TY - JOUR T1 - Protein flexibility and conformational state: A comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin JF - Biophysical Journal Y1 - 2003 A1 - Whitmire, S. E. A1 - Wolpert, D. A1 - Markelz, A. G. A1 - Hillebrecht, J. R. A1 - Galan, J. A1 - Birge, R. R. KW - angstrom resolution KW - Biophysics KW - dna KW - films KW - frequency KW - harmonic-analysis KW - inelastic neutron-scattering KW - large systems KW - mixed basis KW - normal-modes KW - purple membranes KW - structural-changes KW - transform infrared-spectroscopy AB -

Far infrared ( FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses using CHARMM. We find that the FIR absorbance is slowly increasing with frequency and without strong narrow features over the range of 2-60 cm(-1) and up to a resolution of 0.17 cm(-1). The broad absorption shifts in frequency with decreasing temperature as expected with a strongly anharmonic potential and in agreement with neutron inelastic scattering results. Decreasing hydration shifts the absorption to higher frequencies, possibly resulting from decreased coupling mediated by the interior water molecules. Ground-state FIR absorbances have nearly identical frequency dependence, with the mutant having less optical density than the WT. In the M state, the FIR absorbance of the WT increases whereas there is no change for D96N. These results represent the first measurement of FIR absorbance change as a function of conformational state.

VL - 85 SN - 0006-3495 N1 - ISI Document Delivery No.: 705ZZ
Times Cited: 117
Cited Reference Count: 55
Cited References:
AUSTIN RH, 1975, BIOCHEMISTRY-US, V14, P5355, DOI 10.1021/bi00695a021
Birge RR, 1996, J PHYS CHEM-US, V100, P9990, DOI 10.1021/jp953669e
BOUSCHE O, 1992, PHOTOCHEM PHOTOBIOL, V56, P1085, DOI 10.1111/j.1751-1097.1992.tb09732.x
BROOKS BR, 1983, J COMPUT CHEM, V4, P187, DOI 10.1002/jcc.540040211
BROOKS BR, 1995, J COMPUT CHEM, V16, P1522, DOI 10.1002/jcc.540161209
Brooks CL, 1988, PROTEINS THEORETICAL
Brucherseifer M, 2000, APPL PHYS LETT, V77, P4049, DOI 10.1063/1.1332415
Chen Q, 2001, J OPT SOC AM B, V18, P823, DOI 10.1364/JOSAB.18.000823
DENCHER NA, 1989, P NATL ACAD SCI USA, V86, P7876, DOI 10.1073/pnas.86.20.7876
Der A, 2001, BIOCHEMISTRY-MOSCOW+, V66, P1234, DOI 10.1023/A:1013179101782
Diehl M, 1997, BIOPHYS J, V73, P2726, DOI 10.1016/S0006-3495(97)78301-2
DOSTER W, 1989, NATURE, V337, P754, DOI 10.1038/337754a0
FERRAND M, 1993, P NATL ACAD SCI USA, V90, P9668, DOI 10.1073/pnas.90.20.9668
GENZEL L, 1984, SPECTROSCOPY BIOL MO, P609
GRISCHKOWSKY D, 1991, OSA PROC, V9, P9
Guilbert C, 1996, CHEM PHYS, V204, P327, DOI 10.1016/0301-0104(95)00293-6
Han PY, 2000, OPT LETT, V25, P242, DOI 10.1364/OL.25.000242
Hinsen K, 1998, PROTEINS, V33, P417, DOI 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8
JANEZIC D, 1995, J COMPUT CHEM, V16, P1543, DOI 10.1002/jcc.540161210
Kusnetzow A, 1999, BIOPHYS J, V76, P2370, DOI 10.1016/S0006-3495(99)77394-7
Lanyi JK, 1999, INT REV CYTOL, V187, P161, DOI 10.1016/S0074-7696(08)62418-3
Lanyi JK, 2001, TRENDS BIOTECHNOL, V19, P140, DOI 10.1016/S0167-7799(01)01576-1
LINDSAY SM, 1988, BIOPOLYMERS, V27, P1015, DOI 10.1002/bip.360270610
Lisy V, 1997, J BIOMOL STRUCT DYN, V14, P517, DOI 10.1080/07391102.1997.10508150
LONGBOTTOM C, 2002, POTENTIAL USES TERAH
Luecke H, 1999, SCIENCE, V286, P255, DOI 10.1126/science.286.5438.255
Luecke H, 1999, J MOL BIOL, V291, P899, DOI 10.1006/jmbi.1999.3027
MacKerell AD, 1998, J PHYS CHEM B, V102, P3586, DOI 10.1021/jp973084f
Markelz AG, 2000, CHEM PHYS LETT, V320, P42, DOI 10.1016/S0009-2614(00)00227-X
MCINTOSH AR, 1991, BIOPHYS J, V60, P1, DOI 10.1016/S0006-3495(91)82025-2
MOUAWAD L, 1993, BIOPOLYMERS, V33, P599, DOI 10.1002/bip.360330409
Mouawad L, 1996, J MOL BIOL, V258, P393, DOI 10.1006/jmbi.1996.0257
Nagel M, 2002, APPL PHYS LETT, V80, P154, DOI 10.1063/1.1428619
Oesterhelt D, 1974, Methods Enzymol, V31, P667
Palmo K, 1998, J COMPUT CHEM, V19, P754, DOI 10.1002/(SICI)1096-987X(199805)19:7<754::AID-JCC6>3.0.CO;2-P
PERAHIA D, 1995, COMPUT CHEM, V19, P241, DOI 10.1016/0097-8485(95)00011-G
Person W.B., 1982, VIBRATIONAL INTENSIT
Polavarapu P. L., 1998, VIBRATIONAL SPECTRA
POWELL JW, 1991, J MOL STRUCT, V247, P107, DOI 10.1016/0022-2860(91)87067-R
POWELL JW, 1987, PHYS REV A, V35, P3929, DOI 10.1103/PhysRevA.35.3929
Ren L, 2001, BIOCHEMISTRY-US, V40, P13906, DOI 10.1021/bi0116487
ROITBERG A, 1995, SCIENCE, V268, P1319, DOI 10.1126/science.7539156
Sass HJ, 1997, EMBO J, V16, P1484, DOI 10.1093/emboj/16.7.1484
Stuart JA, 1996, BIOMEMBR A&B, V2, P33
Urabe H, 1998, BIOPHYS J, V74, P1533, DOI 10.1016/S0006-3495(98)77865-8
VARO G, 1983, BIOPHYS J, V43, P47, DOI 10.1016/S0006-3495(83)84322-7
Walther M, 2000, CHEM PHYS LETT, V332, P389, DOI 10.1016/S0009-2614(00)01271-9
WEIDLICH T, 1990, BIOPOLYMERS, V30, P477, DOI 10.1002/bip.360300324
WEIDLICH T, 1990, J BIOMOL STRUCT DYN, V8, P139, DOI 10.1080/07391102.1990.10507795
WEIDLICH T, 1987, BIOPOLYMERS, V26, P439, DOI 10.1002/bip.360260310
WEIDLICH T, 1988, J PHYS CHEM-US, V92, P6475
WITTLIN A, 1986, PHYS REV A, V34, P493, DOI 10.1103/PhysRevA.34.493
Woolard DL, 1997, J APPL TOXICOL, V17, P243, DOI 10.1002/(SICI)1099-1263(199707)17:4<243::AID-JAT436>3.0.CO;2-6
Xie AH, 2002, PHYS REV LETT, V88, DOI 10.1103/PhysRevLett.88.018102
Zaccai G, 2000, SCIENCE, V288, P1604, DOI 10.1126/science.288.5471.1604
Whitmire, SE Wolpert, D Markelz, AG Hillebrecht, JR Galan, J Birge, RR
Markelz, Andrea/0000-0003-0443-4319
NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCESUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548] Funding Source: NIH RePORTER; NIGMS NIH HHSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R01 GM034548, R01 GM034548-15] Funding Source: Medline
122
3
31
Cell press
Cambridge
1542-0086 ER -