-
9
-
-
0033616580
-
-
Deniz, A. A.; Dahan, M.; Grunwell, J. R.; Ha, T.; Faulhaber, A. E.; Chemla, D. S.; Weiss, S.; Schultz, P. G. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 3670-3675.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A
, vol.96
, pp. 3670-3675
-
-
Deniz, A.A.1
Dahan, M.2
Grunwell, J.R.3
Ha, T.4
Faulhaber, A.E.5
Chemla, D.S.6
Weiss, S.7
Schultz, P.G.8
-
10
-
-
0034625167
-
-
Deniz, A. A.; Laurence, T. A.; Beligere, G. S.; Dahan, M.; Martin, A. B.; Chemla, D. S.; Dawson, P. E.; Schultz, P. G.; Weiss, S. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5179-5184.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A
, vol.97
, pp. 5179-5184
-
-
Deniz, A.A.1
Laurence, T.A.2
Beligere, G.S.3
Dahan, M.4
Martin, A.B.5
Chemla, D.S.6
Dawson, P.E.7
Schultz, P.G.8
Weiss, S.9
-
15
-
-
14544283620
-
-
Schuler, B.; Lipman, E. A.; Steinbach, P. J.; Kumke, M.; Eaton, W. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2754-2759.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, pp. 2754-2759
-
-
Schuler, B.1
Lipman, E.A.2
Steinbach, P.J.3
Kumke, M.4
Eaton, W.A.5
-
16
-
-
33746408759
-
-
024012/1-02401279
-
Rüttinger, S.; Macdonald, R.; Krämer, B.; Koberling, F.; Roos, M.; Hildt, E. J. Biomed. Optics 2006, 11, 024012/1-02401279.
-
(2006)
J. Biomed. Optics
, vol.11
-
-
Rüttinger, S.1
Macdonald, R.2
Krämer, B.3
Koberling, F.4
Roos, M.5
Hildt, E.6
-
17
-
-
33646416480
-
-
Watkins, L. P.; Chang, H.; Yang, H. J. Phys. Chem. A 2006, 110, 5191-5203.
-
(2006)
J. Phys. Chem. A
, vol.110
, pp. 5191-5203
-
-
Watkins, L.P.1
Chang, H.2
Yang, H.3
-
18
-
-
33745667285
-
-
Sahoo, H.; Roccatano, D.; Zacharias, M.; Nau, W. M. J. Am. Chem. Soc. 2006, 128, 8118-8119.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 8118-8119
-
-
Sahoo, H.1
Roccatano, D.2
Zacharias, M.3
Nau, W.M.4
-
19
-
-
0025694526
-
-
Lakowicz, J. R.; Wiczk, W.; Gryczynski, I.; Johnson, M. L. Proc. SPIE 1990, 1204, 192-205.
-
(1990)
Proc. SPIE
, vol.1204
, pp. 192-205
-
-
Lakowicz, J.R.1
Wiczk, W.2
Gryczynski, I.3
Johnson, M.L.4
-
21
-
-
0025830305
-
-
Chen, R. F.; Knutson, J. R.; Ziffer, H.; Porter, D. Biochemistry 1991, 30, 5184-5195.
-
(1991)
Biochemistry
, vol.30
, pp. 5184-5195
-
-
Chen, R.F.1
Knutson, J.R.2
Ziffer, H.3
Porter, D.4
-
23
-
-
34547748078
-
-
The static quenching fraction was significant (>3%) only for the shortest peptide (n = 1, Table 4) and therefore not analyzed in detail. A small population of conformations with donor-acceptor contact appears reasonable for the shortest peptide, because the attachment of donor and acceptor allows for some flexibility.
-
The static quenching fraction was significant (>3%) only for the shortest peptide (n = 1, Table 4) and therefore not analyzed in detail. A small population of conformations with donor-acceptor contact appears reasonable for the shortest peptide, because the attachment of donor and acceptor allows for some flexibility.
-
-
-
-
25
-
-
34547724733
-
-
ProFit 6.0.3 ed., 2005; QuantumSoft: Zürich, Switzerland.
-
ProFit 6.0.3 ed., 2005; QuantumSoft: Zürich, Switzerland.
-
-
-
-
26
-
-
0005491450
-
Statistical Mechanics of Semiflexible Chains: A meanfield variational approach
-
Grossberg, A, Ed, Academia: New York
-
Thirumalai, D.; Ha, B.-Y. Statistical Mechanics of Semiflexible Chains: A meanfield variational approach. In Theoretical and Mathematical Models in Polymer Research; Grossberg, A., Ed.; Academia: New York, 1998; pp 1-35.
-
(1998)
Theoretical and Mathematical Models in Polymer Research
, pp. 1-35
-
-
Thirumalai, D.1
Ha, B.-Y.2
-
27
-
-
34547738165
-
-
In contrast to the Gaussian model (ref 19), wormlike distributions are somewhat more realistic, especially in the case of flexible peptides, because they do not extend to distances larger than that of the most extended conformation, and because the distributions become negligibly small at distances below the van der Waals limit of ca. 4 Å. When applying the wormlike chain model, one can further calculate an average distance, which is somewhat shorter than the contour lengths due to the asymmetric shape of this distribution. The difference is less than 0.2 Å, except for n = 4 in water (0.6 Å smaller) and n = 6 in water (1.3 Å).
-
In contrast to the Gaussian model (ref 19), wormlike distributions are somewhat more "realistic", especially in the case of flexible peptides, because they do not extend to distances larger than that of the most extended conformation, and because the distributions become negligibly small at distances below the van der Waals limit of ca. 4 Å. When applying the wormlike chain model, one can further calculate an average distance, which is somewhat shorter than the contour lengths due to the asymmetric shape of this distribution. The difference is less than 0.2 Å, except for n = 4 in water (0.6 Å smaller) and n = 6 in water (1.3 Å).
-
-
-
-
29
-
-
0029437733
-
-
Wierzchowski, K. L.; Majcher, K.; Poznanski, J. Acta Biochim. Pol. 1995, 42, 259-268.
-
(1995)
Acta Biochim. Pol
, vol.42
, pp. 259-268
-
-
Wierzchowski, K.L.1
Majcher, K.2
Poznanski, J.3
-
30
-
-
34547798169
-
-
2 peptides in propylene glycol were very similar to those in (deuterated) water, even after the peptides had been incubated for several months (note that the PPII to PPI transition occurs within hours to days; cf. refs 31,32).
-
2 peptides in propylene glycol were very similar to those in (deuterated) water, even after the peptides had been incubated for several months (note that the PPII to PPI transition occurs within hours to days; cf. refs 31,32).
-
-
-
-
31
-
-
12944281484
-
-
Kakinoki, S.; Hirano, Y.; Oka, M. Polym. Bull. 2005, 53, 109-115.
-
(2005)
Polym. Bull
, vol.53
, pp. 109-115
-
-
Kakinoki, S.1
Hirano, Y.2
Oka, M.3
-
33
-
-
0344305773
-
-
Schweitzer-Stenner, R.; Eker, F.; Perez, A.; Griebenow, K.; Cao, X.; Nafie, L. A. Pept. Sci. 2003, 71, 558-568.
-
(2003)
Pept. Sci
, vol.71
, pp. 558-568
-
-
Schweitzer-Stenner, R.1
Eker, F.2
Perez, A.3
Griebenow, K.4
Cao, X.5
Nafie, L.A.6
-
34
-
-
17644422781
-
-
Whittington, S. J.; Chellgren, B. W.; Hermann, V. M.; Creamer, T. P. Biochemistry 2005, 44, 6269-6275.
-
(2005)
Biochemistry
, vol.44
, pp. 6269-6275
-
-
Whittington, S.J.1
Chellgren, B.W.2
Hermann, V.M.3
Creamer, T.P.4
-
35
-
-
34547732617
-
-
2. It was consequently not counted as an amino acid contributing to this CD feature to allow a better absolute comparison.
-
2. It was consequently not counted as an amino acid contributing to this CD feature to allow a better absolute comparison.
-
-
-
-
38
-
-
0000565474
-
-
Vassilian, A.; Wishart, J. F.; van Hemelryck, B.; Schwarz, H.; Isied, S. S. J. Am. Chem. Soc. 1990, 112, 7278-7286.
-
(1990)
J. Am. Chem. Soc
, vol.112
, pp. 7278-7286
-
-
Vassilian, A.1
Wishart, J.F.2
van Hemelryck, B.3
Schwarz, H.4
Isied, S.S.5
-
39
-
-
0001206511
-
-
Bobrowski, K.; Holeman, J.; Poznański, J.; Ciurak, M.; Wierzchowski, K. L. J. Phys. Chem. 1992, 96, 10036-10043.
-
(1992)
J. Phys. Chem
, vol.96
, pp. 10036-10043
-
-
Bobrowski, K.1
Holeman, J.2
Poznański, J.3
Ciurak, M.4
Wierzchowski, K.L.5
-
40
-
-
0001570165
-
-
Ogawa, M. Y.; Wishart, J. F.; Young, Z.; Miller, J. R.; Isied, S. S. J. Phys. Chem. 1993, 97, 11456-11463.
-
(1993)
J. Phys. Chem
, vol.97
, pp. 11456-11463
-
-
Ogawa, M.Y.1
Wishart, J.F.2
Young, Z.3
Miller, J.R.4
Isied, S.S.5
-
41
-
-
0027950714
-
-
Mishra, A. K.; Chandrasekar, R.; Faraggi, M.; Klapper, M. H. J. Am. Chem. Soc. 1994, 116, 1414-1422.
-
(1994)
J. Am. Chem. Soc
, vol.116
, pp. 1414-1422
-
-
Mishra, A.K.1
Chandrasekar, R.2
Faraggi, M.3
Klapper, M.H.4
-
42
-
-
0007758337
-
-
Isied, S. S.; Ogawa, M. Y.; Wishart, J. F. Chem. Rev. 1992, 92, 381-394.
-
(1992)
Chem. Rev
, vol.92
, pp. 381-394
-
-
Isied, S.S.1
Ogawa, M.Y.2
Wishart, J.F.3
-
43
-
-
7444258599
-
-
Malak, R. A.; Gao, Z.; Wishart, J. F.; Isied, S. S. J. Am. Chem. Soc. 2004, 126, 13888-13889.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 13888-13889
-
-
Malak, R.A.1
Gao, Z.2
Wishart, J.F.3
Isied, S.S.4
-
44
-
-
0014243811
-
-
Okabayashi, H.; Isemura, T.; Sakakibara, S. Biopolymers 1968, 6, 323-330.
-
(1968)
Biopolymers
, vol.6
, pp. 323-330
-
-
Okabayashi, H.1
Isemura, T.2
Sakakibara, S.3
-
45
-
-
34547752061
-
-
It should be noted that the closely related Trp-(Pro)n-Tyr-OH peptides, which show the onset for nucleation of the PPII helix only at n, 4, have been extensively employed in studies of long-range electron transfer in polyprolines (refs 39,41, which is also distance dependent and shows an interesting switch-over in mechanism for n, 1-9 ref 43
-
n-Tyr-OH peptides, which show the onset for nucleation of the PPII helix only at n = 4, have been extensively employed in studies of long-range electron transfer in polyprolines (refs 39,41), which is also distance dependent and shows an interesting switch-over in mechanism for n = 1-9 (ref 43).
-
-
-
-
46
-
-
0038344087
-
-
Eker, F.; Griebenow, K.; Schweitzer-Stenner, R. J. Am. Chem. Soc. 2003, 125, 8178-8185.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 8178-8185
-
-
Eker, F.1
Griebenow, K.2
Schweitzer-Stenner, R.3
-
47
-
-
22144480962
-
-
Gokce, I.; Woody, R. W.; Anderluh, G.; Lakey, J. H. J. Am. Chem. Soc. 2005, 127, 9700-9701.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 9700-9701
-
-
Gokce, I.1
Woody, R.W.2
Anderluh, G.3
Lakey, J.H.4
-
48
-
-
33746376976
-
-
Chellgren, B. W.: Miller, A.-F.; Creamer, T. P. J. Mol. Biol. 2006, 361, 362-371.
-
(2006)
J. Mol. Biol
, vol.361
, pp. 362-371
-
-
Chellgren, B.W.1
Miller, A.-F.2
Creamer, T.P.3
-
49
-
-
33847029566
-
-
Schweitzer-Stenner, R.; Measay, T.; Kakalis, L.; Jordan, F.; Pizzanelli, S.; Forte, C.; Griebenow, K. Biochemistry 2007, 46, 1587-1596.
-
(2007)
Biochemistry
, vol.46
, pp. 1587-1596
-
-
Schweitzer-Stenner, R.1
Measay, T.2
Kakalis, L.3
Jordan, F.4
Pizzanelli, S.5
Forte, C.6
Griebenow, K.7
-
51
-
-
0027333695
-
-
Poznański, J.; Ejchart, A.; Wierzchowski, K. L.; Ciurak, M. Biopolymers 1993, 33, 781-795.
-
(1993)
Biopolymers
, vol.33
, pp. 781-795
-
-
Poznański, J.1
Ejchart, A.2
Wierzchowski, K.L.3
Ciurak, M.4
-
52
-
-
0032486107
-
-
Reimer, U.; Scherer, G.; Drewello, M.; Kruber, S.; Schutkowski, M.; Fischer, G. J. Mol. Biol. 1998, 279, 449-460.
-
(1998)
J. Mol. Biol
, vol.279
, pp. 449-460
-
-
Reimer, U.1
Scherer, G.2
Drewello, M.3
Kruber, S.4
Schutkowski, M.5
Fischer, G.6
-
53
-
-
34547778116
-
-
The population of the cis isomer depends on the amino acid type and may vary in dependence on the type of carboxy-terminal amino acid (refs 37, 52), and the charge status (refs 36,51). The presence of carboxy-terminal aromatic amino acids, prominently Tyr, and a deprotonated carboxy terminus favor the relative population of the cis form for the same reasons that they tend to disrupt the PPII helix structure of short polyprolines; see above.
-
The population of the cis isomer depends on the amino acid type and may vary in dependence on the type of carboxy-terminal amino acid (refs 37, 52), and the charge status (refs 36,51). The presence of carboxy-terminal aromatic amino acids, prominently Tyr, and a deprotonated carboxy terminus favor the relative population of the cis form for the same reasons that they tend to disrupt the PPII helix structure of short polyprolines; see above.
-
-
-
-
56
-
-
0003544049
-
-
vdf Hochschulverlag: ETH Zürich, Switzerland
-
van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular simulation: The GROMOS96 manual and user guide; vdf Hochschulverlag: ETH Zürich, Switzerland 1996.
-
(1996)
Biomolecular simulation: The GROMOS96 manual and user guide
-
-
van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hünenberger, P.H.4
Krüger, P.5
Mark, A.E.6
Scott, W.R.P.7
Tironi, I.G.8
-
58
-
-
0016502735
-
-
Haas, E.; Wilchek, M.; Katchalski-Katzir, E.; Steinberg, I. Z. Proc. Natl. Acad. Sci. U.S.A. 1975, 72, 1807-1811.
-
(1975)
Proc. Natl. Acad. Sci. U.S.A
, vol.72
, pp. 1807-1811
-
-
Haas, E.1
Wilchek, M.2
Katchalski-Katzir, E.3
Steinberg, I.Z.4
-
59
-
-
0017875133
-
-
Haas, E.; Katchalski-Katzir, E.; Steinberg, I. Z. Biopolymers 1978, 17, 11-31.
-
(1978)
Biopolymers
, vol.17
, pp. 11-31
-
-
Haas, E.1
Katchalski-Katzir, E.2
Steinberg, I.Z.3
-
62
-
-
0033950079
-
-
Kay, B. K.; Williamson, M. P.; Sudol, M. FASEB J. 2000, 14, 231-241.
-
(2000)
FASEB J
, vol.14
, pp. 231-241
-
-
Kay, B.K.1
Williamson, M.P.2
Sudol, M.3
-
63
-
-
3142658038
-
-
Wong, K. F.; Bagchi, B.; Rossky, P. J. J. Phys. Chem. A 2004, 108, 5752-5763.
-
(2004)
J. Phys. Chem. A
, vol.108
, pp. 5752-5763
-
-
Wong, K.F.1
Bagchi, B.2
Rossky, P.J.3
-
65
-
-
33144461104
-
-
Saini, S.; Singh, H.; Bagchi, B. J. Chem. Sci. 2006, 118, 23-35.
-
(2006)
J. Chem. Sci
, vol.118
, pp. 23-35
-
-
Saini, S.1
Singh, H.2
Bagchi, B.3
-
67
-
-
13244271394
-
-
Wiesenhofer, H.; Beljonne, D.; Scholes, G. D.; Hennebicq, E.; Brédas, J.-L.; Zojer, E. Adv. Funct. Mater. 2005, 15, 155-160.
-
(2005)
Adv. Funct. Mater
, vol.15
, pp. 155-160
-
-
Wiesenhofer, H.1
Beljonne, D.2
Scholes, G.D.3
Hennebicq, E.4
Brédas, J.-L.5
Zojer, E.6
-
68
-
-
0032780521
-
-
Jacob, J.; Baker, B.; Bryant, R. G.; Cafiso, D. S. Biophys. J. 1999, 77, 1086-1092.
-
(1999)
Biophys. J
, vol.77
, pp. 1086-1092
-
-
Jacob, J.1
Baker, B.2
Bryant, R.G.3
Cafiso, D.S.4
-
70
-
-
0014593973
-
-
Eisinger, J.; Feuer, B.; Lamola, A. A. Biochemistry 1969, 8, 3908-3915.
-
(1969)
Biochemistry
, vol.8
, pp. 3908-3915
-
-
Eisinger, J.1
Feuer, B.2
Lamola, A.A.3
-
71
-
-
0011364625
-
-
Wiczk, W.; Eis, P. S.; Fishman, M. N.; Johnson, M. L.; Lakowicz, J. R. J. Fluoresc. 1991, 1, 273-286.
-
(1991)
J. Fluoresc
, vol.1
, pp. 273-286
-
-
Wiczk, W.1
Eis, P.S.2
Fishman, M.N.3
Johnson, M.L.4
Lakowicz, J.R.5
-
72
-
-
0037134857
-
-
Broos, J.; Pas, H. H.; Robillard, G. T. J. Am. Chem. Soc. 2002, 124, 6812-6813.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 6812-6813
-
-
Broos, J.1
Pas, H.H.2
Robillard, G.T.3
-
73
-
-
22844446166
-
-
Azov, V. A.; Schlegel, A.; Diederich, F. Angew. Chem., Int. Ed. 2005, 44, 4635-4638.
-
(2005)
Angew. Chem., Int. Ed
, vol.44
, pp. 4635-4638
-
-
Azov, V.A.1
Schlegel, A.2
Diederich, F.3
-
74
-
-
0035861692
-
-
Arduini, A.; Giorgi, G.; Pochini, A.; Secchi, A.; Ugozzoli, F. J. Org. Chem. 2001, 66, 8302-8308.
-
(2001)
J. Org. Chem
, vol.66
, pp. 8302-8308
-
-
Arduini, A.1
Giorgi, G.2
Pochini, A.3
Secchi, A.4
Ugozzoli, F.5
-
75
-
-
33746211436
-
-
Le Gac, S.; Marrot, J.; Reinaud, O.; Jabin, I. Angew. Chem., Int. Ed. 2006, 45, 3123-3126.
-
(2006)
Angew. Chem., Int. Ed
, vol.45
, pp. 3123-3126
-
-
Le Gac, S.1
Marrot, J.2
Reinaud, O.3
Jabin, I.4
-
76
-
-
33745918325
-
-
Ramanoudjame, G.; Du, M.; Mankiewicz, K. A.; Jayaraman, V. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 10473-10478.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A
, vol.103
, pp. 10473-10478
-
-
Ramanoudjame, G.1
Du, M.2
Mankiewicz, K.A.3
Jayaraman, V.4
-
79
-
-
0032769661
-
-
Hayward, S. Proteins 1999, 36, 425-435.
-
(1999)
Proteins
, vol.36
, pp. 425-435
-
-
Hayward, S.1
-
81
-
-
0037196288
-
-
Hudgins, R. R.; Huang, F.; Gramlich, G.; Nau, W. M. J. Am. Chem. Soc. 2002, 124, 556-564.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 556-564
-
-
Hudgins, R.R.1
Huang, F.2
Gramlich, G.3
Nau, W.M.4
-
82
-
-
0346460133
-
-
Kapusta, P.; Erdmann, R.; Ortmann, U.; Wahl, M. J. Fluoresc. 2003, 13, 179-183.
-
(2003)
J. Fluoresc
, vol.13
, pp. 179-183
-
-
Kapusta, P.1
Erdmann, R.2
Ortmann, U.3
Wahl, M.4
-
85
-
-
34047263387
-
-
Roccatano, D.; Sahoo, H.; Zacharias, M.; Nau, W. M. J. Phys. Chem. B 2007, 111, 2639-2646.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 2639-2646
-
-
Roccatano, D.1
Sahoo, H.2
Zacharias, M.3
Nau, W.M.4
-
86
-
-
10444232877
-
-
Roccatano, D.; Nau, W. M.; Zacharias, M. J. Phys. Chem. B 2004, 108, 18734-18742.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 18734-18742
-
-
Roccatano, D.1
Nau, W.M.2
Zacharias, M.3
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