The role of disaccharides for protein–protein interactions – a SANS study

ABSTRACT

The disaccharide trehalose has shown outstanding anti-aggregation properties for proteins, which are highly important for the possibility to treat neurodegenerative diseases, such as Alzheimer’s and Huntington’s disease. However, the role and mechanism of trehalose for such stabilising effects are still largely unknown, partly because a direct structural picture of how trehalose organises around proteins in an aqueous system is missing. Here we compare small-angle neutron scattering (SANS) data on myoglobin in aqueous solutions of either sucrose or trehalose, in order to investigate their effect on protein–protein interactions. We find that both trehalose and sucrose induces a well-defined protein–protein distance, which could explain why these inhibit protein–protein interactions and associated protein aggregation. It does not however explain the superior anti-aggregation effect of trehalose and suggests that the local solvent structures are highly important for explaining the protein stabilisation mechanism. In a broader perspective, these findings are important for understanding the role of sugars in biological stabilisation, and could provide a structural explanation for why trehalose is a promising candidate for the treatment of neurodegenerative and other protein aggregation related diseases.     

Reminiscence of 40-year research on nitrogen metabolism

This article summarizes my research over 40 years. The main theme of my work is nitrogen metabolism of amino acids, though later I focused on protein turnover in the cell. In the first years of my research work, I was busy dissecting the pathways involved in the metabolism of certain amino acids and their related enzymes. Then I became interested in the physiology and regulation of matabolism of these amino acids. For that, I used primary cultured hepatocytes, which contain many liver-specific enzymes. However, this play field was very rough around 1970 and hence I had to smooth them (differentiated) first. We discovered a specific growth factor (hepatocyte growth factor, HGF) in rat platelets. Exceptionally, I also worked on branched chain amino acids (valine, leucine and isoleucine). These amino acids are not efficiently metabolized in the liver, so I had to consider the physiology of extrahepatic tissues as well. Finally, I came across a huge protease complex, the proteasome. Whether these players, small amino acid metabolizing enzymes and the huge protease complex, danced well in harmony on my playground or not, I still do not know.     

Quantifying amino acid and protein substitution using Raman spectroscopy

Raman spectroscopy can be a powerful tool for the characterization of modified amino acids and proteins. In addition to the potential for quantitative results, it offers the advantage of not requiring any sample preparation. Modification of amines and thiols on amino acids and proteins are common reactions used for medical, biological, food, and agricultural purposes. We hypothesized that the Raman spectrum could be used to quantify the reactions and would be more informative than typical characterization techniques such as the ninhydrin test. To prove the hypothesis, the amino acids alanine, cysteine, and lysine were modified with ethyl vinyl sulfone (EVS) using a nucleophilic addition reaction known as the Michael addition and the product was characterized using Raman spectroscopy. The Raman spectroscopy results were compared with ultraviolet‐visible spectroscopy results based on ninhydrin analysis of the modified amino acids. The Raman spectroscopy analysis was able to discern site‐specific reactions on the amino acids and suggested that more amino acid moieties were substituted than predicted using the ninhydrin test alone. Substitution of the full protein ovalbumin with EVS showed similar results. The ninhydrin test showed the substitution of primary amines and thiols but could not detect substitution of secondary amines remaining after loss of the primary amine. Copyright © 2010 John Wiley & Sons, Ltd.     

Corrections to the cross-polarization dynamics in solids The effect of nonsecular terms of heteronuclear dipolar interaction on cross-relaxation

The dynamic theory of cross-polarization in solids is modified by considering the contribution of the nonsecular terms of the heteronuclear dipolar interaction Hamiltonian in the laboratory frame to cross-relaxation. This contribution is evaluated numerically and confirmed experimentally. It is shown that these nonsecular terms may play a considerable role in cross-relaxation in many systems, especially in those with fast internal molecular motion. The complication in the cross-polarization process is further revealed.     

The structural analysis of protein sequences based on the quasi-amino acids code

Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Genome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system (∑,+,*) is introduced, where ∑ is the set of 64 codons. According to the characteristics of (∑,+,*), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, ⊕,○x) is a field. Furthermore, the operational results display that the codon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of `the 64 codon assignments of mRNA to amino acids is probably completely wrong' proposed by Yang (2006 Progress in Modern Biomedicine 6 3).     

3D HCCH3-TOCSY for Resonance Assignment of Methyl-Containing Side Chains in C-Labeled Proteins

Two 3D experiments, (H)CCH₃-TOCSY and H(C)CH₃-TOCSY, are proposed for resonance assignment of methyl-containing amino acid side chains. After the initial proton–carbon INEPT step, during which either carbon or proton chemical shift labeling is achieved (t₁), the magnetization is spread along the amino acid side chains by a carbon spin lock. The chemical shifts of methyl carbons are labeled (t₂) during the following constant time interval. Finally the magnetization is transferred, in a reversed INEPT step, to methyl protons for detection (t₃). The proposed experiments are characterized by high digital resolution in the methyl carbon dimension (t_2max = 28.6 ms), optimum sensitivity due to the use of proton decoupling during the long constant time interval, and an optional removal of CH₂, or CH₂ and CH, resonances from the F₂F₃ planes. The building blocks used in these experiments can be implemented in a range of heteronuclear experiments focusing on methyl resonances in proteins. The techniques are illustrated using a ¹⁵N, ¹³C-labeled E93D mutant of Schizosacharomyces pombe phosphoglycerate mutase (23.7 kDa).     

Cysteine‐linked aromatic nitriles as UV resonance Raman probes of protein structure

Nitriles introduced into peptides and proteins can serve as useful vibrational spectroscopic probes, because the nitrile C ≡ N stretch is well isolated from backbone and sidechain vibrational bands. Aromatic nitriles offer large νC ≡ N absorption intensity in infrared spectra and resonance enhancement in Raman spectra with ultraviolet excitation. We report the ultraviolet resonance Raman spectra of cyanophenylalanine attached to cysteine, through linkage reactions that are applicable to cysteine residues in proteins. Excitation profiles are reported, and the νC ≡ N detection limit is estimated to be 5 µ m . The band position is sensitive to solvent polarity and especially to strong H‐bonding. The derivatization of mastoparan X peptide at introduced cysteine residues demonstrated the effectiveness of a cyanophenylcysteine probe in reporting the lowered environmental polarity when the peptide was incorporated into liposomes. For an asymmetrical cyanophenyl derivative, 2‐CBCys, the intensity ratio of asymmetric and symmetric ring modes, ν8_b and ν8_a, was found to respond to solvent polarity and not to H‐bonding. Copyright © 2012 John Wiley & Sons, Ltd.     

Development and application of 15N-tracer substances for measuring the whole-body protein turnover rates in the human,especially in neonates: a review

Our research group of the Children's Hospital of the University of Rostock (Rostock group) has long-time experience in ¹⁵N-labelling and in using yeast protein and its hydrolysates for tracer kinetic studies to evaluate parameters of the whole-body protein metabolism in premature infants. The particular advantage of applying an economically convenient, highly ¹⁵N-enriched, and completely labelled yeast protein for evaluating protein turnover rates is the fact that the ¹⁵N dose is spread among all proteinogenic amino acids. The absorption has been improved by hydrolysing [¹⁵N]yeast protein with thermitase into a mixture of amino acids, dipeptides and tripeptides so that faecal analysis becomes unnecessary when determining turnover rates. The review shows that, in contrast to the application of single ¹⁵N-labelled amino acids with resulting overestimation of protein turnover rates, the ¹⁵N-labelled yeast protein thermitase hydrolysate represents the amino acid metabolism more closely without causing amino acid imbalances. The ¹⁵N-labelled yeast protein thermitase hydrolysate leads to the estimation of reliable protein turnover rates, particularly in premature infants.     

Raman spectroscopic analysis of cataract lens: A compendious review

Age-related cataracts is a pressing health issue with the increase in elderly populations. This creates an imminent demand for the development of an early, noninvasive method of cataracts diagnosis. Early detection of cataracts will improve quality of life and may prevent morbidity associated with advanced cataracts and surgery. Raman spectrum of proteins provides characteristic information regarding molecular interactions of peptide residues. Hence Raman spectroscopy is a promising tool for the study of protein-related diseases, such as cataracts. We surveyed the literature to assess the use of Raman technology in the studies of human lens and animal models. These studies included analysis of amino acids (i.e., cysteine, tryptophan, and tyrosine, etc.) and secondary protein structures (i.e., α-helix and β-sheet) in various Raman profiles. Other studies used Raman spectroscopy to analyze and monitor the development of cataracts in lens. Technological advances in the instrumentation of laser Raman spectroscopy, including Fourier transform Raman spectroscopy, Raman microspectroscopy, and confocal Raman microspectroscopy have improved the performance of Raman spectroscopic analysis. How to take advantage of these developments and make it closer to reality using Raman spectroscopic methods to diagnose cataracts in a timely manner is a key challenge for the scientific community of Raman spectroscopy.     

Decrease of free amino acids in high-pressure treated cheese

Abstract

High-pressure treatment of cheese has been studied with a view to preserving fresh cheese [1], and also of developing a method of accelerating its ripening [2-7]. While these objectives can be reached, other changes also occur in cheese when high pressure is applied. One of those changes is the decrease of free amino acids (FAA) in cheese treated in pressures over 200-300MPa. In this paper we will try to summarize the results obtained by different research groups, as well as our own. These results have been published separately, but not previously tied together and explained.     

Thermosonication-induced structural changes and solution properties of mung bean protein

Mung bean protein is considered a highly nutritive food ingredient, but its solution properties are not well defined. In this study, suspensions of mung bean protein isolate (MPI, 10%, w/v) were subjected to high intensity ultrasound (20 kHz, 30% amplitude) at varied durations (5, 10, 20, and 30 min) with controlled temperatures (30, 50, and 70 °C) to determine the effects of thermosonication treatment on physical properties of the protein solution. Results showed that thermosonication treatment significantly reduced the particle size and free sulfhydryl content of MPI in a time-dependent manner. Ultrasound increased surface hydrophobicity, and the exposure of nonpolar groups led to the formation of soluble aggregates. Changes in secondary structure of MPI were minimal at 30 and 50 °C but were significant at 70 °C. The dissociation of native components followed by reaggregation into soluble particles following ultrasound treatment at 70 °C resulted in remarkable improvements of protein solubility (>2 fold), clarity, and stability of the MPI suspensions. The findings indicated that thermosonication could be a promising technology for the processing of mung bean protein beverage.     

Thermodiffusion as a close-to-interface effect that matters in non-isothermal (dis)orderly protein aggregations

The goal of this discussion letter is to argue how and why an inherent nanoscale thermodiffusion (Soret-type) effect can be relevant in (dis)orderly protein aggregation. We propose a model in which the aggregation of proteins, in the presence of temperature gradient, is described in terms of Smoluchowski dynamics in the phase space of nuclei sizes. The Soret coefficient of the aggregation is proportional to the variations of the aggregation free energy over temperature. The free energy is related to the (interface) boundary condition of the system. When boundary condition is of equilibrium Gibbs–Thomson type, with a well-stated surface tension of the nucleus, to the system can be assigned a negative Soret effect. On the contrary, when a non-equilibrium perturbing (salting-out) term enters the boundary condition, a positive Soret effect may manifest. A zero-value Soret regime is expected to occur in between, yielding very soft (“fragile”) non-Kossel protein-type crystals.     

Mass spectrometric study of the decomposition pathways of canonical amino acids and α‐lactones in the gas phase

The dissociation pathways of a gas‐phase amino acid with a canonical (non‐zwitterionic) α‐amino acid moiety are studied by using mass spectrometry. Investigation of the canonical amino acid moiety is possible because the ionized amino acid, a sulfonated phenylalanine, has a charge center that is separated from the amino acid, and dissociation occurs by charge‐remote fragmentation. The amino acid is found to dissociate only by loss of NH₃ upon collision‐induced dissociation to form a substituted α‐lactone. The dissociation is consistent with what has been observed previously upon pyrolysis of other α‐substituted carboxylic acids. Decarboxylation, which has also been reported previously for amino acid pyrolysis, is not observed, likely because the product would be a high‐energy, ammonium ylide. The resulting α‐lactone is found to undergo dissociation by decarbonylation to give an aldehyde, and by loss of CO₂. Decarboxylation is calculated to occur through a transition state involving hydride shift coupled with lactone ring‐opening. The transition state is found to be stabilized by the negative charge, and therefore, decarboxylation is more favorable for anions. The results show that remote ionic groups can be used as mostly inert charge carriers to enable mass spectrometry to be used to investigate the gas‐phase physical and chemical properties of different types of functional groups, including amino acids. Copyright © 2015 John Wiley & Sons, Ltd.     

The Molecular Design of Fluorescent Sensors for Ionic Analytes

Molecular fluorescent sensors can be synthesized by covalently linking a photoactive fragment (e.g., anthracene) to a receptor subunit displaying affinity toward the envisaged substrate. The electron transfer process is the privileged signal transduction mechanism: redox active substrates (e.g., transition metals) typically release/uptake an electron to/from the proximate photoexcited fluorophore, the recognition being signaled through fluorescence quenching; redox inactive substrates (d⁰ and d¹⁰ metals, H⁺) deactivate an existing quenching relay (e.g., a tertiary nitrogen atom close to the fluorophore) and their recognition is signaled through fluorescence enhancement. An-ionic substrates can be conveniently recognized on the basis of the metal–ligand interaction: polyamine receptors containing the photophysically inactive Zn^IIion bind the carboxylate group. In the case of amino acids, , selectivity is improved when the receptor platform bears additional groups capable to interact specifically with the R substituent. If R is capable of transferring an electron to the nearby photoexcited fluorophore, the recognition is signaled through fluorescence quenching.     

The role of hydrogen in negative bias temperature instability of pMOSFET

The NBTI degradation phenomenon and the role of hydrogen during NBT stress are presented in this paper. It is found that PBT stress can recover a fraction of V_th shift induced by NBTI. However, this recovery is unstable. The original degradation reappears soon after reapplication of the NBT stress condition. Hydrogen-related species play a key role during a device's NBT degradation. Experimental results show that the diffusion species are neutral, they repassivate Si dangling bond which is independent of the gate voltage polarity. In addition to the diffusion towards gate oxide, hydrogen diffusion to Si-substrate must be taken into account for it also has important influence on device degradation during NBT stress.     

基于氨基酸位置特异性的蛋白质Loop区结构预测改进方法

蛋白质loop区的结构预测是理解蛋白质功能的重要一环,而长loop区的结构预测至今还是生物信息学中的难题.目前己经出现了多种loop结构的算法,其中LEAP是预测精度最高的算法之一,但它在长loop区初始主链构象采样上仍有较大的改进余地.本文中我们将蛋白质二级结构预测算法SPINE X与LEAP算法结合起来,构建了新的主链扭转角分布图(拉氏图),在主链初始构象采样中引入氨基酸在蛋白序列中的位置特异性信息,使得初始构象的采样更具针对性,对取自CASP10单链蛋白的loop测试集的分析表明,对长度为10,11,12个氨基酸的长loop区,改进后算法都比原始LEAP算法的预测精度有显著提升.这种引入氨基酸位置特异性从而提高预测精度的思路有望进一步推广至loop结构预测的其他算法.     

Fourier transform infrared spectroscopy to detect thermal degradation of vegetable and chrome-tanned leather

Abstract

The present experimental study determined the thermal degradation stages for vegetable and chrome-tanned leathers (goat and sheep) at 90, 100, and 130?°C by using Fourier transform infrared spectroscopy (FTIR) and differential thermal analysis. Infrared spectra revealed that a temperature of 90?°C affected the adsorbed water band at 3400?cm^?1. Moreover, this temperature slightly reduced the vibrations of amide II and amid III (1340?cm^?1) confirming the preliminary decomposition of protein folds, but it is worth noting that the aliphatic side chains remained stable at this stage of aging. At 100?°C, there was a sharp rupturing in the phenolic-OH bond and side-by-side N–H vibrations decreased dramatically. The peak decomposition occurred at 130?°C, where the amide I and amide III intensities significantly increased, which can be considered indicative of protein unfolding. Those changes are substantiation of protein denaturation. Thermal analysis demonstrated that thermal aging significantly reduced the required temperature for the process of oxidation. The oxidation occurred at 217?°C in goat sample aged at 90?°C. Nevertheless, the reference sample suffered from oxidation at about 220?°C, while with increasing aging temperatures (at 100 and 130?°C), endothermic reactions were observed. Such reactions are usually associated with protein denaturation.     

The role of secondary structure in protein structure selection

The presence of highly regular secondary structure motifs in protein structure is a fascinating area of study. The secondary structures play important roles in protein structure and protein folding. We investigate the folding properties of protein by introducing the effect of secondary structure elements. We observed the emergence of several structures with both large average energy gap and high designability. The dynamic study indicates that these structures are more foldable than those without the effect of secondary structures.     

Simultaneous Identification and Quantitative Determination of Amino Acids in Mixture by NMR Spectroscopy Using Chemometric Resolution

Nuclear magnetic resonance (NMR) spectroscopy receives increasing interest in biological and metabolomic studies. It is still, however, a great challenge to analyze the NMR spectra of multicomponent samples, containing overlapping responses of the compositions. In this work, nonnegative independent component analysis (nonnegative ICA) and immune algorithm (IA) were employed for simultaneous identification and quantitative determination of three amino acids in mixture samples from measured multicomponent NMR signals. Results show that the correlation coefficients (R) between the extracted and measured spectra are higher than 0.97 and that those between the calculated relative contents and experimental ones are higher than 0.99. The method may provide an alternative technique for analyzing multicomponent samples like biofluids by using NMR spectroscopy.     

Influence of the Aggregation of Homo-N-Mer Cyanine Dyes on the Nucleic Acids Detection Sensitivity

Novel benzothiazolopyridinium homo-n-mer cyanine dyes are proposed for nucleic acid fluorescent detection. Dependence of the sensitivity of detection in solution from the dye molecules/DNA base pairs ratio was studied. It was shown that the presence of the dye excess could significantly decrease the detection limit. We believe this could be explained by the formation of the dye aggregates on DNA surface.