, E.1
-
35
-
-
0000341366
-
Molecular dynamics simulation of galanin in aqueous and nonaqueous solution
-
DeLoof, H.; Nilsson, L.; Rigler, R. Molecular dynamics simulation of galanin in aqueous and nonaqueous solution. J. Am. Soc. 1992, 114, 4028-4035.
-
(1992)
J. Am. Soc.
, vol.114
, pp. 4028-4035
-
-
DeLoof, H.1
Nilsson, L.2
Rigler, R.3
-
36
-
-
33749535555
-
Interaction of protegrin-1 with lipid bilayers: Membrane thinning effect
-
Jang, H.; Ma, B.; Woolf, T.B.; Nussinov, R. Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophys. J. 2006, 91, 2848-2859.
-
(2006)
Biophys. J.
, vol.91
, pp. 2848-2859
-
-
Jang, H.1
Ma, B.2
Woolf, T.B.3
Nussinov, R.4
-
37
-
-
0004130696
-
-
2nd ed.; Wiley VCH: New York, NY, USA
-
Evans, D.F.; Wennerstrom, H. Colloidal Domain, 2nd ed.; Wiley VCH: New York, NY, USA, 1999; p. 409.
-
(1999)
Colloidal Domain
, pp. 409
-
-
Evans, D.F.1
Wennerstrom, H.2
|