The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water avai...
Collagen is a family of large, fibrous biomacromolecules common in animals, distinguished by unique molecular, structural, and functional properties. Despite the relatively low complexity of their sequences and the repetitive conformation of the trip...
Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, ren...
Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences fou...
(1) Background. Snake venom phosphodiesterases (SVPDEs) are among the least studied venom enzymes. In envenomation, they display various pathological effects, including induction of hypotension, inhibition of platelet aggregation, edema, and paralysi...
Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence–structure–function relationship. Hence, classic sequence- or structure-based bioinformatic appro...
Three-finger toxins (3FTxs) are the largest group of nonenzymatic toxins found in snake venoms. Among them, neurotoxins that target nicotinic acetylcholine receptors are the most well-studied ligands. In addition to the classical neurotoxins, several...
Bioinformatics and biophysical studies of intrinsically disordered proteins and regions (IDRs) note the high entropy at individual sequence positions and in conformations sampled in solution. This prevents application of the canonical sequence-struct...
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, w...
The B cell receptor (BCR) repertoire captures an individual’s immunological history and antigen-driven evolution within a vast, high-dimensional sequence space. Although bulk and single-cell adaptive immune receptor repertoire sequencing (AIRR-...
The first monomeric pyridoxal-5′-phosphate (PLP)-dependent transaminase from a marine, aromatic-compound-degrading, sulfate-reducing bacterium Desulfobacula toluolica Tol2, has been studied using structural, kinetic, and spectral methods. The m...
Sesquiterpenes are important defense and signal molecules for plants to adapt to the environment, cope with stress, and communicate with the outside world, and their evolutionary history is closely related to physiological functions. In this study, t...
Phytopathogenic fungi secrete numerous effector proteins to disrupt plant defenses. At present, their sequence–structure–function relationships remain poorly understood owing to their diversity. Comprehensive understanding of conserved ef...
Biocatalysis has emerged as a mainstay in the field of sustainable chemical synthesis owing to its high selectivity, mild reaction conditions, and reduced environmental impact. Traditional enzyme engineering approaches, such as rational design and di...
Sequence–function relationship in a protein is commonly determined by the three-dimensional protein structure followed by various biochemical experiments. However, with the explosive increase in the number of genome sequences, facilitated by recent...
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...
Recent advances in sequencing technologies have highlighted long non-coding RNAs (lncRNAs) as key regulators that perform essential biological functions without encoding proteins. Despite growing interest, the molecular mechanisms of most lncRNAs rem...
The genomes from complex eukaryotes are enriched in non-coding genes whose transcription products (non-coding RNAs) are involved in the regulation of genomic output at different levels. Non-coding RNA action is predominantly driven by sequence and st...
Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply...
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 function of RNAs is determined by their structure. However, studying the relationship between RNA structure and function often requires altering RNA sequences to modify the structures, which leads to the neglect of the importance of RNA sequences...
Viruses exhibit significantly greater diversity than cellular organisms, posing a complex challenge to their taxonomic classification. While primary sequences may diverge considerably, protein functional domains can maintain conserved 3D structures t...
This study addresses the challenge of DNA sequence similarity analysis by combining deep learning with DNABERT embeddings. Traditional alignment methods based on direct pairwise comparisons often fail to detect deeper biological relationships beyond...
Protein identity and functional roles within the cell provide the landscape of proteomics and other high-throughput technologies. However, not all protein sequences are cataloged with an identity or a functional protein family. The lack of identity a...
Although thousands of long non-coding RNAs (lncRNAs) have been discovered in eukaryotes, very few molecular mechanisms have been characterized due to an insufficient understanding of lncRNA structure. Therefore, investigations of lncRNA structure and...
The molecular design of short peptides to achieve a tailor-made functional architecture has attracted attention during the past decade but remains challenging as a result of insufficient understanding of the relationship between peptide sequence and...
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) functions as the initial enzyme in the dark reactions of photosynthesis, catalyzing reactions that extract CO2 from the atmosphere and fix CO2 into organic compounds. RuBisCO is classified int...
The RTX domains found in some pathogenic proteins encode repetitive peptide sequences that reversibly bind calcium and fold into the unique the β-roll secondary structure. Several of these domains have been studied in isolation, yielding key ins...
In this article, firstly, some basic properties of the sequential
Recently, we proposed a new method, based on protein profiles derived from physicochemical dynamic time warping (PCDTW), to functionally/structurally classify coronavirus spike protein receptor binding domains (RBD). Our method, as used herein, uses...
The deterministic sequence → structure → function relationship is not applicable to describe how proteins dynamically adapt to different cellular conditions. A stochastic model is required to capture functional promiscuity, redundant sequen...
G-quadruplexes (G4s) are non-canonical nucleic acid structures that function as key regulatory elements in crucial cellular processes. Their biological functions are intrinsically linked to thermostability, which is governed by specific sequence feat...
Porcine reproductive and respiratory syndrome (PRRS) has been prevalent in Germany for over 30 years, posing a significant threat to the local swine industry. There are limited analyses to offer German PRRSV ORF5 genetic and evolutionary characterist...
Sorghum (Sorghum bicolor) is an essential bioenergy crop. Cellulosic and non-cellulosic polysaccharides, which can be transformed into biofuels, comprise most of its biomass. Many glycosyltransferases (GT) families, including GT43, are involved in th...
Hallux valgus is increasingly characterized using weight-bearing computed tomography (WBCT), which provides three-dimensional information on first-ray alignment and articular relationships under load. However, structural abnormalities identified on s...
The initial adoption of penicillin as an antibiotic marked the start of exploring other compounds essential for pharmaceuticals, yet resistance to penicillins and their side effects has compromised their efficacy. The N-terminal nucleophile (Ntn) ami...
Studies on 3FTxs around the world are showing the amazing diversity in these proteins both in structure and function. In Brazil, we have not realized the broad variety of their amino acid sequences and probable diversified structures and targets. In...
The great mechanical properties, biocompatibility and biodegradability of silk-based materials make them applicable to the biomedical field. Genetic engineering enables the construction of synthetic equivalents of natural silks. Knowledge about the r...
Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MAL...
Proteins are crucial to the functioning of all lifeforms. Traditional understanding posits that a single protein occupies a single structure (“fold”), which performs a single function. This view is radically challenged with the recognition that high...
Glutathione transferase (GST) is a superfamily of ubiquitous enzymes, multigenic in numerous organisms and which generally present homodimeric structures. GSTs are involved in numerous biological functions such as chemical detoxification as well as c...
We can now sequence and identify genome wide epigenetic patterns and perform a variety of “genomic experiments” within relatively short periods of time—ranging from days to weeks. Yet, despite these technological advances, we have a poor understandin...
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) perform diverse functions in cellular organization, transport and signaling. Unlike the well-defined structures of the classical natively folded proteins, IDPs and I...
Most cellular functions involve proteins’ features based on their physical interactions with other partner proteins. Sketching a map of protein–protein interactions (PPIs) is therefore an important inception step towards understanding the basics of c...
Sixteen novel circular rep-encoding DNA sequences with high sequence homologies to previously described SPHINX and BMMF sequences were isolated for the first time from non-bovine foods (pork, wild boar, chicken meat, Alaska pollock, pangasius, black...
In this paper, we introduce and rigorously define a novel class of difference sequence spaces, denoted by
Adaptive immunity in vertebrates is a complex self-organizing network of molecular interactions. While deep sequencing of the immune-receptor repertoire may reveal clonal relationships, functional interpretation of such data is hampered by the inhere...
The main goal of this research is to study the development of crystalline morphology and compare it to various mechanical properties of microfibrillar composites (MFCs) based on polypropylene (PP) and poly(ethylene terephthalate) (PET), by adding a f...
Proteins are the basic building blocks of life and perform fundamental functions in biology. Predicting protein properties based on amino acid sequences and 3D structures has become a key approach to accelerating drug development. In this study, we p...
Background: Mitochondrial and chloroplast genomes in plants have experienced distinct evolutionary trajectories due to differences in genomic organization, functional constraints, and genome maintenance mechanisms. However, comparative studies of the...
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