New scenarios of protein folding can occur on the ribosome

Identifying and understanding the differences between protein folding in bulk solution and in the cell is a crucial challenge facing biology. Using Langevin dynamics, we have simulated intact ribosomes containing five different nascent chains arrested at different stages of their synthesis such that each nascent chain can fold and unfold at or near the exit tunnel vestibule. We find that the native state is destabilized close to the ribosome surface due to an increase in unfolded state entropy and a decrease in native state entropy; the former arises because the unfolded ensemble tends to behave as an expanded random coil near the ribosome and a semicompact globule in bulk solution. In addition, the unfolded ensemble of the nascent chain adopts a highly anisotropic shape near the ribosome surface and the cooperativity of the folding-unfolding transition is decreased due to the appearance of partially folded structures that are not populated in bulk solution. The results show, in light of these effects, that with increasing nascent chain length folding rates increase in a linear manner and unfolding rates decrease, with larger and topologically more complex folds being the most highly perturbed by the ribosome. Analysis of folding trajectories, initiated by temperature quench, reveals the transition state ensemble is driven toward compaction and greater native-like structure by interactions with the ribosome surface and exit vestibule. Furthermore, the diversity of folding pathways decreases and the probability increases of initiating folding via the N-terminus on the ribosome. We show that all of these findings are equally applicable to the situation in which protein folding occurs during continuous (non-arrested) translation provided that the time scales of folding and unfolding are much faster than the time scale of monomer addition to the growing nascent chain, which results in a quasi-equilibrium process. These substantial ribosome-induced perturbations to almost all aspects of protein folding indicate that folding scenarios that are distinct from those of bulk solution can occur on the ribosome.     

Determination of thiols by titrimetric and chromatographic procedures based on reactions with aromatic thiosulfonates

Semimicro titrimetric procedures and micro high-performance liquid chromatographic procedures are described for the determination of aliphatic and aromatic thiols, based on the highly selective reaction with aromatic thiosulfonates. The reaction products, a sulfinic acid and a mixed disulfide, contain an aromatic moiety, permitting the use of an u.v. detector. The chromatographic procedure offers the advantages of application to mixtures, coupled with cross-checking of the determination by material balance from simultaneous measurement of the two reaction products.     

ortho-Acidic aromatic thiols as efficient catalysts of intramolecular Morita-Baylis-Hillman and Rauhut-Currier reactions

ortho-Mercaptobenzoic acid and ortho-mercaptophenols were discovered as efficient thiol catalysts of both the intramolecular Morita-Baylis-Hillman (MBH) and Rauhut-Currier (RC) reaction. High reaction rates were achieved under mildly basic, aqueous conditions. The unprecedented catalytic activity of these protic nucleophiles could originate from a Brønsted acid induced destabilization of intermediate thioethers and thus represent a unique mechanism of multifunctional Lewis base catalysis.     

Photodissociation of aromatic thiols and disulfides

For the first time, the quantum yields of cleavage of SS and SH bonds in a disulfide and a thiol and also the extinction coefficient of the photoinduced aminophenylthiyl radical were determined, on the basis of which the relation of the photodissociation quantum yield to the energy of an absorbed quantum was observed.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 540–543, March, 1990.     

Steric Effects in Nucleophilic Aromatic Substitution reactions with aromatic amines 12th communication on nucleophilic aromatic substitution reactions

The kinetics of the S_NAr reactions of aniline and N-methylaniline with a variety of substituted nitrochlorobenzenes in acetonitrile demonstrate that the formation of the intermediate σ-complex is rate determining. The ratio of the rate constants of the aniline and the N-methylaniline reactions (k_A/k_M) increases with increasing size of the 6-substituent; with picryl chloride k_A/k_M reaches a value of over 20 000. The reaction of aniline with 4-X-2,6-dinitrochlorobenzenes is subject to considerably larger para-substituent effects than the corresponding reactions with N-methylaniline. These results are interpreted in terms of two effects: (i) A primary steric effect, which renders the approach of N-methylaniline to the substrate difficult. (ii) A shift towards earlier, more reactant-like transition state structures caused by the primary steric effect. In early transition states the activating power of the electron-withdrawing substituents in the substrate is expected to be relatively small. An early transition state for the slow N-methylaniline reaction and a late transition state for the fast aniline reaction is in apparent contradiction to what would be expected on the basis of the Hammond postulate.     

The synthesis of water soluble decalin-based thiols and S-nitrosothiols--model systems for studying the reactions of nitric oxide with protein thiols

The syntheses of three decalin-based tert-thiols displaying varying degrees of solubility in aqueous milieu are described. The S-nitroso derivatives of these compounds have also been prepared and the structures of two of these determined by single crystal X-ray diffraction. These compounds have been designed for studying the interaction of nitric oxide (NO) with thiols under physiological conditions.     

Mechanism of thiolate-disulfide interchange reactions in biochemistry

Both density functional theory (DFT) (B3LYP) and CCSD ab initio calculations were employed in a theoretical investigation of the mechanism of thiolate-disulfide exchange reactions. The reaction pathway for degenerate thiolate-disulfide exchange reactions with dimethyl disulfide has been shown to proceed through a SN2-like transition structure that is very close in energy to the corresponding trisulfur anionic intermediate ([delta-S-S-Sdelta(-)]). When relatively small substituents are involved, the level of theory must be increased to CCSD to make this rather subtle mechanistic distinction. With the more sterically hindered exchange reaction involving t-butyl mercaptide and di-t-butyl disulfide, the potential energy surface exhibits a distinct preference for the S(N)2 displacement pathway with an activation barrier of 9.8 kcal/mol. When corrections for solvent polarity are included (COSMO), an S(N)2 mechanism is also implicated in both polar and nonpolar solvents. DFT studies on thiolate-disulfide exchange, when the substituent is a model peptide, strongly support the intermediacy of a trisulfur intermediate that lies 10.7 kcal/mol below isolated reactants. A well depth of this magnitude should provide a sufficient lifetime of the intermediate to accommodate the requisite conformational adjustments that accompanies formation of the new disulfide bond.     

Effects of long-range electrostatic forces on simulated protein folding kinetics

Molecular dynamics simulations are a useful tool for characterizing protein folding pathways. There are several methods of treating electrostatic forces in these simulations with varying degrees of physical fidelity and computational efficiency. In this article, we compare the reaction field (RF) algorithm, particle-mesh Ewald (PME), and tapered cutoffs with increasing cutoff radii to address the impact of the electrostatics method employed on the folding kinetics. We quantitatively compare different methods by a correlation of quantitative measures of protein folding kinetics. The results of these comparisons show that for protein folding kinetics, the RF algorithm can quantitatively reproduce the kinetics of the more costly PME algorithm. These results not only assist the selection of appropriate algorithms for future simulations, but also give insight on the role that long-range electrostatic forces have in protein folding.     

The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel

Protein folding is a dynamic process with continuous transitions among different conformations. In this work, the dynamics in the protein folding network of villin headpiece subdomain (HP35) has been investigated based on multiple reversible folding trajectories of HP35 and its ultrafast folding mutant where sub-angstrom folding was achieved. The four folding states were clearly separated on the network, validating the classification of the states. Examination of the eight conformers with different formation of the individual helices revealed high plasticity of the three helices in all the four states. A consistent feature between the wild type and mutant protein is the dominant conformer 111 (all three helices formed) in the folded state and conformers 111 and 011 (helices II and III formed) in the major intermediate state, indicating the critical role of helices II and III in the folding mechanism. When compared to the wild type, the folding landscape of the ultrafast folding mutant exhibited a deeper folding funnel towards the folded state. The very beginning of the folding (0-10 ns) was very similar for both protein variants but it soon diverged and displayed different folding pathways. Although going through the major intermediate state is the dominant pathway for both, it was also observed that some folding went through the minor intermediate state for the mutant. The intriguing difference resulting from the mutation at two residues in helix III has been carefully analyzed and discussed in details.     

Place exchange reactions of alkyl thiols on gold nanoparticles

The kinetics and equilibrium position of place exchange (alkylthiol-for-alkylthiol) reactions of gold nanoparticles are reported. These reactions were monitored via a gas chromatography analysis of structurally similar incoming and outgoing alkylthiols, as a function of time. The place exchange reactions described here proceed to an equilibrium position, where Keq approximately 1. The product-time data follow Langmuir diffusion kinetics.     

A semi-analytical description of protein folding that incorporates detailed geometrical information

Much has been done to study the interplay between geometric and energetic effects on the protein folding energy landscape. Numerical techniques such as molecular dynamics simulations are able to maintain a precise geometrical representation of the protein. Analytical approaches, however, often focus on the energetic aspects of folding, including geometrical information only in an average way. Here, we investigate a semi-analytical expression of folding that explicitly includes geometrical effects. We consider a Hamiltonian corresponding to a Gaussian filament with structure-based interactions. The model captures local features of protein folding often averaged over by mean-field theories, for example, loop contact formation and excluded volume. We explore the thermodynamics and folding mechanisms of beta-hairpin and alpha-helical structures as functions of temperature and Q, the fraction of native contacts formed. Excluded volume is shown to be an important component of a protein Hamiltonian, since it both dominates the cooperativity of the folding transition and alters folding mechanisms. Understanding geometrical effects in analytical formulae will help illuminate the consequences of the approximations required for the study of larger proteins.     

Kinetics of OH reactions with aliphatic thiols

The kinetics of OH reactions with 1–4 carbon aliphatic thiols have been investigated over the temperature range 252–430 K. OH radicals were produced by flash photolysis of water vapor at λ > 165 nm and detected by time-resolved resonance fluorescence spectroscopy. All thiols investigated react with OH at nearly the same rate; k(298 K) = 3.2–4.6 × 10^?11 cm³ molecule^?1 s^?1, -E_act = 0.6–1.0 kcal/mol, A = 0.6–1.2 × 10^?11 cm³ molecule^?1 s^?1. CH₃SH and CH₃SD react with OH at identical rates over the entire temperature range investigated. We conclude that the dominant reaction pathway is addition to the sulfur atom.     

Solvent-induced forces in protein folding reflections on the protein folding problem

It is shown that the solvent induced forces on hydrophilic groups are the strongest ones. The relevance of this finding to protein folding is discussed.     

Synthesis of copolyesters via interchange reactions with polypivalolactone

The synthesis of copolyesters via interchange reactions of polypivalolactone (PPVL) with bisphenol-A polycarbonate (PC) and dimethyl terephthalate (DMT) was studied. Random copolyesters with high thermal stability were obtained by heating PPVL with PC and DMT in the melt at 280 °C in the presence of tetrabutylorthotitanate (TnBT) as a catalyst. Results from SEC measurements showed that the values for M_n of these copolyesters ranged from 7,000 to 16,000. The process for preparing these copolyesters was studied in detail and based on the results of these studies, the reactions occurring during copolyester synthesis were discussed. It was found that in the early stages of the process mainly interchange reactions occurred between PPVL and PC chains, whereas the amount of terephthalate units increased only after longer reaction times.     

Substituent dependence of the reactions of [RuCl2(PPh3)3] with bulky aromatic thiols

2,4,6-trialkylbenzenethiols react with [RuCl2(PPh3)3] to give Ru products with the alkyl substituents forming M-C sigma bonds, carbene, carbene with a S alpha-heteroatom, agostic hydrogen interaction or a simple tetrahedral Ru(II) species, depending on the substituent.     

Reactions that occur during the synthesis of 3-phenyl-5-phenoxymethyl-2-N-phenyliminooxazolidine

Conclusions 3-Phenyl-5-phenoxymethyl-2-N-phenyliminooxazolidine, formed by the reaction of diphenyl-carbodiimide with phenyl glycidyl ether, reacts with an excess of the latter to give 3-phenyl-5-phenoxymethyl-2-oxazolidone.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 2152–2153, September, 1983.