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Volumn , Issue , 2016, Pages 59-107

Quantitative molecular electro-optics: Macromolecular structures and their dynamics in solution

Author keywords

[No Author keywords available]

Indexed keywords

MACROMOLECULAR STRUCTURES;

EID: 85052233093     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter
Times cited : (4)

References (116)
  • 1
    • 0020490833 scopus 로고
    • Structure of the complex between lac repressor headpiece and operator DNA from measurements of the orientation relaxation and the electric dichroism
    • Porschke, D., Geisler, N., and Hillen, W., Structure of the complex between lac repressor headpiece and operator DNA from measurements of the orientation relaxation and the electric dichroism, Nucleic Acids Res., 10, 3791, 1982.
    • (1982) Nucleic Acids Res , vol.10 , pp. 3791
    • Porschke, D.1    Geisler, N.2    Hillen, W.3
  • 2
    • 0031837979 scopus 로고    scopus 로고
    • Time-resolved analysis of macromolecular structures during reactions by stoppedflow electrooptics
    • Porschke, D., Time-resolved analysis of macromolecular structures during reactions by stoppedflow electrooptics, Biophys. J., 75, 528, 1998.
    • (1998) Biophys. J , vol.75 , pp. 528
    • Porschke, D.1
  • 3
    • 0022187785 scopus 로고
    • Effects of electric fields on biopolymers
    • Porschke, D., Effects of electric fields on biopolymers, Annu. Rev. Phys. Chem., 36, 159, 1985.
    • (1985) Annu. Rev. Phys. Chem , vol.36 , pp. 159
    • Porschke, D.1
  • 6
    • 0020130381 scopus 로고
    • Electric properties and structure of DNA restriction fragments from measurements of the electric dichroism
    • Diekmann, S., et al., Electric properties and structure of DNA restriction fragments from measurements of the electric dichroism, Biophys. Chem., 15, 157, 1982.
    • (1982) Biophys. Chem , vol.15 , pp. 157
    • Diekmann, S.1
  • 7
    • 0023442745 scopus 로고
    • Electric optical and hydrodynamic parameters of lac repressor from measurements of the electric dichroism-high permanent dipole-moment associated with the protein
    • Porschke, D., Electric, optical and hydrodynamic parameters of lac repressor from measurements of the electric dichroism-high permanent dipole-moment associated with the protein, Biophys. Chem., 28, 137, 1987.
    • (1987) Biophys. Chem , vol.28 , pp. 137
    • Porschke, D.1
  • 8
    • 0024788820 scopus 로고
    • The nature of protein dipole-moments-experimental and calculated permanent dipole of a-chymotrypsin
    • Antosiewicz, J.M. and Porschke, D., The nature of protein dipole-moments-experimental and calculated permanent dipole of a-chymotrypsin, Biochemistry, 28, 10072, 1989.
    • (1989) Biochemistry , vol.28 , pp. 10072
    • Antosiewicz, J.M.1    Porschke, D.2
  • 9
    • 0342502240 scopus 로고    scopus 로고
    • Electrooptical analysis of a-chymotrypsin at physiological salt concentration
    • Schonknecht, T. and Porschke, D., Electrooptical analysis of a-chymotrypsin at physiological salt concentration, Biophys. Chem., 58, 21, 1996.
    • (1996) Biophys. Chem , vol.58 , pp. 21
    • Schonknecht, T.1    Porschke, D.2
  • 10
    • 0029769803 scopus 로고    scopus 로고
    • Electrostatics and electrodynamics of bacteriorhodopsin
    • Porschke, D., Electrostatics and electrodynamics of bacteriorhodopsin, Biophys. J., 71, 3381, 1996.
    • (1996) Biophys. J , vol.71 , pp. 3381
    • Porschke, D.1
  • 11
    • 0000125188 scopus 로고
    • Relaxation methods
    • S. Friess, E. Lewis, and A.Weissberger, Eds., of Technique of Organic Chemistry, Interscience, New York
    • Eigen, M. and DeMaeyer, L., Relaxation methods, in Investigation of Rates and Mechanisms of Reactions, S. Friess, E. Lewis, and A.Weissberger, Eds., Vol. VIII, Part II of Technique of Organic Chemistry, Interscience, New York, 1963, pp. 895-1054.
    • (1963) Investigation of Rates and Mechanisms of Reactions , vol.8 , pp. 895-1054
    • Eigen, M.1    DeMaeyer, L.2
  • 12
    • 9244229410 scopus 로고
    • Entwicklung einer E-Feldsprung-Apparatur mit optischer Detektion und ihre Anwendung auf die Assoziation amphiphiler Elektrolyte
    • Ph.D. thesis, Braunschweig
    • Grünhagen, H.H., Entwicklung einer E-Feldsprung-Apparatur mit optischer Detektion und ihre Anwendung auf die Assoziation amphiphiler Elektrolyte, Ph.D. thesis, Braunschweig, 1974.
    • (1974)
    • Grünhagen, H.H.1
  • 13
    • 0015159414 scopus 로고
    • Nanosecond temperature-jump apparatus
    • Hoffman, G.W., Nanosecond temperature-jump apparatus, Rev. Sci. Instrum., 42, 1643, 1971.
    • (1971) Rev. Sci. Instrum , vol.42 , pp. 1643
    • Hoffman, G.W.1
  • 14
    • 0017020199 scopus 로고
    • Cable temperature jump apparatus with improved sensitivity and time resolution
    • Porschke, D., Cable temperature jump apparatus with improved sensitivity and time resolution, Rev. Sci. Instrum., 47, 1363, 1976.
    • (1976) Rev. Sci. Instrum , vol.47 , pp. 1363
    • Porschke, D.1
  • 15
    • 0001286652 scopus 로고
    • An electric-field jump apparatus with ns time resolution for electrooptical measurements at physiological salt concentrations
    • Porschke, D. and Obst, A., An electric-field jump apparatus with ns time resolution for electrooptical measurements at physiological salt concentrations, Rev. Sci. Instrum., 62, 818, 1991.
    • (1991) Rev. Sci. Instrum , vol.62 , pp. 818
    • Porschke, D.1    Obst, A.2
  • 16
    • 0029112706 scopus 로고
    • Electric parameters ofNa+/K+-Atpase by measurements of the fluorescence-detected electric dichroism
    • Porschke, D. and Grell, E., Electric parameters ofNa+/K+-Atpase by measurements of the fluorescence-detected electric dichroism, Biochim. Biophys. Acta Bioen., 1231, 181, 1995.
    • (1995) Biochim. Biophys. Acta Bioen , vol.1231 , pp. 181
    • Porschke, D.1    Grell, E.2
  • 17
    • 0038051825 scopus 로고    scopus 로고
    • Dipole reversal in bacteriorhodopsin and separation of dipole components
    • Wang, G.Y. and Porschke, D., Dipole reversal in bacteriorhodopsin and separation of dipole components, J. Phys. Chem. B, 107, 4632, 2003.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 4632
    • Wang, G.Y.1    Porschke, D.2
  • 18
    • 33646937708 scopus 로고    scopus 로고
    • Analysis of chemical and physical relaxation processes of polyelectrolytes by electric field pulse methods: A comparison of critical comments with facts
    • Porschke, D., Analysis of chemical and physical relaxation processes of polyelectrolytes by electric field pulse methods: A comparison of critical comments with facts, Ber. Bunsengesell. Phys. Chem., 100, 715, 1996.
    • (1996) Ber. Bunsengesell. Phys. Chem , vol.100 , pp. 715
    • Porschke, D.1
  • 19
    • 0020161682 scopus 로고
    • Orientation relaxation of DNA restriction fragments and the internal mobility of the double helix
    • Diekmann, S., et al., Orientation relaxation of DNA restriction fragments and the internal mobility of the double helix, Biophys. Chem., 15, 263, 1982.
    • (1982) Biophys. Chem , vol.15 , pp. 263
    • Diekmann, S.1
  • 20
    • 0021870990 scopus 로고
    • The conformation of single stranded oligonucleotides and of oligonucleotide-oligopeptide complexes from their rotation relaxation in the nanosecond time range
    • Porschke, D. and Jung, M., The conformation of single stranded oligonucleotides and of oligonucleotide-oligopeptide complexes from their rotation relaxation in the nanosecond time range, J. Biomol. Struct. Dyn., 2, 1173, 1985.
    • (1985) J. Biomol. Struct. Dyn , vol.2 , pp. 1173
    • Porschke, D.1    Jung, M.2
  • 21
    • 0028282252 scopus 로고
    • Deconvolution of electrooptical data in the frequency-domain- relaxation processes of DNA from rigid rods to coiled spheres
    • Porschke, D. and Nolte, G., Deconvolution of electrooptical data in the frequency-domain- relaxation processes of DNA from rigid rods to coiled spheres, Macromolecules, 27, 590, 1994.
    • (1994) Macromolecules , vol.27 , pp. 590
    • Porschke, D.1    Nolte, G.2
  • 22
    • 0041592685 scopus 로고    scopus 로고
    • Strong bending of purple membranes in the M-state
    • Porschke, D., Strong bending of purple membranes in the M-state, J. Mol. Biol., 331, 667, 2003.
    • (2003) J. Mol. Biol , vol.331 , pp. 667
    • Porschke, D.1
  • 23
    • 0034632864 scopus 로고    scopus 로고
    • Molecular mechanism of vectorial proton translocation by bacteriorhodopsin
    • Subramaniam, S. and Henderson, R., Molecular mechanism of vectorial proton translocation by bacteriorhodopsin, Nature, 406, 653, 2000.
    • (2000) Nature , vol.406 , pp. 653
    • Subramaniam, S.1    Henderson, R.2
  • 24
    • 0038111667 scopus 로고    scopus 로고
    • Bacteriorhodopsin-the movie
    • Kühlbrandt, W., Bacteriorhodopsin-the movie, Nature, 406, 569, 2000.
    • (2000) Nature , vol.406 , pp. 569
    • Kühlbrandt, W.1
  • 25
    • 0041608233 scopus 로고    scopus 로고
    • Molecular electro-optics, in Protein-Ligand Interactions: Hydrodynamics and Calorimetry
    • S.E. Harding and B.Z. Chowdhry, Eds., Oxford University Press, Oxford
    • Porschke, D., Molecular electro-optics, in Protein-Ligand Interactions: Hydrodynamics and Calorimetry, S.E. Harding and B.Z. Chowdhry, Eds., Oxford University Press, Oxford, 2001, pp. 197-221.
    • (2001) , pp. 197-221
    • Porschke, D.1
  • 26
    • 33947480381 scopus 로고
    • Electric properties of macromolecules. IV. Determination of electric and optical parameters from saturation of electric birefringence in solutions
    • Okonski, C.T., Yoshioka, K., and Orttung, W.H., Electric properties of macromolecules. IV. Determination of electric and optical parameters from saturation of electric birefringence in solutions, J. Phys. Chem., 63, 1558, 1959.
    • (1959) J. Phys. Chem , vol.63 , pp. 1558
    • Okonski, C.T.1    Yoshioka, K.2    Orttung, W.H.3
  • 28
    • 0011257308 scopus 로고
    • Brownian dynamics simulation of electrooptical transients for solutions of rigid macromolecules
    • Antosiewicz, J.M., Grycuk, T., and Porschke, D., Brownian dynamics simulation of electrooptical transients for solutions of rigid macromolecules, J. Chem. Phys., 95, 1354, 1991.
    • (1991) J. Chem. Phys , vol.95 , pp. 1354
    • Antosiewicz, J.M.1    Grycuk, T.2    Porschke, D.3
  • 29
    • 0008217485 scopus 로고
    • Brownian dynamics simulation of electrooptical transients for complex macrodipoles
    • Antosiewicz, J.M. and Porschke, D., Brownian dynamics simulation of electrooptical transients for complex macrodipoles, J. Phys. Chem., 97, 2767, 1993.
    • (1993) J. Phys. Chem , vol.97 , pp. 2767
    • Antosiewicz, J.M.1    Porschke, D.2
  • 30
    • 36849142014 scopus 로고
    • Rotational diffusion constant of a cylindrical particle
    • Broersma, S., Rotational diffusion constant of a cylindrical particle, J. Chem. Phys., 32, 1626, 1960.
    • (1960) J. Chem. Phys , vol.32 , pp. 1626
    • Broersma, S.1
  • 31
    • 4243642135 scopus 로고
    • Comparison of theories for the translational and rotational diffusion-coefficients of rod-like macromolecules-application to short DNA fragments
    • Tirado, M.M., Martinez, C.L., and Garcia de la Torre, J.G., Comparison of theories for the translational and rotational diffusion-coefficients of rod-like macromolecules-application to short DNA fragments, J. Chem. Phys., 81, 2047, 1984.
    • (1984) J. Chem. Phys , vol.81 , pp. 2047
    • Tirado, M.M.1    Martinez, C.L.2    Garcia de la Torre, J.G.3
  • 32
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman, H.M., et al., The Protein Data Bank, Nucleic Acids Res., 28, 235, 2000.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235
    • Berman, H.M.1
  • 33
    • 0030003578 scopus 로고    scopus 로고
    • NAMOT2-A redesigned nucleic acid modeling tool: construction of non-canonical DNA structures
    • Carter, E.S. and Tung, C.S., NAMOT2-A redesigned nucleic acid modeling tool: construction of non-canonical DNA structures, Comp. Appl. Biosci., 12, 25, 1996.
    • (1996) Comp. Appl. Biosci , vol.12 , pp. 25
    • Carter, E.S.1    Tung, C.S.2
  • 34
    • 0344154480 scopus 로고
    • Anisotropie der Lichtabsorption gelster Molekle im elektrischen Feld
    • Kuhn, W., Dührkop, H., and Martin, H., Anisotropie der Lichtabsorption gelster Molekle im elektrischen Feld, Z. Phys. Chem., B45, 121, 1939.
    • (1939) Z. Phys. Chem , vol.B45 , pp. 121
    • Kuhn, W.1    Dührkop, H.2    Martin, H.3
  • 35
    • 0017698551 scopus 로고
    • Dichroic tensor of flexible helices
    • Wilson, R.W. and Schellman, J.A., Dichroic tensor of flexible helices, Biopolymers, 16, 2143, 1977.
    • (1977) Biopolymers , vol.16 , pp. 2143
    • Wilson, R.W.1    Schellman, J.A.2
  • 36
    • 0021403295 scopus 로고
    • Matrix-method calculation of linear and circular-dichroism spectra of nucleic-acids and polynucleotides
    • Rizzo, V. and Schellman, J.A., Matrix-method calculation of linear and circular-dichroism spectra of nucleic-acids and polynucleotides, Biopolymers, 23, 435, 1984.
    • (1984) Biopolymers , vol.23 , pp. 435
    • Rizzo, V.1    Schellman, J.A.2
  • 37
    • 84984084960 scopus 로고
    • Absorption spectra of nucleotides polynucleotides, and nucleic acids in the far ultraviolet
    • Voet, D., et al., Absorption spectra of nucleotides, polynucleotides, and nucleic acids in the far ultraviolet, Biopolymers, 1, 193, 1963.
    • (1963) Biopolymers , vol.1 , pp. 193
    • Voet, D.1
  • 38
    • 0017595418 scopus 로고
    • Circular-dichroism calculations for double-stranded polynucleotides of repeating sequence
    • Cech, C.L. and Tinoco, I., Circular-dichroism calculations for double-stranded polynucleotides of repeating sequence, Biopolymers, 16, 43, 1977.
    • (1977) Biopolymers , vol.16 , pp. 43
    • Cech, C.L.1    Tinoco, I.2
  • 39
    • 84943917679 scopus 로고
    • Applications of linear dichroism spectroscopy
    • Norden, B., Applications of linear dichroism spectroscopy, App. Spectrosc. Rev., 14, 157, 1978.
    • (1978) App. Spectrosc. Rev , vol.14 , pp. 157
    • Norden, B.1
  • 40
    • 2342651908 scopus 로고
    • Dichroic spectra of biopolymers oriented by flow
    • Wada, A., Dichroic spectra of biopolymers oriented by flow, Appl. Spectrosc. Rev., 6, 1, 1972.
    • (1972) Appl. Spectrosc. Rev , vol.6 , pp. 1
    • Wada, A.1
  • 41
    • 0011205264 scopus 로고
    • Structure of an alternating-B DNA helix and its relationship to A-tract DNA
    • Yoon, C., et al., Structure of an alternating-B DNA helix and its relationship to A-tract DNA, Proc. Natl. Acad. Sci. USA, 85, 6332, 1988.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 6332
    • Yoon, C.1
  • 42
    • 0019558179 scopus 로고
    • Structure of a B-DNA dodecamer-conformation and dynamics
    • Drew, H.R., et al., Structure of a B-DNA dodecamer-conformation and dynamics, Proc. Natl. Acad. Sci. USA, 78, 2179, 1981.
    • (1981) Proc. Natl. Acad. Sci. USA , vol.78 , pp. 2179
    • Drew, H.R.1
  • 43
    • 0016778737 scopus 로고
    • Atomic coordinates for yeast phenylalanine transfer-RNA
    • Ladner, J.E., et al., Atomic coordinates for yeast phenylalanine transfer-RNA, Nucleic Acids Res., 2, 1629, 1975.
    • (1975) Nucleic Acids Res , vol.2 , pp. 1629
    • Ladner, J.E.1
  • 44
    • 0000581846 scopus 로고
    • Polarized absorption-spectra of crystals of indole and its related compounds
    • Yamamoto, Y. and Tanaka, J., Polarized absorption-spectra of crystals of indole and its related compounds, Bull. Chem. Soc. Jpn., 45, 1362, 1972.
    • (1972) Bull. Chem. Soc. Jpn , vol.45 , pp. 1362
    • Yamamoto, Y.1    Tanaka, J.2
  • 46
    • 85022818235 scopus 로고
    • Effect of sigma-2 interaction on electronic-structure of molecules in excited-states. 2. Oscillator strength
    • Maki, I., Kitaura, K., and Nishimoto, K., Effect of sigma-2 interaction on electronic-structure of molecules in excited-states. 2. Oscillator strength, Bull. Chem. Soc. Jpn., 51, 401, 1978.
    • (1978) Bull. Chem. Soc. Jpn , vol.51 , pp. 401
    • Maki, I.1    Kitaura, K.2    Nishimoto, K.3
  • 47
    • 36549091193 scopus 로고
    • The rotationally resolved electronic-spectrum of indole in the gasphase
    • Philips, L.A. and Levy, D.H., The rotationally resolved electronic-spectrum of indole in the gasphase, J. Chem. Phys., 85, 1327, 1986.
    • (1986) J. Chem. Phys , vol.85 , pp. 1327
    • Philips, L.A.1    Levy, D.H.2
  • 48
    • 0023953148 scopus 로고
    • Turn of promotor DNA by camp receptor protein characterized by bead model simulation of rotational diffusion
    • Antosiewicz, J.M. and Porschke, D., Turn of promotor DNA by camp receptor protein characterized by bead model simulation of rotational diffusion, J. Biomol. Struct. Dyn., 5, 819, 1988.
    • (1988) J. Biomol. Struct. Dyn , vol.5 , pp. 819
    • Antosiewicz, J.M.1    Porschke, D.2
  • 49
    • 0028851189 scopus 로고
    • Electrostatics of hemoglobins from measurements of the electric dichroism and computer-simulations
    • Antosiewicz, J.M. and Porschke, D., Electrostatics of hemoglobins from measurements of the electric dichroism and computer-simulations, Biophys. J., 68, 655, 1995.
    • (1995) Biophys. J , vol.68 , pp. 655
    • Antosiewicz, J.M.1    Porschke, D.2
  • 50
    • 0343387160 scopus 로고
    • Electric polarizability of polar ions
    • Mysels, K.J., Electric polarizability of polar ions, J. Chem. Phys., 21, 201, 1953.
    • (1953) J. Chem. Phys , vol.21 , pp. 201
    • Mysels, K.J.1
  • 51
    • 0024241856 scopus 로고
    • An unusual electrooptical effect observed for DNA fragments and its apparent relation to a permanent electric moment associated with bent DNA
    • Antosiewicz, J.M. and Porschke, D., An unusual electrooptical effect observed for DNA fragments and its apparent relation to a permanent electric moment associated with bent DNA, Biophys. Chem., 33, 19, 1989.
    • (1989) Biophys. Chem , vol.33 , pp. 19
    • Antosiewicz, J.M.1    Porschke, D.2
  • 52
    • 0030059821 scopus 로고    scopus 로고
    • Direct measurement of the aspartic acid 26 pKa for reduced Escherichia coli thioredoxin by C-13 NMR
    • Jeng, M.F. and Dyson, H.J., Direct measurement of the aspartic acid 26 pKa for reduced Escherichia coli thioredoxin by C-13 NMR, Biochemistry, 35, 1, 1996.
    • (1996) Biochemistry , vol.35 , pp. 1
    • Jeng, M.F.1    Dyson, H.J.2
  • 53
    • 0025718561 scopus 로고
    • The conserved buried aspartic-acid in oxidized Escherichia-coli thioredoxin has a pKa of 7.5-Its titration produces a related shift in global stability
    • Langsetmo, K., Fuchs, J.A., and Woodward, C., The conserved, buried aspartic-acid in oxidized Escherichia-coli thioredoxin has a pKa of 7.5-Its titration produces a related shift in global stability, Biochemistry, 30, 7603, 1991.
    • (1991) Biochemistry , vol.30 , pp. 7603
    • Langsetmo, K.1    Fuchs, J.A.2    Woodward, C.3
  • 54
    • 0029116114 scopus 로고
    • Aspartic-acid 26 in reduced Escherichia-coli thioredoxin has a pKa greaterthan-9
    • Wilson, N.A., et al., Aspartic-acid 26 in reduced Escherichia-coli thioredoxin has a pKa greaterthan-9, Biochemistry, 34, 8931, 1995.
    • (1995) Biochemistry , vol.34 , pp. 8931
    • Wilson, N.A.1
  • 55
    • 0027383705 scopus 로고
    • Active-site labeling of the Yersinia protein-tyrosine-phosphatase- the determination of the pKa of the active-site cysteine and the function of the conserved histidine-402
    • Zhang, Z.Y. and Dixon, J.E., Active-site labeling of the Yersinia protein-tyrosine-phosphatase- the determination of the pKa of the active-site cysteine and the function of the conserved histidine-402, Biochemistry, 32, 9340, 1993.
    • (1993) Biochemistry , vol.32 , pp. 9340
    • Zhang, Z.Y.1    Dixon, J.E.2
  • 56
    • 0019889036 scopus 로고
    • Calculations of enzymatic-reactions-calculations of pKa proton-transfer reactions, and general acid catalysis reactions in enzymes
    • Warshel, A., Calculations of enzymatic-reactions-calculations of pKa, proton-transfer reactions, and general acid catalysis reactions in enzymes, Biochemistry, 20, 3167, 1981.
    • (1981) Biochemistry , vol.20 , pp. 3167
    • Warshel, A.1
  • 57
    • 33947468892 scopus 로고
    • Theory of protein titration curves. I. General equations for impenetrable spheres
    • Tanford, C. and Kirkwood, J.G., Theory of protein titration curves. I. General equations for impenetrable spheres, J. Am. Chem. Soc., 79, 5333, 1957.
    • (1957) J. Am. Chem. Soc , vol.79 , pp. 5333
    • Tanford, C.1    Kirkwood, J.G.2
  • 58
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz, J.M., McCammon, J.A., and Gilson, M.K., Prediction of pH-dependent properties of proteins, J. Mol. Biol., 238, 415, 1994.
    • (1994) J. Mol. Biol , vol.238 , pp. 415
    • Antosiewicz, J.M.1    McCammon, J.A.2    Gilson, M.K.3
  • 59
    • 0000945505 scopus 로고    scopus 로고
    • Computing ionization states of proteins with a detailed charge model
    • Antosiewicz, J.M., et al., Computing ionization states of proteins with a detailed charge model, J. Comput. Chem., 17, 1633, 1996.
    • (1996) J. Comput. Chem , vol.17 , pp. 1633
    • Antosiewicz, J.M.1
  • 60
    • 0025197061 scopus 로고
    • pKa's of ionizable groups in proteins-atomic detail from a continuum electrostatic model
    • Bashford, D. and Karplus, M., pKa's of ionizable groups in proteins-atomic detail from a continuum electrostatic model, Biochemistry, 29, 10219, 1990.
    • (1990) Biochemistry , vol.29 , pp. 10219
    • Bashford, D.1    Karplus, M.2
  • 61
    • 0026612756 scopus 로고
    • Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin
    • Bashford, D. and Gerwert, K., Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin, J. Mol. Biol., 224, 473, 1992.
    • (1992) J. Mol. Biol , vol.224 , pp. 473
    • Bashford, D.1    Gerwert, K.2
  • 62
    • 0027563464 scopus 로고
    • On the calculation of pKa's in proteins
    • Yang, A.S., et al., On the calculation of pKa's in proteins, Proteins: Struct. Funct. Genet., 15, 252, 1993.
    • (1993) Proteins: Struct. Funct. Genet , vol.15 , pp. 252
    • Yang, A.S.1
  • 63
    • 33748593093 scopus 로고    scopus 로고
    • Improving the continuum dielectric approach to calculating pKa's of ionizable groups in proteins
    • Demchuk, E. and Wade, R.C., Improving the continuum dielectric approach to calculating pKa's of ionizable groups in proteins, J. Phys. Chem., 100, 17373, 1996.
    • (1996) J. Phys. Chem , vol.100 , pp. 17373
    • Demchuk, E.1    Wade, R.C.2
  • 64
    • 0030945495 scopus 로고    scopus 로고
    • Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
    • Alexov, E.G. and Gunner, M.R., Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties, Biophys. J., 72, 2075, 1997.
    • (1997) Biophys. J , vol.72 , pp. 2075
    • Alexov, E.G.1    Gunner, M.R.2
  • 65
    • 0031719963 scopus 로고    scopus 로고
    • Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles-application to the photosynthetic reaction center
    • Rabenstein, B., Ullmann, G.M., and Knapp, E.W., Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles-application to the photosynthetic reaction center, Eur. Biophys. J. Biophys. Lett., 27, 626, 1998.
    • (1998) Eur. Biophys. J. Biophys. Lett , vol.27 , pp. 626
    • Rabenstein, B.1    Ullmann, G.M.2    Knapp, E.W.3
  • 66
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein-structure
    • Richards, F.M., Areas, volumes, packing, and protein-structure, Annu. Rev. Biophys. Bioeng., 6, 151, 1977.
    • (1977) Annu. Rev. Biophys. Bioeng , vol.6 , pp. 151
    • Richards, F.M.1
  • 67
    • 0020475509 scopus 로고
    • Calculation of the electric-potential in the active-site cleft due to alpha-helix dipoles
    • Warwicker, J. and Watson, H.C., Calculation of the electric-potential in the active-site cleft due to alpha-helix dipoles, J. Mol. Biol., 157, 671, 1982.
    • (1982) J. Mol. Biol , vol.157 , pp. 671
    • Warwicker, J.1    Watson, H.C.2
  • 68
    • 0022964504 scopus 로고
    • Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification
    • Klapper, I., et al., Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification, Proteins: Struct. Funct. Genet., 1, 47, 1986.
    • (1986) Proteins: Struct. Funct. Genet , vol.1 , pp. 47
    • Klapper, I.1
  • 69
    • 5744249209 scopus 로고
    • Equation of state calculations by fast computing machines
    • Metropolis, N., et al., Equation of state calculations by fast computing machines, J. Chem. Phys., 21, 1087, 1953.
    • (1953) J. Chem. Phys , vol.21 , pp. 1087
    • Metropolis, N.1
  • 70
    • 0026095641 scopus 로고
    • Protonation of interacting residues in a protein by a Monte-Carlo Method- application to lysozyme and the photosynthetic reaction center of Rhodobacter-sphaeroides
    • Beroza, P., et al., Protonation of interacting residues in a protein by a Monte-Carlo Method- application to lysozyme and the photosynthetic reaction center of Rhodobacter-sphaeroides, Proc. Natl. Acad. Sci. USA, 88, 5804, 1991.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 5804
    • Beroza, P.1
  • 71
    • 0029100915 scopus 로고
    • Computation of the dipole-moments of proteins
    • Antosiewicz, J.M. Computation of the dipole-moments of proteins, Biophys. J., 69, 1344, 1995.
    • (1995) Biophys. J , vol.69 , pp. 1344
    • Antosiewicz, J.M.1
  • 72
    • 33751499830 scopus 로고
    • Multiple-site titration curves of proteins-an analysis of exact and approximate methods for their calculation
    • Bashford, D. and Karplus, M., Multiple-site titration curves of proteins-an analysis of exact and approximate methods for their calculation, J. Phys. Chem., 95, 9556, 1991.
    • (1991) J. Phys. Chem , vol.95 , pp. 9556
    • Bashford, D.1    Karplus, M.2
  • 73
    • 0027477251 scopus 로고
    • Multiple-site titration and molecular modeling-2 rapid methods for computing energies and forces for ionizable groups in proteins
    • Gilson, M.K., Multiple-site titration and molecular modeling-2 rapid methods for computing energies and forces for ionizable groups in proteins, Proteins: Struct. Funct. Genet., 15, 266, 1993.
    • (1993) Proteins: Struct. Funct. Genet , vol.15 , pp. 266
    • Gilson, M.K.1
  • 74
    • 0026124585 scopus 로고
    • Electrostatics and diffusion of molecules in solution-simulations with the University of Houston Brownian Dynamics program
    • Davis, M.E., et al., Electrostatics and diffusion of molecules in solution-simulations with the University of Houston Brownian Dynamics program, Comput. Phys. Commun., 62, 187, 1991.
    • (1991) Comput. Phys. Commun , vol.62 , pp. 187
    • Davis, M.E.1
  • 75
    • 0029633152 scopus 로고
    • Electrostatics and diffusion of molecules in solution-simulations with the University of Houston Brownian Dynamics program
    • Madura, J.D., et al., Electrostatics and diffusion of molecules in solution-simulations with the University of Houston Brownian Dynamics program, Comput. Phys. Commun., 91, 57, 1995.
    • (1995) Comput. Phys. Commun , vol.91 , pp. 57
    • Madura, J.D.1
  • 76
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell, A.D., et al., All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B, 102, 3586, 1998.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586
    • MacKerell, A.D.1
  • 77
    • 0001461682 scopus 로고
    • Examination of titration behaviour
    • C. Hirs, Ed., volume XI of Methods in Enzymology, Academic Press, New York
    • Nozaki, Y. and Tanford, C., Examination of titration behaviour, in Enzyme Structure, C. Hirs, Ed., volume XI of Methods in Enzymology, Academic Press, New York, 1967, pp. 715-734.
    • (1967) Enzyme Structure , pp. 715-734
    • Nozaki, Y.1    Tanford, C.2
  • 78
    • 0004155427 scopus 로고
    • Freeman, New York
    • Stryer, L., Biochemistry, 4th ed., Freeman, New York, 1995.
    • (1995) Biochemistry
    • Stryer, L.1
  • 79
    • 0018749496 scopus 로고
    • Electrostatic effects in hemoglobin-hydrogen-ion equilibria in human deoxyhemoglobin and oxyhemoglobin-A
    • Matthew, J.B., Hanania, G.I.H., and Gurd, F.R.N., Electrostatic effects in hemoglobin-hydrogen-ion equilibria in human deoxyhemoglobin and oxyhemoglobin-A, Biochemistry, 18, 1919, 1979.
    • (1979) Biochemistry , vol.18 , pp. 1919
    • Matthew, J.B.1    Hanania, G.I.H.2    Gurd, F.R.N.3
  • 80
    • 84977586068 scopus 로고
    • Uber die von der molekularkinetischen Theorie der Wrme geforderte Bewegung von in ruhenden Flssigkeiten suspendierten Teilchen
    • Einstein, A., Uber die von der molekularkinetischen Theorie der Wrme geforderte Bewegung von in ruhenden Flssigkeiten suspendierten Teilchen, Ann. Physik, 17, 549, 1905.
    • (1905) Ann. Physik , vol.17 , pp. 549
    • Einstein, A.1
  • 81
    • 5244227523 scopus 로고
    • Coupling between translational and rotational Brownian motions of rigid particles of arbitrary shape. I. Helicoidally isotropic particles
    • Brenner, H., Coupling between translational and rotational Brownian motions of rigid particles of arbitrary shape. I. Helicoidally isotropic particles, J. Coll. Sci., 20, 104, 1965.
    • (1965) J. Coll. Sci , vol.20 , pp. 104
    • Brenner, H.1
  • 82
    • 0003502177 scopus 로고
    • Low Reynolds number hydrodynamics. With special applications to particulate media, Mechanics of fluids and transport processes
    • ed edition, Noordhoff International Publishing, Leyden
    • Happel, J. and Brenner, H., Low Reynolds number hydrodynamics. With special applications to particulate media, Mechanics of fluids and transport processes, 2., rev. ed edition, Noordhoff International Publishing, Leyden, 1973.
    • (1973) , vol.2
    • Happel, J.1    Brenner, H.2
  • 83
    • 33645084334 scopus 로고
    • The Stokes resistance of an arbitrary particle. II. An extension
    • Brenner, H., The Stokes resistance of an arbitrary particle. II. An extension, Chem. Eng. Sci., 19, 599, 1964.
    • (1964) Chem. Eng. Sci , vol.19 , pp. 599
    • Brenner, H.1
  • 84
    • 0040169959 scopus 로고
    • The Stokes resistance of an arbitrary particle. III. Shear fields
    • Brenner, H., The Stokes resistance of an arbitrary particle. III. Shear fields, Chem. Eng. Sci., 19, 631, 1964.
    • (1964) Chem. Eng. Sci , vol.19 , pp. 631
    • Brenner, H.1
  • 85
    • 0001006091 scopus 로고
    • Coordinate systems for modeling the hydrodynamic resistance and diffusion-coefficients of irregularly shaped rigid macromolecules
    • Harvey, S.C. and Garcia de la Torre, J.G., Coordinate systems for modeling the hydrodynamic resistance and diffusion-coefficients of irregularly shaped rigid macromolecules, Macromolecules, 13, 960, 1980.
    • (1980) Macromolecules , vol.13 , pp. 960
    • Harvey, S.C.1    Garcia de la Torre, J.G.2
  • 86
    • 85052221000 scopus 로고
    • Neuere Methoden und Ergebnisse in der Hydrodynamik, Mathematik und ihre Anwendungen
    • Oseen, C.W., Neuere Methoden und Ergebnisse in der Hydrodynamik, Mathematik und ihre Anwendungen, Akad. Verl. Ges., Leipzig, 1927.
    • (1927) Akad. Verl. Ges., Leipzig
    • Oseen, C.W.1
  • 87
    • 84949208823 scopus 로고
    • Langevin theory of polymer dynamics in dilute solution
    • K. Shuler, Ed., Interscience, New York
    • Zwanzig, R., Langevin theory of polymer dynamics in dilute solution, in Stochastic Processes in Chemical Physics, K. Shuler, Ed., Interscience, New York, 1969, pp. 325-331.
    • (1969) Stochastic Processes in Chemical Physics , pp. 325-331
    • Zwanzig, R.1
  • 88
    • 84933517499 scopus 로고
    • Variational treatment of hydrodynamic interaction in polymers
    • Rotne, J. and Prager, S., Variational treatment of hydrodynamic interaction in polymers, J. Chem. Phys., 50, 4831, 1969.
    • (1969) J. Chem. Phys , vol.50 , pp. 4831
    • Rotne, J.1    Prager, S.2
  • 89
    • 36849101815 scopus 로고
    • Transport properties of polymer chains in dilute solution-hydrodynamic interaction
    • Yamakawa, H., Transport properties of polymer chains in dilute solution-hydrodynamic interaction, J. Chem. Phys., 53, 436, 1970.
    • (1970) J. Chem. Phys , vol.53 , pp. 436
    • Yamakawa, H.1
  • 90
    • 0017403408 scopus 로고
    • Hydrodynamic properties of macromolecular complexes. I. Translation
    • Garcia de la Torre, J.G. and Bloomfield, V.A., Hydrodynamic properties of macromolecular complexes. I. Translation, Biopolymers, 16, 1747, 1977.
    • (1977) Biopolymers , vol.16 , pp. 1747
    • Garcia de la Torre, J.G.1    Bloomfield, V.A.2
  • 91
    • 0017391665 scopus 로고
    • Hydrodynamics of macromolecular complexes. II. Rotation
    • Garcia de la Torre, J.G. and Bloomfield, V.A., Hydrodynamics of macromolecular complexes. II. Rotation, Biopolymers, 16, 1765, 1977.
    • (1977) Biopolymers , vol.16 , pp. 1765
    • Garcia de la Torre, J.G.1    Bloomfield, V.A.2
  • 92
    • 0019526265 scopus 로고
    • Hydrodynamic properties of complex rigid, biological macromolecules-theory and applications
    • Garcia de la Torre, J.G. and Bloomfield, V.A., Hydrodynamic properties of complex, rigid, biological macromolecules-theory and applications, Q. Rev. Biophys., 14, 81, 1981.
    • (1981) Q. Rev. Biophys , vol.14 , pp. 81
    • Garcia de la Torre, J.G.1    Bloomfield, V.A.2
  • 93
    • 0001753999 scopus 로고
    • Low Reynolds-number translational friction of ellipsoids cylinders, dumbbells, and hollow spherical caps-numerical testing of validity of modified Oseen tensor in computing friction of objects modeled as beads on a shell
    • Swanson, E., Teller, D.C., and Haen, C.D., Low Reynolds-number translational friction of ellipsoids, cylinders, dumbbells, and hollow spherical caps-numerical testing of validity of modified Oseen tensor in computing friction of objects modeled as beads on a shell, J. Chem. Phys., 68, 5097, 1978.
    • (1978) J. Chem. Phys , vol.68 , pp. 5097
    • Swanson, E.1    Teller, D.C.2    Haen, C.D.3
  • 94
    • 36749114754 scopus 로고
    • Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models
    • Garcia de la Torre, J.G. and Rodes, V., Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models, J. Chem. Phys., 79, 2454, 1983.
    • (1983) J. Chem. Phys , vol.79 , pp. 2454
    • Garcia de la Torre, J.G.1    Rodes, V.2
  • 95
    • 0001741346 scopus 로고
    • Volume correction for bead model simulations of rotational friction coefficients of macromolecules
    • Antosiewicz, J.M. and Porschke, D., Volume correction for bead model simulations of rotational friction coefficients of macromolecules, J. Phys. Chem., 93, 5301, 1989.
    • (1989) J. Phys. Chem , vol.93 , pp. 5301
    • Antosiewicz, J.M.1    Porschke, D.2
  • 96
    • 0015222647 scopus 로고
    • Interpretation of protein structures-estimation of static accessibility
    • Lee, B. and Richards, F.M., Interpretation of protein structures-estimation of static accessibility, J. Mol. Biol., 55, 379, 1971.
    • (1971) J. Mol. Biol , vol.55 , pp. 379
    • Lee, B.1    Richards, F.M.2
  • 97
    • 0000741446 scopus 로고
    • Time-dependent birefringence linear dichroism, and optical-rotation resulting from rigid-body rotational diffusion
    • Wegener, W.A., Dowben, R.M., and Koester, V.J., Time-dependent birefringence, linear dichroism, and optical-rotation resulting from rigid-body rotational diffusion, J. Chem. Phys., 70, 622, 1979.
    • (1979) J. Chem. Phys , vol.70 , pp. 622
    • Wegener, W.A.1    Dowben, R.M.2    Koester, V.J.3
  • 98
    • 0008664122 scopus 로고
    • Sinusoidal electric birefringence of dilute rigid-body suspensions at low field strengths
    • Wegener, W.A., Sinusoidal electric birefringence of dilute rigid-body suspensions at low field strengths, J. Chem. Phys., 84, 6005, 1986.
    • (1986) J. Chem. Phys , vol.84 , pp. 6005
    • Wegener, W.A.1
  • 99
    • 0030989905 scopus 로고    scopus 로고
    • Influence of static and dynamic bends on the birefringence decay profile of RNA helices: Brownian dynamics simulations
    • Zacharias, M. and Hagerman, P.J., Influence of static and dynamic bends on the birefringence decay profile of RNA helices: Brownian dynamics simulations, Biophys. J., 73, 318, 1997.
    • (1997) Biophys. J , vol.73 , pp. 318
    • Zacharias, M.1    Hagerman, P.J.2
  • 100
    • 13244299277 scopus 로고    scopus 로고
    • Strong effect of hydrodynamic coupling on the electric dichroism of bent rods
    • Porschke, D. and Antosiewicz, J.M., Strong effect of hydrodynamic coupling on the electric dichroism of bent rods, J. Phys. Chem. B, 109, 1034, 2005.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 1034
    • Porschke, D.1    Antosiewicz, J.M.2
  • 101
    • 0024993099 scopus 로고
    • Permanent dipole-moment of transfer-RNAs and variation of their structure in solution
    • Porschke, D. and Antosiewicz, J.M., Permanent dipole-moment of transfer-RNAs and variation of their structure in solution, Biophys. J., 58, 403, 1990.
    • (1990) Biophys. J , vol.58 , pp. 403
    • Porschke, D.1    Antosiewicz, J.M.2
  • 102
    • 0002557374 scopus 로고
    • The electric moments and the relaxation times of proteins as measured from their influence upon the dielectric constants of solutions
    • E. Cohn and J. Edsall, Eds., Reinhold Publication Corporation, New York
    • Oncley, J., The electric moments and the relaxation times of proteins as measured from their influence upon the dielectric constants of solutions, in Proteins, Amino Acids and Peptides, E. Cohn and J. Edsall, Eds., Reinhold Publication Corporation, New York, 1943.
    • (1943) Proteins, Amino Acids and Peptides
    • Oncley, J.1
  • 103
    • 0000824742 scopus 로고
    • The influence of dipole moment fluctuations on the dielectric increment of proteins in solution
    • Kirkwood, J.G. and Shumaker, J.B., The influence of dipole moment fluctuations on the dielectric increment of proteins in solution, Proc. Natl. Acad. Sci. USA, 38, 855, 1952.
    • (1952) Proc. Natl. Acad. Sci. USA , vol.38 , pp. 855
    • Kirkwood, J.G.1    Shumaker, J.B.2
  • 104
    • 0021926711 scopus 로고
    • The mechanism of ion polarization along DNA double helices
    • Porschke, D., The mechanism of ion polarization along DNA double helices, Biophys. Chem., 22, 237, 1985.
    • (1985) Biophys. Chem , vol.22 , pp. 237
    • Porschke, D.1
  • 105
    • 0000463977 scopus 로고
    • Contribution a l'étude de l'effet Kerr présenté par les solutions diluées de macromolécules rigide
    • Benoit, H., Contribution a l'étude de l'effet Kerr présenté par les solutions diluées de macromolécules rigides, Ann. de Phys., 12e Serie, 6, 561, 1951.
    • (1951) Ann. de Phys., 12e Serie , vol.6 , pp. 561
    • Benoit, H.1
  • 106
    • 0029004903 scopus 로고
    • Crystal-structure of lac repressor core tetramer and its implications for DNA looping
    • Friedman, A.M., Fischmann, T.O., and Steitz, T.A., Crystal-structure of lac repressor core tetramer and its implications for DNA looping, Science, 268, 1721, 1995.
    • (1995) Science , vol.268 , pp. 1721
    • Friedman, A.M.1    Fischmann, T.O.2    Steitz, T.A.3
  • 107
    • 0029938053 scopus 로고    scopus 로고
    • Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
    • Lewis, M., et al., Crystal structure of the lactose operon repressor and its complexes with DNA and inducer, Science, 271, 1247, 1996.
    • (1996) Science , vol.271 , pp. 1247
    • Lewis, M.1
  • 108
    • 0025914242 scopus 로고
    • Crystal-structure of a cap-DNA complex-the DNA is bent by 90-degrees
    • Schultz, S.C., Shields, G.C., and Steitz, T.A., Crystal-structure of a cap-DNA complex-the DNA is bent by 90-degrees, Science, 253, 1001, 1991.
    • (1991) Science , vol.253 , pp. 1001
    • Schultz, S.C.1    Shields, G.C.2    Steitz, T.A.3
  • 109
    • 0031588024 scopus 로고    scopus 로고
    • The cyclic AMP receptor promoter DNA complex: A comparison of crystal and solution structure by quantitative molecular electrooptics
    • MeyerAlmes, F.J. and Porschke, D., The cyclic AMP receptor promoter DNA complex: A comparison of crystal and solution structure by quantitative molecular electrooptics, J. Mol. Biol., 269, 842, 1997.
    • (1997) J. Mol. Biol , vol.269 , pp. 842
    • MeyerAlmes, F.J.1    Porschke, D.2
  • 111
    • 0028325140 scopus 로고
    • DNA double helices with positive electric dichroism and permanent dipole-moments- nonsymmetrical charge-distributions and frozen configurations
    • Porschke, D., DNA double helices with positive electric dichroism and permanent dipole-moments- nonsymmetrical charge-distributions and frozen configurations, Biophys. Chem., 49, 127, 1994.
    • (1994) Biophys. Chem , vol.49 , pp. 127
    • Porschke, D.1
  • 112
    • 0006379005 scopus 로고
    • Brownian dynamics of the polarization of rodlike polyelectrolytes
    • Grycuk, T., Antosiewicz, J.M., and Porschke, D., Brownian dynamics of the polarization of rodlike polyelectrolytes, J. Phys. Chem., 98, 10881, 1994.
    • (1994) J. Phys. Chem , vol.98 , pp. 10881
    • Grycuk, T.1    Antosiewicz, J.M.2    Porschke, D.3
  • 113
    • 0025911729 scopus 로고
    • Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations
    • Porschke, D., Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations, Biophys. Chem., 40, 169, 1991.
    • (1991) Biophys. Chem , vol.40 , pp. 169
    • Porschke, D.1
  • 114
    • 0024372454 scopus 로고
    • Electric dichroism and bending amplitudes of DNA fragments according to a simple orientation function for weakly bent rods
    • Porschke, D., Electric dichroism and bending amplitudes of DNA fragments according to a simple orientation function for weakly bent rods, Biopolymers, 28, 1383, 1989.
    • (1989) Biopolymers , vol.28 , pp. 1383
    • Porschke, D.1
  • 115
    • 2342637689 scopus 로고    scopus 로고
    • Dynamics of the B-A transition of DNA double helices
    • Jose, D. and Porschke, D., Dynamics of the B-A transition of DNA double helices, Nucleic Acids Res., 32, 2251, 2004.
    • (2004) Nucleic Acids Res , vol.32 , pp. 2251
    • Jose, D.1    Porschke, D.2
  • 116
    • 28044465975 scopus 로고    scopus 로고
    • The dynamics of the B-A transition of natural DNA double helices
    • Jose, D. and Porschke, D., The dynamics of the B-A transition of natural DNA double helices, J. Am. Chem. Soc. 127, 16120, 2005.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 16120
    • Jose, D.1    Porschke, D.2


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