Signal recognition particle binds to translating ribosomes before emergence of a signal anchor sequence.

The bacterial signal recognition particle (SRP) is part of the machinery that targets ribosomes synthesizing membrane proteins to membrane-embedded translocons co-translationally. Recognition of nascent membrane proteins occurs by virtue of a hydrophobic signal-anchor sequence (SAS) contained in the nascent chain, usually at the N terminus. Here we use fluorescence-based stopped-flow to monitor SRP-ribosome interactions with actively translating ribosomes while an SRP substrate is synthesized and emerges from the peptide exit tunnel. The kinetic analysis reveals that, at cellular concentrations of ribosomes and SRP, SRP rapidly binds to translating ribosomes prior to the emergence of an SAS and forms an initial complex that rapidly rearranges to a more stable engaged complex. When the growing peptide reaches a length of ∼50 amino acids and the SAS is partially exposed, SRP undergoes another conformational change which further stabilizes the complex and initiates targeting of the translating ribosome to the translocon. These results provide a reconciled view on the timing of high-affinity targeting complex formation, while emphasizing the existence of preceding SRP recruitment steps under conditions of ongoing translation

Reversible dynamic isomerism change in the solid state, from Bi4I16 clusters to BiI4 1D chains in L-cystine based hybrids: templating effect of cations in iodobismuthate network formation

The dehydration of a iodobismuthate hybrid built up from Bi4I16 clusters and protonated L-cystine molecules involves an unprecedented reversible dynamic structural change in the solid state leading to 1D BiI4 chains and 1D helical molecular chains, highlighting the templating effect of cations in the formation of iodobismuthate network

Structural diversity and retro-crystal engineering analysis of iodometalate hybrids

With guidance from retro-crystal engineering, iodometalate structures based on MI6 octahedra of group 14 (M = Sn(II), Pb(II)) and group 15 (M = Sb(III) and Bi(III)) are analysed. The criterion of I/M ratio, with the function of indicating the degree of condensation of octahedra in inorganic networks and the average charge density at the organic–inorganic interface, is introduced to classify all of the iodometalate networks, resulting in an easy and clear way to identify isomers with different dimensionalities. Of all iodometalates, the 2D M(II)I4 anion derived from the perovskite network is special since it can be easily stabilized by a range of common organic cations. We provide here the up-to-date progress in this extensively studied field, focusing on crystal engineering of hybrids in the aim of getting materials with a reduced band gap. Relationships between the molecular layouts of cationic entities and the structures of several non-perovskite anionic networks, focusing on the organic–inorganic interface, are highlighted. Distinct dependences between different types of cations and different types of anions are revealed, although it is still unfeasible to apply them in the actual control, design, or prediction of specific hybrid structures

Solid Phase DNA Amplification: A Brownian Dynamics Study of Crowding Effects

AbstractSolid phase amplification (SPA), a new method to amplify DNA, is characterized by the use of surface-bound primers. This limits the amplification to two-dimensional surfaces and therefore allows the easy parallelization of DNA amplification in a single system. SPA leads to the formation of small but dense DNA brushes, called DNA colonies. For a molecule to successfully duplicate itself, it needs to bend so that its free end can find a matching primer, located on the surface. We used Brownian dynamics simulations (with a united-atom model) to model the basic kinetics of an SPA experiment. The simulations mimic the temperature cycles and the molecule duplication process found in SPA. Our results indicate that the steric interaction between molecules leads to a decreased duplication probability for molecules in the center of a colony and to an outward leaning for the molecules on the perimeter. These effects result in slower amplification (compared to solution PCR) and indicate that steric interaction alone can explain the loss of the exponential growth (characteristic of solution PCR) of the number of molecules in an SPA experiment. Furthermore, the growth of the colony as a function of the number of thermal cycles is found to be similar to the one obtained with a simple Monte Carlo simulation

Signal recognition particle prevents N-terminal processing of bacterial membrane proteins.

Bacterial proteins are synthesized with an N-formylated amino-terminal methionine, and N-formylated peptides elicit innate-immunity responses against bacterial infections. However, the source of these formylated peptides is not clear, as most bacterial proteins are co-translationally deformylated by peptide deformylase. Here we develop a deformylation assay with translating ribosomes as substrates, to show that the binding of the signal recognition particle (SRP) to signal sequences in nascent proteins on the ribosome prevents deformylation, whereas deformylation of nascent proteins without signal sequence is not affected. Deformylation and its inhibition by SRP are not influenced by trigger factor, a chaperone that interacts with nascent chains on the ribosome. We propose that bacterial inner-membrane proteins, in particular those with N-out topology, can retain their N-terminal formyl group during cotranslational membrane insertion and supply formylated peptides during bacterial infections

Cotranslational biogenesis of membrane proteins in bacteria

Nascent polypeptides emerging from the ribosome during translation are rapidly scanned and processed by ribosome-associated protein biogenesis factors (RPBs). RPBs cleave the N-terminal formyl and methionine groups, assist cotranslational protein folding, and sort the proteins according to their cellular destination. Ribosomes translating inner- membrane proteins are recognized and targeted to the translocon with the help of the signal recognition particle, SRP, and SRP receptor, FtsY. The growing nascent peptide is then inserted into the phospholipid bilayer at the translocon, an inner-membrane protein complex consisting of SecY, SecE, and SecG. Folding of membrane proteins requires that transmembrane helices (TMs) attain their correct topology, the soluble domains are inserted at the correct (cytoplasmic or periplasmic) side of the membrane, and – for polytopic membrane proteins – the TMs find their interaction partner TMs in the phospholipid bilayer. This review describes the recent progress in understanding how growing nascent peptides are processed and how inner-membrane proteins are targeted to the translocon and find their correct orientation at the membrane, with the focus on biophysical approaches revealing the dynamics of the process. We describe how spontaneous fluctuations of the translocon allow diffusion of TMs into the phospholipid bilayer and argue that the ribosome orchestrates cotranslational targeting not only by providing the binding platform for the RPBs or the translocon, but also by helping the nascent chains to find their correct orientation in the membrane. Finally, we present the auxiliary role of YidC as a chaperone for inner-membrane proteins. We show how biophysical approaches provide new insights into the dynamics of membrane protein biogenesis and raise new questions as to how translation modulates protein folding

Lateral gate dynamics of the bacterial translocon during cotranslational membrane protein insertion

During synthesis of membrane proteins, transmembrane segments (TMs) of nascent proteins emerging from the ribosome are inserted into the central pore of the translocon (SecYEG in bacteria) and access the phospholipid bilayer through the open lateral gate formed of two helices of SecY. Here we use single-molecule fluorescence resonance energy transfer to monitor lateral-gate fluctuations in SecYEG embedded in nanodiscs containing native membrane phospholipids. We find the lateral gate to be highly dynamic, sampling the whole range of conformations between open and closed even in the absence of ligands, and we suggest a statistical model-free approach to evaluate the ensemble dynamics. Lateral gate fluctuations take place on both short (submillisecond) and long (subsecond) timescales. Ribosome binding and TM insertion do not halt fluctuations but tend to increase sampling of the open state. When YidC, a constituent of the holotranslocon, is bound to SecYEG, TM insertion facilitates substantial opening of the gate, which may aid in the folding of YidC-dependent polytopic membrane proteins. Mutations in lateral gate residues showing in vivo phenotypes change the range of favored states, underscoring the biological significance of lateral gate fluctuations. The results suggest how rapid fluctuations of the lateral gate contribute to the biogenesis of inner-membrane proteins

Photochromism, Electrical Properties, and Structural Investigations of a Series of Hydrated Methylviologen Halobismuthate Hybrids: Influence of the Anionic Oligomer Size and Iodide Doping on the Photoinduced Properties and on the Dehydration Process

Syntheses, X-ray structural analyses, thermal behaviors, photochromism, and electrical properties of a series of methylviologen (MV2+) halobismuthate hybrids, namely, (MV)3[Bi4Cl18](H2O)y (1a, y~1.7), (MV)4[Bi6Cl26](H2O)y (2a, y~1.7), (MV)4[Bi6Cl25.6I0.4](H2O)y (3a, y~1.5), and (MV)4[Bi6Cl24.6I1.4](H2O)y (4a, y~1.3), are reported. Because of the thermal effect of a UV lamp or as a result of being heated up to 100 °C, all of the above compounds undergo a complete (1a, 2a, and 3a) or a partial (4a) dehydration together, in 2a and 3a, with an impressive structural reorganization involving a 90° rotation of methylviologen dimers and, in 3a, a new Cl/I distribution, finally leading to (MV)3[Bi4Cl18] (1b), (MV)4[Bi6Cl26] (2b), (MV)4[Bi6Cl25.6I0.4] (3b), and (MV)4[Bi6Cl24.6I1.4](H2O)x (4a, x ~ 0.65), respectively. In its turn, 4a (x ~ 0.65) undergoes an abrupt structural change at 160 °C when water molecules are completely removed, leading to (MV)4[Bi6Cl24.6I1.4] (4b). Obviously, the two first dehydrated phases can be considered as the n = 2 (1b) and n = 3 (2b) members of the (MV)(2n+2)/2[Bi2nCl8n+2] family, and the ultimate member (n = ∞) with an infinite 1D double-chain inorganic framework, namely, (MV)[Bi2Cl8], has already been reported. According to the results of structural refinements, some positions of the Cl atoms in the [Bi6Cl26]8− anionic cluster of 3a and 4a have been occupied by I atoms, finally leading to iodide-doped materials of the 2a type (percentage of doping: 3a, 1.5%; 4a, 5.4%). Upon UV irradiation, yellow crystals of 2a and 3a (which become 2b and 3b because of the thermal effect of the UV lamp) or yellow crystals of 2b, 3b, and 4a undergo a color change to black crystals (in the case of 2b), as observed in (MV)[Bi2Cl8], or light-brown crystals (in the cases of 3b and 4a). These photochromic properties are probably due to the photoinduced electron transfer from the anionic part to the methylviologen dications. In contrast, no color change is observed when yellow crystals of 1a or 1b and the iodide-doped (MV)[Bi2Cl8−εIε] material are irradiated. Because the relative positions of methylviologen to the host anionic frameworks are comparable in all structures (the N···Cl distances are about 3.4 Å), these results indicate that such kinds of photochemical reactions depend on the dimension of the anionic networks, as well as the iodide doping. The single-crystal electrical conductivity measurements of 2b before and after irradiation were carried out between 150 and 393 K. The results prove that both of them are semiconductors with weak room temperature conductivity and that the band gap of the irradiated crystal (2b, 0.35 eV) is much smaller than that of the original hybrid 2a (1.0 eV)