Tamara Senyushkina

Dynamic switch of the signal recognition particle from scanning to targeting

Ribosomes synthesizing inner membrane proteins in Escherichia coli are targeted to the membrane by the signal recognition particle (SRP) pathway. By rapid kinetic analysis we show that after initial binding to the ribosome, SRP undergoes dynamic fluctuations in search of additional interactions. Non-translating ribosomes, or ribosomes synthesizing non-membrane proteins, do not provide these contacts, allowing SRPs to dissociate rapidly. A nascent peptide in the exit tunnel stabilizes SRPs in a standby state. Binding to the emerging signal-anchor sequence (SAS) of a nascent membrane protein halts the fluctuations of SRP, resulting in complex stabilization and recruitment of the SRP receptor. We propose a kinetic model where SRP rapidly scans all ribosomes until it encounters a ribosome exposing an SAS. Binding to the SAS switches SRP into the targeting mode, in which dissociation is slow and docking of the SRP receptor is accelerated.

Ultrafast Intramolecular Charge Transfer with N-(4-Cyanophenyl)carbazole. Evidence for a LE Precursor and Dual LE + ICT Fluorescence

The photophysics of N-(4-cyanophenyl)carbazole (NP4CN) was investigated by using absorption and fluorescence spectra, picosecond fluorescence decays, and femtosecond transient absorption. In the nonpolar n-hexane as well as in the polar solvent acetonitrile (MeCN), a locally excited (LE) state is detected, as a precursor for the intramolecular charge transfer (ICT) state. A LE → ICT reaction time τ(2) at 22 °C of 0.95 ps in ethyl cyanide (EtCN) and 0.32 ps in MeCN is determined from the decay of the LE excited state absorption (ESA) maximum around 620 nm. In the ESA spectrum of NP4CN in n-hexane at a pump-probe delay time of 100 ps, an important contribution of the LE band remains alongside the ICT band, in contrast to what is observed in EtCN and MeCN. This shows that a LE ⇄ ICT equilibrium is established in this solvent and the ICT reaction time of 0.5 ps is equal to the reciprocal of the sum of the forward and backward ICT rate constants 1/(k(a) + k(d)). In the photostationary S(0) → S(n) absorption spectrum of NP4CN in n-hexane and MeCN, an additional CT absorption band appears, absent in the sum of the spectra of its electron donor (D) and acceptor (A) subgroups carbazole and benzonitrile. This CT band is located at an energy of ∼4000 cm(-1) lower than for N-phenylcarbazole (NPC), due to the larger electron affinity of the benzonitrile moiety of NP4CN than the phenyl subunit of NPC. The fluorescence spectrum of NP4CN in n-hexane at 25 °C mainly consists of a structured LE emission, with a small ICT admixture, indicating that a LE → ICT reaction just starts to occur under these conditions. In di-n-pentyl ether (DPeE) and di-n-butyl ether (DBE), a LE emission is found upon cooling at the high-energy edge of the ICT fluorescence band, caused by the onset of dielectric solvent relaxation. This is not the case in more polar solvents, such as diethyl ether (DEE) and MeCN, in which a structureless ICT emission band fully overlaps the strongly quenched LE fluorescence. For the series of D/A molecules NPC, N-(4-fluorophenyl)carbazole (NP4F), N-[4-(trifluoromethyl)phenyl]carbazole (NP4CF), and NP4CN, with increasing electron affinity of their phenyl subgroup, an ICT emission in n-hexane 25 °C only is present for NP4CN, whereas in MeCN an ICT fluorescence is observed with NP4CF and NP4CN. The ICT fluorescence appears when for the energies E(ICT) of the ICT state and E(S(1)) of the lowest excited singlet state the condition E(ICT) ≤ E(S(1)) holds. E(ICT) is calculated from the difference E(D/D(+)) - E(A(-)/A) of the redox potentials of the D and A subgroups of the N-phenylcarbazoles. From solvatochromic measurements with NP4CN an ICT dipole moment μ(e)(ICT) = 19 D is obtained, somewhat larger than the literature values of 10-16 D, because of a different Onsager radius ρ. The carbazole/phenyl twist angle θ = 45° of NP4CN in the S(0) ground state, determined from X-ray crystal analysis, has become smaller for its ICT state, in analogy with similar conclusions for related N-phenylcarbazoles and other D/A molecules in the literature.

Intramolecular charge transfer of 4-(dimethylamino)benzonitrile probed by time-resolved fluorescence and transient absorption: No evidence for two ICT states and a pisigma( *) reaction intermediate.

For the double exponential fluorescence decays of the locally excited (LE) and intramolecular charge transfer (ICT) states of 4-(dimethylamino)benzonitrile (DMABN) in acetonitrile (MeCN) the same times tau(1) and tau(2) are observed. This means that the reversible LE<==>ICT reaction, starting from the initially excited LE state, can be adequately described by a two state mechanism. The most important factor responsible for the sometimes experimentally observed differences in the nanosecond decay time, with tau(1)(LE)<tau(1)(ICT), is photoproduct formation. By employing a global analysis of the LE and ICT fluorescence response functions with a time resolution of 0.5 ps/channel in 1200 channels reliable kinetic and thermodynamic data can be obtained. The arguments presented in the literature in favor of a pisigma( *) state with a bent CN group as an intermediate in the ICT reaction of DMABN are discussed. From the appearance of an excited state absorption (ESA) band in the spectral region between 700 and 800 nm in MeCN for N,N-dimethylanilines with CN, Br, F, CF(3), and C(=O)OC(2)H(2) p-substituents, it is concluded that this ESA band cannot be attributed to a pisigma( *) state, as only the C-C[Triple Bond]N group can undergo the required 120 degrees bending.

Fluctuations between multiple EF-G-induced chimeric tRNA states during translocation on the ribosome

The coupled translocation of transfer RNA and messenger RNA through the ribosome entails large-scale structural rearrangements, including step-wise movements of the tRNAs. Recent structural work has visualized intermediates of translocation induced by elongation factor G (EF-G) with tRNAs trapped in chimeric states with respect to 30S and 50S ribosomal subunits. The functional role of the chimeric states is not known. Here we follow the formation of translocation intermediates by single-molecule fluorescence resonance energy transfer. Using EF-G mutants, a non-hydrolysable GTP analogue, and fusidic acid, we interfere with either translocation or EF-G release from the ribosome and identify several rapidly interconverting chimeric tRNA states on the reaction pathway. EF-G engagement prevents backward transitions early in translocation and increases the fraction of ribosomes that rapidly fluctuate between hybrid, chimeric and posttranslocation states. Thus, the engagement of EF-G alters the energetics of translocation towards a flat energy landscape, thereby promoting forward tRNA movement.

Intramolecular charge transfer with 4-fluorofluorazene and the flexible 4-fluoro-N-phenylpyrrole

With 4-fluorofluorazene (FPP4F) and its flexible counterpart 4-fluoro-N-phenylpyrrole (PP4F) an intramolecular charge transfer (ICT) reaction occurs in the singlet excited state in sufficiently polar solvents. The ICT reaction begins to appear in tetrahydrofuran (epsilon = 7.4) for FPP4F and in the more polar 1,2-dichloroethane (epsilon = 10.4) with PP4F, showing its presence by dual fluorescence from a locally excited (LE) and an ICT state. Only LE fluorescence is observed in less polar solvents such as n-hexane. The ICT reaction is more pronounced with FPP4F than for PP4F, due to the smaller energy gap DeltaE(S1,S2) of the former molecule, in accordance with the PICT model. The occurrence of an ICT reaction is confirmed by the ICT dipole moments mu(e)(ICT) of 12 D (FPP4F) and 10 D (PP4F), clearly larger than mu(e)(LE) of approximately 4 D for FPP4F and PP4F. Isoemissive points are found in the fluorescence spectra of FPP4F and PP4F in acetonitrile (MeCN), ethyl cyanide (EtCN), and n-propyl cyanide (PrCN) as a function of temperature, confirming the two-state (LE and ICT) reaction mechanism. From plots of the logarithm of the ICT/LE fluorescence quantum yield ratio versus the reciprocal absolute temperature in these solvents, the ICT reaction enthalpies DeltaH are determined, with larger -DeltaH values for FPP4F than for PP4F: 19.2 as compared with 14.9 kJ/mol in MeCN, as an example. The picosecond fluorescence decay of PP4F at -45 degrees C becomes slower with decreasing solvent polarity, 5.1 ps (MeCN), 14 ps (EtCN), and 35 ps (PrCN), from which the LE --> ICT reaction rate constant is calculated, decreasing from 19 x 10(10) to 2.1 x 10(10) s(-1) between MeCN and PrCN. The femtosecond LE excited-state absorption spectra of FPP4F and PP4F do not undergo any time development in n-hexane (no ICT reaction), but show a fast ICT reaction in MeCN at 22 degrees C, with decay times of 1.1 ps (FPP4F) and 3.3 ps (PP4F). It is concluded that FPP4F and PP4F have a planar ICT state (PICT model), indicating that a perpendicular twist of the donor and acceptor subgroups in a donor/acceptor molecule is not a requirement for fast and efficient ICT. The molecular structures of FPP4F and PP4F obtained from X-ray crystal analysis reveal that the pyrrole group of PP4F is twisted over an angle theta = 25 degrees relative to the fluorophenyl moiety in the ground state, whereas as expected FPP4F is practically planar (theta = 2 degrees). The pyrrole-phenyl bond length of FPP4F (140.7 pm) is shorter than that for PP4F (141.8 pm).

Counterintuitive absence of an excited-state intramolecular charge transfer reaction with 2,4,6-tricyanoanilines. Experimental and computational results.

The fluorescence spectra of 2,4,6-tricyano-N,N-dimethylaniline (TCDMA), 2,4,6-tricyano-N-methylaniline (TCMA), and 2,4,6-tricyanoaniline (TCA) consist of a single emission band, even in the polar solvent acetonitrile (MeCN). This indicates that an intramolecular charge transfer (ICT) reaction from the initially prepared locally excited (LE) state does not take place with these molecules, in contrast to 4-(dimethylamino)benzonitrile (DMABN), although the electron accepting capability of the tricyanobenzene moiety in TCDMA, TCMA, and TCA is substantially larger than that of the benzonitrile group in DMABN. In support of this conclusion, the picosecond fluorescence decays of the tricyanoanilines are single-exponential. Only with TCDMA in MeCN at the highest time resolution, double-exponential decays are observed. On the basis of a similar temporal evolution of around 2 ps in the femtosecond excited-state absorption (ESA) spectra of TCDMA in this solvent, the time development is attributed to the presence of two rapidly interconverting S(1) conformers. The same conclusion is reached from CASPT2/CASSCF computations on TCDMA, in which two S(1) minima are identified. The ESA spectra of TCDMA, TCMA, and TCA resemble that of the LE state of DMABN, but are different from its ICT ESA spectrum, likewise showing that an ICT reaction does not occur with the tricyanoanilines. From the luminescence spectrum of TCDMA in n-propyl cyanide at -160 degrees C, it follows that intersystem crossing and not internal conversion is the main S(1) deactivation channel. The radiative rate constant of TCDMA in MeCN is smaller than that of TCMA and TCA, which indicates that the S(1) state of TCDMA has a larger ICT contribution than in the case of TCMA and TCA, in accordance with the results of the calculations, which show that the S(1) state displays ICT valence bond character. Extrapolated gas-phase data for TCDMA and TCA are compared with the results of the computations, revealing a good agreement. The calculations on TCDMA and TCA also lead to the conclusion that the lowest excited singlet state S(1) determines its photophysical behavior, without the occurrence of an LE --> ICT reaction, in the sense that the initially excited LE state has already a strong ICT character and there is no equilibrium between two electronic states with strongly different electronic structures (i.e., LE and ICT with very different dipole moments) leading to dual (LE + ICT) fluorescence.

Dynamics of ribosomes and release factors during translation termination in E. coli

Release factors RF1 and RF2 promote hydrolysis of peptidyl-tRNA during translation termination. The GTPase RF3 promotes recycling of RF1 and RF2. Using single molecule FRET and biochemical assays, we show that ribosome termination complexes that carry two factors, RF1–RF3 or RF2–RF3, are dynamic and fluctuate between non-rotated and rotated states, whereas each factor alone has its distinct signature on ribosome dynamics and conformation. Dissociation of RF1 depends on peptide release and the presence of RF3, whereas RF2 can dissociate spontaneously. RF3 binds in the GTP-bound state and can rapidly dissociate without GTP hydrolysis from termination complex carrying RF1. In the absence of RF1, RF3 is stalled on ribosomes if GTP hydrolysis is blocked. Our data suggest how the assembly of the ribosome–RF1–RF3–GTP complex, peptide release, and ribosome fluctuations promote termination of protein synthesis and recycling of the release factors.