构象电子系统的集体激发,跃迁过程和合作现象

本文给出了一套对分子生物学问题进行理论分析的方法并列举简单应用的实例.以分子构象和前沿电子为变数,引入了构家电子场,给出了研究其集体激发的Green函数途径,指出生物凝聚态中存在新型局域激发.导出了构象电子跃迁哈密顿量,特别研究了光致构家电子跃迁,指出低阶跃迁为非Franck—Condon型的.研究了链式分子的合作现象,阐明了振动激发对于实现合作转变的重要性及转变中可能存在反常温度依赖.     

发菜藻胆体的分离和光谱特性的研究

完整藻胆体和不完整藻胆体的吸收峰都在618nm。完整藻胆体的室温荧光峰位于670nm以上,而不完整藻胆体则在670nm以下。完整藻胆体的77K荧光发射光谱中只有648nm一个荧光发射带;而在不完整藻胆体,则有2个或3个发射带,它们位于684nm,666nm和648nm,依次属于别藻蓝蛋白-B,别藻蓝蛋白和C-藻蓝蛋白的荧光。     

发菜藻胆体分离和光谱特性的研究

完整藻胆体和不完整藻胆体的吸收峰都在618nm。完整藻胆体的室温荧光峰位于670nm 以上,而不完整藻胆体则在670nm以下。完整藻胆体的77K荧光发射光谱中只有648nm一个荧光发射带;而在不完整藻胆体,则有2个或3个发射带,它们位于684nm,666nm和648nm, 依次属于别藻蓝蛋白 — B,别藻蓝蛋白和C — 藻蓝蛋白的荧光。     

螺旋藻（Spirulina platensis）藻胆体在解离过程中荧光发射光谱和光能传递的研究

对螺旋藻（Ｓｐｉｒｕｌｉｎａｐｌａｔｅｎｓｉｓ）藻胆体在室温和７７Ｋ处于不同浓度磷缓冲溶液和不同解离时间的荧光发射光谱进行了研究。藻胆体在０．９ｍｏｌ／Ｌ磷酸缓冲溶液中,由于没有发生解离,光能传递效率高,在７７Ｋ荧光发射光谱中只有一个峰,位于６８７ｎｍ,属于别藻蓝蛋白－Ｂ。当藻胆体悬浮在０．３ｍｏｌ／Ｌ磷酸缓冲溶液中１分钟,７７Ｋ荧光光谱的主峰出现在６８４ｎｍ．又出现６５５ｎｍ和６６６ｎｍ荧光峰,它们依次属子Ｃ－藻蓝蛋白和别藻蓝蛋白。在２小时;６５５ｎｍ荧先峰成为主峰,６８４ｎｍ荧光峰为次峰,６６６ｎｍ荧光肩消失。这表明Ｃ－藻蓝蛋白所捕获的先能已不能传递给别藻蓝蛋白,但能传给别藻蓝蛋白－Ｂ。我们提出在螺旋藻藻胆体中存在两类Ｃ－藻蓝蛋白,一是与别藻蓝蛋白相连接,另一是与别藻蓝蛋白－Ｂ相连接。     

螺旋藻（Spirulina platensis）藻胆体在解离过程中荧光发射光谱和光能传递的研究

对螺旋藻（Ｓｐｉｒｕｌｉｎａｐｌａｔｅｎｓｉｓ）藻胆体在室温和７７Ｋ处于不同浓度磷缓冲溶液和不同解离时间的荧光发射光谱进行了研究。藻胆体在０．９ｍｏｌ／Ｌ磷酸缓冲溶液中,由于没有发生解离,光能传递效率高,在７７Ｋ荧光发射光谱中只有一个峰,位于６８７ｎｍ,属于别藻蓝蛋白－Ｂ。当藻胆体悬浮在０．３ｍｏｌ／Ｌ磷酸缓冲溶液中１分钟,７７Ｋ荧光光谱的主峰出现在６８４ｎｍ．又出现６５５ｎｍ和６６６ｎｍ荧光峰,它们依次属子Ｃ－藻蓝蛋白和别藻蓝蛋白。在２小时;６５５ｎｍ荧先峰成为主峰,６８４ｎｍ荧光峰为次峰,６６６ｎｍ荧光肩消失。这表明Ｃ－藻蓝蛋白所捕获的先能已不能传递给别藻蓝蛋白,但能传给别藻蓝蛋白－Ｂ。我们提出在螺旋藻藻胆体中存在两类Ｃ－藻蓝蛋白,一是与别藻蓝蛋白相连接,另一是与别藻蓝蛋白－Ｂ相连接。     

别藻蓝蛋白藻蓝胆素发色团分子构象研究

主要研究了蓝绿藻污棕席藻(Phormidium luridum)别藻蓝蛋白在不同 pH值条件下的吸收光谱和共振拉曼光谱.发现低聚化的结果导致了三聚体别藻蓝蛋白 650nm 特征吸收峰的消失和一些共振拉曼带强度和位置的移动.结果表明在低 pH 值作用下的低聚化的别藻蓝蛋白中藻蓝胆素发色团分子的构象和自由胆素分子类似,比三聚体的别藻蓝蛋白的发色团分子更趋于卷曲,折叠的构象态.而三聚体的别藻蓝蛋白,主要的拉曼带 1645cm^-1是其发色团分子构象处于更线性延展的标志,其光谱行为和吸收光谱 A_vis/A_uv所表征的发色团分子构象的结果相一致.     

嗜热蓝藻层理鞭枝藻（Mastigocladus laminosus）藻胆体在解离过程中荧光发射光谱和光能传递的研究

研究了层理鞭枝藻藻胆体在不同浓度磷酸缓冲溶液中解离过程中荧光发射光谱的变化和光能传递。完整藻胆体的７７Ｋ荧光光谱中只有一个峰,位于６８５ｎｍ它是末端发射体（核心－膜连接多肽和别藻蓝蛋白－Ｂ）的荧光峰。部分解离藻胆体的荧光光谱的主峰位移至６５２ｎｍ：次峰位于６８５ｎｍ;６６０ｎｍ为一弱荧光发射肩。它们依次为Ｃ－藻蓝蛋白,末端发射体和别藻蓝蛋白的荧光。严重解离藻胆体的荧光主峰移６４４ｎｍ;次峰由６８５ｎｍ移至６８２ｎｍ;６６０ｎｍ荧光发射肩消失。这表明Ｃ－藻蓝蛋白所捕获的光能已不能传递给别藻蓝蛋白,但可传递给末端发射体洞时又表明Ｃ－藻蓝蛋白不仅与别藻蓝蛋白相连接而且还与末端发射体相连接。提出该藻胆体光能传递链如下：核心－膜连接多肽藻红蓝蛋白→Ｃ－藻蓝蛋白→别藻蓝蛋白别藻蓝蛋白－Ｂ     

几种绿藻、褐藻和红藻的吸收光谱的比较研究

1.用乳白玻璃法测定了我国黄海常见的属于绿藻门、褐藻门和红藻门的十种海藻的吸收光谱。讨论了这三门海藻的吸收光谱的特点。通过对吸收光谱及红藻、褐藻相对于绿藻的差异光谱的分析,讨论了各种色素在活体中的吸收峰和吸收带的位置。2.根据褐藻与绿藻的吸收光谱的差异及差异光谱的比较分析,认为绿藻吸收光谱中位于485(或480)毫微米的吸收峰是叶绿素 b 的蓝光吸收峰。叶绿素 b 的红光吸收峰位于655毫微米附近。岩藻黄素的吸收峰位于525毫微米附近。根据红藻吸收光谱及其同绿藻的差异光谱中的红光吸收峰和负峰的特点,初步认为红藻中的叶绿素 d 的红光吸收峰比叶绿素 a 的红光吸收峰位于较长波长处。3.对几种红藻的吸收光谱进行了比较。观察到原始红藻纲的条斑紫菜(Porphyra yezoen-sis)的藻胆素与真红藻纲的藻类有显著的差异。这种差异及条斑紫菜的藻胆素的含量和组成上的易变性值得进一步研究。     

左手螺旋Z-DNA的研究 Ⅴ 环境因子对Oligo-d(G-C)_6构象的影响

脱氧寡聚核苷酸ｄ（Ｇ－Ｃ）６是迄今所报道的同类脱氧多聚核苷酸中能形成左手螺旋ＤＮＡ（Ｚ－ＤＮＡ）的最短序列。环境因子如ＰＨ,温度和离子的类别与浓度对ｄ（Ｇ－Ｃ）６在溶液中的Ｚ－构象的形成和Ｂ－、Ｚ－构象的相对稳定性有着明显的影响。在合适的条件下,ｄ（Ｇ－Ｃ）６在溶液中可呈现Ｂ－构象区,Ｚ－构象相对稳定区和Ｂ－、Ｚ－构象跃迁过渡区。     

左手螺旋Z—DNA的研究：V 环境因子对Oligo—d（G—C）6构象的影响

脱氧寡聚核苷酸ｄ（Ｇ－Ｃ）６是迄今所报道的同类脱氧多聚核苷酸中能形成左手螺旋ＤＮＡ（Ｚ－ＤＮＡ）的最短序列。环境因子如ＰＨ,温度和离子的类别与浓度对ｄ（Ｇ－Ｃ）６在溶液中的Ｚ－构象的形成和Ｂ－、Ｚ－构象的相对稳定性有着明显的影响。在合适的条件,ｄ（Ｇ－Ｃ）６在溶液中可呈现Ｂ－构象区,Ｚ－构象相对稳定区和Ｂ－、Ｚ－构象跃迁过渡区。     

Excited-state structure and isomerization dynamics of the retinal chromophore in rhodopsin from resonance Raman intensities.

Resonance Raman excitation profiles have been measured for the bovine visual pigment rhodopsin using excitation wavelengths ranging from 457.9 to 647.1 nm. A complete Franck-Condon analysis of the absorption spectrum and resonance Raman excitation profiles has been performed using an excited-state, time-dependent wavepacket propagation technique. This has enabled us to determine the change in geometry upon electronic excitation of rhodopsin's 11-cis-retinal protonated Schiff base chromophore along 25 normal coordinates. Intense low-frequency Raman lines are observed at 98, 135, 249, 336, and 461 cm-1 whose intensities provide quantitative, mode-specific information about the excited-state torsional deformations that lead to isomerization. The dominant contribution to the width of the absorption band in rhodopsin results from Franck-Condon progressions in the 1,549 cm-1 ethylenic normal mode. The lack of vibronic structure in the absorption spectrum is shown to be caused by extensive progressions in low-frequency torsional modes and a large homogeneous linewidth (170 cm-1 half-width) together with thermal population of low-frequency modes and inhomogeneous site distribution effects. The resonance Raman cross-sections of rhodopsin are unusually weak because the excited-state wavepacket moves rapidly (approximately 35 fs) and permanently away from the Franck-Condon geometry along skeletal stretching and torsional coordinates.     

Correct interpretation of heme protein spectra allows distinguishing between the heme and the protein dynamics

It is shown by using the vibronic approach that the iron displacement out of the porphyrin plane in deoxyheme proteins intermixes the porphyrin pi and axial iron-histidine sigma electronic subsystems. This intermixing explains the substantial coupling of the iron-histidine vibration to the heme Soret excitation, the appearance of the iron-histidine band in the corresponding resonance Raman spectra, and a number of other experimental data, including the dependence of the iron-histidine vibrational frequency on the extent of the iron displacement out of the porphyrin plane. This dependence implies that there is an anharmonic coupling between the corresponding vibrations, which is shown to be the cause of the specific temperature dependence of the iron-histidine band. The anharmonic coupling and the dependence of the dipole transition moment of the charge transfer optical absorption band III on the iron-porphyrin distance cause the anomalous temperature and pressure dependencies of this band. It is shown that the change in both the magnitude and the distribution of the iron-porphyrin distance is expected to affect the band III intensity. Consequently, the stationarity of the band III intensity can be considered as a signature of the stationarity of the iron-porphyrin distance and its distribution in deoxyheme proteins, whereas the band III position and width could be also affected by the change in the protein electric field, caused by the protein globule dynamics.     

Regulation of the distribution of chlorophyll and phycobilin-absorbed excitation energy in cyanobacteria. A structure-based model for the light state transition

The light state transition regulates the distribution of absorbed excitation energy between the two photosystems (PSs) of photosynthesis under varying environmental conditions and/or metabolic demands. In cyanobacteria, there is evidence for the redistribution of energy absorbed by both chlorophyll (Chl) and by phycobilin pigments, and proposed mechanisms differ in the relative involvement of the two pigment types. We assayed changes in the distribution of excitation energy with 77K fluorescence emission spectroscopy determined for excitation of Chl and phycobilin pigments, in both wild-type and state transition-impaired mutant strains of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803. Action spectra for the redistribution of both Chl and phycobilin pigments were very similar in both wild-type cyanobacteria. Both state transition-impaired mutants showed no redistribution of phycobilin-absorbed excitation energy, but retained changes in Chl-absorbed excitation. Action spectra for the Chl-absorbed changes in excitation in the two mutants were similar to each other and to those observed in the two wild types. Our data show that the redistribution of excitation energy absorbed by Chl is independent of the redistribution of excitation energy absorbed by phycobilin pigments and that both changes are triggered by the same environmental light conditions. We present a model for the state transition in cyanobacteria based on the x-ray structures of PSII, PSI, and allophycocyanin consistent with these results.     

Excitation energy transfer in the LHC-II trimer: a model based on the new 2.72 Å structure

Energy transfer of the light harvesting complex LHC-II trimer, extracted from spinach, was studied in the Q(y) region at room temperature by femtosecond transient absorption spectroscopy. Configuration interaction exciton method [Linnanto et al. (1999) J Phys Chem B 103: 8739-8750] and 2.72 A structural information reported by Liu et al. was used to calculate spectroscopic properties and excitation energy transfer rates of the complex. Site energies of the pigments and coupling constants of pigment pairs in close contact were calculated by using a quantum chemical configuration interaction method. Gaussian random variation of the diagonal and off-diagonal exciton matrix elements was used to account for inhomogeneous broadening. Rate calculations included only the excitonic states initially excited and probed in the experiments. A kinetic model was used to simulate time and wavelength dependent absorption changes after excitation on the blue side of the Q(y) transition and compared to experimentally recorded rates. Analysis of excitonic wavefunctions allowed identification of pigments initially excited and probed into later. It was shown that excitation of the blue side of the Q(y) band of a single LHC-II complex results in energy transfer from chlorophyll b's of the lumenal side to chlorophyll a's located primarly on one of the monomers of the stromal side.     

Local dynamic properties of the heme pocket in native and solvent-induced molten-globule-like states of cytochrome c

We report the Soret absorption band, down to cryogenic temperature, of native and molten-globule-like state of horse heart cytochrome c. The band profile is analyzed in terms of vibronic coupling of the heme normal modes to the electronic transition in the framework of the Franck-Condon approximation. From the temperature dependence of the Gaussian broadening and of the peak position, we obtain information on the 'bath' of low frequency harmonic motions of the heme group within the heme pocket. The reported data indicate that, compared to the native state, the less rigid tertiary structure of the molten globule is reflected in a higher flexibility of the heme pocket and in greater conformational disorder, allowing the transduction of large-amplitude motion of the protein to the dynamics of the heme pocket.     

Protein dynamics: conformational disorder,vibrational coupling and anharmonicity in deoxy-hemoglobin and myoglobin

In this work we study the temperature dependence of the Soret band lineshape of deoxymyoglobin and deoxyhemoglobin, in the range 300–20 K. To fit the measured spectra we use an approach originally proposed by Champion and coworkers (Srajer et al. 1986; Srajer and Champion 1991). The band profile is modelled as a Voigt function that accounts for the coupling with low frequency vibrational modes, whereas the coupling with high frequency modes is responsible for the vibronic structure of the spectra. Moreover, owing to the position of the iron atom out of the mean heme plane, inhomogeneous broadening brings about a non-Gaussian distribution of 0–0 electronic transition frequencies. The reported analysis enables us to isolate the various contributions to the overall bandwidth, and their temperature dependence points out the relevance of low frequency vibrations and of large scale anharmonic motions starting at temperatures higher than 170 K. Information on the mean iron-heme plane distance and on its temperature dependence, as well as on the heme pocket conformational disorder, is also obtained.Abbreviations Cc Carbon monoxide - Hb Human deoxyhemoglobin A - HbCO human carbonmonoxyhemoglobin A - SWMb spermwhale deoxymyoglobin - SWMbCO spermwhale carbonmonoxymyoglobin - HbO₂ human oxyhemoglobin A - SWMb³⁺-H₂O spermwhale aquometmyoglobin     

Photo-induced charge transfer. A critical test of the mechanism and range of biological electron transfer processes.

The vibronic coupling theory of electron tunneling between biomolecules requires that all such tunnelings involve vibronic coupling, finds temperature dependence to tunneling at finite temperatures, and predicts relatively short tunneling distances. This theory might be expected to apply to most electron transfers involved in the membrane-bound electron transfer reactions of photosynthesis and oxidative phosphorylation. This paper calculates the properties of a weak charge-transfer optical absorption band, whose predicted characteristics are a direct and simple consequence of the model that describes vibronically coupled tunneling. The new absorption band provides the basis for a critical experimental test of the constructs and parameters of the tunneling theory. If the tunneling theory is valid, the oscillator strength of such bands will be the most reliable measure of the tunneling matrix element and of the distance between the sites exchanging an electron.     

The low-energy forms of photosystem I light-harvesting complexes: spectroscopic properties and pigment-pigment interaction characteristics

In this work the spectroscopic properties of the special low-energy absorption bands of the outer antenna complexes of higher plant Photosystem I have been investigated by means of low-temperature absorption, fluorescence, and fluorescence line-narrowing experiments. It was found that the red-most absorption bands of Lhca3, Lhca4, and Lhca1-4 peak, respectively, at 704, 708, and 709 nm and are responsible for 725-, 733-, and 732-nm fluorescence emission bands. These bands are more red shifted compared to "normal" chlorophyll a (Chl a) bands present in light-harvesting complexes. The low-energy forms are characterized by a very large bandwidth (400-450 cm(-1)), which is the result of both large homogeneous and inhomogeneous broadening. The observed optical reorganization energy is untypical for Chl a and resembles more that of BChl a antenna systems. The large broadening and the changes in optical reorganization energy are explained by a mixing of an Lhca excitonic state with a charge transfer state. Such a charge transfer state can be stabilized by the polar residues around Chl 1025. It is shown that the optical reorganization energy is changing through the inhomogeneous distribution of the red-most absorption band, with the pigments contributing to the red part of the distribution showing higher values. A second red emission form in Lhca4 was detected at 705 nm and originates from a broad absorption band peaking at 690 nm. This fluorescence emission is present also in the Lhca4-N-47H mutant, which lacks the 733-nm emission band.     

Heme symmetry, vibronic structure, and dynamics in heme proteins: ferrous nicotinate horse myoglobin and soybean leghemoglobin

We report the visible and Soret absorption bands, down to cryogenic temperatures, of the ferrous nicotinate adducts of native and deuteroheme reconstituted horse heart myoglobin in comparison with soybean leghemoglobin-a. The band profile in the visible region is analyzed in terms of vibronic coupling of the heme normal modes to the electronic transition in the framework of the Herzberg-Teller approximation. This theoretical approach makes use of the crude Born-Oppenheimer states and therefore neglects the mixing between electronic and vibrational coordinates; however, it takes into account the vibronic nature of the visible absorption bands and allows an estimate of the vibronic side bands for both Condon and non-Condon vibrational modes. In this framework, an x-y splitting of the Q transition for native and deuteroheme reconstituted horse myoglobin is clearly assessed and attributed to electronic perturbations that, in turn, are caused by a reduction of the typical D(4h) symmetry of the system due to heme distortions of B(1g)-type symmetry and/or to an x-y asymmetric position of the nicotinate ring; in deuteroheme reconstituted horse myoglobin the asymmetric heme peripheral substituents add to the above effect(s). On the contrary, in leghemoglobin-a no spectral splitting upon nicotinate binding is observed, pointing to a planar heme configuration in which only distortions of A(1g)-type symmetry are effective and to which the nicotinate ring is bound in an x - y symmetric position. The local dynamic properties of the heme pocket of the three proteins are investigated through the temperature dependence of spectral line broadening. Leghemoglobin-a behaves as a softer matrix with respect to horse myoglobin, thus validating the hypothesis of a looser heme pocket conformation in the former protein, which allows a nondistorted heme configuration and a symmetric binding of the bulky nicotinate ligand.     

Measurement of the electronic properties of the flavoprotein old yellow enzyme (OYE) and the OYE:p-Cl phenol charge-transfer complex using Stark spectroscopy

Low-temperature absorption and Stark spectroscopy have been used to study the electronic properties of oxidized flavin mononucleotide (FMN) in old yellow enzyme (OYE) and OYE complexed with p-chlorophenol (p-Cl phenol). The low-temperature absorbance spectrum of OYE showed splittings of the blue and near-UV vibronic bands, which appears to be due to hydrogen bonding between the isoalloxazine moiety and the protein. A Stark spectroscopic analysis showed that the electronic structure of the FMN cofactor in OYE is not significantly perturbed relative to flavins in simple solvents. However, the charge-transfer band in the OYE:p-Cl phenol complex showed a large Stark effect indicative of substantial charge displacement. The magnitude and direction of this charge displacement are consistent with significant charge transfer along the charge-transfer transition dipole moment direction. In addition, the Stark spectrum of the CT band showed unexpected fine structure that could correlate with vibrational progressions in either the p-Cl phenol donor or the flavin acceptor.