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Recent advancements in artificial intelligence (AI) have accelerated the prediction of unknown protein structures. However, accurately predicting the three‐dimensional (3D) structures of fusion proteins remains a difficult task because the current AI‐based protein structure predictions are focused on the WT proteins rather than on the newly fused proteins in nature. Following the central dogma of biology, fusion proteins are translated from fusion transcripts, which are made by transcribing the fusion genes between two different loci through the chromosomal rearrangements in cancer. Accurately predicting the 3D structures of fusion proteins is important for understanding the functional roles and mechanisms of action of new chimeric proteins. However, predicting their 3D structure using a template‐based model is challenging because known template structures are often unavailable in databases. Deep learning (DL) models that utilize multi‐level protein information have revolutionized the prediction of protein 3D structures. In this review paper, we highlighted the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using DL models. We aim to explore both the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr‐Rosetta and D‐I‐TASSER for modelling the 3D structures. Highlights: This review provides the overall pipeline and landscape of the prediction of the 3D structure of fusion protein.This review provides the factors that should be considered in predicting the 3D structures of fusion proteins using AI approaches in each step.This review highlights the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using deep learning models.This review explores the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta, and D-I-TASSER to model 3D structures. [ABSTRACT FROM AUTHOR]

Summary: Peanuts produce millions of tons of high‐protein peanut meal (after oil extraction) annually that can be used for food. Peanut protein, as a plant‐based protein, is a great alternative to animal protein to address protein deficiencies and rising health problems in the world. It has a high nutritional value, while the globular structure results in poor functional properties, limiting its application. Better functional properties can be obtained through processing and modification. This paper elaborates the nutritional and functional properties of peanut protein and highlights the application of peanut protein in food industry in recent years. Applications for peanut protein include meat and milk substitutes, edible films, nanoparticles, and some new technologies such as electrostatic spinning and three‐dimensional (3D) printing in recent years. This paper could improve people's understanding of the molecular structure of peanut protein and the physicochemical properties associated with the structure changes during processing. It could also contribute to better utilisation of peanut protein, providing more varieties of peanut protein products for the food industry. [ABSTRACT FROM AUTHOR]

Protein structure prediction (PSP) is the prediction of the three‐dimensional (3D) folding of a protein (its tertiary structure) starting from its amino acid sequence (its primary structure). The state of the art in PSP is achieved by deep learning pipelines that require several input features extracted from amino acid sequences. It has been demonstrated that features that grasp the relative orientation of amino acids positively impact the prediction accuracy of the 3D coordinates of atoms in the protein backbone. In this paper, we demonstrate the relevance of geometric algebra (GA) in instantiating orientational features for PSP problems. We do so by proposing two novel GA‐based metrics which contain information on relative orientations of amino acid residues. We then employ these metrics as additional input features to a graph transformer (GT) architecture to aid the prediction of the 3D coordinates of a protein, and compare them to classical angle‐based metrics. We show how our GA features yield comparable results to angle maps in terms of accuracy of the predicted coordinates. This is despite being constructed from less initial information about the protein backbone. The features are also fewer and more informative and can be (i) closely associated to protein secondary structures and (ii) more easily predicted compared to angle maps. We hence deduce that GA can be employed as a tool to simplify the modeling of protein structures and pack orientational information in a more natural and meaningful way. [ABSTRACT FROM AUTHOR]

Summary: The advancement of the modern food industry has prompted a shift away from traditional protein extraction methods due to their inherent limitations. As a result, there is a growing interest in exploring alternative methods for protein extraction and modification such as ultrasonic (US) treatment. This shift towards more sustainable and efficient protein extraction methods is a key research focus in obtaining safe proteins in an environmentally friendly manner. Furthermore, enhancing the functional properties of proteins through modification can expand their application. This paper reviews recent research progress and applications of US treatment on protein extraction and modification as well as the impact on protein structure and functional properties. In addition, the latest applications of ultrasound‐modified‐proteins, including nano‐proteins, 3D printing and interactions between proteins and other food components, are reviewed. This review may provide some inspiration for the potential application of US technologies in food fields. [ABSTRACT FROM AUTHOR]

Vibrational optical activity (VOA) consisting of infrared vibrational circular dichroism (VCD) and vibrational Raman optical activity (ROA) was predicted, discovered, and confirmed between 1971 and 1975. My path to VOA was mentored by three pioneers of chirality and vibrational spectroscopy: Professors Albert Moscowitz, Warner L. Peticolas, and Philip J. Stephens, and while they are no longer alive today, the Chirality Medal, my award address, and this paper are dedicated to each of them. Since the discovery of VOA, a number of key advances have made possible the current era of widespread applications. The principal instrumental advances were Fourier‐transform VCD (FT‐VCD) and multichannel charge coupled detector (CCD) ROA. Computational advances include the first complete quantum chemistry formulation of VCD leading to the magnetic field perturbation (MFP) and the nuclear velocity perturbation (NVP) theories. The strength of VOA is the comparison between measured and calculated spectra that enables the determination of absolute configuration and solution‐state conformations. More recently, VCD has uncovered supramolecular chirality in amyloid fibrils and ROA to high‐order protein structure. Future challenges for VOA include describing the effects of weak intermolecular interactions, transfer of chirality, solvent effects, supramolecular chirality, and the generation of nuclear velocity electron current density. [ABSTRACT FROM AUTHOR]

BL19U1, an energy‐tunable protein complex crystallography beamline at the Shanghai Synchrotron Radiation Facility, has emerged as one of the most productive MX beamlines since opening to the public in July 2015. As of October 2023, it has contributed to over 2000 protein structures deposited in the Protein Data Bank (PDB), resulting in the publication of more than 1000 scientific papers. In response to increasing interest in structure‐based drug design utilizing X‐ray crystallography for fragment library screening, enhancements have been implemented in both hardware and data collection systems on the beamline to optimize efficiency. Hardware upgrades include the transition from MD2 to MD2S for the diffractometer, alongside the installation of a humidity controller featuring a rapid nozzle exchanger. This allows users to opt for either low‐temperature or room‐temperature data collection modes. The control system has been upgraded from Blu‐Ice to MXCuBE3, which supports website‐mode data collection, providing enhanced compatibility and easy expansion with new features. An automated data processing pipeline has also been developed to offer users real‐time feedback on data quality. [ABSTRACT FROM AUTHOR]

Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X‐ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X‐ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X‐ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66000 spots. We then discuss the open source extensible U‐Net‐based spotfinder Bragg Spot Finder (BSF), with image pre‐processing, a U‐Net segmentation backbone, and post‐processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages (Dozor and DIALS), demonstrating that this is an appropriate framework to support future extensions and improvements. [ABSTRACT FROM AUTHOR]

Bismuth is a xenobiotic metal with a high affinity to sulfur that is used in a variety of therapeutic applications. Bi(III) induces the cysteine-rich metallothionein (MT), a protein known to form two-domain cluster structures with certain metals such as Zn(II), Cd(II), or Cu(I). The binding of Bi(III) to MTs has been previously studied, but there are conflicting reports on the stoichiometry and binding pathway, which appear to be highly dependent on pH and initial metal-loading status of the MT. Additionally, domain specificity has not been thoroughly investigated. In this paper, ESI-MS was used to determine the binding constants of [Bi(EDTA)]-binding to apo-MT1a and its individual aMT fragment. The results were compared to previous experiments using ßMT1a and βαMT3. Domain specificity was investigated using proteolysis methods and the initial cooperatively formed Bi2MT was found to bind to cysteines that spanned across the traditional metal binding domain regions. Titrations of [Bi-(EDTA)]-into Zn7MT were performed and were found to result in a maximum stoichiometry of Bi7MT, contrasting the Bi6MT formed when [Bi(EDTA)] was added to apo-MT. These results show that the initial structure of the apo-MT determines the stoichiometry of new incoming metals and explains the previously observed differences in stoichiometry. [ABSTRACT FROM AUTHOR]

Synchrotron protein crystallography (PX) is one of the most powerful and dominant tools for determining the three‐dimensional structures of biological macromolecules. At the National Synchrotron Radiation Research Center, TLS 13B1 is the first dedicated energy‐tunable and highly automated PX beamline for efficiently solving de novo protein structures in Taiwan and has been open for users since September 2005. With remote access, user support services, and annual PX training courses over 17 years, the number of user groups at TLS 13B1 has grown from 11 to 139. In total, 1,429 projects were supported, and 2090 experiments were hosted during 67,846 hr of beamtime. This paper describes the photon source, beamline components, experimental station equipment, beamline software, beamline application process, and results from our users. [ABSTRACT FROM AUTHOR]

Vitamin B12 (cobalamin, Cbl) is required as a cofactor by two human enzymes, 5‐methyltetrahydrofolate‐homocysteine methyltransferase (MTR) and methylmalonyl‐CoA mutase (MMUT). Within the body, a vast array of transporters, enzymes and chaperones are required for the generation and delivery of these cofactor forms. How they perform these functions is dictated by the structure and interactions of the proteins involved, the molecular bases of which are only now being elucidated. In this review, we highlight recent insights into human Cbl metabolism and address open questions in the field by employing a protein structure and interactome based perspective. We discuss how three very similar proteins—haptocorrin, intrinsic factor and transcobalamin—exploit slight structural differences and unique ligand receptor interactions to effect selective Cbl absorption and internalisation. We describe recent advances in the understanding of how endocytosed Cbl is transported across the lysosomal membrane and the implications of the recently solved ABCD4 structure. We detail how MMACHC and MMADHC cooperate to modify and target cytosolic Cbl to the client enzymes MTR and MMUT using ingenious modifications to an ancient nitroreductase fold, and how MTR and MMUT link with their accessory enzymes to sustainably harness the supernucleophilic potential of Cbl. Finally, we provide an outlook on how future studies may combine structural and interactome based approaches and incorporate knowledge of post‐translational modifications to bring further insights. Click here to access the podcast for this paper. [ABSTRACT FROM AUTHOR]

As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label‐free and high‐throughput protein sequencing. In recent years, nanopore‐based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing. [ABSTRACT FROM AUTHOR]

The flexibility of protein structure is related to various biological processes, such as molecular recognition, allosteric regulation, catalytic activity, and protein stability. At the molecular level, protein dynamics and flexibility are important factors to understand protein function. DNA‐binding proteins and Coronavirus proteins are of great concern and relatively unique proteins. However, exploring the flexibility of DNA‐binding proteins and Coronavirus proteins through experiments or calculations is a difficult process. Since protein dihedral rotational motion can be used to predict protein structural changes, it provides key information about protein local conformation. Therefore, this paper introduces a method to improve the accuracy of protein flexibility prediction, DihProFle (Prediction of DNA‐binding proteins and Coronavirus proteins flexibility introduces the calculated dihedral Angle information). Based on protein dihedral Angle information, protein evolution information, and amino acid physical and chemical properties, DihProFle realizes the prediction of protein flexibility in two cases on DNA‐binding proteins and Coronavirus proteins, and assigns flexibility class to each protein sequence position. In this study, compared with the flexible prediction using sequence evolution information, and physicochemical properties of amino acids, the flexible prediction accuracy based on protein dihedral Angle information, sequence evolution information and physicochemical properties of amino acids improved by 2.2% and 3.1% in the nonstrict and strict conditions, respectively. And DihProFle achieves better performance than previous methods for protein flexibility analysis. In addition, we further analyzed the correlation of amino acid properties and protein dihedral angles with residues flexibility. The results show that the charged hydrophilic residues have higher proportion in the flexible region, and the rigid region tends to be in the angular range of the protein dihedral angle (such as the ψ angle of amino acid residues is more flexible than rigid in the range of 91°–120°). Therefore, the results indicate that hydrophilic residues and protein dihedral angle information play an important role in protein flexibility. [ABSTRACT FROM AUTHOR]

Proteins are macromolecules that perform essential biological functions which depend on their three‐dimensional structure. Determining this structure involves complex laboratory and computational work. For the computational work, multiple software pipelines have been developed to build models of the protein structure from crystallographic data. Each of these pipelines performs differently depending on the characteristics of the electron‐density map received as input. Identifying the best pipeline to use for a protein structure is difficult, as the pipeline performance differs significantly from one protein structure to another. As such, researchers often select pipelines that do not produce the best possible protein models from the available data. Here, a software tool is introduced which predicts key quality measures of the protein structures that a range of pipelines would generate if supplied with a given crystallographic data set. These measures are crystallographic quality‐of‐fit indicators based on included and withheld observations, and structure completeness. Extensive experiments carried out using over 2500 data sets show that the tool yields accurate predictions for both experimental phasing data sets (at resolutions between 1.2 and 4.0 Å) and molecular‐replacement data sets (at resolutions between 1.0 and 3.5 Å). The tool can therefore provide a recommendation to the user concerning the pipelines that should be run in order to proceed most efficiently to a depositable model. [ABSTRACT FROM AUTHOR]

Background: With the change in consumers' lifestyles, the global demand for meat analogs is growing rapidly. However, soy has many drawbacks as a raw material to produce meat analogs, such as its allergy potential (glycinin and β‐conglycinin) and some unpredictable alterations in genetic DNA, proteins, and biochemical processing due to genetic modification. This paper aims to study the physicochemical and textural properties of meat analogs obtained under different pea protein contents and extrusion types to explore the potential of applying pea protein to meat analogs. Results: High‐moisture meat analog (HMMA) is superior to low‐moisture meat analog (LMMA) based on the physical properties (integrity index and nitrogen solubility index) and texture properties (texture profile analysis and cutting strength). The higher the amount of pea protein added, the higher the degree of sample texturization. At low‐moisture extrusion cooking (LMEC), higher isolated pea protein content is accompanied by lower water holding capacity and higher texturization. Hydrophobic interactions play a slightly greater role than disulfide bonds in stabilizing the protein structure of the extrudates. The type of extrusion significantly affected the free sulfhydryl and disulfide bond content of the extrudate, while the source of raw material has an important relationship with protein solubility and free sulfhydryl content. Dodecyl sulfated gel electrophoresis (SDS‐PAGE) showed that most of the protein subunits remained after extrusion. Conclusions: Extrusion types and isolated pea protein contents showed significant effects on the properties of meat analogs, and isolated pea protein has great potential for application in the production of meat analogs. [ABSTRACT FROM AUTHOR]

Principal component analysis (PCA) has been widely proposed to analyze flexibility and heterogeneity in cryo‐electron microscopy (cryoEM). In this paper, it is argued that (i) PCA is an excellent technique to describe continuous flexibility at low resolution (but not so much at high resolution) and (ii) PCA components should be analyzed in a concerted manner (and not independently). [ABSTRACT FROM AUTHOR]

Deep learning techniques can recognize complex patterns in noisy, multidimensional data. In recent years, researchers have started to explore the potential of deep learning in the field of structural biology, including protein crystallography. This field has some significant challenges, in particular producing high‐quality and well ordered protein crystals. Additionally, collecting diffraction data with high completeness and quality, and determining and refining protein structures can be problematic. Protein crystallographic data are often high‐dimensional, noisy and incomplete. Deep learning algorithms can extract relevant features from these data and learn to recognize patterns, which can improve the success rate of crystallization and the quality of crystal structures. This paper reviews progress in this field. [ABSTRACT FROM AUTHOR]

The chemical modification of proteins is an effective technique for manipulating the properties and functions of proteins, and for creating protein‐based materials. The N‐terminus is a promising target for single‐site modification that provides modified proteins with uniform structures and properties. In this paper, a copper(II)‐mediated aldol reaction with 2‐pyridinecarboxaldehyde (2‐PC) derivatives is proposed as an operationally simple method to selectively modify the N‐terminus of peptides and proteins at room temperature and physiological pH. The copper(II) ion activates the N‐terminal amino acids by complexation with an imine of the N‐terminal amino acid and 2‐PCs, realizing the selective formation of the nucleophilic intermediate at the N‐terminus. This results in a stable carbon‐carbon bond between the 2‐PCs and the α‐carbon of various N‐terminal amino acids. The reaction is applied to four different proteins, including biopharmaceuticals such as filgrastim and trastuzumab. The modified trastuzumab retains the human epidermal growth factor receptor 2 recognition activity. [ABSTRACT FROM AUTHOR]

Cupin proteins share a double‐stranded β‐helix fold, form one of the largest protein superfamilies, and possess remarkable functional diversity. They usually exist in homooligomeric states. Goss and co‐workers recently reported that the cupin protein Pac13, which is a dehydratase that mediates the formation of the 3′‐deoxy nucleoside of pacidamycins, is an unusual small monomer. However, a careful analysis of the biophysical and structural data provided by the authors suggests that Pac13 is in fact a homodimer, similar to many other cupin proteins. [ABSTRACT FROM AUTHOR]

Gums are complex carbohydrate molecules which have the ability to bind water and form gels at low concentration. These carbohydrates are often associated with proteins and minerals in their structure. Gums are of various types such as seed gums, exudate gums, microbial gums, mucilage gums, seaweeds gums, etc. Exudate gums are plant gums which ooze out from bark as a result of a protection mechanism upon injury. Exudate gums have been used by humans since ancient times for various applications due to their easy availability. The main characteristics which make them fit for use in various applications are viscosity, adhesive property, stabilization effect, emulsification action and surface‐active property. Major applications of these gums are in food products, the paper, textile, cosmetics and pharmaceutical industries, oil‐well drilling, etc. In the present paper, the chemistry, properties, processing and applications of commercially available exudate gums such as acacia gum or gum arabic, karaya gum, ghatti gum and tragacanth gum are discussed. Recent literature reveals that apart from the above mentioned applications, these gums also have nutritional properties which are being explored. Other gums cannot replace them because of their certain unique characteristics. © 2020 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

The rapidly growing animal protein demand of Chinese residents has caused multiple pressures, including on food security, health, and the environment. It is critical to study the reasons for the changes in Chinese residents' protein intake structure and make a reasonable judgment about its future trend. This paper uses the Nationwide Urban Household Survey Date from 1992 to 2009 to construct a pseudo panel and conduct research based on the habit formation theory. We find that there is a significant habit formation effect in the consumption of the main protein source foods of Chinese urban residents, especially animal foods. It weakens with the passage of time, which may be the reason for the continuous increase in urbanites' animal protein intake. There are differences in the protein intake structure and changing trend of urban residents in China's different regions. We suggest that government should pay more attention to the development of animal husbandry and the supply security of feed grains; strengthen nutritional intervention efforts to guide residents toward balanced and healthy dietary patterns, with moderate intake of animal protein; and formulate more detailed nutritional standards by region and population to cope with the impact of the growing animal protein demand among China's residents. [EconLit Citations: D12, E21, Q18]. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The prediction of protein-ligand complexes (PLC), using both experimental and predicted structures, is an active and important area of research, underscored by the inclusion of the Protein-Ligand Interaction category in the latest round of the Critical Assessment of Protein Structure Prediction experiment CASP15. The prediction task in CASP15 consisted of predicting both the three-dimensional structure of the receptor protein as well as the position and conformation of the ligand. This paper addresses the challenges and proposed solutions for devising automated benchmarking techniques for PLC prediction. The reliability of experimentally solved PLC as ground truth reference structures is assessed using various validation criteria. Similarity of PLC to previously released complexes are employed to judge PLC diversity and the difficulty of a PLC as a prediction target. We show that the commonly used PDBBind time-split test-set is inappropriate for comprehensive PLC evaluation, with state-of-the-art tools showing conflicting results on a more representative and high quality dataset constructed for benchmarking purposes. We also show that redocking on crystal structures is a much simpler task than docking into predicted protein models, demonstrated by the two PLC-prediction-specific scoring metrics created. Finally, we introduce a fully automated pipeline that predicts PLC and evaluates the accuracy of the protein structure, ligand pose, and protein–ligand interactions. [ABSTRACT FROM AUTHOR]

Prediction categories in the Critical Assessment of Structure Prediction (CASP) experiments change with the need to address specific problems in structure modeling. In CASP15, four new prediction categories were introduced: RNA structure, ligandprotein complexes, accuracy of oligomeric structures and their interfaces, and ensembles of alternative conformations. This paper lists technical specifications for these categories and describes their integration in the CASP data management system. [ABSTRACT FROM AUTHOR]

Conformational space annealing (CSA), a global optimization method, has been applied to various protein structure modeling tasks. In this paper, we applied CSA to the cryo‐EM structure modeling task by combining the python subroutine of CSA (PyCSA) and the fast relax (FastRelax) protocol of PyRosetta. Refinement of initial structures generated from two methods, rigid fitting of predicted structures to the Cryo‐EM map and de novo protein modeling by tracing the Cryo‐EM map, was performed by CSA. In the refinement of the rigid‐fitted structures, the final models showed that CSA can generate reliable atomic structures of proteins, even when large movements of protein domains were required. In the de novo modeling case, although the overall structural qualities of the final models were rather dependent on the initial models, the final models generated by CSA showed improved MolProbity scores and cross‐correlation coefficients to the maps. These results suggest that CSA can accomplish flexible fitting and refinement together by sampling diverse conformations effectively and thus can be utilized for cryo‐EM structure modeling. [ABSTRACT FROM AUTHOR]

Pathogenic variants occurring in protein‐coding regions underlie human genetic disease through various mechanisms. They can lead to a loss of function (LOF) such as in recessive conditions or in dominant conditions due to haploinsufficiency. Dominant‐negative (DN) effects, counteracting the activity of the normal gene‐product, and gain of function (GOF) are also mechanisms driving dominance. Here, I discuss a few papers on these specific mechanisms. In short, there is accumulating evidence pointing to differences between LOF versus non‐LOF variants (DN and GOF). The latter are thought to have milder effects on protein structure and, as expected, DN variants are enriched at protein interfaces. This tendency to cluster in 3D space can help improve the ability of computational tools to predict the pathogenicity of DN variants, which is currently a challenging issue. More recent results support the hypothesis whereby cotranslational assembly of macromolecular complexes can buffer deleterious consequences of variants that would otherwise lead to DN effects (DNEs). Indeed, subunits the variants of which are responsible for DNEs tend to elude cotranslational assembly, thus poisoning complexes involving wild‐type subunits. The constraints explaining why the buffering of DNEs is not universal require further investigation. [ABSTRACT FROM AUTHOR]

Acquisition of X‐ray crystallographic data is always accompanied by structural degradation owing to the absorption of energy. The application of high‐fluency X‐ray sources to large biomolecules has increased the importance of finding ways to curtail the onset of X‐ray‐induced damage. A significant effort has been under way with the aim of identifying strategies for protecting protein structure. A comprehensive model is presented that has the potential to explain, both qualitatively and quantitatively, the structural changes induced in crystalline protein at ∼100 K. The first step is to consider the qualitative question: what are the radiation‐induced intermediates and expected end products? The aim of this paper is to assist in optimizing these strategies through a fundamental understanding of radiation physics and chemistry, with additional insight provided by theoretical calculations performed on the many schemes presented. [ABSTRACT FROM AUTHOR]

Spermidine N‐acetyltransferase (SpeG) transfers an acetyl group from acetyl‐coenzyme A to an N‐terminal amino group of intracellular spermidine. This acetylation inactivates spermidine, reducing the polyamine toxicity that tends to occur under certain chemical and physical stresses. The structure of the SpeG protein from Vibrio cholerae has been characterized: while the monomer possesses a structural fold similar to those of other Gcn5‐related N‐acetyltransferase superfamily members, its dodecameric structure remains exceptional. In this paper, structural analyses of SpeG isolated from Escherichia coli are described. Like V. cholerae SpeG, E. coli SpeG forms dodecamers, as revealed by two crystal structures of the ligand‐free E. coli SpeG dodecamer determined at 1.75 and 2.9 Å resolution. Although both V. cholerae SpeG and E. coli SpeG can adopt an asymmetric open dodecameric state, solution analysis showed that the oligomeric composition of ligand‐free E. coli SpeG differs from that of ligand‐free V. cholerae SpeG. Based on these data, it is proposed that the equilibrium balance of SpeG oligomers in the absence of ligands differs from one species to another and thus might be important for SpeG function. [ABSTRACT FROM AUTHOR]

A method for the estimation of coordinates of atoms in proteins from coarse‐grained geometry by simple analytical formulas (ESCASA), for use in nuclear‐magnetic‐resonance (NMR) data‐assisted coarse‐grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side‐chain Hβ protons, given the Cα‐trace, have been derived and parameterized, by using the interproton distances calculated from a set of 140 high‐resolution non‐homologous protein structures. The mean standard deviation over all types of proton pairs in the set was 0.44 Å after fitting. Validation against a set of 41 proteins with NMR‐determined structures, which were not considered in parameterization, resulted in average standard deviation from average proton–proton distances of the NMR‐determined structures of 0.25 Å, compared to 0.21 Å obtained with the PULCHRA all‐atom‐chain reconstruction algorithm and to the 0.12 Å standard deviation of the average‐structure proton–proton distance of NMR‐determined ensembles. The formulas provide analytical forces and can, therefore, be used in coarse‐grained molecular dynamics. [ABSTRACT FROM AUTHOR]

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Background: Discovered and described 40 years ago, non‐specific lipid transfer proteins (nsLTP) are present in many plant species and play an important role protecting plants from stressors such as heat or drought. In the last 20 years, sensitization to nsLTP and consequent reactions to plant foods has become an increasing concern. Aim: The aim of this paper is to review the evidence for the structure and function of nsLTP allergens, and cross‐reactivity, sensitization, and epidemiology of nsLTP allergy. Materials and Methods: A Task Force, supported by the European Academy of Allergy & Clinical Immunology (EAACI), reviewed current evidence and provide a signpost for future research. The search terms for this paper were "Non‐specific Lipid Transfer Proteins", "LTP syndrome", "Pru p 3", "plant food allergy", "pollen‐food syndrome". Results: Most nsLTP allergens have a highly conserved structure stabilised by 4‐disulphide bridges. Studies on the peach nsLTP, Pru p 3, demonstrate that nsLTPs are very cross‐reactive, with the four major IgE epitopes of Pru p 3 being shared by nsLTP from other botanically related fruits. These nsLTP allergens are to varying degrees resistant to heat and digestion, and sensitization may occur through the oral, inhaled or cutaneous routes. In some populations, Pru p 3 is the primary and sole sensitizing allergen, but many are poly‐sensitised both to botanically un‐related nsLTP in foods, and non‐food sources of nsLTP such as Cannabis sativa, Platanus acerifolia, (plane tree), Ambrosia artemisiifolia (ragweed) and Artemisia vulgaris (mugwort). Initially, nsLTP sensitization appeared to be limited to Mediterranean countries, however more recent studies suggest clinically relevant sensitization occurs in North Atlantic regions and also countries in Northern Europe, with nsLTP sensitisation profiles being broadly similar. Discussion: These robust allergens have the potential to sensitize and provoke symptoms to a large number of plant foods, including those which are raw, cooked or processed. It is unknown why some sensitized individuals develop clinical symptoms to foods whereas others do not, or indeed what other allergens besides Pru p 3 may be primary sensitising allergens. It is clear that these allergens are also relevant in non‐Mediterranean populations and there needs to be more recognition of this. Conclusion: Non‐specific LTP allergens, present in a wide variety of plant foods and pollens, are structurally robust and so may be present in both raw and cooked foods. More studies are needed to understand routes of sensitization and the world‐wide prevalence of clinical symptoms associated with sensitization to these complex allergens. [ABSTRACT FROM AUTHOR]

Consumers' preference to have a healthy eating pattern has led to an increasing demand for more nutrient‐dense and healthier plant‐based foods. Pulse proteins are exceptional quality ingredients with potential nutritional benefits, and might act as health‐promoting agents for addressing the new‐generation foods. However, the utilization of pulse protein in foods has been hampered by its relatively poor functionality and unpleasant flavor. Protein structure modification has been proved to be a useful means to improve the functionality and flavor profile of pulse protein. This paper begins with a brief introduction of hierarchical structure of pulse protein materials to better understand the structure characteristics. A comprehensive review is presented on the current techniques including chemical and enzymatic modifications and molecular breeding on pulse protein structure and functionality/flavor. The mechanism and the limitations and the toxicological concerns of these approaches are discussed. We conclude that understanding protein structure‒functionality relationship is extremely valuable in tailoring proteins for specific functional outcomes and expanding the availability of pulse proteins. Furthermore, selective protein modification is a valuable in‐depth toolkit for generating novel protein constructs with preferable functional attributes and flavor profiles. Innovative structure modification with special focus on the molecular basis for the exquisite protein designs is a pillar of pulse protein access to the desired functionality. [ABSTRACT FROM AUTHOR]

Proximal noncovalent forces are commonplace in natural systems and understanding the consequences of their juxtaposition is critical. This paper experimentally quantifies for the first time a Hydrogen Bond‐Enhanced Halogen Bond (HBeXB) without the complexities of protein structure or preorganization. An HBeXB is a halogen bond that has been strengthened when the halogen donor simultaneously accepts a hydrogen bond. Our theoretical studies suggest that electron‐rich halogen bond donors are strengthened most by an adjacent hydrogen bond. Furthermore, stronger hydrogen bond donors enhance the halogen bond the most. X‐ray crystal structures of halide complexes (X−=Br−, I−) reveal that HBeXBs produce shorter halogen bonds than non‐hydrogen bond analogues. 19F NMR titrations with chloride highlight that the HBeXB analogue exhibits stronger binding. Together, these results form the foundation for future studies concerning hydrogen bonds and halogen bonds in close proximity. [ABSTRACT FROM AUTHOR]

Summary: Advanced structures of food proteins are maintained by many forces such as hydrophobic activities, electrostatic interaction, and disulphide bond interaction, which can affect their functional characteristics to a certain extent. Therefore, many approaches have been utilised to improve functional characteristics of food proteins. pH‐shift process refers to the method that food proteins are treated under extreme alkaline or acid conditions followed by adjusting pH to isoelectric point or neutral pH. Many studies have showed that pH‐shift process can significantly affect the functional characteristics of food proteins, for example emulsifying activities, forming property, solubility and water/oil adsorption ability. pH‐shift process has been utilised to recover protein isolates from many sources including fish, fish by‐products, meat processing products. Many researches have indicated that the functional and physicochemical characteristics of recovered protein isolates are significantly influenced by pH‐shift process. In this paper, the latest studies regarding the functional and physicochemical characteristics of proteins treated or recovered through pH‐shift process, and potential applications of obtained protein isolates in the production of the hydrolysates or used as a delivery system were reviewed. [ABSTRACT FROM AUTHOR]

The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal-organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein-ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure refinement. [ABSTRACT FROM AUTHOR]

A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein--ligand complexes, develop threedimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics--the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals. [ABSTRACT FROM AUTHOR]

The motto of this Virtual Issue of The FEBS Journal is a paraphrase of the statement made in 1897 by Mark Twain, which is usually quoted as 'Reports of my death have been greatly exaggerated'. With the incredible progress in the utilization of cryo‐EM for the determination of high‐resolution macromolecular structures that led to the award of the Nobel Prize in Chemistry to Jacques Dubochet, Joachim Frank, and Richard Henderson in 2017, it became a common assumption that crystallography was dead. However, as this Virtual Issue should show very clearly, that is emphatically not the case. To put the current relative importance of different technologies of determination of macromolecular structures into perspective, 78% of structures deposited in the Protein Data Bank since January 2020 were still determined by X‐ray crystallography. The reasons why that is the case will be clear after reading the papers gathered here. [ABSTRACT FROM AUTHOR]

The results of computer modeling of plant kinesin‐8/αβ‐tubulin complexes with such αβ‐tubulins' modified amino acid residues as phosphorylated Tyr262 and Tyr107 are reported in this paper. The molecular dynamics of these modified complexes in comparison with the dynamics of non‐modified ones suggests that the phosphorylation of both α‐ and β‐tubulins reveals stabilizing effect on the protein structure around the modified residue. It was found also that the phosphorylation of Tyr107 in β‐tubulin molecule favors to more advantageous kinesin‐8 binding with the phosphorylated microtubule surface in terms of energy. [ABSTRACT FROM AUTHOR]

This paper presents the effects of microwave on the structure changes of myofibrillar protein compared with traditional water bath heating method. Under microwave or water bath heating conditions, α‐helix conformation of myofibrillar protein was converted into β‐turn, β‐sheet and randomly coiled structures gradually. The fluorescence intensity of myofibrillar protein exhibited a marked red shift of the maximum absorption wavelength after microwave or water bath treatment. Total sulfhydryls groups and surface hydrophobicity contents were increased with progressing microwave or water bath treatment time. Results indicated that the thermal effects of microwave dominated the structure changes of myofibrillar protein, and microwaving also had an apparent influence on myofibrillar protein structure compared with water bath heating due to its nonthermal effects, and thus affecting the retention and release of ketone flavour compounds. [ABSTRACT FROM AUTHOR]

Invited for this month's cover are the groups of Annalisa Martucci and Luisa Pasti at the University of Ferrara (Italy). The cover picture shows L‐lysine amino acid adsorption on zeolite L. The role of zeolite channels in the stabilization of the lysine absorbed and the effect of water on protein structure are elucidated at atomistic level. The stabilization of the L α‐helical conformation is related to strong H‐bonds between the tail aminogroups of lysine molecules and the Brønsted acid site as well as to complex intermolecular H‐bond system between water molecules, zeolite and amino acid. Read the full text of their Full Paper at 10.1002/open.202000183. [ABSTRACT FROM AUTHOR]

Human NOTCH1 receptor contains 36 epidermal growth factor (EGF)‐like repeating domains, in which O‐glycosylation status of the EGF12 domain regulates the interaction with Notch ligands. In their Full Paper on page 12363 ff., Y. Yokoi and S.‐I. Nishimura carried out chemical synthesis and NMR studies of site‐specifically O‐glycosylated EGF11 and EGF10. Four EGF11 and five EGF10 modules were synthesized. The specific O‐glycosylation states affected in vitro folding of EGF10 more than EGF11, while calcium ion had a larger effect on EGF11 folding. Comprehensive NMR studies shed light on the new type “sugar bridges” crosslinking Thr‐O‐GlcNAc in the consensus sequence C5‐X‐X‐G‐X‐(T/S)‐G‐X‐X‐C6 and an amino acid in the hinge region between the domains, 445Thr‐O‐GlcNAc—IIe451 in domain 11 and 405Thr‐O‐GlcNAc—Gln411 in domain 10. [ABSTRACT FROM AUTHOR]

The enzyme nitrogenase converts N2 to NH3, and hydrogenates many other small unsaturated molecules, using multiple electrons and multiple protons. The protein contains a number of water structures in the vicinity of the active site, FeMo‐co, and functional roles have been assigned to two of these with detailed mechanisms proposed for the serial ingress of protons and the egress of product NH3. A separate small water pool (SWP), in a different part of the protein surrounding FeMo‐co, has unknown function. A recent investigation of protein crystals soaked in low‐pH buffer revealed changes in residues near this SWP, and suggested that it could be involved in proton transfer steps. This paper examines the SWP in three protein crystal structures, Azotobacter vinelandii (Av1) and Clostridium pasterianum (Cp1) in their neutral resting states, and Cp1 at low pH. The H atoms, not observed crystallographically, were patched in through density functional calculations using large protein models. Optimisation of the various possibilities, with assessment against crystal dimensions, yielded the most probable distributions of hydrogen atoms in the hydrogen bonds, and the location of H3O+ in the low‐pH state. These detailed structures vary in water content and water involvement with surrounding residues, and vary also in their hydrogen bonding to S atoms of FeMo‐co. A conserved mechanism for proton transfer to FeMo‐co is not evident, and it is concluded that the SWP has no role in the mechanism of nitrogenase. [ABSTRACT FROM AUTHOR]

Abstract: The analysis of protein‐ligand interactions is complex because of the many factors at play. Most current methods for visual analysis provide this information in the form of simple 2D plots, which, besides being quite space hungry, often encode a low number of different properties. In this paper we present a system for compact 2D visualization of molecular simulations. It purposely omits most spatial information and presents physical information associated to single molecular components and their pairwise interactions through a set of 2D InfoVis tools with coordinated views, suitable interaction, and focus+context techniques to analyze large amounts of data. The system provides a wide range of motifs for elements such as protein secondary structures or hydrogen bond networks, and a set of tools for their interactive inspection, both for a single simulation and for comparing two different simulations. As a result, the analysis of protein‐ligand interactions of Molecular Simulation trajectories is greatly facilitated. [ABSTRACT FROM AUTHOR]

Abstract: The essay reviews John Kendrew's pioneering work on the structure of myoglobin for which he shared the Nobel Prize for Chemistry in 1962. It reconstructs the status of protein X‐ray crystallography at the time Kendrew entered the field in 1945, after distinctive service in operational research during the war. It reflects on the choice of sperm whale myoglobin as research material. In particular, it highlights Kendrew's early use of digital electronic computers for crystallographic computations and the marshaling of other tools and approaches that made it possible to solve the structure at increasing resolution. The essay further discusses the role of models in structure resolution and their broader reception. It ends by briefly reviewing Kendrew's other contributions in the formation and institutionalization of molecular biology. [ABSTRACT FROM AUTHOR]

Abstract: IgE and not IgG is usually associated with allergy. IgE lodged on mast cells in skin or gut and basophils in the blood allows for the prolonged duration of allergy through the persistent expression of high affinity IgE receptors. However, many allergic reactions are not dependent on IgE and are generated in the absence of allergen specific and even total IgE. Instead, IgG plasma cells are involved in induction of, and for much of the pathogenesis of, allergic diseases. The pattern of IgG producing plasma cells in atopic children and the tendency for direct or further class switching to IgE are the principle factors responsible for long‐lasting sensitization of mast cells in allergic children. Indirect class switching from IgG producing plasma cells has been shown to be the predominant pathway for production of IgE while a Th2 microenvironment, genetic predisposition, and the concentration and nature of allergens together act on IgG plasma cells in the atopic tendency to undergo further immunoglobulin gene recombination. The seminal involvement of IgG in allergy is further indicated by the principal role of IgG4 in the natural resolution of allergy and as the favourable immunological response to immunotherapy. This paper will look at allergy through the role of different antibodies than IgE and give current knowledge of the nature and role of IgG antibodies in the start, maintenance and resolution of allergy. [ABSTRACT FROM AUTHOR]

Background: Phosphoserine aminotransferase deficiency (PSATD) is an autosomal recessive disorder associated with hypertonia, psychomotor retardation, and acquired microcephaly. Patients with PSATD have low concentrations of serine in plasma and cerebrospinal fluid. Methods: We reported a 2‐year‐old female child with developmental delay, dyskinesia, and microcephaly. LC–MS/MS was used to detect amino acid concentration in the blood and whole‐exome sequencing (WES) was used to identify the variants. PolyPhen‐2 web server and PyMol were used to predict the pathogenicity and changes in the 3D model molecular structure of protein caused by variants. Results: WES demonstrated compound heterozygous variants in PSAT1, which is associated with PSATD, with a paternal likely pathogenic variant (c.235G>A, Gly79Arg) and a maternal likely pathogenic variant (c.43G>C, Ala15Pro). Reduced serine concentration in LC–MS/MS further confirmed the diagnosis of PSATD in this patient. Conclusions: Our findings demonstrate the importance of WES combined with LC–MS/MS reanalysis in the diagnosis of genetic diseases and expand the PSAT1 variant spectrum in PSATD. Moreover, we summarize all the cases caused by PSAT1 variants in the literature. This case provides a vital reference for the diagnosis of future cases. [ABSTRACT FROM AUTHOR]

Akkermansia muciniphila, an anaerobic Gram‐negative bacterium, is a major intestinal commensal bacterium that can modulate the host immune response. It colonizes the mucosal layer and produces nutrients for the gut mucosa and other commensal bacteria. It is believed that mucin desulfation is the rate‐limiting step in the mucin‐degradation process, and bacterial sulfatases that carry out mucin desulfation have been well studied. However, little is known about the structural characteristics of A. muciniphila sulfatases. Here, the crystal structure of the premature form of the A. muciniphila sulfatase AmAS was determined. Structural analysis combined with docking experiments defined the critical active‐site residues that are responsible for catalysis. The loop regions I–V were proposed to be essential for substrate binding. Structure‐based sequence alignment and structural superposition allow further elucidation of how different subclasses of formylglycine‐dependent sulfatases (FGly sulfatases) adopt the same catalytic mechanism but exhibit diverse substrate specificities. These results advance the understanding of the substrate‐recognition mechanisms of A. muciniphila FGly‐type sulfatases. Structural variations around the active sites account for the different substrate‐binding properties. These results will enhance the understanding of the roles of bacterial sulfatases in the metabolism of glycans and host–microbe interactions in the human gut environment. [ABSTRACT FROM AUTHOR]

IUBMB Life (2014) 66:793-802. DOI: The above article, published online on November 15, 2014 in Wiley Online Library (), has been retracted by agreement between the journal's Editors-in-Chief, Angelo Azzi and William J. Whelan, Corresponding Author Tina Wenz, the University of Cologne, and Wiley Periodicals, Inc. The article has been retracted on request of the University of Cologne that, after an investigation, established that the data reported in it are not reproducible. Note from the Corresponding Author: 'The paper reports on the influence of mitochondrial acetylation on protein synthesis. After publication, several irregularities appeared and have been thoroughly investigated by the lab of the Corresponding Author in cooperation with the commission of Research integrity of the University of Cologne. Both came to the conclusion that data used for the publication are erroneous and that the presented data are not reproducible by the lab of the Corresponding Author and other labs. The Corresponding Author takes responsibility and regrets not having detected these issues before publication. The appropriate corrective action is retraction of the paper. The Corresponding Author apologizes to the scientific community.' Reference [ABSTRACT FROM AUTHOR]

Alpha-synuclein ( α-syn) is a 140 residue protein that plays a central role in Parkinson's disease and other neurological disorders. The precise function and pathological properties of α-syn remain however poorly understood. While α-syn is considered to be a flexible and disordered protein under native conditions, its ability to adopt a variety of conformational ensembles depending on the environment is considered to be related to its pathology. Raman optical activity (ROA) is a chiroptical spectroscopic technique that is uniquely sensitive to the secondary structure of proteins in solution and was used here for the first time to study the different conformational ensembles of α-syn. In this paper, the Raman and ROA spectral characteristics of these different conformations of α-syn are investigated. We show that Raman and ROA spectroscopy are sensitive enough not only to detect transitions from a disordered to an α-helical or a β-sheet rich ensemble but also to differentiate between the α-helical forms of wild-type and C-terminal truncated α-syn 107. Using increasing concentrations of fluorinated alcohols, we induce the aggregation pathway of α-syn and identify a molten globule intermediate structure and β-sheet rich oligomers. Taken together, these results demonstrate the power of Raman and ROA spectroscopies for the structural elucidation of proteins that are challenging to characterise. Copyright © 2017 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

BACKGROUND The predominant use of anionic surfactants to precipitate high isoelectric point (pI) proteins has increased in recent years, simplifying downstream separations. However, few researchers have tested cationic and non-ionic surfactants, whose properties are more desirable. This paper examines the effect of these surfactants on the precipitation efficiency of lysozyme, trypsin inhibitor and bovine serum albumin (BSA). RESULTS Precipitation of BSA and trypsin inhibitor using the cationics, trioctylmethylammonium chloride (TOMAC) and dimethyl dioctadecyl ammonium chloride (DODMAC) was evaluated, with TOMAC being superior. More than 90% of BSA was precipitated using TOMAC at pH 9.0 with a molar ratio of surfactant/protein (R) of 100:1, while 88% was precipitated using DODMAC. However, for trypsin inhibitor, only 58% was precipitated at an R of 61:1 and pH 6.2 using TOMAC. Protein precipitate recovery using the anionic surfactant sodium bis-[2-ethylhexyl] sulfosuccinate (AOT) was effective only with trypsin inhibitor, with 100% of the protein being recovered. CONCLUSIONS This study shows the potential of cationics to precipitate low pI proteins, and recover them using the counterionic surfactant AOT, with 100% recovery of trypsin inhibitor. However, non-ionic surfactants were ineffective. The method not only separates, but also preserves protein structure; hence cationic surfactants for low pI protein separation are promising. © 2016 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Proteopedia (proteopedia.org) is an open resource to explore the structure–function relationship of proteins and other biomolecules. This guide provides practical advice on how to incorporate Proteopedia into teaching the structure and function of proteins and other biomolecules. For 11 activities, we discuss desired outcomes, setting expectations, preparing students for the tasks, using resources within Proteopedia, and evaluating student work. We point out features of Proteopedia that make it especially suitable for teaching and give examples of how to avoid common pitfalls. [ABSTRACT FROM AUTHOR]