Differential dehydration effects on globular proteins and intrinsically disordered proteins during film formation

Analytical approaches for assessing protein structure in protein-rich food: A comprehensive review

This review focuses on changes in nutrition and functional properties of protein-rich foods, primarily attributed to alterations in protein structures. We provide a comprehensive overview and comparison of commonly used laboratory methods for protein structure identification, aiming to offer readers a convenient understanding of these techniques. The review covers a range of detection technologies employed in food protein analysis and conducts an extensive comparison to identify the most suitable method for various proteins. While these techniques offer distinct advantages for protein structure determination, the inherent complexity of food matrices presents ongoing challenges. Further research is necessary to develop and enhance more robust detection methods to improve accuracy in protein conformation and structure analysis.

Probing the structure of water in individual living cells

Water regulates or even governs a wide range of biological processes. Despite its fundamental importance, surprisingly little is known about the structure of intracellular water. Herein we employ a Raman micro-spectroscopy technique to uncover the composition, abundance and vibrational spectra of intracellular water in individual living cells. In three different cell types, we show a small but consistent population (~3%) of non-bulk-like water. It exhibits a weakened hydrogen-bonded network and a more disordered tetrahedral structure. We attribute this population to biointerfacial water located in the vicinity of biomolecules. Moreover, our whole-cell modeling suggests that all soluble (globular) proteins inside cells are surrounded by, on average, one full molecular layer (about 2.6 Angstrom) of biointerfacial water. Furthermore, relative invariance of biointerfacial water is observed among different single cells. Overall, our study not only opens up experimental possibilities of interrogating water structure in vivo but also provides insights into water in life.

DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources

Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically-disordered proteins.

Processing Characteristics of Freeze-Dried Pork Powder for Meat Emulsion Gel

The processing characteristics of freeze-dried pork powder as raw meat for comminuted meat products were compared with those of freeze-thawed pork. The tertiary structural properties, oxidation, and solubility of proteins in the freeze-dried pork powder were investigated. In addition, the properties of the emulsion gels manufactured with freeze-dried pork powder (GFD) and freeze-thawed pork (GFT) at 1.5% and 2.0% NaCl were evaluated. The surface hydrophobicity and intrinsic tryptophan fluorescence intensity of myofibrillar proteins between the freeze-dried pork powder and freeze-thawed pork were similar. However, freeze-dried pork powder had higher carbonyl compounds and lower solubility of sarcoplasmic and myofibrillar proteins than freeze-thawed pork (p<0.05). GFD had higher cooking loss than GFT in 2.0% NaCl, and lower hardness and a* value of GFD were observed regardless of NaCl level (p<0.05). Moreover, GFD had higher malondialdehyde content than GFT at the two NaCl concentrations (p<0.05). Therefore, our study demonstrated that freeze-dried pork powder has lower functional properties than freeze-thawed pork as raw meat for comminuted meat products.

Moisture Content of Bacterial Cells Determines Thermal Resistance of Salmonella enterica Serotype Enteritidis PT 30

Salmonella spp. are resilient bacterial pathogens in low-moisture foods. There has been a general lack of understanding of critical factors contributing to the enhanced thermal tolerance of Salmonella spp. in dry environments. In this study, we hypothesized that the moisture content (X_W ) of bacterial cells is a critical intrinsic factor influencing the resistance of Salmonella spp. to thermal inactivation. We selected Salmonella enterica serotype Enteritidis PT 30 to test this hypothesis. We first produced viable freeze-dried S. Enteritidis PT 30, conditioned the bacterial cells to different X_W s (7.7, 9.2, 12.4, and 15.7 g water/100 g dry solids), and determined the thermal inactivation kinetics of those cells at 80°C. The results show that the D-value (the time required to achieve a 1-log reduction) decreased exponentially with increasing X_W We further measured the water activities (a_w) of the freeze-dried S. Enteritidis PT 30 as influenced by temperatures between 20 and 80°C. By using those data, we estimated the X_W of S. Enteritidis PT 30 from the published papers that related the D-values of the same bacterial strain at 80°C with the a_w of five different food and silicon dioxide matrices. We discovered that the logarithmic D-values of S. Enteritidis PT 30 in all those matrices also decreased linearly with increasing X_W of the bacterial cells. The findings suggest that the amount of moisture in S. Enteritidis PT 30 is a determining factor of its ability to resist thermal inactivation. Our results may help future research into fundamental mechanisms for thermal inactivation of bacterial pathogens in dry environments.IMPORTANCE This study established a logarithmic relationship between the thermal death time (D-value) of S. Enteritidis PT 30 and the moisture content (X_W ) of the bacterial cells by conducting thermal inactivation tests on freeze-dried S Enteritidis PT 30. We further verified this relationship using literature data for S. Enteritidis PT 30 in five low-moisture matrices. The findings suggest that the X_W of S. Enteritidis PT 30, which is rapidly adjusted by microenvironmental a_w, or relative humidity, during heat treatments, is the key intrinsic factor determining the thermal resistance of the bacterium. The quantitative relationships reported in this study may help guide future designs of industrial thermal processes for the control of S. Enteritidis PT 30 or other Salmonella strains in low-moisture foods. Our findings highlight a need for further fundamental investigation into the role of water in protein denaturation and the accumulation of compatible solutes during thermal inactivation of bacterial pathogens in dry environments.

Proximate analysis and fatty acid of Corbicula fluminea (C. fluminea) tissue in Kelantan, Malaysia

Corbicula fluminea (C. fluminea) is one of the mollusc species commonly eaten as a popular snack in Kelantan, Malaysia. This species contributes to the local economic activity. However, the handling process of C. fluminea at different processing stages (raw, smoke and selling stages) is believed to have affected the nutritional value in their soft tissue. Hence, this study aims to provide information about the chemical content (moisture, crude fat, ash, crude protein and carbohydrate) of C. fluminea and fatty acid of smoked C. fluminea at different processing stages. Samples were collected from Pasir Mas and Tumpat, Kelantan, Malaysia. The chemical content analysis was carried out based on the Association of Official Analytical Chemists (AOAC) standard procedures. The results have indicated that moisture (80.93 ± 0.37%) and crude fat (10.82 ± 0.21%) in C. fluminea were significantly higher (p < 0.05) at the raw stage. On the other hand, the ash (2.09 ± 0.03%) and crude protein (9.45 ± 0.42%) were significantly higher (p < 0.05) at smoked stage. Meanwhile, carbohydrate (3.39 ± 0.49%) was significantly higher (p < 0.05) at the selling stage. The fatty acid percentage of smoked C. fluminea indicates that the total saturated fatty acid (SFA) content was higher than the total of both monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA). The obtained data indicates that the composition percentage of omega-6 (n-6) in PUFA is significantly greater than omega-3 (n-3). The n-6/n-3 ratio of smoked C. fluminea is 2.95-3.11 and therefore can be considered as a healthy diet. The findings of this study can improve consumers' health through sufficient nutrient consumption and also provide economic benefits by increasing sellers' income in Kelantan.

Structural Characterization of Individual α-Synuclein Oligomers Formed at Different Stages of Protein Aggregation by Atomic Force Microscopy-Infrared Spectroscopy

Aberrant α-synuclein aggregation is strongly associated with the onset and development of Parkinson's disease (PD). Therefore, characterizing the structure of toxic intermediate oligomers plays an essential role in better understanding their neurotoxicity. Using atomic force microscopy-infrared spectroscopy (AFM-IR), we were able to reveal the structure of α-synuclein oligomers present at different stages of protein aggregation and establish a relationship between morphology and structure on the single oligomer level. We were also able to probe the secondary structure evolution of individual oligomers. Moreover, the IR spectra of individual oligomers suggest structural rearrangement that is necessary for oligomers with an antiparallel β-sheet to propagate into fibrils that have a parallel-β-sheet secondary structure. Detailed investigation of structural organization of α-synuclein oligomers reported in this study is critically important to understand the toxicity of these protein species. We also anticipate that this work will help developing approaches for oligomer detection and consequently presymptomatic diagnostic of PD.

Conformational Evolution of Molecular Signatures during Amyloidogenic Protein Aggregation

Aggregation is a pathological hallmark of proteinopathies such as Alzheimer's disease and results in the deposition of β-sheet-rich amyloidogenic protein aggregates. Such proteinopathies can be classified by the identity of one or more aggregated proteins, with recent evidence also suggesting that distinct molecular conformers (strains) of the same protein can be observed in different diseases, as well is in subtypes of the same disease. Therefore, methods for the quantification of pathological changes in protein conformation are central to understanding and treating proteinopathies. In this work, the evolution of Raman spectroscopic molecular signatures of three conformationally distinct proteins, bovine serum albumin (α-helical-rich), β2-microglobulin (β-sheet-rich), and tau (natively disordered), was assessed during aggregation into oligomers and fibrils. The morphological evolution was tracked using atomic force microscopy and corresponding conformational changes were assessed by their Raman signatures acquired in both wet and dried conditions. A deconvolution model was developed which allowed us to quantify the conformation of the nonregular protein tau, as well as for the oligomeric and fibrillar species of each of the proteins. Principle component analysis of the fingerprint region allowed further identification of the distinguishing spectral features and unsupervised distinction. While an increase in β-sheet is seen on aggregation, crucially, however, each protein also retains a significant proportion of its native monomeric structure after aggregation. Thus, spectral analysis of each aggregated species, oligomeric, as well as fibrillar, for each protein resulted in a unique and quantitative "conformational fingerprint". This approach allowed us to provide the first differential detection of both oligomers and fibrils of the three different amyloidogenic proteins, including tau, whose aggregates have never before been interrogated using spontaneous Raman spectroscopy. Quantitative "conformational fingerprinting" by Raman spectroscopy thus demonstrates its huge potential and utility in understanding proteinopathic disease mechanisms and for providing strain-specific early diagnostic markers and targets for disease-modifying therapies.

Spectral and Photochemical Properties of Rhodobacter sphaeroides R-26 Reaction Center Films in Vacuum

Using absorption spectroscopy in the visible/near-IR and mid-IR regions, spectral and photochemical properties of isolated reaction centers (RCs) from Rhodobacter sphaeroides R-26 were studied in dried films on the inorganic support surface (quartz or CaF₂ plates) under vacuum dehydration conditions (10^-2 or 7·10^-5 mm Hg). Three detergents, N,N-dimethyldodecylamine N-oxide (LDAO), Triton X-100 (TX100), and n-dodecyl-β-D-maltoside (DM), were tested for their ability to stabilize the RC-detergent complexes in the vacuum-dried state. It was shown that in the presence of LDAO, RC complexes underwent destruction in vacuum. In contrast, DM provided an environment that minimized irreversible disruptive changes in the RCs in vacuum. The effects of vacuum dehydration on the RC-DM films included a small increase in the content of α-helices in the RC protein, a short-wavelength reversible shift in the optical transitions of pigments, and minor changes in the electronic structure of the P⁺ dimer. The films retained their photochemical activity upon excitation with high-intensity light (200 mW/cm²). TX100 also helped to maintain spectral and functional properties of the RCs in vacuum; however, in this case, the stabilizing effect was less pronounced than in the presence of DM, especially, at high detergent concentrations. The results are discussed within the framework of a model suggesting that the detergent-protein interactions and the properties of detergent micelles play a dominant role in maintaining the structure of the RCs upon vacuum dehydration of the RC complexes. The obtained data can be useful for developing hybrid photoconverting systems based on bacterial RCs.

Protecting Enzymes from Stress-Induced Inactivation

The pharmaceutical and chemical industries depend on additives to protect enzymes and other proteins against stresses that accompany their manufacture, transport, and storage. Common stresses include vacuum-drying, freeze-thawing, and freeze-drying. The additives include sugars, compatible osmolytes, amino acids, synthetic polymers, and both globular and disordered proteins. Scores of studies have been published on protection, but the data have never been analyzed systematically. To spur efforts to understand the sources of protection and ultimately develop more effective formulations, we review ideas about the mechanisms of protection, survey the literature searching for patterns of protection, and then compare the ideas to the data.

Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.

Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases

Structural information of biological macromolecules is crucial and necessary to deliver predictions about the effects of mutations-whether polymorphic or deleterious (i.e., disease causing), wherein, thermodynamic parameters, namely, folding and binding free energies potentially serve as effective biomarkers. It may be emphasized that the effect of a mutation depends on various factors, including the type of protein (globular, membrane or intrinsically disordered protein) and the structural context in which it occurs. Such information may positively aid drug-design. Furthermore, due to the intrinsic plasticity of proteins, even mutations involving radical change of the structural and physico⁻chemical properties of the amino acids (native vs. mutant) can still have minimal effects on protein thermodynamics. However, if a mutation causes significant perturbation by either folding or binding free energies, it is quite likely to be deleterious. Mitigating such effects is a promising alternative to the traditional approaches of designing inhibitors. This can be done by structure-based in silico screening of small molecules for which binding to the dysfunctional protein restores its wild type thermodynamics. In this review we emphasize the effects of mutations on two important biophysical properties, stability and binding affinity, and how structures can be used for structure-based drug design to mitigate the effects of disease-causing variants on the above biophysical properties.

The ionic liquid [C4mpy][Tf2N] induces bound-like structure in the intrinsically disordered protein FlgM

The ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide is shown to induce secondary structure similar to a bioactive state in the protein FlgM.

CDtoolX, a downloadable software package for processing and analyses of circular dichroism spectroscopic data

Circular dichroism (CD) spectroscopy is a highly used method for the examination and characterization of proteins, including, amongst other features, their secondary and tertiary structures, thermal stability, comparisons of wildtype and mutant proteins, and monitoring the binding of small molecules, folding/unfolding pathways, and formation of macromolecular complexes. This article describes CDtoolX, a new, user-friendly, free-to-download-and-use software program that enables processing, displaying, archiving, calibrating, comparisons, and analyses of CD and synchrotron radiation circular dichroism spectroscopic data.

Disorder-to-order transitions in the molten globule-like Golgi Reassembly and Stacking Protein

BACKGROUND

Golgi Reassembly and Stacking Proteins (GRASPs) are widely spread among eukaryotic cells (except plants) and are considered as key components in both the stacking of the Golgi cisternae and its lateral connection. Furthermore, GRASPs were also proved essential in the unconventional secretion pathway of several proteins, even though the mechanism remains obscure. It was previously observed that the GRASP homologue in Cryptococcus neoformans has a molten globule-like behavior in solution.

METHODS

We used circular dichroism, synchrotron radiation circular dichroism and steady-state as well as time-resolved fluorescence.

RESULTS

We report the disorder-to-order transition propensities for a native molten globule-like protein in the presence of different mimetics of cell conditions. Changes in the dielectric constant (such as those experienced close to the membrane surface) seem to be the major factor in inducing multiple disorder-to-order transitions in GRASP, which shows very distinct behavior when in conditions that mimic the vicinity of the membrane surface as compared to those found when free in solution. Other folding factors such as molecular crowding, counter ions, pH and phosphorylation exhibit lower or no effect on GRASP secondary structure and/or stability.

GENERAL SIGNIFICANCE

To the best of our knowledge, this is the first study focusing on understanding the disorder-to-order transitions of a molten globule structure without the need of any mild denaturing condition. A model is also introduced aiming at describing how the cell could manipulate the GRASP sensitivity to changes in the dielectric constant during different cell-cycle periods.

Going deep into protein secondary structure with synchrotron radiation circular dichroism spectroscopy

Circular dichroism (CD) spectroscopy is a fast, powerful, well-established, and widely used analytical technique in the biophysical and structural biology community to study protein secondary structure and to track changes in protein conformation in different environments. The use of the intense light of a synchrotron beam as the light source for collecting CD measurements has emerged as an enhanced method, known as synchrotron radiation circular dichroism (SRCD) spectroscopy, that has several advantages over the conventional CD method, including a significant spectral range extension for data collection, deeper access to the lower limit (cut-off) of conventional CD spectroscopy, an improved signal-to-noise ratio to increase accuracy in the measurements, and the possibility to collect measurements in highly absorbing solutions. In this review, we discuss different applications of the SRCD technique by researchers from Latin America. In this context, we specifically look at the use of this method for examining the secondary structure and conformational behavior of proteins belonging to the four main classes of the hierarchical protein domain classification CATH (Class, Architecture, Topology, Homology) database, focusing on the advantages and improvements associated with SRCD spectroscopy in terms of characterizing proteins composed of different structural elements.