Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates

Richard W. Hendler, Curtis W. Meuse, Mark S Braiman, Paul D. Smith, John W. Kakareka

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

We have used new kinetic fitting procedures to obtain infrared (IR) absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear-algebra-based procedures of Hendler et al. (J. Phys. Chem. B, 105, 3319-3228 (2001)) for obtaining clean absolute visible spectra of bR photocycle intermediates were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its MF and MS components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm -1 for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the MF pathway of the parallel cycles model of the photocycle.

Original languageEnglish (US)
Pages (from-to)1029-1045
Number of pages17
JournalApplied Spectroscopy
Volume65
Issue number9
DOIs
StatePublished - Sep 2011

Fingerprint

Bacteriorhodopsins
Infrared radiation
cryogenic temperature
visible spectrum
confidence
isolation
algebra
infrared spectra
Deprotonation
cycles
Linear algebra
protons
kinetics
room temperature
Cryogenics
water
Protons
Hydrogen
Temperature
Kinetics

Keywords

  • Arginine 82 deprotonation
  • Flash photolysis
  • Infrared spectroscopy
  • Kinetic analysis
  • Parallel cycles
  • PRG
  • Proton release group
  • Purple membrane
  • Reversible homogeneous model

ASJC Scopus subject areas

  • Spectroscopy
  • Instrumentation

Cite this

Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates. / Hendler, Richard W.; Meuse, Curtis W.; Braiman, Mark S; Smith, Paul D.; Kakareka, John W.

In: Applied Spectroscopy, Vol. 65, No. 9, 09.2011, p. 1029-1045.

Research output: Contribution to journalArticle

Hendler, Richard W. ; Meuse, Curtis W. ; Braiman, Mark S ; Smith, Paul D. ; Kakareka, John W. / Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates. In: Applied Spectroscopy. 2011 ; Vol. 65, No. 9. pp. 1029-1045.
@article{4132b16680b947808ad4ca14db7d0b9e,
title = "Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates",
abstract = "We have used new kinetic fitting procedures to obtain infrared (IR) absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear-algebra-based procedures of Hendler et al. (J. Phys. Chem. B, 105, 3319-3228 (2001)) for obtaining clean absolute visible spectra of bR photocycle intermediates were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its MF and MS components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm -1 for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the MF pathway of the parallel cycles model of the photocycle.",
keywords = "Arginine 82 deprotonation, Flash photolysis, Infrared spectroscopy, Kinetic analysis, Parallel cycles, PRG, Proton release group, Purple membrane, Reversible homogeneous model",
author = "Hendler, {Richard W.} and Meuse, {Curtis W.} and Braiman, {Mark S} and Smith, {Paul D.} and Kakareka, {John W.}",
year = "2011",
month = "9",
doi = "10.1366/11-06302",
language = "English (US)",
volume = "65",
pages = "1029--1045",
journal = "Applied Spectroscopy",
issn = "0003-7028",
publisher = "Society for Applied Spectroscopy",
number = "9",

}

TY - JOUR

T1 - Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates

AU - Hendler, Richard W.

AU - Meuse, Curtis W.

AU - Braiman, Mark S

AU - Smith, Paul D.

AU - Kakareka, John W.

PY - 2011/9

Y1 - 2011/9

N2 - We have used new kinetic fitting procedures to obtain infrared (IR) absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear-algebra-based procedures of Hendler et al. (J. Phys. Chem. B, 105, 3319-3228 (2001)) for obtaining clean absolute visible spectra of bR photocycle intermediates were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its MF and MS components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm -1 for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the MF pathway of the parallel cycles model of the photocycle.

AB - We have used new kinetic fitting procedures to obtain infrared (IR) absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear-algebra-based procedures of Hendler et al. (J. Phys. Chem. B, 105, 3319-3228 (2001)) for obtaining clean absolute visible spectra of bR photocycle intermediates were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its MF and MS components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm -1 for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the MF pathway of the parallel cycles model of the photocycle.

KW - Arginine 82 deprotonation

KW - Flash photolysis

KW - Infrared spectroscopy

KW - Kinetic analysis

KW - Parallel cycles

KW - PRG

KW - Proton release group

KW - Purple membrane

KW - Reversible homogeneous model

UR - http://www.scopus.com/inward/record.url?scp=80052920162&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80052920162&partnerID=8YFLogxK

U2 - 10.1366/11-06302

DO - 10.1366/11-06302

M3 - Article

C2 - 21929858

AN - SCOPUS:80052920162

VL - 65

SP - 1029

EP - 1045

JO - Applied Spectroscopy

JF - Applied Spectroscopy

SN - 0003-7028

IS - 9

ER -