-
2
-
-
0022308218
-
Describing patterns of protein tertiary structure
-
Richardson, J. S. (1985) Describing patterns of protein tertiary structure Methods Enzymol. 115, 341-358
-
(1985)
Methods Enzymol.
, vol.115
, pp. 341-358
-
-
Richardson, J.S.1
-
3
-
-
0019934717
-
The helical hydrophobic moment: A measure of the amphiphilicity of a helix
-
Eisenberg, D., Weiss, R. M., and Terwilliger, T. C. (1982) The helical hydrophobic moment: A measure of the amphiphilicity of a helix Nature 299, 371-374
-
(1982)
Nature
, vol.299
, pp. 371-374
-
-
Eisenberg, D.1
Weiss, R.M.2
Terwilliger, T.C.3
-
4
-
-
0014062165
-
Use of helical wheels to represent the structures of proteins and to identify segments with helical potential
-
Shiffer, M. and Edmunson, A. B. (1967) Use of helical wheels to represent the structures of proteins and to identify segments with helical potential Biophys. J. 7, 121-135
-
(1967)
Biophys. J.
, vol.7
, pp. 121-135
-
-
Shiffer, M.1
Edmunson, A.B.2
-
5
-
-
0014307971
-
The use of helical net-diagrams to represent protein structures
-
Dunnill, P. (1968) The use of helical net-diagrams to represent protein structures Biophys. J. 8, 865-875
-
(1968)
Biophys. J.
, vol.8
, pp. 865-875
-
-
Dunnill, P.1
-
6
-
-
0024461439
-
A common cytolytic region in myotoxins, hemolysins, cardiotoxins and antibacterial peptides
-
Kini, R. M. and Evans, H. J. (1989) A common cytolytic region in myotoxins, hemolysins, cardiotoxins and antibacterial peptides Int. J. Pept. Protein Res. 34, 277-286
-
(1989)
Int. J. Pept. Protein Res.
, vol.34
, pp. 277-286
-
-
Kini, R.M.1
Evans, H.J.2
-
7
-
-
0022497150
-
Interactions between membranes and cytolytic peptides
-
Bernheimer, A. W. and Rudy, B. (1986) Interactions between membranes and cytolytic peptides Biochim. Biophys. Acta 864, 123-141
-
(1986)
Biochim. Biophys. Acta
, vol.864
, pp. 123-141
-
-
Bernheimer, A.W.1
Rudy, B.2
-
8
-
-
84960963081
-
Surface tension of lung extracts
-
Clements, J. A. (1957) Surface tension of lung extracts Proc. Soc. Exp. Biol. Med. 95, 170-172
-
(1957)
Proc. Soc. Exp. Biol. Med.
, vol.95
, pp. 170-172
-
-
Clements, J.A.1
-
9
-
-
0000136017
-
Properties, function, and origin of the alveolar lining layer
-
Pattle, R. E. (1958) Properties, function, and origin of the alveolar lining layer Proc. R. Soc. London, Ser. B 148, 217-240
-
(1958)
Proc. R. Soc. London, Ser. B
, vol.148
, pp. 217-240
-
-
Pattle, R.E.1
-
10
-
-
0025935264
-
The biophysics of peptide models of ion channels
-
Sansom, M. S. (1991) The biophysics of peptide models of ion channels Prog. Biophys. Mol. Biol. 55, 139-235
-
(1991)
Prog. Biophys. Mol. Biol.
, vol.55
, pp. 139-235
-
-
Sansom, M.S.1
-
11
-
-
0024570141
-
Structural significance of the C-terminal amphiphilic helix of interleukin-2
-
Landgraf, B., Cohen, F. E., Smith, K. A., Gadski, R., and Ciardelli, T. L. (1989) Structural significance of the C-terminal amphiphilic helix of interleukin-2 J. Biol. Chem. 264, 816-822
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 816-822
-
-
Landgraf, B.1
Cohen, F.E.2
Smith, K.A.3
Gadski, R.4
Ciardelli, T.L.5
-
12
-
-
0000555628
-
Role of glycopeptides and peptides in inhibition of crystallization of water in polar fishes
-
DeVries, A. L. (1984) Role of glycopeptides and peptides in inhibition of crystallization of water in polar fishes Philos. Trans. R. Soc., B 304, 575-588
-
(1984)
Philos. Trans. R. Soc., B
, vol.304
, pp. 575-588
-
-
Devries, A.L.1
-
13
-
-
0020447080
-
Insect antifreezes and ice-nucleating agents
-
Duman, J. G. (1982) Insect antifreezes and ice-nucleating agents Cryobiology 19, 613-627
-
(1982)
Cryobiology
, vol.19
, pp. 613-627
-
-
Duman, J.G.1
-
14
-
-
33644601596
-
Peptide helices based on α-amino acids
-
Crisma, M., Formaggio, F., Moretto, A., and Toniolo, C. (2006) Peptide helices based on α-amino acids Biopolymers 84, 3-12
-
(2006)
Biopolymers
, vol.84
, pp. 3-12
-
-
Crisma, M.1
Formaggio, F.2
Moretto, A.3
Toniolo, C.4
-
17
-
-
0038054286
-
A structural and functional role for 11-mer repeats in α-synuclein and other exchangeable lipid binding proteins
-
Jr, R. B. and Eliezer, D. (2003) A structural and functional role for 11-mer repeats in α-synuclein and other exchangeable lipid binding proteins J. Mol. Biol. 329, 763-778
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 763-778
-
-
Eliezer, D.1
-
18
-
-
0033527736
-
A detailed molecular belt model for apolipoprotein A-I in discoidal high density lipoprotein
-
Segrest, J. P., Jones, M. K., Klon, A. E., Sheldahl, C. J., Hellinger, M., Loof, H. D., and Harvey, S. C. (1999) A detailed molecular belt model for apolipoprotein A-I in discoidal high density lipoprotein J. Biol. Chem. 274, 31755-31758
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 31755-31758
-
-
Segrest, J.P.1
Jones, M.K.2
Klon, A.E.3
Sheldahl, C.J.4
Hellinger, M.5
Loof, H.D.6
Harvey, S.C.7
-
19
-
-
0028814090
-
10-helices in peptides and proteins as studied by modified Zimm-Bragg theory
-
10-helices in peptides and proteins as studied by modified Zimm-Bragg theory J. Am. Chem. Soc. 117, 10098-10103
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 10098-10103
-
-
Sheinerman, F.B.1
Brooks, C.L.2
-
20
-
-
0024278714
-
Helix geometry in proteins
-
Barlow, D. J. and Thornton, J. M. (1988) Helix geometry in proteins J. Mol. Biol. 201, 601-619
-
(1988)
J. Mol. Biol.
, vol.201
, pp. 601-619
-
-
Barlow, D.J.1
Thornton, J.M.2
-
21
-
-
0034826730
-
10-helix interconversion: A quantum-chemical study on polyalanine systems in the gas phase and in aqueous solvent
-
10-helix interconversion: A quantum-chemical study on polyalanine systems in the gas phase and in aqueous solvent J. Am. Chem. Soc. 123, 6054-6060
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 6054-6060
-
-
Topol, I.A.1
Burt, S.K.2
Deretey, E.3
Tang, T.H.4
Perczel, A.5
Rashin, A.6
Csizmadia, I.G.7
-
23
-
-
0025777309
-
Analysis of protein loop closure: Two types of hinges produce one motion in lactate dehydrogenase
-
Gerstein, M. and Chothia, C. H. (1991) Analysis of protein loop closure: Two types of hinges produce one motion in lactate dehydrogenase J. Mol. Biol. 220, 133-149
-
(1991)
J. Mol. Biol.
, vol.220
, pp. 133-149
-
-
Gerstein, M.1
Chothia, C.H.2
-
24
-
-
0026767761
-
Domain closure in mitochondrial aspartate aminotransferase
-
McPhalen, C. A., Vincent, M. G., Picot, P., and Jansonius, J. N. (1992) Domain closure in mitochondrial aspartate aminotransferase J. Mol. Biol. 227, 197-213
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 197-213
-
-
McPhalen, C.A.1
Vincent, M.G.2
Picot, P.3
Jansonius, J.N.4
-
25
-
-
0025345233
-
Structural characteristics of α-helical peptide molecules containing Aib residues
-
Karle, I. L. and Balaram, P. (1990) Structural characteristics of α-helical peptide molecules containing Aib residues Biochemistry 29, 6747-6756
-
(1990)
Biochemistry
, vol.29
, pp. 6747-6756
-
-
Karle, I.L.1
Balaram, P.2
-
29
-
-
0025022683
-
Factors governing helical preference of peptides containing multiple α,α-dialkyl amino acids
-
Marshall, G. R., Hodgkin, E. E., Langs, D. A., Smith, G. D., Zabrocki, J., and Leplawy, M. T. (1990) Factors governing helical preference of peptides containing multiple α,α-dialkyl amino acids Proc. Natl. Acad. Sci. U.S.A. 87, 487-491
-
(1990)
Proc. Natl. Acad. Sci. U.S.A.
, vol.87
, pp. 487-491
-
-
Marshall, G.R.1
Hodgkin, E.E.2
Langs, D.A.3
Smith, G.D.4
Zabrocki, J.5
Leplawy, M.T.6
-
30
-
-
0026882368
-
A molecular mechanical study of the structure of poly(α- aminoisobutyric acid)
-
Aleman, C., Subirana, J. A., and Perez, J. J. (1992) A molecular mechanical study of the structure of poly(α-aminoisobutyric acid) Biopolymers 32, 621-631
-
(1992)
Biopolymers
, vol.32
, pp. 621-631
-
-
Aleman, C.1
Subirana, J.A.2
Perez, J.J.3
-
31
-
-
0025059854
-
Conformational analysis and helical preferences of normal and α,α-dialkyl amino acids
-
Hodgkin, E. E., Clark, J. D., Miller, K. R., and Marshall, G. R. (1990) Conformational analysis and helical preferences of normal and α,α-dialkyl amino acids Biopolymers 30, 533-546
-
(1990)
Biopolymers
, vol.30
, pp. 533-546
-
-
Hodgkin, E.E.1
Clark, J.D.2
Miller, K.R.3
Marshall, G.R.4
-
32
-
-
0028167446
-
10-helix transitions in α-methylalanine homopeptides: Conformational transition pathway and potential of mean force
-
10-helix transitions in α-methylalanine homopeptides: Conformational transition pathway and potential of mean force Biopolymers 34, 75-90
-
(1994)
Biopolymers
, vol.34
, pp. 75-90
-
-
Huston, S.E.1
Marshall, G.R.2
-
33
-
-
33846217858
-
α-tetrasubstituted amino acids
-
α-tetrasubstituted amino acids Chem.-Eur. J. 13, 407-416
-
(2007)
Chem. - Eur. J.
, vol.13
, pp. 407-416
-
-
Bellanda, M.1
Mammi, S.2
Geremia, S.3
Demitri, N.4
Randaccio, L.5
Broxterman, Q.B.6
Kaptein, B.7
Pengo, P.8
Pasquato, L.9
Scrimin, P.10
-
35
-
-
0020823063
-
Stereochemistry of α-aminoisobutyric acid peptides in solution: Helical conformations of protected decapeptides with repeating Aib- l -Ala and Aib- l -Val sequences
-
Vijayakumar, E. K. and Balaram, P. (1983) Stereochemistry of α-aminoisobutyric acid peptides in solution: Helical conformations of protected decapeptides with repeating Aib- l -Ala and Aib- l -Val sequences Biopolymers 22, 2133-2140
-
(1983)
Biopolymers
, vol.22
, pp. 2133-2140
-
-
Vijayakumar, E.K.1
Balaram, P.2
-
36
-
-
0034613390
-
Crystal structure of Pseudomonas aeruginosa lipase in the open conformation
-
Nardini, M., Lang, D. A., Liebeton, K., Jaeger, K., and Dijkstra, B. W. (2000) Crystal structure of Pseudomonas aeruginosa lipase in the open conformation J. Biol. Chem. 275, 31219-31225
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 31219-31225
-
-
Nardini, M.1
Lang, D.A.2
Liebeton, K.3
Jaeger, K.4
Dijkstra, B.W.5
-
37
-
-
0030732162
-
Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation
-
Borhani, D. W., Rogers, D. P., Engler, J. A., and Brouillette, C. G. (1997) Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation Proc. Natl. Acad. Sci. U.S.A. 94, 12291-12296
-
(1997)
Proc. Natl. Acad. Sci. U.S.A.
, vol.94
, pp. 12291-12296
-
-
Borhani, D.W.1
Rogers, D.P.2
Engler, J.A.3
Brouillette, C.G.4
-
38
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M. J., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.J.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
39
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 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
-
40
-
-
0004023353
-
Amber molecular dymnamics package
-
University of California, San Francisco.
-
Case, D. A., Darden, T. A., Cheatham, T. E. I., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Crowly, M., Walker, R. C., Zhang, W., Merz, K. M., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossvry, I., Wong, K. F., Pasani, F., Vanicek, J., Wu, X., Brozell, S. R., Steinbrecher, T., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Mathews, D. H., Seetin, M. G., Sagui, C., Babin, V., and Kollman, P. A. (2008) Amber molecular dymnamics package. AMBER 10, University of California, San Francisco.
-
(2008)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.I.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowly, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossvry, I.16
Wong, K.F.17
Pasani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.A.33
more..
-
41
-
-
84864678581
-
Solvent-dependent gating motions of an extremophilic lipase from Pseudomonas aeruginosa
-
Johnson, Q. R., Nellas, R. B., and Shen, T. (2012) Solvent-dependent gating motions of an extremophilic lipase from Pseudomonas aeruginosa Biochemistry 51, 6238-6245
-
(2012)
Biochemistry
, vol.51
, pp. 6238-6245
-
-
Johnson, Q.R.1
Nellas, R.B.2
Shen, T.3
-
42
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22, 2577-2637
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
44
-
-
32544446167
-
Peptide secondary structure folding reaction coordinate: Correlation between UV Raman amide III frequency, Ψ Ramachandran angle, and hydrogen bonding
-
Mikhonin, A., Bykov, S., Myshakina, N., and Asher, S. (2006) Peptide secondary structure folding reaction coordinate: Correlation between UV Raman amide III frequency, Ψ Ramachandran angle, and hydrogen bonding J. Phys. Chem. B 110, 1928-1943
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 1928-1943
-
-
Mikhonin, A.1
Bykov, S.2
Myshakina, N.3
Asher, S.4
-
45
-
-
84859991838
-
High-pressure effect on the dynamics of solvated peptides
-
Nellas, R. B., Glover, M. M., Hamelberg, D., and Shen, T. (2012) High-pressure effect on the dynamics of solvated peptides J. Chem. Phys. 136, 145103
-
(2012)
J. Chem. Phys.
, vol.136
, pp. 145103
-
-
Nellas, R.B.1
Glover, M.M.2
Hamelberg, D.3
Shen, T.4
-
46
-
-
77956587811
-
Water's contribution to the energetic roughness from peptide dynamics
-
Johnson, Q., Doshi, U., Shen, T., and Hamelberg, D. (2010) Water's contribution to the energetic roughness from peptide dynamics J. Chem. Theory Comput. 6, 2591-2597
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2591-2597
-
-
Johnson, Q.1
Doshi, U.2
Shen, T.3
Hamelberg, D.4
-
47
-
-
35748952477
-
Cloning and expression of gene, and activation of an organic solvent-stable lipase from Pseudomonas aeruginosa LST-03
-
Ogino, H., Katou, Y., Akagi, R., Mimitsuka, T., Hiroshima, S., Gemba, Y., Doukyu, N., Yasuda, M., Ishimi, K., and Ishikawa, H. (2007) Cloning and expression of gene, and activation of an organic solvent-stable lipase from Pseudomonas aeruginosa LST-03 Extremophiles 11, 809-817
-
(2007)
Extremophiles
, vol.11
, pp. 809-817
-
-
Ogino, H.1
Katou, Y.2
Akagi, R.3
Mimitsuka, T.4
Hiroshima, S.5
Gemba, Y.6
Doukyu, N.7
Yasuda, M.8
Ishimi, K.9
Ishikawa, H.10
-
48
-
-
0033917914
-
Purification and characterization of organic solvent-stable lipase from organic solvent-tolerant Pseudomonas aeruginosa LST-03
-
Ogino, H., Nakagawa, S., Shinya, K., Muto, T., Fujimura, N., Yasuda, M., and Ishikawa, H. (2000) Purification and characterization of organic solvent-stable lipase from organic solvent-tolerant Pseudomonas aeruginosa LST-03 J. Biosci. Bioeng. 89, 451-457
-
(2000)
J. Biosci. Bioeng.
, vol.89
, pp. 451-457
-
-
Ogino, H.1
Nakagawa, S.2
Shinya, K.3
Muto, T.4
Fujimura, N.5
Yasuda, M.6
Ishikawa, H.7
-
49
-
-
0037098857
-
Extracting hydration sites around proteins from explicit water simulations
-
Henchman, R. H. and McCammon, J. A. (2002) Extracting hydration sites around proteins from explicit water simulations J. Comput. Chem. 23, 861-869
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 861-869
-
-
Henchman, R.H.1
McCammon, J.A.2
-
50
-
-
75349095771
-
-
(Siddiqui, K. S. and Thomas, T. Eds.) pp, Nova Biomedical, New York
-
Ogino, H. (2008) in Protein adaptation in extremophiles (Siddiqui, K. S. and Thomas, T., Eds.) pp 193-236, Nova Biomedical, New York.
-
(2008)
Protein Adaptation in Extremophiles
, pp. 193-236
-
-
Ogino, H.1
-
51
-
-
77955926979
-
Isolation and characterization of a novel thermophilic-organic solvent stable lipase from Acinetobacter baylyi
-
Uttatree, S., Winayanuwattikun, P., and Charoenpanich, J. (2010) Isolation and characterization of a novel thermophilic-organic solvent stable lipase from Acinetobacter baylyi Appl. Biochem. Biotechnol. 162, 1362-1376
-
(2010)
Appl. Biochem. Biotechnol.
, vol.162
, pp. 1362-1376
-
-
Uttatree, S.1
Winayanuwattikun, P.2
Charoenpanich, J.3
|