Literature DB >> 2009362

Solving complex photocycle kinetics. Theory and direct method.

J F Nagle1.   

Abstract

A direct nonlinear least squares method is described that obtains the true kinetic rate constants and the temperature-independent spectra of n intermediates from spectroscopic data taken in the visible at three or more temperatures. A theoretical analysis, which is independent of implementation of the direct method, proves that well determined local solutions are not possible for fewer than three temperatures. This analysis also proves that measurements at more than n wavelengths are redundant, although the direct method indicates that convergence is faster if n + m wavelengths are measured, where m is of order one. This suggests that measurements should concentrate on high precision for a few measuring wavelengths, rather than lower precision for many wavelengths. Globally, false solutions occur, and the ability to reject these depends upon the precision of the data, as shown by explicit example. An optimized way to analyze vibrational spectroscopic data is also presented. Such data yield unique results, which are comparably accurate to those obtained from data taken in the visible with comparable noise. It is discussed how use of both kinds of data is advantageous if the data taken in the visible are significantly less noisy.

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Year:  1991        PMID: 2009362      PMCID: PMC1281164          DOI: 10.1016/S0006-3495(91)82241-X

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  11 in total

1.  Bacteriorhodopsin: a light-driven proton pump in Halobacterium Halobium.

Authors:  R H Lozier; R A Bogomolni; W Stoeckenius
Journal:  Biophys J       Date:  1975-09       Impact factor: 4.033

2.  How Many M Forms are there in the Bacteriorhodopsin Photocycle?

Authors:  G I Groma; Z Dancshazy
Journal:  Biophys J       Date:  1986-08       Impact factor: 4.033

3.  The role of back-reactions and proton uptake during the N----O transition in bacteriorhodopsin's photocycle: a kinetic resonance Raman study.

Authors:  J B Ames; R A Mathies
Journal:  Biochemistry       Date:  1990-08-07       Impact factor: 3.162

4.  Flash spectroscopy of purple membrane.

Authors:  A H Xie; J F Nagle; R H Lozier
Journal:  Biophys J       Date:  1987-04       Impact factor: 4.033

5.  Bacteriorhodopsin photoreaction: identification of a long-lived intermediate N (P,R350) at high pH and its M-like photoproduct.

Authors:  T Kouyama; A Nasuda-Kouyama; A Ikegami; M K Mathew; W Stoeckenius
Journal:  Biochemistry       Date:  1988-08-09       Impact factor: 3.162

6.  Photocycles of bacteriorhodopsin in light- and dark-adapted purple membrane studied by time-resolved absorption spectroscopy.

Authors:  J Hofrichter; E R Henry; R H Lozier
Journal:  Biophys J       Date:  1989-10       Impact factor: 4.033

7.  Testing kinetic models for the bacteriorhodopsin photocycle--II. Inclusion of an O to M backreaction.

Authors:  L A Parodi; R H Lozier; S M Bhattacharjee; J F Nagle
Journal:  Photochem Photobiol       Date:  1984-10       Impact factor: 3.421

8.  Events in proton pumping by bacteriorhodopsin.

Authors:  G W Rayfield
Journal:  Biophys J       Date:  1983-02       Impact factor: 4.033

9.  Procedure for testing kinetic models of the photocycle of bacteriorhodopsin.

Authors:  J F Nagle; L A Parodi; R H Lozier
Journal:  Biophys J       Date:  1982-05       Impact factor: 4.033

10.  Tyrosine and carboxyl protonation changes in the bacteriorhodopsin photocycle. 1. M412 and L550 intermediates.

Authors:  P Roepe; P L Ahl; S K Das Gupta; J Herzfeld; K J Rothschild
Journal:  Biochemistry       Date:  1987-10-20       Impact factor: 3.162

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  17 in total

1.  Multicolored protein conformation states in the photocycle of transducer-free sensory rhodopsin-I.

Authors:  I Szundi; T E Swartz; R A Bogomolni
Journal:  Biophys J       Date:  2001-01       Impact factor: 4.033

2.  Interpretation of the spatial charge displacements in bacteriorhodopsin in terms of structural changes during the photocycle.

Authors:  A Dér; L Oroszi; A Kulcsár; L Zimányi; R Tóth-Boconádi; L Keszthelyi; W Stoeckenius; P Ormos
Journal:  Proc Natl Acad Sci U S A       Date:  1999-03-16       Impact factor: 11.205

3.  Singular value decomposition with self-modeling applied to determine bacteriorhodopsin intermediate spectra: analysis of simulated data.

Authors:  L Zimányi; A Kulcsár; J K Lanyi; D F Sears; J Saltiel
Journal:  Proc Natl Acad Sci U S A       Date:  1999-04-13       Impact factor: 11.205

4.  Fluctuations and the Hofmeister effect.

Authors:  A Neagu; M Neagu; A Dér
Journal:  Biophys J       Date:  2001-09       Impact factor: 4.033

5.  Pressure dependence of the photocycle kinetics of bacteriorhodopsin.

Authors:  B U Klink; R Winter; M Engelhard; I Chizhov
Journal:  Biophys J       Date:  2002-12       Impact factor: 4.033

6.  Intermediate spectra and photocycle kinetics of the Asp96 --> asn mutant bacteriorhodopsin determined by singular value decomposition with self-modeling.

Authors:  L Zimányi; A Kulcsár; J K Lanyi; D F Sears; J Saltiel
Journal:  Proc Natl Acad Sci U S A       Date:  1999-04-13       Impact factor: 11.205

7.  Structural comparison of metarhodopsin II, metarhodopsin III, and opsin based on kinetic analysis of Fourier transform infrared difference spectra.

Authors:  A L Klinger; M S Braiman
Journal:  Biophys J       Date:  1992-11       Impact factor: 4.033

8.  A priori resolution of the intermediate spectra in the bacteriorhodopsin photocycle: the time evolution of the L spectrum revealed.

Authors:  László Zimányi; Jack Saltiel; Leonid S Brown; Janos K Lanyi
Journal:  J Phys Chem A       Date:  2006-02-23       Impact factor: 2.781

9.  Kinetic and thermodynamic study of the bacteriorhodopsin photocycle over a wide pH range.

Authors:  K Ludmann; C Gergely; G Váró
Journal:  Biophys J       Date:  1998-12       Impact factor: 4.033

10.  Protein structural change at the cytoplasmic surface as the cause of cooperativity in the bacteriorhodopsin photocycle.

Authors:  G Váró; R Needleman; J K Lanyi
Journal:  Biophys J       Date:  1996-01       Impact factor: 4.033

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