Engineering a beta-sheet protein toward the folding speed limit

Recent experimental studies have shown that alpha-helical proteins can approach the folding "speed limit", where folding switches from an activated to a downhill process in free energy. beta-sheet proteins are generally thought to fold more slowly than helix bundles. However, based on studies of hairpins, folding should still be able to approach the microsecond time scale. Here we demonstrate how the hPin1 WW domain, a triple-stranded beta-sheet protein with a sharp thermodynamic melting transition, can be engineered toward the folding "speed limit" without a significant loss in thermal denaturation cooperativity.     

Folding kinetics of a polymer

We present the results of computer simulations giving a kinetic insight into the liquid-to-solid transition of a homopolymer chain with short-range interactions. By calculating the absolute rates in each direction of the transition, using molecular dynamics employing the forward flux sampling scheme, we provide the phase diagram based on purely kinetic data, and compare it with the results from Monte Carlo simulations. Additionally, we present and discuss a remarkably simple and general relation between the polymer topology and the folding pathway, and show that the eigenvalue spectrum of a matrix defined by non-bonded contacts (the Laplacian matrix) provides an insight into the nonequilibrium ensembles of these trajectories. In particular, the Laplacian matrix seems to identify a large fraction of configurations on the folding pathway at the free energy maximum that have a very low probability of reaching the crystallized state. This implies that the eigenvalues of this matrix may be suitable additional reaction coordinates to describe the folding transition of chain molecules.     

Molecular dynamics simulation of folding of a short helical peptide with many charged residues

A molecular dynamics simulation of the folding of conantokin-T (con-T), a short helical peptide with 5 helical turns of 21 amino acids with 10 charged residues, was carried out to examine folding pathways for this peptide and to predict the folding rate. In the 18 trajectories run at 300 K, 16 trajectories folded, with an averaged folding time of approximately 50 ns. Two trajectories did not fold in up to 200 ns simulation. The folded structure in folded trajectories is in good agreement with experimental structure. An analysis of the trajectories showed that, at the beginning of a few nanoseconds, helix formation started from residues 5-9 with assistance of a hydrophobic clustering involving Tyr5, Met8, and Leu9. The peptide formed a U-shape mainly due to charge-charge interactions between charged residues at the N- and C-terminus segments. In the next approximately 10 ns, several nonnative charge-charge interactions were broken and nonnative Gla10-Lys18 (this denotes a salt bridge between Gal10 and Lys18) and/or Gla10-Lys19 interactions appeared more frequently in this folding step and the peptide became a fishhook J-shape. From this structure, the peptide folded to the folded state in 7 of all 16 folded trajectories in approximately 15 ns. Alternatively, in approximately 30 ns, the con-T went to a conformation in an L-shape with 4 helical turns and a kink at the Arg13 and Gla14 segment in the other 9 trajectories. Con-T in the L-shape then required another approximately 15 ns to fold into the folded state. In addition, in overall folding times, the former 7 trajectories folded faster with the total folding times all shorter than 45 ns, while the latter 9 trajectories folded at a time longer than 45 ns, resulting in an average folding time of approximately 50 ns. Two major folding intermediates found in 2 nonfolded trajectories are stabilized by charge clusters of 5 and 6 charged residues, respectively. With inclusion of friction and solvent-solvent interactions, which were ignored in the present GB/SA solvation model, the folding time obtained above should be multiplied by a factor of 1.25-1.7 according to a previous, similar simulation study. This results in a folding time of 65-105 ns, slightly shorter than the folding time of 127 ns for an alanine-based peptide of the same length. This suggests that the energy barrier of folding for this type of peptides with many charged residues is slightly lower than alanine-based helical peptides by less than 1 kcal/mol.     

Thermal behavior and dehydroxylation kinetics of naturally occurring sepiolite and bentonite

Sepiolite and bentonite have a wide range of industrial applications based on their physicochemical properties such as surface area, thermal behavior, chemical composition, and mineralogic composition. The thermal behavior and kinetics of naturally occurring sepiolite and bentonite were determined in order to give an idea about the potential use of naturally occurring clay minerals in possible applications. Naturally occurring sepiolite and bentonite samples were heated to the temperature that was achieved at the end of the dehydroxylation process. Mineralogic and thermal characteristics of raw and heat treated samples were investigated by X-ray diffraction, Fourier transform infrared spectroscopy, and nitrogen adsorption/desorption analyses. Changes in the structure following heat treatment were used for the evaluation of the dehydroxylation properties of the samples. The dehydroxylation properties of the minerals are strongly affected by the crystal structure. Kinetic analyses, which were related to the dehydroxylation of naturally occurring sepiolite and bentonite, were conducted using dynamic thermogravimetry/derivative thermogravimetry analysis under nitrogen atmosphere. Flynn–Wall–Ozawa, Kissenger–Akahira–Sunose, and Friedman isoconversional methods were used to determine the activation energies of the dehydroxylation reactions of the samples. The results indicate that the activation energy of naturally occurring sepiolite showed a little variation at a particular conversion rate (0.3–0.7), while the activation energy of naturally occurring bentonite showed a significant variation within the range of variation of the conversion rate. The present study shows that the dehydroxylation reactions of naturally occurring sepiolite and bentonite were single mechanism reaction and complex mechanism reaction, respectively.     

Examination of the folding of a short alanine-based helical peptide with salt bridges using molecular dynamics simulation

A molecular dynamics simulation of the folding of a short alanine-based helical peptide of 17 residues with three Glu...Lys (i, i + 4) salt bridge pairs, referred to as the AEK17 peptide, was carried out. The simulation gave an estimated simulation folding time of 2.5 ns, shorter than 12 ns for an alanine-based peptide of 16 residues with three Lys residues only, referred to as the AK16 peptide, simulated previously. After folded, the AEK17 peptide had a helical content of 77%, in excellent agreement with the experimentally determined value of 80%. An examination of the folding pathways of AEK17 indicated that the peptide proceeded via three-turn helix conformations more than the helix-turn-helix conformation in the folding pathways. An analysis of interactions indicated that the formation of hydrogen bonds between Lys residue side chains and backbone carbonyls is a major factor in the abundant conformation of the three-turn helix intermediate. The substitution of three Ala with Glu residues reduces the extent of hydrophobic interaction in alanine-based AK peptides with the result that the breaking of the interactions of Lys epsilon-NH3+(side chain)...C=O(backbone) is a major activation action for the AEK17 to achieve a complete fold, in contrast to the AK16 peptide, in which breaking non-native hydrophobic interaction is the rate-determining step.     

probing the gas-phase folding kinetics of peptide ions by IR activated DR-ECD

The effect of infrared (IR) irradiation on the electron capture dissociation (ECD) fragmentation pattern of peptide ions was investigated. IR heating increases the internal energy of the precursor ion, which often amplifies secondary fragmentation, resulting in the formation of w-type ions as well as other secondary fragments. Improved sequence coverage was observed with IR irradiation before ECD, likely due to the increased conformational heterogeneity upon IR heating, rather than faster breakdown of the initially formed product ion complex, as IR heating after ECD did not have similar effect. Although the ECD fragment ion yield of peptide ions does not typically increase with IR heating, in double resonance (DR) ECD experiments, fragment ion yield may be reduced by fast resonant ejection of the charge reduced molecular species, and becomes dependent on the folding state of the precursor ion. In this work, the fragment ion yield was monitored as a function of the delay between IR irradiation and the DR-ECD event to study the gas-phase folding kinetics of the peptide ions. Furthermore, the degree of intracomplex hydrogen transfer of the ECD fragment ion pair was used to probe the folding state of the precursor ion. Both methods gave similar refolding time constants of approximately 1.5 s(-1), revealing that gaseous peptide ions often refold in less than a second, much faster than their protein counterparts. It was also found from the IR-DR-ECD study that the intramolecular H. transfer rate can be an order of magnitude higher than that of the separation of the long-lived c/z product ion complexes, explaining the common observation of c. and z type ions in ECD experiments.     

Folding of ubiquitin: a simple model describes the strange kinetics

The ubiquitin mutant UbG folding experiments of Sabelko et al., in which "strange kinetics" were observed, are interpreted in terms of a simple kinetic model. A minimal set of states consisting of a semicompact globule, two off-pathway traps, and the native state are included; the fully unfolded state is not considered because folding to the semicompact globule is fast. Both the low- and the high-temperature experiments of Sabelko et al. are fitted by a system of kinetic equations determining the transitions between these states. It is possible that cold- and heat-denaturated states of UbG are the basis of the off-pathway traps. The fits of the kinetic model to the experimental results provides an estimate of the rate constants for the various reaction channels and show how their contributions vary with temperature. Introduction of an on-pathway intermediate instead of one of the off-pathway traps does not lead to agreement with the experiments.     

Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model

The theoretical concept of folding probability, p(fold), has proven to be a useful means to characterize the kinetics of protein folding. Here, we illustrate the practical importance of p(fold) and demonstrate how it can be determined theoretically. We derive a general analytical expression for p(fold) and show how it can be estimated from simulations for systems where the transition rates between the relevant microstates are not known. By analyzing the Ising model we are able to determine the scaling behavior of the numerical error in the p(fold) estimate as function of the number of analyzed Monte Carlo runs. We apply our method to a simple, newly developed protein folding model for the formation of alpha helices. It is demonstrated that our technique highly parallelizes the calculation of p(fold) and that it is orders of magnitude more efficient than conventional approaches.     

Metallacyclopeptides: artificial analogues of naturally occurring peptides

Naturally occurring metalloproteins contain metal ions either to introduce a special reactivity or to stabilize a peptide structure. Since the early 1990s, chemists have been trying to use metal coordination for the fixation of short artificial peptides in well-defined cyclic structures. In this tutorial review a survey of the general approaches towards metallacyclopeptides as small cyclic peptide derivatives or as a part of a bigger alpha-helix (or beta-sheet) structure is given. In three case studies it is shown how naturally occurring compounds can be mimicked by metal coordination to non-natural peptide derivatives.     

Synthesis of erythrinin A,a naturally occurring pyranoisoflavone

Erythrinin A ($\text{10}$) has been synthesised by the oxidative rearrangement of dihydropyranochalcone $\text{1}$ with thallium(III) nitrate (TTN) in trimethyl orthoformate (TMOF) to the dimethyl acetal $\text{2}$, followed by cyclisation to $\text{3}$, demethylation to $\text{6}$ and dehydrogenation. Compound $\text{10}$ could also be obtained from chalcone $\text{4}$ on similar rearrangement followed by cyclisation, demethoxymethylation and dehydrogenation. In another route, chalcone $\text{7}$ was oxidatively rearranged with TTN in TMOF, to $\text{8}$ which on treatment with HCl yielded $\text{10}$.     

Synthesis of naturally occurring polyacetylenes via a bis-silylated diyne

A straightforward synthesis of a series of naturally occurring polyacetylenes has been developed, including the montiporynes A and C, possessing cytotoxic activity against several human solid tumor cells, the atractylodin, with antibiotic activity against Escherichia coli, and triynes, which display insecticidal activities, starting from the readily available 1,4-bis(trimethylsilyl)-1,3-butadiyne.     

Synthesis of a naturally occurring nucleopeptide fragment via a phosphotriester approach

The phosphorylating agent 2-chlorophenyl-O,O-bis[1-benzotriazolyl]phosphate has been used for the introduction of a phosphodiester bond between the hydroxyl group of the tyrosine containing dipeptide (H-Ala-Tyr-NH₂) and the 5′-OH of the RNA dimer UpU.     

Regiospecific synthesis of isopestacin, a naturally occurring isobenzofuranone antioxidant

A DBU promoted aldol cyclocondensation of hydroxyisobenzofuranone 15 with cyclohexane-1,3-dione, followed by aromatization has resulted in the first short synthesis of isopestacin (1).     

Adsorption kinetics of proteins onto solid surfaces in the limit of the interfacial interaction control

We have developed an experimental set-up using radiolabelled proteins for the continuous measurement, as a function of time, of the excess concentration of superficial protein at a solid/liquid interface. The experimental conditions were designed in order to minimize the coupling of the interfacial interaction with bulk diffusion, and therefore to work within the limit of the interfacial interaction control. Chemical kinetics were assumed to follow a Langmuir equation. The absorption (K_a) and desorption (K_d) rate constants have been evaluated in the case of fibrinogen and albumin adsorption, onto glass beads and synthetic hydroxyapatite powder, respectively. In order to determine these parameters, a non-linear differential equation (obtained by combining the Langmuir rate equation and a mass-balance equation) was solved by the fourth-order Runge-Kutta method. The results obtained are consistent with the hypothesis of an adsorption rate controlled by the interfacial interaction.     

Viscosamine: the first naturally occurring trimeric 3-alkyl pyridinium alkaloid

[structure: see text] Pyridinium alkaloids are widely distributed in marine sponges of different genera. Chemical investigation of the Arctic sponge Haliclona viscosa led to the isolation of a new trimeric 3-alkyl pyridinium alkaloid (viscosamine). Trimers have not been described as natural products yet. The isolation and the structure elucidation of viscosamine are discussed in detail.     

7‐Fluorotubercidin: a halogenated derivative of a naturally occurring nucleoside antimetabolite

The title compound [systematic name: 4‐amino‐5‐fluoro‐7‐(β‐d ‐ribofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine], C₁₁H₁₃FN₄O₄, exhibits an anti glycosylic bond conformation, with a χ torsion angle of −124.7 (3)°. The furanose moiety shows a twisted C2′‐endo sugar pucker (S‐type), with P = 169.8 (3)° and τ_m = 38.7 (2)°. The orientation of the exocyclic C4′—C5′ bond is +sc (gauche, gauche), with a γ torsion angle of 59.3 (3)°. The nucleobases are stacked head‐to‐head. The extended crystal structure is a three‐dimensional hydrogen‐bond network involving O—H...O, O—H...N and N—H...O hydrogen bonds. The crystal structure of the title nucleoside demonstrates that the C—C bonds nearest the F atom of the pyrrole system are significantly shortened by the electronegative halogen atom.