TY - JOUR T1 - Terahertz spectroscopy of bacteriorhodopsin and rhodopsin: Similarities and differences JF - Biophysical Journal Y1 - 2008 A1 - Balu, R. A1 - Zhang, H. A1 - Zukowski, E. A1 - Chen, J. Y. A1 - Markelz, A. G. A1 - Gregurick, S. K. KW - Biophysics KW - bovine rhodopsin KW - conformational-changes KW - elastic KW - frequency normal-modes KW - light activation KW - molecular-dynamics simulation KW - neutron-scattering KW - protein-coupled receptors KW - transmembrane helices KW - vibrational-modes KW - wild-type AB -

We studied the low-frequency terahertz spectroscopy of two photoactive protein systems, rhodopsin and bacteriorhodopsin, as a means to characterize collective low-frequency motions in helical transmembrane proteins. From this work, we found that the nature of the vibrational motions activated by terahertz radiation is surprisingly similar between these two structurally similar proteins. Specifically, at the lowest frequencies probed, the cytoplasmic loop regions of the proteins are highly active; and at the higher terahertz frequencies studied, the extracellular loop regions of the protein systems become vibrationally activated. In the case of bacteriorhodopsin, the calculated terahertz spectra are compared with the experimental terahertz signature. This work illustrates the importance of terahertz spectroscopy to identify vibrational degrees of freedom which correlate to known conformational changes in these proteins.

VL - 94 SN - 0006-3495 N1 - ISI Document Delivery No.: 280IP
Times Cited: 50
Cited Reference Count: 72
Cited References:
Abdulaev NG, 1998, P NATL ACAD SCI USA, V95, P12854, DOI 10.1073/pnas.95.22.12854
Alexandrov V, 2005, PROTEIN SCI, V14, P633, DOI 10.1110/ps.04882105
Alexiev U, 2003, J MOL BIOL, V328, P705, DOI 10.1016/S0022-2836(03)00326-7
Altenbach C, 2001, BIOCHEMISTRY-US, V40, P15493, DOI 10.1021/bi011545o
AMADEI A, 1993, PROTEINS, V17, P412, DOI 10.1002/prot.340170408
Balog E, 2004, PHYS REV LETT, V93, DOI 10.1103/PhysRevLett.93.028103
Beck M, 1998, BIOCHEMISTRY-US, V37, P7630, DOI 10.1021/bi9801560
Bizzarri AR, 2001, EUR BIOPHYS J BIOPHY, V30, P443, DOI 10.1007/s002490100167
BROOKS B, 1983, P NATL ACAD SCI-BIOL, V80, P6571, DOI 10.1073/pnas.80.21.6571
BROOKS BR, 1995, J COMPUT CHEM, V16, P1522, DOI 10.1002/jcc.540161209
Bu ZM, 2000, J MOL BIOL, V301, P525, DOI 10.1006/jmbi.2000.3978
Chen JY, 2005, PHYS REV E, V72, DOI 10.1103/PhysRevE.72.040901
Chen Q, 2001, J OPT SOC AM B, V18, P823, DOI 10.1364/JOSAB.18.000823
Chung HS, 2005, P NATL ACAD SCI USA, V102, P612, DOI 10.1073/pnas.0408646102
Crozier PS, 2003, J MOL BIOL, V333, P493, DOI 10.1016/j.jmb.2003.08.045
Farrens DL, 1996, SCIENCE, V274, P768, DOI 10.1126/science.274.5288.768
Filippovich S. Y., 2004, PHOTOCHEM PHOTOBIOL, V3, P1
Fotiadis D, 2006, CURR OPIN STRUC BIOL, V16, P252, DOI 10.1016/j.sbi.2006.03.013
Gabel F, 2005, BIOPHYS J, V89, P3303, DOI 10.1529/biophysj.105.061028
Gabel F, 2002, Q REV BIOPHYS, V35, P327, DOI 10.1017/S0033583502003840
Getmanova E, 2004, BIOCHEMISTRY-US, V43, P1126, DOI 10.1021/bi030120u
Giraud G, 2003, BIOPHYS J, V85, P1903, DOI 10.1016/S0006-3495(03)74618-9
GRISCHKOWSKY D, 1991, FEMTOSECOND PULSES T
Groma GI, 2001, BIOPHYS J, V81, P3432, DOI 10.1016/S0006-3495(01)75975-9
Hendler RW, 2003, EUR J BIOCHEM, V270, P1920, DOI 10.1046/j.1432-1033.2003.03547.x
Hu KS, 2000, J PHOTOCH PHOTOBIO B, V58, P163, DOI 10.1016/S1011-1344(00)00125-1
Humphrey W, 1996, J MOL GRAPH MODEL, V14, P33, DOI 10.1016/0263-7855(96)00018-5
ICHIYE T, 1991, PROTEINS, V11, P205, DOI 10.1002/prot.340110305
Jaaskelainen S, 1998, PROTEIN SCI, V7, P1359
Joti Y, 2004, PHYSICA B, V350, pE627, DOI 10.1016/j.physb.2004.03.167
Kamikubo H, 1997, BIOCHEMISTRY-US, V36, P12282, DOI 10.1021/bi9712302
Kataoka M, 2000, BBA-BIOENERGETICS, V1460, P166, DOI 10.1016/S0005-2728(00)00137-7
Keskin O, 2000, BIOPHYS J, V78, P2093, DOI 10.1016/S0006-3495(00)76756-7
Kim JE, 2003, BIOCHEMISTRY-US, V42, P5169, DOI 10.1021/bi030026d
Kim JE, 2002, J PHYS CHEM A, V106, P8508, DOI 10.1021/jp021069r
Knab J, 2006, BIOPHYS J, V90, P2576, DOI 10.1529/biophysj.105.069088
KONIG B, 1989, P NATL ACAD SCI USA, V86, P6878, DOI 10.1073/pnas.86.18.6878
Korter TM, 2006, CHEM PHYS LETT, V418, P65, DOI 10.1016/j.cplett.2005.10.097
Koutsopoulos S, 2005, PROTEINS, V61, P377, DOI 10.1002/prot.20606
Langen R, 1999, BIOCHEMISTRY-US, V38, P7918, DOI 10.1021/bi990010g
Lee AG, 2004, BBA-BIOMEMBRANES, V1666, P62, DOI 10.1016/j.bbamem.2004.05.012
Li J, 2004, J MOL BIOL, V343, P1409, DOI 10.1016/j.jmb.2004.08.090
Liang Y, 2003, J BIOL CHEM, V278, P21655, DOI 10.1074/jbc.M302536200
MacKerell AD, 2001, BIOPOLYMERS, V56, P257
Markelz A, 2002, PHYS MED BIOL, V47, P3797, DOI 10.1088/0031-9155/47/21/318
Markelz AG, 2000, CHEM PHYS LETT, V320, P42, DOI 10.1016/S0009-2614(00)00227-X
McCamant DW, 2005, J PHYS CHEM B, V109, P10449, DOI 10.1021/jp050095x
Niv MY, 2006, J COMPUT AID MOL DES, V20, P437, DOI 10.1007/s10822-006-9061-3
Oesterhelt D, 1974, Methods Enzymol, V31, P667
Okada T, 2001, CURR OPIN STRUC BIOL, V11, P420, DOI 10.1016/S0959-440X(00)00227-X
Pitman MC, 2005, J AM CHEM SOC, V127, P4576, DOI 10.1021/ja042715y
Rader AJ, 2004, P NATL ACAD SCI USA, V101, P7246, DOI 10.1073/pnas.0401429101
Ridge KD, 2003, TRENDS BIOCHEM SCI, V28, P479, DOI 10.1016/S0968-0004(03)00172-5
Ruprecht JJ, 2004, EMBO J, V23, P3609, DOI 10.1038/sj.emboj.7600374
Saam J, 2002, BIOPHYS J, V83, P3097, DOI 10.1016/S0006-3495(02)75314-9
Sass HJ, 2000, NATURE, V406, P649, DOI 10.1038/35020607
Schmuttenmaer CA, 2004, CHEM REV, V104, P1759, DOI 10.1021/cr020685g
Siegel PH, 2004, IEEE T MICROW THEORY, V52, P2438, DOI 10.1109/TMTT.2004.835916
Siegrist K, 2006, J AM CHEM SOC, V128, P5764, DOI 10.1021/ja058176u
Subramaniam S, 2000, BBA-BIOENERGETICS, V1460, P157, DOI 10.1016/S0005-2728(00)00136-5
Tajkhorshid E, 2000, BIOPHYS J, V78, P683, DOI 10.1016/S0006-3495(00)76626-4
Tama F, 2000, PROTEINS, V41, P1
Tama F, 2002, J MOL BIOL, V321, P297, DOI 10.1016/S0022-2836(02)00627-7
Tama F, 2001, PROTEIN ENG, V14, P1, DOI 10.1093/protein/14.1.1
Teller DC, 2001, BIOCHEMISTRY-US, V40, P7761, DOI 10.1021/bi0155091
Thomas A, 1999, PROTEINS, V34, P96, DOI 10.1002/(SICI)1097-0134(19990101)34:1<96::AID-PROT8>3.0.CO;2-0
Ujj L, 1998, BIOPHYS J, V74, P1492, DOI 10.1016/S0006-3495(98)77861-0
Vogel R, 2004, J MOL BIOL, V338, P597, DOI 10.1016/j.jmb.2004.03.006
Vogel R, 2003, BIOPOLYMERS, V72, P133, DOI 10.1002/bip.10407
Whitmire SE, 2003, BIOPHYS J, V85, P1269, DOI 10.1016/S0006-3495(03)74562-7
Yan ECY, 2004, BIOCHEMISTRY-US, V43, P10867, DOI 10.1021/bi0400148
Zhang J, 2006, PROTEIN PEPTIDE LETT, V13, P33, DOI 10.2174/092986606774502027
Balu, R. Zhang, H. Zukowski, E. Chen, J. -Y. Markelz, A. G. Gregurick, S. K.
Zhang, Hailiang/F-8325-2010
Markelz, Andrea/0000-0003-0443-4319
52

27
Cell press
Cambridge
1542-0086 ER -