Prion protein insertional mutations increase aggregation propensity but not fiber stability

Background  

Mutations in the PRNPgene account for ~15% of all prion disease cases. Little is understood about the mechanism of how some of these mutations in PRNPcause the protein to aggregate into amyloid fibers or cause disease. We have taken advantage of a chimeric protein system to study the oligopeptide repeat domain (ORD) expansions of the prion protein, PrP, and their effect on protein aggregation and amyloid fiber formation. We replaced the ORD of the yeast prion protein Sup35p with that from wild type and expanded ORDs of PrP and compared their biochemical properties in vitro. We previously determined that these chimeric proteins maintain the [PSI⁺] yeast prion phenotype in vivo. Interestingly, we noted that the repeat expanded chimeric prions seemed to be able to maintain a stronger strain of [PSI ⁺] and convert from [psi ^-] to [PSI ⁺] with a much higher frequency. In this study we have attempted to understand the biochemical properties of these chimeric proteins and to establish a system to study the properties of the ORD of PrP both in vivoand in vitro.     

Hsp104 Drives “Protein-Only” Positive Selection of Sup35 Prion Strains Encoding Strong [PSI+]

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Highlights? Hsp104 disrupts intermolecular contacts of different synthetic NM prion strains ? Hsp104 selectively amplifies NM prions that confer strong [PSI⁺] phenotypes ? Hsp104 selectively eliminates NM prions that confer weak [PSI⁺] phenotypes ? Hsp104 drives strain selection events that favor prions encoding strong [PSI⁺]     

Light-induced hydrogen production by photosystem I–Pt nanoparticle conjugates immobilized in porous glass plate nanopores

In recent years, a number of light-induced hydrogen production systems composed of photosystem I (PSI) and hydrogen production catalysts (e.g. hydrogenases and Pt nanoparticles) have been reported. However, the utility of these systems under aerobic conditions is limited due to their poor stability in the presence of oxygen. The development of light-induced hydrogen production systems that work under aerobic conditions is, therefore, of great importance to establish artificial photosynthetic devices. Ideally, these systems should utilise water as an electron source, via water splitting by photosystem II (PSII). We report the construction of a novel light-induced hydrogen production system composed of PSI-platinum nanoparticle conjugates and cytochrome c ₆ (cyt c ₆) immobilised in nanoporous glass plates (PGP50, 50-nm pore diameter). PSI trimer (PSI_t) from Thermosynechococcus elongatus and Pt nanoparticles (PtNPs) were conjugated via electrostatic interactions (PSI_t-PtNP). PSI_t-PtNP and cyt c ₆ were spontaneously absorbed in nanopores of PGP50 without denaturation. Upon irradiation in the presence of ascorbate as a sacrificial electron donor, catalytic H₂ evolution was observed for PSI_t-PtNP immobilised in the pores of PGP50 (PSI_t-PtNP/PGP50) under both anaerobic and aerobic conditions, indicating that an effective photoinduced electron transfer system had been established. PSI_t-PtNP/PGP50 was found to exhibit improved oxygen resistivity over the homogeneous solution system consisting of PSI_t-PtNP, cyt c ₆, and ascorbate, suggesting that the PSI_t-PtNP/PGP50 system could be a potential candidate for artificial photosynthetic systems. The distribution of the components, PSI_t-PtNP and cyt c ₆, in PGP50 was characterised to discuss the efficiency of light-induced hydrogen production.     

Fluorometric and molecular modeling deciphering the non-covalent interaction between cyromazine and human serum albumin

Cyromazine (CMZ) had been believed to be one of the safest pesticides and widely used for many years until its carcinogenesis was revealed recently. In this work, the interaction between cyromazine and human serum albumin (HSA) was systematically investigated by multiple spectroscopic methods and molecular docking techniques using warfarin and flufenamic acid as probes. The results demonstrated the fluorescence of HSA had been quenched by CMZ through static mechanism, with new non-covalent complexes formed at ground state. Fluorescence probe experiments indicated CMZ bound to Sudlow’s site I in subdomain IIA of HSA, having no competition with site marker in site II. The number of binding sites, equilibrium constants and thermodynamic parameters were calculated by monitoring the binding equilibriums at different temperatures. The positive enthalpy change (ΔH ^θ) and entropy change (ΔS ^θ) implied the binding was mainly conducted by hydrophobic interactions. The binding was an endothermic, spontaneous (ΔG ^θ?<?0) and entropy-driven process which made the energy distribution of the system more evenly. The force of interaction and the conformation of binding pocket were displayed by molecular simulation and discussed at molecular level. Circular dichroism (CD) spectra indicated distorted α-helix content of HSA decreased while other fine secondary structure increased when CMZ was added.     

Spectroscopic Studies on the Interaction of 2,4-Dichlorophenol with Bovine Serum Albumin

The interaction between 2,4-dichlorophenol (DCP) and bovine serum albumin (BSA) was investigated by fluorescence spectroscopy combined with UV-vis absorption and circular dichroism (CD) spectroscopy under simulative physiological conditions. The experiment results show that the fluorescence intensity of BSA is dramatically decreased owing to the formation of a DCP–BSA complex. The corresponding effective quenching constants (K _a) between DCP and BSA at four different temperatures (292, 298, 304 and 310 K) were determined to be 10.08×10⁴, 9.082×10⁴, 8.177×10⁴, and 7.260×10⁴ L?mol^?1, respectively. The thermodynamics parameters enthalpy change (ΔH) and entropy change (ΔS) were calculated to be ?13.64 kJ?mol^?1 and 49.08 J?mol^?1?K^?1, which suggested that hydrophobic interaction was the predominant intermolecular force. Site marker competitive experiments indicated that the binding of DCP to BSA primarily takes place in subdomain IIA. The binding distance (r) between DCP and the tryptophan residue of BSA ias 4.09 nm according to Förster’s theory of non-radioactive energy transfer. The conformational investigation demonstrated that the presence of DCP decreased the α-helical content of BSA and induced a slight unfolding of the polypeptides of protein, which confirmed the occurrence some micro environmental and conformational changes of BSA molecules.     

CO<Subscript>2</Subscript>-responsive Polymeric Fluorescent Sensor with Ultrafast Response

Abstract Response speed is one of the most important evaluation criteria for CO₂ sensors. In this work, we report an ultrafast CO₂ fluorescent sensor based on poly[oligo(ethylene glycol) methyl ether methacrylate]-b-poly[N,N-diethylaminoethyl methacrylate-r-4-(2-methylacryloyloxyethylamino)-7-nitro-2,1,3-benzoxadiazole] [POEGMA-b-P(DEAEMA-r-NBDMA)], in which DEAEMA units act as the CO₂-responsive segment and 4-nitrobenzo-2-oxa-1,3-diazole (NBD) is the chromophore. The micelles composed of this copolymer could disassemble in 2 s upon CO₂ bubbling, accompanying with enhanced fluorescence emission with bathochromic shift. Furthermore, the quantum yield of the NBD chromophore increases with both the CO₂ aeration time and the NBD content. Thus we attribute the fluorescent enhancement to the inhibition of the photo-induced electron transfer between unprotonated tertiary amine groups and NBD fluorophores. The sensor is durable although it is based on “soft” materials. These micellar sensors could be facilely recycled by alternative CO₂/Ar purging for at least 5 times, indicating good reversibility.     

Structural and Thermodynamic Investigation into the Protein-Binding Properties of a Natural Product Crytotanshinone

Crytotanshinone (CTSO) is a Chinese herbal medicine active ingredient isolated from Salvia miltiorrhiza. In this work, the interaction of CTSO and human serum albumin (HSA) was studied by fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that the endogenous fluorescence of HSA was quenched by CTSO through a static mechanism. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at three different temperatures. The positive enthalpy change (ΔH^θ) and entropy change (ΔS^θ) revealed that the interaction was an endothermic as well as an entropy-driven process, where hydrophobic power played the major role in stabilizing the structure of the new complex. Site-selective binding experiments were carried out using warfarin and ibuprofen as probes, which proved that CTSO binds to Sudlow’s site II in subdomain IIIA of the HSA molecule. Circular dichroism (CD) spectra was employed to detect the α-helix and β-strand contents in HSA before and after the binding of CTSO. Based on the experimental results, the structure of the CTSO–HSA complex was calculated by docking CTSO to the proven site using molecular modeling. The study obtained comprehensive information on structure and thermodynamics, which is essential for understanding the bioaffinity, delivery process and pharmacological mechanism.     

Comparative sequence analysis and mutagenesis of Ethylene Forming Enzyme (EFE) 2-oxoglutarate/Fe(II)-dependent dioxygenase homologs

Background

Ethylene is one of the most used chemical monomers derived from non-renewable sources and we are investigating the possibility of producing it in yeast via the ethylene forming enzyme (EFE) from Pseudomonas syringae. To enable engineering strategies to improve the enzyme, it is necessary to identify the regions and amino acid residues involved in ethylene formation.

Results

We identified the open reading frame for the EFE homolog in Penicillium digitatum and also showed its capability of mediating ethylene production in yeast. The sequence of the EFE homologs from P.digitatum and P. syringae was compared to that of the non-functional EFE-homolog from Penicillium chrysogenum and ten amino acids were found to correlate with ethylene production. Several of these amino acid residues were found to be important for ethylene production via point mutations in P. syringae EFE. The EFE homolog from P. chrysogenum was engineered at 10 amino acid residues to mimic the P. syringae EFE, but this did not confer ethylene producing capability.Furthermore, we predicted the structure of EFE by homology to known structures of 2-oxoglutarate/Fe(II) dependent dioxygenases. Three of the amino acids correlating with ethylene production are located in the predicted 2-oxoglutarate binding domain. A protein domain specific for the EFE-class was shown to be essential for activity. Based on the structure and alanine substitutions, it is likely that amino acids (H189, D191 and H268) are responsible for binding the Fe(II) ligand.

Conclusion

We provide further insight into the structure and function of the ethylene forming (EFE) - subclass of 2-oxoglutarate/Fe(II) dependent dioxygenases. We conclude that residues in addition to the 10 identified positions implicated in ethylene production by sequence comparison, are important for determining ethylene formation. We also demonstrate the use of an alternative EFE gene. The data from this study will provide the basis for directed protein engineering to enhance the ethylene production capability and properties of EFE.

     

Influence of <Emphasis Type="Italic">gauche</Emphasis> effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies

The neutral oxime reactivator RS194B with a seven-membered ring has shown better efficacy towards the tabun-inhibited AChE than that of RS69N with a six-membered ring and RS41A with a five-membered ring. The difference in the efficacy of these reactivators has remained unexplored. We report here the origin of the difference of efficacy of these reactivators based on the conformational analysis, quantum chemical calculations and steered molecular dynamics (SMD) simulations. The conformational analysis using B3LYP/6-31G(d) level of theory revealed that RS41A and RS194B are more stable in gauche conformation due to the gauche effect (–N–C–C–N– bonds) whereas RS69N prefers anti-conformation. The SMD simulations show that RS194B retains in more stable gauche conformation inside the active gorge of AChE during different time intervals that experiences more hydrogen bonding, hydrophobic interactions with the catalytic anionic site (CAS) residues and weaker interactions with the peripheral anionic site (PAS) residues compared to RS41A and RS69N. In an effort to design an even superior reactivator, RS194B-S has been chosen with a subtle change in the geometry of RS194B by replacing the carbonyl oxygen with the sulfur atom. The newly designed reactivator RS194B-S can also be a promising candidate to reactivate tabun-inhibited AChE.     

Structure and dynamics of a free aquaporin (AQP1) by a coarse-grained Monte Carlo simulation

Structure and dynamics of a free aquaporin (AQP1) are studied by a coarse-grained Monte Carlo simulation as a function of temperature using a phenomenological potential with the input of a knowledge-based residue–residue interaction. Response of the radius of gyration (R _g) of the protein to the temperature (T) is found to be nonlinear: Decay of R _g at T ≤ T _c is followed by a continuous increase at T ≥ T _c before reaching its saturation. In thermo-responsive regime, the protein exhibits segmental globularization with the persistence of three regions along its sequence involving residues ¹M–²⁵V and ²⁵⁰V–²⁶⁹K toward the beginning and end segments with a narrow intermediate region around ¹⁵⁵A–¹⁶³D. A detail analysis of the structure factor S(q) shows a global random coil conformation at high temperatures with an effective dimension D _e ~ 1.74 and a globular structure (D _e ~ 3) at low temperatures. In thermo-responsive regime, the variation of S(q) with the wave vector q reveals a systematic redistribution of self-organizing residues (in globular and fibrous sections) that depends on the length scale and the temperature.     

Study of the Binding of Herbacetin to Bovine Serum Albumin by Fluorescence Spectroscopy

In this paper, the interaction between herbacetin and BSA was investigated by fluorescence and three-dimensional fluorescence spectroscopy under simulated physiological conditions. It was proved that the fluorescence quenching of BSA by herbacetin was mainly the result of the formation of a herbacetin–BSA complex. The modified Stern–Volmer quenching constant and the corresponding thermodynamic parameters ΔH ⁰, ΔG ⁰ and ΔS ⁰ were calculated at different temperatures. The results indicated that electrostatic interactions were the predominant intermolecular forces in stabilizing the complex. The distance r=3.23 nm between the donor (BSA) and acceptor (herbacetin) was obtained according to Förster’s nonradioactive energy transfer theory. The synchronous fluorescence and three-dimensional fluorescence spectra results showed that the hydrophobity of amino acid residues increased in the presence of herbacetin. These results revealed that the microenvironment and conformation of BSA changed during the binding reaction.     

Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics

Heat-shock proteins 70 (Hsp70s) are key molecular chaperones which assist in the folding and refolding/disaggregation of proteins. Hsp70s, which consist of a nucleotide-binding domain (NBD, consisting of NBD-I and NBD-II subdomains) and a substrate-binding domain [SBD, further split into the β-sheet (SBD-β) and α-helical (SBD-α) subdomains], occur in two major conformations having (a) a closed SBD, in which the SBD and NBD domains do not interact, (b) an open SBD, in which SBD-α interacts with NBD-I and SBD-β interacts with the top parts of NBD-I and NBD-II. In the SBD-closed conformation, SBD is bound to a substrate protein, with release occurring after transition to the open conformation. While the transition from the closed to the open conformation is triggered efficiently by binding of adenosine triphosphate (ATP) to the NBD, it also occurs, although less frequently, in the absence of ATP. The reverse transition occurs after ATP hydrolysis. Here, we report canonical and multiplexed replica exchange simulations of the conformational dynamics of Hsp70s using a coarse-grained molecular dynamics approach with the UNRES force field. The simulations were run in the following three modes: (i) with the two halves of the NBD unrestrained relative to each other, (ii) with the two halves of the NBD restrained in an "open" geometry as in the SBD-closed form of DnaK (2KHO), and (iii) the two halves of NBD restrained in a "closed" geometry as in known experimental structures of ATP-bound NBD forms of Hsp70. Open conformations, in which the SBD interacted strongly with the NBD, formed spontaneously during all simulations; the number of transitions was largest in simulations carried out with the "closed" NBD domain, and smallest in those carried out with the "open" NBD domain; this observation is in agreement with the experimentally-observed influence of ATP-binding on the transition of Hsp70's from the SBD-closed to the SBD-open form. Two kinds of open conformations were observed: one in which SBD-α interacts with NBD-I and SBD-β interacts with the top parts of NBD-I and NBD-II (as observed in the structures of nucleotide exchange factors), and another one in which this interaction pattern is swapped. A third type of motion, in which SBD-α binds to NBD without dissociating from SBD-β was also observed. It was found that the first stage of interdomain communication (approach of SBD-β, to NBD) is coupled with the rotation of the long axes of NBD-I and NBD-II towards each other. To the best of our knowledge, this is the first successful simulation of the full transition of an Hsp70 from the SBD-closed to the SBD-open conformation.     

Functional Analysis of Ribonucleotide Reductase from <Emphasis Type="Italic">Cordyceps militaris</Emphasis> Expressed in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Cordyceps militaris produces cordycepin (3′-deoxyadenosine), which has various activities, including anti-oxidant, anti-tumoral, anti-viral, and anti-inflammatory. Ribonucleotide reductase (RNR) seems to be a candidate to produce cordycepin in C. militaris because RNR catalyzes the reduction of nucleotides to 2′-deoxynucleotides, whose structures are similar to that of cordycepin. However, the role of RNR has not been confirmed yet. In this study, complementary DNAs (cDNAs) of C. militaris RNR (CmRNR) large and small subunits (CmR1 and CmR2) were cloned from C. militaris NBRC9787 to investigate the function of CmRNR for its cordycepin production. C. militaris NBRC9787 began to produce cordycepin when grown in a liquid surface culture in medium composed of glucose and yeast extract for 15 days. CmR1 cDNA and CmR2 cDNA were obtained from its genomic DNA and from total RNA extracted from its mycelia after cultivation for 21 days, respectively. Recombinant CmR1 and CmR2 were expressed individually in Escherichia coli and purified. Purified recombinant CmR1 and CmR2 showed RNR activity toward adenosine diphosphate (ADP) only when two subunits were mixed but only show the reduction of ADP to 2′-deoxyADP. These results indicate that the pathway from ADP to 3′deoxyADP via CmRNR does not exist in C. militaris and cordycepin production in C. militaris may be mediated by other enzymes.     

Modelling of proton and metal exchange in the alginate biopolymer

Acid–base behaviour of a commercial sodium alginate extracted from brown seaweed (Macrocystis pyrifera) has been investigated at different ionic strengths (0.1≤I/mol l^?1≤1.0) and in different supporting electrolytes (Et₄NI, NaCl, KCl, LiCl, NaCl+MgCl₂), with the aim of examining the influence of ionic medium on the proton-binding capacity and of quantifying the strength of interaction with light metal ions in the perspective of speciation studies in natural aqueous systems. Potentiometric ([H⁺]-glass electrode) and titration calorimetric data were expressed as a function of the dissociation degree (α) using different models (Henderson–Hasselbalch modified, Högfeldt three parameters and linear equations). The dependence on ionic strength of the protonation constants was taken into account by a modified specific interaction theory model. Differences among different media were explained in terms of the interaction between polyanion and metal cations of the supporting electrolytes. Quantitative information on the proton-binding capacity, together with the stabilities of different species formed, is reported. Protonation thermodynamic parameters, at α=0.5, are log K ^H=3.686±0.005, ΔG ⁰=?21.04±0.03 kJ mol^?1, ΔH ⁰=4.8±0.2 kJ mol^?1 and TΔS ⁰=35.7±0.3 kJ mol^?1, at infinite dilution. Protonation enthalpies indicate that the main contribution to proton binding arises from the entropy term. A strict correlation between ΔG and TΔS was found, TΔS=?9.5–1.73 ΔG. Results are reported in light of building up a chemical complexation model of general validity to explain the binding ability of naturally occurring polycarboxylate polymers and biopolymers. Speciation profiles of alginate in the presence of sodium and magnesium ions, naturally occurring cations in natural waters, are also reported.     

Production of ethanol from waste paper using immobilized yeasts

This work is aimed at a selection of yeast strains suitable for simultaneous saccharification and fermentation of waste paper. The waste paper, as a lignocellulosic material, represents an unconventional source for the production of ethanol which is a promising alternative fuel. The yeast strains Saccharomyces cerevisiae and Pichia kudriavzevii produced the highest amounts of ethanol at 30 °C and were also resistant at 40 °C during the first 92 h of fermentation. These two strains were immobilized by entrapment into poly(vinyl alcohol) hydrogel lens-shaped particles LentiKats^®. The immobilized S. cerevisiae was a better ethanol producer and retained higher metabolic activity in repeated batch fermentations than P. kudriavzevii. The immobilized S. cerevisiae was also suitable for a long-term storage, with 23% decrease in the ethanol production ability after 1-year storage of yeast cells.     

Secretory Expression and Characterization of Chinese <Emphasis Type="Italic">Narcissus</Emphasis> GNA-Like Lectin in <Emphasis Type="Italic">Pichia pastoris</Emphasis>

Narcissus tazetta lectin (NTL) is a GNA-like lectin, which has a wide potential application in medicine, agriculture, and glycobiology. In the present paper, the codon-optimized ntl gene was transformed into the yeast Pichia pastoris; SDS–PAGE gel and western blotting analysis revealed that the recombinant lectin was expressed successfully in Pichia yeast. The similarity between the recombinant NTL and the native NTL was confirmed by circular dichroism (CD) and hemagglutination assay further. In the 5-L scale fermentator, the protein yield was as high as 1.2 g/L after fermentation for 96 h. In addition, the effect of metal ions (K⁺, Mg²⁺, Ca²⁺, and Cu²⁺), acid, and alkaline on hemagglutinating activity of NTL was tested, which provided biochemical characterizations of the mannose-binding lectin from Chinese Narcissus.     

Effect of magnesium cations on the activity and stability of β-galactosidases

It was shown that the presence of magnesium cations in the reaction mixture increases, approximately twofold, the activity of bacterial Escherichia coli and yeast Kluyveromyces lactis β-galactosidases but does not affect the activity of bovine liver and fungous Penicillium canescens β-galactosidases. The catalytic constants for E. coli and yeast K. lactis β-galactosidases in the presence of 0.01 M and in the absence of Mg²⁺ cations were determined (490 and 220 s^?1 and 59.8 and 37.4 s^?1, respectively). It was shown that the Michaelis constants for these two enzymes are higher in the presence of Mg²⁺ cations, that the thermal stability of E. coli and K. Lactis β-galactosidases is higher in the presence of 0.01 M Mg²⁺, and that the effective rate constants of thermal inactivation of the enzymes are two-to eightfold lower, depending on conditions, in the presence of Mg²⁺ cations. The maximum stabilizing effect of magnesium cations was observed at weak alkaline pH values (7.5–8.5).     

Spectroscopic Studies on the Interaction of Vitamin C with Bovine Serum Albumin

The mechanism of binding of vitamin C (VC) with bovine serum albumin (BSA) was investigated by spectroscopic methods under simulated physiological conditions. VC effectively quenched the intrinsic fluorescence of BSA. The binding constants K _A, and the number of binding sites, n, and corresponding thermodynamic parameters ΔG ^Θ , ΔH ^Θ and ΔS ^Θ between VC and BSA were calculated at different temperatures. The primary binding pattern between VC and BSA was interpreted as being a hydrophobic interaction. The interaction between VC and BSA occurs through static quenching and the effect of VC on the conformation of BSA was also analyzed using synchronous fluorescence spectroscopy. The average binding distance, r, between the donor (BSA) and acceptor (VC) was determined based on Förster’s theory and was found to be 3.65 nm. The effects of common ions on the binding constant of VC-BSA were also examined.     

Thermochemistry of the Reaction of Solvated Sodium Ion Clusters with Thymine in the Gas Phase: An Example of the Reaction in Microcosmic Environment

The thermochemistry of the reaction of the microsolvated Na⁺ such as [Na(H₂O) _n ; n?=?1?6]⁺, [Na(NH₃) _n ; n?=?1?6]⁺ and [Na(H₂O) _n (NH₃) _m ; n?+?m?=?2?6]⁺ with thymine (Thy), as an example of a reaction in the microcosmic environment, have been studied in this work, theoretically. It was found that the increase of the number of solvent molecules in the structure of microsolvated Na⁺ is accompanied by the decrease of the standard enthalpy (\(\Delta H_{r}^{^\circ }\)) and Gibbs free (\(\Delta G_{r}^{^\circ }\)) energies of the reaction (Thy?+?[Na(X) _n ]⁺→Thy-Na(X) _n ⁺ ; X?=?solvent molecule). Also, the calculations showed that the electronic intermolecular interaction (?E_int) between the Thy and microslovated Na⁺ decreased with the increase of solvent molecules. For the interaction of the [Na(H₂O) _n ; n?=?4, 5 and 6]⁺ ions with the Thy, there was the probability of forming of the hydrogen bond between water molecules in the structure of solvated Na⁺ and the Thy. The gas phase infrared (IR) spectra of the complexes of the microsolvated Na⁺ with the Thy for different values of n were calculated and compared with each other to follow the change in the frequency of the stretching vibration of the interaction path between the C=O group of the Thy and Na (O…Na) with n. Using the calculated values of \(\Delta G_{r}^{^\circ }\) of the reactions, the mole fractions of the complexes of microsolvated Na⁺ ions with the Thy were calculated at different humidity.