Evaluation of intrinsic chemical kinetics and transient product spectra from time-resolved spectroscopic data
Evaluation of intrinsic chemical kinetics and transient product spectra from time-resolved spectroscopic data
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DOI：
10.1016/s0301-4622(96)02268-5
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发表时间：
1997-09-01
影响因子：
3.8
通讯作者：
Dioumaev, AK
中科院分区：
文献类型：
--
作者：
Dioumaev, AK
这种通信是致力于从时间分辨光谱实验监测多中间体系统的复杂弛豫动力学测量的表观动力学的真实光谱和内在（微观）速率常数的评估。视网膜蛋白、细胞色素氧化酶、光敏色素、血红蛋白和光敏黄蛋白都是自然系统的例子，在这些系统中，几种瞬态（中间体）在时间和光谱域上重叠得如此强烈，以至于它们的分离和完全表征不可能通过经典的生物化学方法进行，并且需要对它们的真实光谱和微观动力学常数进行数学评估。大多数流行的动力学数据分析方法，全局拟合（GF），奇异值分解（SVD），主成分分析（PCA）和因子分析（FA），适用于二维（二维，在时间和频谱域）阵列的数据。所有这些方法只产生数据的现象学描述，仅用表观动力学近似测量数据。一个基本的限制，即，在2D数据中的信息不足，不允许任何这些方法达到最终目标：重新计算，但在任何最微不足道的情况下，从表观到内在的价值。提出了一项战略（J.F.内格尔生物物理J.，59（1991）476-487），以将另外的（第三）信息丰富的维度温度包括到同步计算机分析中。三维数据阵列的微分速率方程系统的同时直接拟合允许重新计算的表观动力学到真正的光谱和内在的速率常数。尽管这种策略在理论上有明显的优势，但在真实的数据上并不成功。在这里，我们描述了另一个定制的程序，方案，开发用于相同的目的：直接拟合测得的动力学耦合微分速率方程描述的光致变色的弛豫动力学系统。虽然与以前的方法共享主要策略，但SCHEMEFIT基于不同的数值算法集，并且其应用需要不同的策略。仿真结果表明了该方法的有效性，并与GF和SVD进行了比较。本文还报道了一个将Schemefit应用于盐视紫红质光循环的例子。(C)1997年Elsevier Science B.V.
This communication is devoted to the evaluation of true spectra and intrinsic (microscopic) rate constants from apparent kinetics measured in time-resolved spectroscopic experiments monitoring complex relaxation dynamics of multi-intermediate systems. Retinal proteins, cytochrom c oxidase, phytochrome, hemoglobin, and photoactive yellow protein are examples of natural systems in which several transient states (intermediates) overlap so strongly, both in time and spectral domains, that their isolation and full characterization by classical biochemical methods is impossible, and mathematical evaluation of their true spectra and microscopic kinetic constants is required. Most of the popular methods for analysis of kinetic data, global fitting (GF), singular value decomposition (SVD), principal component analysis (PCA) and factor analysis (FA), are applicable to two-dimensional (2D, in time and spectral domains) arrays of data. All these methods produce only a phenomenological description of data, that approximates the measured data only with apparent kinetics. A fundamental limitation, namely, insufficient information in 2D data, does not allow any of these methods to reach the final goal: to recalculate from apparent to intrinsic values in any but the most trivial cases. A strategy was proposed (J.F. Nagle, Biophys. J., 59 (1991) 476-487) to include an additional (third) information-rich dimension, temperature, into the simultaneous computer analysis. A simultaneous direct fitting of 3D data arrays to systems of differential rate equations allows recalculation of apparent kinetics into true spectra and intrinsic rate constants. In spite of its evident theoretical advantages, this strategy has not been successful on real data. Here we describe another custom-built program, SCHEMEFIT, developed for the same purpose: to fit measured kinetics directly to the system of coupled differential rate equations describing the photochrome's relaxation dynamics. Though sharing the main strategy with the previous approach, SCHEMEFIT is based on a different set of numeric algorithms, and its application requires different tactics. Its performance is illustrated on synthetic data, and compared with GF and SVD. An example of applying SCHEMEFIT to the photocycle of halorhodopsin is also reported. (C) 1997 Elsevier Science B.V.