Express primer tool for high-throughput gene cloning and expression.

High-throughput approaches for gene cloning and expression require the development of new nonstandard tools for molecular biologists and biochemists. We introduce a Web-based tool to design primers specifically for the generation of expression clones for both laboratory-scale and high-throughput projects. The application is designed not only to allow the user complete flexibility to specify primer design parameters but also to minimize the amount of manual intervention needed to generate a large number of primers for the simultaneous amplification of multiple target genes.

The structure of a mutant photosynthetic reaction center shows unexpected changes in main chain orientations and quinone position.

We report on the unexpected structural changes caused by substitution of acidic amino acids in the Q(B) binding pocket of the bacterial photosynthetic reaction center by alanines. The mutations targeted key residues L212Glu and L213Asp of this transmembrane protein-cofactor complex. The amino acid substitutions in the L212Ala-L213Ala mutant reaction center ("AA") were known to affect the delivery of protons after the light-induced generation of Q(B)(-), which renders the AA strain incapable of photosynthetic growth. The AA structure not only revealed side chain rearrangements but also showed movement of the main chain segments that are contiguous with the mutation sites. The alanine substitutions caused an expansion of the cavity rather than its collapse. In addition, Q(B) is found mainly in the binding site that is proximal to the iron-ligand complex (closest to Q(A)) as opposed to its distal binding site (furthest from Q(A)) in the structure of the wild-type reaction center. The observed rearrangements in the structure of the AA reaction center establish a new balance between charged residues of an interactive network near Q(B). This structurally and electrostatically altered complex forms the basis for future understanding of the structural basis for proton transfer in active reaction centers which retain the alanine substitutions but carry a distant compensatory mutation.

Protein modifications affecting triplet energy transfer in bacterial photosynthetic reaction centers.

The efficiency of triplet energy transfer from the special pair (P) to the carotenoid (C) in photosynthetic reaction centers (RCs) from a large family of mutant strains has been investigated. The mutants carry substitutions at positions L181 and/or M208 near chlorophyll-based cofactors on the inactive and active sides of the complex, respectively. Light-modulated electron paramagnetic resonance at 10 K, where triplet energy transfer is thermally prohibited, reveals that the mutations do not perturb the electronic distribution of P. At temperatures > or = 70 K, we observe reduced signals from the carotenoid in most of the RCs with L181 substitutions. In particular, triplet transfer efficiency is reduced in all RCs in which a lysine at L181 donates a sixth ligand to the monomeric bacteriochlorophyll B(B). Replacement of the native Tyr at M208 on the active side of the complex with several polar residues increased transfer efficiency. The difference in the efficiencies of transfer in the RCs demonstrates the ability of the protein environment to influence the electronic overlap of the chromophores and thus the thermal barrier for triplet energy transfer.

Influence of iron-removal procedures on sequential electron transfer in photosynthetic bacterial reaction centers studied by transient EPR spectroscopy.

Electron spin polarized electron paramagentic resonance (ESP EPR) spectra were obtained with deuterated iron-removed photosynthetic bacterial reaction centers (RCs) to specifically investigate the effect of the rate of primary charge separation, metal-site occupancy, and H-subunit content on the observed P865+QA- charge-separated state. Fe-removed and Zn-substituted RCs from Rb. sphaeroides R-26 were prepared by refined procedures, and specific electron transfer rates (kQ) from the intermediate acceptor H- to the primary acceptor QA of (200 ps)-1 vs (3-6 ns)-1 were observed. Correlation of the transient EPR and optical results shows that the observed slow kQ rate in Fe-removed RCs is H-subunit-independent, and, in some cases, independent of Fe-site occupancy as Zn2+ substitution does not ensure retention of the native kQ. In addition, shifts in the optical spectrum of P865 and differences in the high-field region of the Q-band ESP spectrum for Fe-removed RCs with slow kQ indicate possible structural changes near P865. The experimental X-band and Q-band spin-polarized EPR spectra for deuterated Fe-removed RCs where kQ is at least 15-fold slower at room temperature than the (200 ps)-1 rate observed for native Fe-containing RCs have different relative amplitudes and small g-value shifts compared to the spectra of Zn-RCs which have a kQ unchanged from native RCs. These differences reflect the trends in polarization predicted from the sequential electron transfer polarization (SETP) model [Morris et al. (1995) J. Phys. Chem. 99, 3854-3866; Tang et al. (1996) Chem. Phys. Lett. 253, 293-298]. Thus, SETP modeling of these highly resolved ESP spectra obtained with well-characterized proteins will provide definitive information about any light-induced structural changes of P865, H, and QA that occur upon formation of the P865+QA- charge-separated state.

Antenna excited state decay kinetics establish primary electron transfer in reaction centers as heterogeneous.

The decay of the excited primary electron donor P* in bacterial photosynthetic reaction centers (both membrane-bound and detergent-isolated) has been observed to be nonexponential on a time scale of some tens of picoseconds. Although the multipicosecond nonexponentiality of P* has been ascribed to heterogeneity in teh rate of primary electron transfer (PET), the decay kinetics can be interpreted equally well using homogeneous models. To address this ambiguity, we studied the decay of excited bacteriochlorophyll (Bchl) in the membrane-bound core antenna/reaction center complexes of wild-type and mutant reaction center strains of Rhodobacter capsulatus. Reaction centers isolated from these same strains display a range of multiexponentiality in primary charge separation. The mutant strains carry substitutions of amino acids residing near the monomeric Bchl on the active and/or inactive sides of the reaction center. Transient absorption measurements monitoring the Qy bleach of antenna Bchls require at least two exponential components to fit all decays. The wild type was fitted with equal-amplitude components whose lifetimes are 24 and 65 ps. The shortest-lived component is relatively insensitive to mutation, in contrast to the longer-lived component(s) whose amplitude and magnitude were dramatically perturbed by amino acid substitutions. Unlike the situation with isolated reaction centers, here the only kinetic models consistent with the data are those in which the primary electron-transfer rate constant is heterogeneous, suggesting at least two structural populations of RCs. PET in the population with the shortest-lived antenna decay causes the kinetics to be transfer-to-trap-limited, whereas the kinetics in the other population(s)--having longer-lived antenna decays--are limited by the rate of PET. Observation of both types of kinetic limitation within a single light-harvesting system is unexpected and complicates any discussion of the rate-limiting step of light energy utilization in photosynthesis.

Chemical platinization and its effect on excitation transfer dynamics and P700 photooxidation kinetics in isolated photosystem I.

Isolated photosystem I (PSI) reaction center/core antenna complexes (PSI-40) were platinized by reduction of [PtCl6]2- at 20 degrees C and neutral pH. PSI particles were visualized directly on a gold surface by scanning tunneling microscopy (STM) before and after platinization. STM results showed that PSI particles were monomeric and roughly ellipsoidal with major and minor axes of 6 and 5 nm, respectively. Platinization deposited approximately 1000 platinum atoms on each PSI particle and made the average size significantly larger (9 x 7 nm). In addition to direct STM visualization, the presence of metallic platinum on the PSI complexes was detected by its effect of actinic shading and electrostatic shielding on P700 photooxidation and P700+ reduction. The reaction centers (P700) in both platinized and nonplatinized PSI-40 were photooxidized by light and reduced by ascorbate repeatedly, although at somewhat slower rates in platinized PSI because of the presence of platinum. The effect of platinization on excitation transfer and trapping dynamics was examined by measuring picosecond fluorescence decay kinetics in PSI-40. The fluorescence decay kinetics in both platinized and control samples can be described as a sum of three exponential components. The dominant (amplitude 0.98) and photochemically limited excitation lifetime remained the same (16 ps) before and after platinization. The excitation transfer and trapping in platinized PSI-40 was essentially as efficient as that in the control (without platinization) PSI. The platinization also did not affect the intermediate-lifetime (400-600 ps) and long-lifetime (> 2500 ps) components, which likely are related to intrinsic electron transport and to functionally uncoupled chlorophylls, respectively. The amplitudes of these two components were exceptionally small in both of the samples. These results provide direct evidence that although platinization dramatically alters the photocatalytic properties of PSI, it does not alter the intrinsic excitation dynamics and initial electron transfer reactions in PSI.

Excited state dynamics in chlorophyll-based antennae: the role of transfer equilibrium.

We present computer simulations of excited state dynamics in models of PS I and PS II which are based upon known structural and spectral properties of the antennae. In particular, these models constrain the pigment binding sites to three-dimensional volumes determined from molecular properties of the antenna complexes. The simulations demonstrate that within a 10-30 ps after light absorption, rapid energy transfer among coupled antenna chlorophylls leads to a quasiequilibrium state in which the fraction of the excited state on any antenna chlorophyll, normalized to the total excited state remaining on the model, remains constant with time. We describe this quasiequilibrium state as a "transfer equilibrium" (TE) state because of its dependence on the rates of processes that couple excited state motion and quenching in the antenna as well as on the individual antenna site energies and temperature. The TE state is not a true equilibrium in that loss of the excited state primarily due to photochemistry (but also due to fluorescence, thermal emission, and intersystem crossing) continues once TE is established. Depending on the dynamics of the system, the normalized distribution of excited state at TE may differ substantially from the Boltzmann distribution (the state of the model at infinite time in the absence of any avenues for decay of excited state). The models predict lifetimes, equilibration times, and photochemical yields that are in agreement with experimental data and affirm trap-limited dynamics in both photosystems. The rapid occurrence of TE states implies that any excited state dynamics that depends on antenna structure and excitation wavelength must occur before the TE state is established. We demonstrate that the excited state distribution of the TE state is central to determining the excited state lifetime and quantum efficiency of photochemistry.