Most non-communicable diseases are associated with dysfunction of proteins or protein complexes. The relationship between sequence and structure has been analyzed for a long time, and the analysis of the sequences organization in domains and motifs r...
High-Mobility Group (HMG) chromosomal proteins are the most numerous nuclear non-histone proteins. HMGB domain proteins are the most abundant and well-studied HMG proteins. They are involved in variety of biological processes. HMGB1 and HMGB2 were th...
HMGB3 protein belongs to the group of HMGB proteins from the superfamily of nuclear proteins with high electrophoretic mobility. HMGB proteins play an active part in almost all cellular processes associated with DNA—repair, replication, recombi...
To date, in-cell NMR has elucidated various aspects of protein behaviour by associating structures in physiological conditions. Meanwhile, current studies of this method mostly have deduced protein states in cells exclusively based on ‘indirect...
Protein structure information is essential to understand protein function. Computational methods to accurately predict protein structure from the sequence have primarily been evaluated on protein sequences representing full-length native proteins. He...
The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades. Recently, the widespread integration of artificial intelligence (AI)...
8 January 2024
The three-dimensional protein structure is pivotal in comprehending biological phenomena. It directly governs protein function and hence aids in drug discovery. The development of protein prediction algorithms, such as AlphaFold2, ESMFold, and trRose...
Among available structuring agents that have been used to provide solid properties to liquid oils, protein is a more recent candidate. Due to their nutritional value and high consumer acceptance, proteins are of special interest for the preparation o...
Obtaining an accurate description of protein structure is a fundamental step toward understanding the underpinning of biology. Although recent advances in experimental approaches have greatly enhanced our capabilities to experimentally determine prot...
Dansyl labeling is a widely used approach for enhancing the detection of small molecules by UV spectroscopy and mass spectrometry. It has been successfully applied to identify and quantify a variety of biological and environmental specimens. Despite...
This review discusses different protein sources and their role in human nutrition, focusing on their structure, digestibility, and bioavailability. Plant-based proteins, such as those found in legumes, nuts, and seeds, may contain anti-nutritional fa...
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopula...
Secondary structure prediction (SSP) of proteins is an important structural biology technique with many applications. There have been ~300 algorithms published in the past seven decades with fierce competition in accuracy. In the first 60 years, the...
Protein structure analysis is essential in various bioinformatics domains such as drug discovery, disease diagnosis, and evolutionary studies. Within structural biology, the classification of protein structures is pivotal, employing machine learning...
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly u...
Protein structure prediction is important for understanding their function and behavior. This review study presents a comprehensive review of the computational models used in predicting protein structure. It covers the progression from established pr...
DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both prote...
Protein–Protein Interaction (PPI) prediction plays a pivotal role in understanding cellular processes and uncovering molecular mechanisms underlying health and disease. Structure-based PPI prediction has emerged as a robust alternative to seque...
Protein therapeutics play an important role in controlling the functions and activities of disease-causing proteins in modern medicine. Despite protein therapeutics having several advantages over traditional small-molecule therapeutics, further devel...
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for studying the structure and dynamics of proteins in their native state. For high-resolution NMR structure determination, the collection of a rich restraint dataset is necessary. Th...
The assignment of secondary structure elements in protein conformations is necessary to interpret a protein model that has been established by computational methods. The process essentially involves labeling the amino acid residues with H (Helix), E...
Living organisms are composed of biopolymers (proteins, nucleic acids, carbohydrates and lipid polymers) that are used to keep or transmit information relevant to the state of these organisms at any given time. In these processes, proteins play a cen...
A super-secondary structure (SSS) is a spatially unique ensemble of secondary structural elements that determine the three-dimensional shape of a protein and its function, rendering SSSs attractive as folding cores. Understanding known types of SSSs...
The high moisture extrusion of plant proteins is well suited for the production of protein-rich products that imitate meat in their structure and texture. The desired anisotropic product structure of these meat analogues is achieved by extrusion at h...
With the accumulation of next generation sequencing data, there is increasing interest in the study of intra-species difference in molecular biology, especially in relation to disease analysis. Furthermore, the dynamics of the protein is being identi...
Thermal green protein Q66E (TGP-E) has previously shown increased thermal stability compared to thermal green protein (TGP), a thermal stable fluorescent protein produced through consensus and surface protein engineering. In this paper, we describe t...
Protein structure and protein function should be related, yet the nature of this relationship remains unsolved. Mapping the critical residues for protein function with protein structure features represents an opportunity to explore this relationship,...
A tertiary structure governs, to a great extent, the biological activity of a protein in the living cell and is consequently a central focus of numerous studies aiming to shed light on cellular processes central to human health. Here, we aim to eluci...
Brugia malayi is a filarial nematode, which causes lymphatic filariasis in humans. In 1995, the disease has been identified by the World Health Organization (WHO) as one of the second leading causes of permanent and long-term disability and thus it i...
The quality prediction of quaternary structure models of a protein complex, in the absence of its true structure, is known as the Estimation of Model Accuracy (EMA). EMA is useful for ranking predicted protein complex structures and using them approp...
Protein secondary structure prediction is an important topic in bioinformatics. This paper proposed a novel model named WS-BiLSTM, which combined the wavelet scattering convolutional network and the long-short-term memory network for the first time t...
Although it is one of the most studied proteins, p53 continues to be an enigma. This protein has numerous biological functions, possesses intrinsically disordered regions crucial for its functionality, can form both homo-tetramers and isoform-based h...
Native soy protein isolate (N-SPI) has a low denaturation point and low solubility, limiting its industrial application. The influence of different industrial modification methods (heat (H), alkaline (A), glycosylation (G), and oxidation (O)) on the...
One of the most important lessons we have learned from sequencing the human genome is that not all proteins have a 3D structure. In fact, a large part of the human proteome is made up of intrinsically disordered proteins (IDPs) which can adopt multip...
The structure and shape of the polypeptide chains of proteins are determined by the hybridized states of the atomic orbitals in the molecular chain. The calculated s ratio in the spn hybrid orbitals is computed from the fractal dimension D of the ter...
Plant proteins are constantly gaining attention as potential substitutes for dairy proteins, due to their suitable functionality and nutritional value. This study was designed to compare the structural and functional responses of different plant prot...
The continued development of X-ray free-electron lasers and serial crystallography techniques has opened up new experimental frontiers. Nanoscale dynamical processes such as crystal growth can now be probed at unprecedented time and spatial resolutio...
The new advances in deep learning methods have influenced many aspects of scientific research, including the study of the protein system. The prediction of proteins’ 3D structural components is now heavily dependent on machine learning techniques tha...
Significant efforts in wet and dry laboratories are devoted to resolving molecular structures. In particular, computational methods can now compute thousands of tertiary structures that populate the structure space of a protein molecule of interest....
While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary stru...
The refinement of predicted 3D protein models is crucial in bringing them closer towards experimental accuracy for further computational studies. Refinement approaches can be divided into two main stages: The sampling and scoring stages. Sampling str...
High-temperature cooking can induce oxidation and structural changes in myofibrillar protein (MP), harming meat product quality. 6-gingerol is a key part of ginger and a natural antioxidant. In this study, MP was mixed with 6-gingerol and cooked at d...
Few studies have examined dietary protein intake and sources, in combination with longitudinal changes in brain structure markers. Our study aimed to examine the association between dietary protein intake and different sources of dietary protein, wit...
Ribosome-inactivating proteins (RIPs) are cytotoxic enzymes that inhibit protein translation by depurinating ribosomal RNA. Although most plant RIPs are synthesized with leader sequences that sequester them away from the host ribosomes, several RIPs...
The recent successes of AlphaFold and RoseTTAFold have demonstrated the value of AI methods in highly accurate protein structure prediction. Despite these advances, the role of these methods in the context of small-molecule drug discovery still needs...
Predicting the secondary structure from protein sequence plays a crucial role in estimating the 3D structure, which has applications in drug design and in understanding the function of proteins. As new genes and proteins are discovered, the large siz...
The lack of adequate guidance and control of the extraction conditions as well as the gap between bench- and industrial-scale production, contributes to the poor functionality of commercial pea protein isolate (cPPI). Therefore, pea protein extractio...
Oxygen is a key atom that maintains biomolecular structures, regulates various physiological processes, and mediates various biomolecular interactions. Oxygen-17 (17O), therefore, has been proposed as a useful probe that can provide detailed informat...
The subcellular locations of proteins are closely related to their functions. In the past few decades, the application of machine learning algorithms to predict protein subcellular locations has been an important topic in proteomics. However, most st...
The B-factor, also known as the atomic displacement parameter, is a fundamental metric in crystallography for quantifying the positional flexibility of atoms within crystal lattices. In structural biology, various developments have expanded the use o...
of 565