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Publications related to Protein Chemistry (1,394)
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Plant-derived antimicrobial peptides Jane Mary Lafayette Neves Gelinski1, Bernadette Dora Gombossy de Melo Franco2 and Gustavo Graciano Fonseca3 1Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia-Federal District, Brasilia, 2Food Research Center FoRC, Sao Paulo University, USP, Sao Paulo, SP, Brazi...
Article
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Light‐guided soft actuators with dynamic polymer networks have drawn much attention in recent years. However, the application of such actuators is limited by their synthetic strategies, polymer structures, and shape‐morphing modes. This work reports a new class of liquid crystalline elastomer (LCE) actuators crosslinked by mussel‐inspired catechol‐...
Article
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Off-the-shelf small diameter vascular grafts are an attractive alternative to eliminate the shortcomings of autologous tissues for vascular grafting. Bovine saphenous vein (SV) extracellular matrix (ECM) scaffolds are potentially ideal small diameter vascular grafts, due to their inherent architecture and signaling molecules capable of driving repo...
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The major focus of an interdisciplinary field of study termed proteomics is a comprehensive analysis of proteins to evaluate their genetic variety, examine their distinctions, and respond to stresses. Proteomics' major goal is to use protein chemistry, bioinformatics, and biology to detect and measure proteins as well as analyze their post-translat...
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ConspectusThis Account summarizes the progress in protein-calixarene complexation, tracing the developments from binary recognition to the glue activity of calixarenes and beyond to macrocycle-mediated frameworks. During the past 10 years, we have been tackling the question of protein-calixarene complexation in several ways, mainly by cocrystalliza...
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HaloTag labeling technology has introduced unrivaled potential in protein chemistry and molecular and cellular biology. A wide variety of ligands have been developed to meet the specific needs of diverse applications, but only a single protein tag, DhaAHT, is routinely used for their incorporation. Following a systematic kinetic and computational a...
Article
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Amyloid crystals, a form of ordered protein aggregates documented relatively recently, have not been studied as extensively as amyloid fibres. This study investigates the formation of amyloid crystals with low frequency ultrasound (20 kHz) using β-lactoglobulin, as a model protein for amyloid synthesis. Acoustic cavitation generates localised zones...
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Non-native disulfide bonds are dynamic covalent bridges that form post-translationally between two cysteines within the same protein (intramolecular) or with a neighboring protein (intermolecular), frequently due to changes in the cellular redox potential. The reversible formation of non-native disulfides is intimately linked to alterations in prot...
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Although the tools based on split proteins have found broad applications, ranging from controlled biological signaling to advanced molecular architectures, many of them suffer from drawbacks such as background reassembly, low thermodynamic stability, and static structural features. Here, we present a chemically inducible protein assembly method ena...
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Polyglutamylation is a posttranslational modification (PTM) that adds several glutamates on glutamate residues in the form of conjugated peptide chains by a family of enzymes known as polyglutamylases. Polyglutamylation is well documented in microtubules. Polyglutamylated microtubules consist of different α- and β-tubulin subunits with varied numbe...
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This review addresses nine areas of knowledge revealed by micromanipulations performed with Paramecium. Microinjection has shown that sexual maturation and senescence of Paramecium caudatum is a programmed process conducted by a specific gene and its product protein. In P. tetraurelia, autogamy was revealed to depend on the number of DNA syntheses...
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The study of nonlinear evolution equations is a subject of active interest in different fields including physics, chemistry, and engineering. The exact solutions to nonlinear evolution equations provide insightful details and physical descriptions into many problems of interest that govern the real world. The Kadomtsev–Petviashvili (kp) equation, w...
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Proteins: Chemistry and classification of amino acids and proteins, Physico-Chemical properties of protein and their structure, general methods of analysis of proteins and amino acids, Digestion, absorption and metabolism of proteins.
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G protein-coupled receptors (GPCRs) make up the largest superfamily of integral membrane proteins and play critical signal transduction roles in many physiological processes. Developments in molecular biology, biophysical, biochemical, pharmacological, and computational techniques aimed at these important therapeutic targets are beginning to provid...
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The advent of soft-ionization mass spectrometry for biomolecules has opened up new possibilities for the structural analysis of proteins. Combining protein chemistry methods with modern mass spectrometry has led to the emergence of the distinct field of structural proteomics. Multiple protein chemistry approaches, such as surface modification, limi...
Preprint
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HaloTag labeling technology has introduced unrivaled potential in protein chemistry, molecular and cellular biology. A wide variety of ligands have been developed to meet the specific needs of diverse applications, but only a single protein tag, DhaAHT, is routinely used for their incorporation. Following a systematic kinetic and computational anal...
Article
Full-text available
MhuD is a noncanonical heme oxygenase (HO) from Mycobacterium tuberculosis (Mtb) that catalyzes unique heme degradation chemistry distinct from canonical HOs, generating mycobilin products without releasing carbon monoxide. Its crucial role in the Mtb heme uptake pathway has identified MhuD as an auspicious drug target. MhuD is capable of binding e...
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Sortase-mediated ligation (SML) is a powerful tool of protein chemistry allowing the ligation of peptides containing LPxTG sorting motifs and N-terminal glycine nucleophiles. The installation of a sorting motif into the product prohibits the assembly of multiple fragments by SML. Here we report multi-fragment SML based on switchable sortase substra...
Article
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Successful proteome analysis requires reliable sample preparation beginning with protein solubilization and ending with a sample free of contaminants, ready for downstream analysis. Most proteome sample preparation technologies utilize precipitation or filter-based separation, both of which have significant disadvantages. None of the current techno...
Article
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Protein synthesis and semisynthesis offer immense promise for life science and have impacted pharmaceutical innovation. Nevertheless, the absence of a generally applicable method for traceless peptide conjugation with a flexible choice of junction sites remains a bottleneck for accessing many important synthetic targets. Here we introduce the prote...
Article
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Protecting group chemistry for the cysteine thiol group has enabled a vast array of peptide and protein chemistry over the last several decades. Increasingly sophisticated strategies for the protection, and subsequent deprotection, of cysteine have been developed, facilitating synthesis of complex disulfide-rich peptides, semisynthesis of proteins,...
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Dan Tawfik suddenly left us on 4 May, 2021. His scientific intuition led him to articulate, and solve, many key questions related to protein chemistry and molecular evolution. Although science, particularly for his students, postdoctoral fellows and colleagues, is dimmer after his loss, his legacy will persist.
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Shape memory polymers (SMPs) with the permanent shape reconfiguration capability have received much research interest because they are capable of diversified tasks and the ability to work in conditions that required complex geometry. However, most of such SMPs are thermally triggered, which limits their applications. Inspired by reversible mussel a...
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The functions of most proteins result from their 3D structures, but determining their structures experimentally remains a challenge, despite steady advances in crystallography, NMR and single-particle cryoEM. Computationally predicting the structure of a protein from its primary sequence has long been a grand challenge in bioinformatics, intimately...
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LI-cadherin is a member of the cadherin superfamily, which encompasses a group of Ca²⁺-dependent cell adhesion proteins. The expression of LI-cadherin is observed on various types of cells in the human body, such as normal small intestine and colon cells, and gastric cancer cells. Because its expression is not observed on normal gastric cells, LI-c...
Book
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Engineering Chemistry-I (Concepts & applications) is a Textbook that offers an exclusive coverage of the topics and proper explanation of concepts as per the students' needs. Key Features: • Detailed discussion with point-wise explanation of the concepts • Let’s Think sections – In-text questions with answers after each section • A large number of...
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Background: Triple-negative breast cancer (TNBC) is highly metastatic and lethal. Due to a lack of druggable targets for this disease, there are no effective therapies in the clinic. Methods: We explored the ability of active compounds derived from natural herbs to inhibit TNBC metastasis using the methods of molecular biology, cell biology, protei...
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Epigenetics research focuses on the study of heritable gene regulatory mechanisms that do not involve changes of the DNA sequence. Such mechanisms include post-translational modifications of histone proteins that organize the genome in the nucleus into a nucleoprotein complex called chromatin, and which are of key importance in development and dise...
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Michael J. Behe writes a controversial 300-page book that takes a challenging view of the current state of the failure of biological orthodoxy to provide detailed biochemical explanations for several of the vital processes in living cells. He accuses too many biologists of ignorance of protein chemistry and regards their view of the cell's chemical...
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Tangential flow filtration (TFF) is a chemical unit operation used to purify and concentrate liquid suspensions of colloids, proteins, or cells. The solution flows tangentially across a membrane, such that a selective part of the fluid permeates the membrane while the filtrated matter is retained, increasing its concentration. Tmild mechanical puri...
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A major role for the intracellular post-translational modification O-GlcNAc appears to be the inhibition of protein aggregation. Most of the previous studies in this area focused on O-GlcNAc modification of the amyloid-forming proteins themselves. Here we used synthetic protein chemistry to discover that O-GlcNAc also activates the anti-amyloid act...
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Human glutathione transferase A1-1 (hGSTA1-1) contributes to developing resistance to anticancer drugs and, therefore, is promising in terms of drug-design targets for coping with this phenomenon. In the present study, the interaction of anthraquinone and diazo dichlorotriazine dyes (DCTD) with hGSTA1-1 was investigated. The anthraquinone dye Proci...
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Purpose: The risk for age-related macular degeneration has been tied to an overactive complement system. Despite combined attempts by academia and industry to develop therapeutics that modulate the complement response, particularly in the late geographic atrophy form of advanced AMD, to date, there is no effective treatment. We have previously dem...
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The thiol group of the cysteine side chain is arguably the most versatile chemical handle in proteins. To expand the scope of established and commercially available thiol bioconjugation reagents, we genetically encoded a second such functional moiety in form of a latent thiol group that can be unmasked under mild physiological conditions. Phenylace...
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Enzymatic deprotection of a latent thiol under mild and physiological conditions expands the scope of classic thiol bioconjugation. New reaction schemes enable regioselective labeling and dual modifications for a variety of preparative applications and using the established and commercially available plethora of thiol-directed reagents. Abstract T...
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Die Rezeptor‐bindende Domäne (RBD) des SARS‐CoV‐2 Spike‐Glykoproteins kann durch Semisynthese als homogene Glykoform hergestellt werden. Ping Wang et al. berichten in ihrem Forschungsartikel (DOI: 10.1002/ange.202100543) über die erstmalige Synthese von glykosylierten RBDs mit strukturell definierten Glykanen. Das Titelbild illustriert die Kombinat...
Article
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Comprehensive analysis of proteins to evaluate their genetic diversity, study their differences, and respond to the tensions is the main subject of an interdisciplinary field of study called proteomics. The main objective of the proteomics is to detect and quantify proteins and study their post-translational modifications and interactions using pro...
Preprint
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The mechanism which adapts the T-cell antigen receptor (TCR) within a given major histocompatibility complex ( MHC/HLA ) genotype is essential for protection against pathogens. Historically attributed to relative affinity, genetically vast TCRs are surprisingly focused towards a micromolar affinity for their respective peptide (p) plus MHC (pMHC) l...
Article
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Water-soluble, anionic calix[n]arenes are useful receptors for protein recognition and assembly. For example, sulfonato-calix[8]arene (sclx 8 ) can encapsulate proteins and direct their assembly into porous frameworks. In this work, we turned our attention to an "extended arm" calixarene with 16 phenyl rings. We hypothesized that this larger recept...
Article
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The Neisseria meningitidis protein FrpC contains a self-processing module (SPM) undergoing autoproteolysis via an aspartic anhydride. Herein, we establish NeissLock, using a binding protein genetically fused to SPM. Upon calcium triggering of SPM, the anhydride at the C-terminus of the binding protein allows nucleophilic attack by its target protei...
Preprint
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Protein synthesis and semisynthesis offer immense promise for life science and have impacted pharmaceutical innovation. Nevertheless, the absence of a generally applicable method for traceless peptide conjugation with flexible choices of junction sites remains a bottleneck to accessing many important synthetic targets. Here we introduce the protein...
Article
Full-text available
Two decades ago Lau and Dill developed a computer program based on a two-dimensional lattice model. With this program they showed that between 10-6 to 10-10 random polypeptides, a hundred residues long, would produce stable protein-like folds. Ever after, their seminal work has been quoted as evidence for the claim that randomly formed polypeptides...
Chapter
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This chapter begins with an account of the early developments in protein chemistry and supramolecular chemistry. We have attempted to summarize the seminal achievements in each of these vast fields, highlighting how one has informed the other over the past century. We focus on the central topic of molecular recognition and noncovalent interactions....
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Carbodiimide-catalyzed carboxyl and amine conjugation (amidation) has been widely used to protect carboxyl groups. N-(3-(Dimethylamino)propyl)-N'-ethylcarbodiimide (EDC) is the most common carbodiimide reagent in protein chemistry due to its high catalytic efficiency in aqueous media. The reaction has also been applied in different proteomic studie...
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The transpeptidase sortase A of Staphylococcus aureus (Sa‐SrtA) is a valuable tool in protein chemistry. The native enzyme anchors surface proteins containing a highly conserved LPxTG sorting motif to a terminal glycine residue of the peptidoglycan layer in gram‐positive bacteria. This reaction is exploited for sortase‐mediated ligation (SML), allo...
Article
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Matrix metalloproteinase (MMP) is a class of metalloenzyme that cleaves peptide bonds in extracellular matrices. Their functions are important in both health and disease of animals. Here using quantum mechanics simulations of the MMP8 protein, the coordination chemistry of different metal cofactors is examined. Structural comparisons reveal that Jh...
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Tuberculosis (TB) remains a foremost poverty-related disease with a high rate of mortality despite global immunization with Bacille Calmette−Guerin (BCG). Several adjuvanted recombinant proteins are in clinical development for TB to protect against the disease in infants and adults. Nevertheless, simple mixing of adjuvants with antigens may not be...
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Virulent strains of Streptococcus pyogenes (GAS) recruit host single-chain human plasminogen (hPg) to the cell surface - where in the case of Pattern D strains of GAS - hPg binds directly to the cells through a surface receptor, plasminogen-binding group A streptococcal M-protein (PAM). The coinherited Pattern D GAS-secreted streptokinase (SK2b) th...
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amino acids and protein chemistry part 3
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amino acids and protein chemistry part 2
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amino acids and protein chemistry part 4
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Amino acids and protein chemistry part 1
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Hexokinase (HK) catalyzes the first step in glucose metabolism, making it an exciting target for the inhibition of tumor initiation and progression due to their elevated glucose metabolism. The upregulation of hexokinase-2 (HK2) in many cancers and its limited expression in normal tissues makes it a particularly attractive target for the selective...
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Durante la segunda mitad del siglo 20, se produjo una revolución en la aplicación práctica de las ciencias biológicas; en particular, de la bioquímica. Su interrelación con disciplinas basadas en la física y la electrónica provocaron una explosión en el desarrollo de nuevas tec-nologías y productos. De todas estas tecnologías de base interdisci-pli...
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Alkylating reagents based on thioimidazolium ionic liquids were synthesized and the influence of the anion on the alkylation reaction mechanism explored in detail using both experimental and computational methods. Thioimidazolium cations transfer alkyl substituents to nucleophiles, however the reaction rate was highly dependent on anion identity, d...
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The genetic code, once believed to be universal and immutable, is now known to contain many variations and is not quite universal. The basis for genome recoding strategy is genetic code variation that can be harnessed to improve cellular properties. Thus, genome recoding is a promising strategy for the enhancement of genome flexibility, allowing fo...
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Axon regeneration constitutes a fundamental challenge for regenerative neurobiology, which necessitates the use of tailor-made biomaterials for controllable delivery of cells and biomolecules. An increasingly popular approach for creating these materials is to directly assemble engineered proteins into high-order structures, a process that often re...
Article
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Protein aggregation is among the most challenging new frontiers in protein chemistry as well as in molecular medicine and has direct implications in protein misfolding. This study investigated the role of sugar molecules (glucose, fructose, sucrose, and the mixture of glucose and fructose) in protecting the structural integrity of α-lactalbumin (α-...
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There has been increasing interest in recent years in the use of agro-based raw materials for the production of bio-friendly and sustainable products. Plant-based proteins are among the popular materials being studied. In particular, cottonseed protein (a byproduct of cotton fiber production) is widely available and has useful properties. Although...
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Structural biology is the study of the molecular arrangement and dynamics of biological macromolecules, particularly proteins. The resulting structures are then used to help explain how proteins function. This article gives the reader an insight into protein structure and the underlying chemistry and physics that is used to uncover protein structur...
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Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibod...
Article
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An approach is presented for the facile generation of a vacant initiation codon, based on preventing formylation of the endogenous initiator. This can be achieved by either removing its substrate or adding an inhibitor, and it enables the generation of peptides and proteins reprogrammed with multiple and diverse functional groups and reactive handl...
Article
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A particularly powerful approach to controlled protein modification is through the use genetic code reprogramming. One remaining challenge, however, is the convenient generation of vacant codons. In this work we target the initiation machinery of Escherichia coli , showing that simple restriction of formyl donor or inhibition of the formyl transfer...
Chapter
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Fibrillation and aggregation of protein are some of the most exciting frontiers in protein chemistry and molecular medicine. It is also expected to shed light on the molecular and biochemical basis of various pathological conditions having a dramatic social impact such as Alzheimer’s, Parkinson’s diseases, and type II diabetes. The role of insulin...
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La comunidad de Ojos Negros está ubicada en el municipio de Ensenada Baja California, México. Desde 1930, los residentes locales fabrican un queso artesanal muy apreciado en la región; sin embargo, la leche cruda y el queso nunca han sido analizados por la calidad microbiológica y de higiene del producto final. El objetivo del presente estudio fue...
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The attachment of differently linked ubiquitin (Ub) chains of varying length to proteins is a prevalent posttranslational modification in eukaryotic cells. The fate of a modified protein is determined by Ub‐binding proteins (UBPs) that interact with Ub chains in a linkage‐selective manner. Therefore, proteome‐wide interaction studies using differen...
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Über kurz oder lang : Es wurde eine effiziente Methode entwickelt, um homogene, Triazol‐verknüpfte Ub‐Ketten zu trennen. Affinitätsbasierte Proteomikstudien ermöglichten die Identifikation von längenspezifischen Interaktionspartnern von K27‐, L29‐ und K33‐verknüpften Ketten zum Nachweis der Auswirkungen der Kettenlänge auf die Ub‐Kettenerkennung....