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Methods in Molecular Biology (Clifton,... 2022Proteins with a functionalized C-terminus are critical to synthesizing large proteins via expressed protein ligation. To overcome the limitations of currently available...
Proteins with a functionalized C-terminus are critical to synthesizing large proteins via expressed protein ligation. To overcome the limitations of currently available C-terminus functionalization strategies, we established an approach based on a small molecule cyanylating reagent that chemically activates a cysteine in a recombinant protein at its N-side amide for undergoing nucleophilic acyl substitution with amines. We demonstrated the versatility of this approach by successfully synthesizing RNAse H with its RNA hydrolyzing activity restored and in vitro nucleosome build with a C-terminal posttranslational modified histone H2A. This technique will expand the landscape of protein chemical synthesis and its application in new research fields significantly.
Topics: Cysteine; Histones; Nucleosomes; Protein Biosynthesis; RNA
PubMed: 35761048
DOI: 10.1007/978-1-0716-2489-0_11 -
Biochemistry. Biokhimiia Jun 2022Solving the structures of bacterial, archaeal, and eukaryotic ribosomes by crystallography and cryo-electron microscopy has given an impetus for studying intracellular... (Review)
Review
Solving the structures of bacterial, archaeal, and eukaryotic ribosomes by crystallography and cryo-electron microscopy has given an impetus for studying intracellular regulatory proteins affecting various stages of protein translation. Among them are ribosome hibernation factors, which have been actively investigated during the last decade. These factors are involved in the regulation of protein biosynthesis under stressful conditions. The main role of hibernation factors is the reduction of energy consumption for protein biosynthesis and preservation of existing functional ribosomes from degradation, which increases cell survival under unfavorable conditions. Despite a broad interest in this topic, only a few articles have been published on the ribosomal silencing factor S (RsfS). According to the results of these studies, RsfS can be assigned to the group of hibernation factors. However, recent structural studies of the 50S ribosomal subunit maturation demonstrated that RsfS has the features inherent to biogenesis factors for example, ability to bind to the immature ribosomal subunit (similar to the RsfS mitochondrial ortholog MALSU1, mitochondrial assembly of ribosomal large subunit 1). In this review, we summarized the information on the function and structural features RsfS, as well as compared RsfS with MALSU1 in order to answer the emerging question on whether RsfS is a hibernation factor or a ribosome biogenesis factor. We believe that this review might promote future studies of the RsfS-involving molecular mechanisms, which so far remain completely unknown.
Topics: Biotin; Cryoelectron Microscopy; Eukaryotic Cells; Protein Biosynthesis; Ribosomes
PubMed: 35790407
DOI: 10.1134/S0006297922060025 -
International Journal of Molecular... Jan 2022Among the 20 amino acids needed for protein synthesis, Tryptophan (Trp) is an aromatic amino acid fundamental not only for the synthesis of the major components of...
Among the 20 amino acids needed for protein synthesis, Tryptophan (Trp) is an aromatic amino acid fundamental not only for the synthesis of the major components of living cells (namely, the proteins), but also for the maintenance of cellular homeostasis [...].
Topics: Disease Susceptibility; Homeostasis; Humans; Metabolic Networks and Pathways; Protein Biosynthesis; Tryptophan
PubMed: 35054973
DOI: 10.3390/ijms23020787 -
Current Opinion in Chemical Biology Oct 2019Synthetic biology aims to rewire cellular activities and functionality by implementing genetic circuits with high biocomputing capabilities. Recent efforts led to the... (Review)
Review
Synthetic biology aims to rewire cellular activities and functionality by implementing genetic circuits with high biocomputing capabilities. Recent efforts led to the development of smart sensing interfaces which integrate multiple inputs to activate desired outputs in a highly specific and sensitive manner. In this review, we highlight protein-based interfaces that sense intracellular or extracellular cues providing information about dynamic environmental changes and cellular state. We will also discuss different mechanisms of regulation of gene expression connected to the sensors to develop diagnostic and therapeutic devices. We conclude discussing challenges and opportunities for biomedical applications of synthetic mammalian protein-based devices.
Topics: Animals; Gene Expression Regulation; Gene Regulatory Networks; Mammals; Protein Biosynthesis; Protein Processing, Post-Translational; Proteins; Signal Transduction; Synthetic Biology; Transcription, Genetic
PubMed: 31158655
DOI: 10.1016/j.cbpa.2019.04.014 -
Cell Systems Feb 2020How do cells maintain relative proportions of protein complex components? Advances in quantitative, genome-wide measurements have begun to shed light onto the roles of... (Review)
Review
How do cells maintain relative proportions of protein complex components? Advances in quantitative, genome-wide measurements have begun to shed light onto the roles of protein synthesis and degradation in establishing the precise proportions in living cells: on the one hand, ribosome profiling studies indicate that proteins are already produced in the correct relative proportions. On the other hand, proteomic studies found that many complexes contain subunits that are made in excess and subsequently degraded. Here, we discuss these seemingly contradictory findings, emerging principles, and remaining open questions. We conclude that establishing precise protein levels involves both coordinated synthesis and post-translational fine-tuning via protein degradation.
Topics: Protein Biosynthesis; Proteins
PubMed: 32105631
DOI: 10.1016/j.cels.2020.01.004 -
Essays in Biochemistry Oct 2019Nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), carry genetic information which is read in cells to make the RNA and proteins by which living... (Review)
Review
Nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), carry genetic information which is read in cells to make the RNA and proteins by which living things function. The well-known structure of the DNA double helix allows this information to be copied and passed on to the next generation. In this article we summarise the structure and function of nucleic acids. The article includes a historical perspective and summarises some of the early work which led to our understanding of this important molecule and how it functions; many of these pioneering scientists were awarded Nobel Prizes for their work. We explain the structure of the DNA molecule, how it is packaged into chromosomes and how it is replicated prior to cell division. We look at how the concept of the gene has developed since the term was first coined and how DNA is copied into RNA (transcription) and translated into protein (translation).
Topics: Bacteria; DNA; DNA Replication; Eukaryota; Genes; History, 20th Century; Nucleic Acid Conformation; Protein Biosynthesis; RNA; Ribosomes
PubMed: 31652314
DOI: 10.1042/EBC20180038 -
Cancer Letters Apr 2022Hypoxia-inducible factor-1 (HIF-1), an essential promoter of tumor progression, has attracted increasing attention as a therapeutic target. In addition to hypoxic... (Review)
Review
Hypoxia-inducible factor-1 (HIF-1), an essential promoter of tumor progression, has attracted increasing attention as a therapeutic target. In addition to hypoxic cellular conditions, HIF-1 activation can be triggered by cancer treatment, which causes drug tolerance and therapeutic failure. To date, a series of effective strategies have been explored to suppress HIF-1 function, including silencing the HIF-1α gene, inhibiting HIF-1α protein translation, degrading HIF-1α protein, and inhibiting HIF-1 transcription. Furthermore, nanoparticle-based drug delivery systems have been widely developed to improve the stability and pharmacokinetics of HIF-1 inhibitors or achieve HIF-1-targeted combination therapies as a nanoplatform. In this review, we summarize the current literature on nanomedicines targeting HIF-1 to combat cancer and discuss their potential for future development.
Topics: Humans; Hypoxia; Hypoxia-Inducible Factor 1; Nanomedicine; Neoplasms; Protein Biosynthesis
PubMed: 35041892
DOI: 10.1016/j.canlet.2022.01.012 -
Nature Structural & Molecular Biology Dec 2021Close coordination between chaperones is essential for protein biosynthesis, including the delivery of tail-anchored (TA) proteins containing a single C-terminal...
Close coordination between chaperones is essential for protein biosynthesis, including the delivery of tail-anchored (TA) proteins containing a single C-terminal transmembrane domain to the endoplasmic reticulum (ER) by the conserved GET pathway. For successful targeting, nascent TA proteins must be promptly chaperoned and loaded onto the cytosolic ATPase Get3 through a transfer reaction involving the chaperone SGTA and bridging factors Get4, Ubl4a and Bag6. Here, we report cryo-electron microscopy structures of metazoan pretargeting GET complexes at 3.3-3.6 Å. The structures reveal that Get3 helix 8 and the Get4 C terminus form a composite lid over the Get3 substrate-binding chamber that is opened by SGTA. Another interaction with Get4 prevents formation of Get3 helix 4, which links the substrate chamber and ATPase domain. Both interactions facilitate TA protein transfer from SGTA to Get3. Our findings show how the pretargeting complex primes Get3 for coordinated client loading and ER targeting.
Topics: Animals; Arsenite Transporting ATPases; Cryoelectron Microscopy; Endoplasmic Reticulum; Humans; Models, Molecular; Molecular Chaperones; Protein Biosynthesis; Protein Conformation; Ubiquitins; Zebrafish; Zebrafish Proteins
PubMed: 34887561
DOI: 10.1038/s41594-021-00690-7 -
Methods (San Diego, Calif.) Sep 2019Protein synthesis is critical to cell survival and translation regulation is essential to post-transcriptional gene expression regulation. Disorders of this process,... (Review)
Review
Protein synthesis is critical to cell survival and translation regulation is essential to post-transcriptional gene expression regulation. Disorders of this process, particularly through RNA-binding proteins, is associated with the development and progression of a number of diseases, including cancers. However, the molecular mechanisms underlying the initiation of protein synthesis are intricate, making it difficult to find a drug that interferes with this process. Chemical probes are useful in elucidating the structures of RNA-protein complex and molecular mechanism of biological events. Moreover, some of these chemical probes show certain therapeutic benefits and can be further developed as leading compounds. Here, we will briefly review the general process and mechanism of protein synthesis, and emphasis on chemical probes in examples of probing the RNA structural changes and RNA-protein interactions. Moreover, the therapeutic potential of these probes is also discussed to give a comprehensive understanding.
Topics: Gene Expression Regulation; Humans; Molecular Biology; Nucleic Acid Conformation; Protein Biosynthesis; RNA; RNA-Binding Proteins; Small Molecule Libraries
PubMed: 31185274
DOI: 10.1016/j.ymeth.2019.06.004 -
Advances in Experimental Medicine and... 2023Protein folding accuracy is fundamental to all cells. In spite of this, it is difficult to maintain the fidelity of protein synthesis and folding due to the fact that...
Protein folding accuracy is fundamental to all cells. In spite of this, it is difficult to maintain the fidelity of protein synthesis and folding due to the fact that the implicit genetic and biochemical systems are inherently prone to error, which leads to the constant production of a certain amount of misfolded proteins. This problem is further compounded by genetic variation and the effects of environmental stress. To that end, the prediction of protein structures for tertiary protein structure analysis and prediction might be an ideal approach for the study of mutation effects in macromolecules and their complexes. With the development and accessibility to increasingly powerful computational systems, this type of study will enable a wide variety of opportunities for the creation of better-targeted peptide-based pharmacotherapy and prospects for precision medicine in future.
Topics: Proteins; Protein Folding; Protein Structure, Tertiary; Protein Biosynthesis
PubMed: 37486480
DOI: 10.1007/978-3-031-31982-2_7