2,633 results match your criteria unnatural amino


Current Advances in Covalent Stabilization of Macromolecular Complexes for Structural Biology.

Bioconjug Chem 2021 Apr 16. Epub 2021 Apr 16.

Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.

Structural characterization of macromolecular assemblies is often limited by the transient nature of the interactions. The development of specific chemical tools to covalently tether interacting proteins to each other has played a major role in various fundamental discoveries in recent years. To this end, protein engineering techniques such as mutagenesis, incorporation of unnatural amino acids, and methods using synthetic substrate/cosubstrate derivatives were employed. Read More

View Article and Full-Text PDF

Host-Guest Induced Peptide Folding with Sequence-Specific Structural Chirality.

J Am Chem Soc 2021 Apr 16. Epub 2021 Apr 16.

Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

Controlling the spatial and temporal behavior of peptide segments is essential in the fabrication of functional peptide-based materials and nanostructures. To achieve a desired structure, complex sequence design is often required, coupled with the inclusion of unnatural amino acids or synthetic modifications. Herein, we investigate the structural properties of 1:1 inclusion complexes between specific oligopeptides and cucurbit[8]uril (CB[8]), inducing the formation of turns, and by alteration of the peptide sequence, tunable structural chirality. Read More

View Article and Full-Text PDF

Imaging Commensal Microbiota and Pathogenic Bacteria in the Gut.

Acc Chem Res 2021 Apr 15. Epub 2021 Apr 15.

Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.

ConspectusAs a newly discovered organ, gut microbiota has been extensively studied in the last two decades, with their highly diverse and fundamental roles in the physiology of many organs and systems of the host being gradually revealed. However, most of the current research heavily relies on DNA sequencing-based methodologies. To truly understand the complex physiological and pathological functions demonstrated by commensal and pathogenic gut bacteria, we need more powerful methods and tools, among which imaging strategies suitable for approaching this ecosystem in different settings are one of the most desirable. Read More

View Article and Full-Text PDF

Switchable CAR-T Cells Outperformed Traditional Antibody-Redirected Therapeutics Targeting Breast Cancers.

ACS Synth Biol 2021 Apr 15. Epub 2021 Apr 15.

California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, California 92037, United States.

Various antibody-redirected immunotherapeutic approaches, including antibody-drug conjugates (ADCs), bispecific antibodies (bsAbs), and chimeric antigen receptor-T (CAR-T) cells, have been devised to produce specific activity against various cancer types. Using genetically encoded unnatural amino acids, we generated a homogeneous Her2-targeted ADC, a T cell-redirected bsAb, and a FITC-modified antibody capable of redirecting anti-FITC CAR-T (switchable CAR-T; sCAR-T) cells to target different Her2-expressing breast cancers. sCAR-T cells showed activity against Her2-expressing tumor cells comparable to that of conventional anti-Her2 CAR-T cells and superior to that of ADC- and bsAb-based approaches. Read More

View Article and Full-Text PDF

Amber codon is genetically unstable in generation of premature termination codon (PTC)-harbouring Foot-and-mouth disease virus (FMDV) via genetic code expansion.

RNA Biol 2021 Apr 14:1-12. Epub 2021 Apr 14.

State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China.

The foot-and-mouth disease virus (FMDV) is the causative agent of FMD, a highly infectious and devastating viral disease of domestic and wild cloven-hoofed animals. FMD affects livestock and animal products' national and international trade, causing severe economic losses and social consequences. Currently, inactivated vaccines play a vital role in FMD control, but they have several limitations. Read More

View Article and Full-Text PDF

Chemogenetic and optogenetic control of post-translational modifications through genetic code expansion.

Curr Opin Chem Biol 2021 Apr 9;63:123-131. Epub 2021 Apr 9.

Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA. Electronic address:

Post-translational modifications (PTMs) of proteins extensively diversify the biological information flow from the genome to the proteome and thus have profound pathophysiological implications. Precise dissection of the regulatory networks of PTMs benefits from the ability to achieve conditional control through external optogenetic or chemogenetic triggers. Genetic code expansion provides a unique solution by allowing for site-specific installation of functionally masked unnatural amino acids (UAAs) into proteins, such as enzymes and enzyme substrates, rendering them inert until rapid activation through exposure to light or small molecules. Read More

View Article and Full-Text PDF

In-Cell Characterization of the Stable Tyrosyl Radical in E. coli Ribonucleotide Reductase via Advanced EPR Spectroscopy.

Angew Chem Int Ed Engl 2021 Apr 12. Epub 2021 Apr 12.

Technische Universitat Dortmund, Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, GERMANY.

The E. coli ribonucleotide reductase (RNR), a paradigm for class Ia enzymes including human RNR, catalyzes the biosynthesis of DNA building blocks and requires a di-iron tyrosyl radical (Y122•) cofactor for activity. The knowledge on in vitro Y122• structure and its radical distribution within ß2 subunit has accumulated over the years; yet, little information exists on in vivo Y122•. Read More

View Article and Full-Text PDF

The Benefits of Unnatural Amino Acid Incorporation as Protein Labels for Single Molecule Localization Microscopy.

Front Chem 2021 25;9:641355. Epub 2021 Mar 25.

European Molecular Biology Laboratory (EMBL) Australia Node in Single Molecule Sciences, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.

Single Molecule Localization Microscopy (SMLM) is an imaging method that allows for the visualization of structures smaller than the diffraction limit of light (~200 nm). This is achieved through techniques such as stochastic optical reconstruction microscopy (STORM) and photoactivated localization microscopy (PALM). A large part of obtaining ideal imaging of single molecules is the choice of the right fluorescent label. Read More

View Article and Full-Text PDF

Synthesis of six-membered carbocyclic ring α,α-disubstituted amino acids and arginine-rich peptides to investigate the effect of ring size on the properties of the peptide.

Bioorg Med Chem 2021 Mar 19;38:116111. Epub 2021 Mar 19.

Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.

Cell-penetrating peptides (CPPs) have been attracting attention as tools for intracellular delivery of membrane-impermeant functional molecules. Among the variety of CPPs that have been developed, many are composed of both natural and unnatural amino acids. We previously synthesized α,α-disubstituted α-amino acids (dAAs) containing a five-membered carbocyclic ring in its side chain and revealed the utility of dAAs for the development of novel CPPs. Read More

View Article and Full-Text PDF

Mechanistic Similarities of Sesquiterpene Cyclases PenA, Omp6/7, and BcBOT2 Are Unraveled by an Unnatural "FPP-Ether" Derivative.

Org Lett 2021 Apr 7;23(8):3162-3166. Epub 2021 Apr 7.

Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167 Hannover, Germany.

The sesquiterpene cyclases pentalenene synthase (PenA) and two Δ-protoilludene synthases Omp6 and Omp7 convert a FPP ether into several new tetrahydrofurano terpenoids, one of which is also formed as the main product by the sesquiterpene cyclase BcBOT2. Thus, PenA, Omp6/7, and BcBOT2 follow closely related catalytic pathways and induce similar folding of their diphosphate substrates despite low levels of amino acid sequence similarity. Some of the new terpenoids show pronounced olfactoric properties. Read More

View Article and Full-Text PDF

Abiological Catalysis by Myoglobin Mutant with a Genetically Incorporated Unnatural Amino Acid.

Biochem J 2021 Apr 6. Epub 2021 Apr 6.

The University of Texas, Arlington, Texas, United States.

To inculcate biocatalytic activity in the oxygen-storage protein myoglobin (Mb), a genetically engineered myoglobin mutant H64DOPA (DOPA = L-3,4-dihydroxyphenylalanine) has been created.  Incorporation of unnatural amino acids has already demonstrated their ability to accomplish many non-natural functions in proteins efficiently.  Herein, the presence of redox-active DOPA residue in the active site of mutant Mb presumably stabilizes the compound I in the catalytic oxidation process by participating in an additional hydrogen bonding (H-bonding) as compared to the WT Mb. Read More

View Article and Full-Text PDF

Molecular Oxygen-Mediated Radical Alkylation of C(sp)-H Bonds with Boronic Acids.

Org Lett 2021 Apr 6;23(8):3207-3210. Epub 2021 Apr 6.

Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China.

A direct and site-specific alkylation of (sp)C-H bond with aliphatic boronic acid was achieved. By simply heating glycinates and amines together with alkylboronic acids under an oxygen atmosphere, a variety of unnatural α-amino acids and peptides could be obtained in good yields. Read More

View Article and Full-Text PDF

Bioorthogonal dissection of the replicase assembly of hepatitis C virus.

Cell Chem Biol 2021 Mar 26. Epub 2021 Mar 26.

Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai 201052, China. Electronic address:

Positive-strand RNA viruses such as hepatitis C virus (HCV), flaviviruses, and coronaviruses are medically important. Assembly of replicase on host membranes is a conserved replication strategy and an attractive antiviral target. The mechanisms of replicase assembly are largely unknown, due to the technical difficulties in purifying the replicase and carrying out structural studies. Read More

View Article and Full-Text PDF

Contribution of the μ opioid receptor and enkephalin to the antinociceptive actions of endomorphin-1 analogs with unnatural amino acid modifications in the spinal cord.

Peptides 2021 Mar 29;141:170543. Epub 2021 Mar 29.

Department of Pharmacology, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, PR China. Electronic address:

Endomorphin analogs containing unnatural amino acids have demonstrated potent analgesic effects in our previous studies. In the present study, the differences in antinociception and the mechanisms thereof for analogs 1-3 administered intracerebroventricularly and intrathecally were explored. All analogs at different routes of administration produced potent analgesia compared to the parent peptide endomorphin-1. Read More

View Article and Full-Text PDF

Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores.

J Am Chem Soc 2021 Apr 30;143(14):5497-5507. Epub 2021 Mar 30.

Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.

Genetically encoded macrocyclic peptide libraries with unnatural pharmacophores are valuable sources for the discovery of ligands for many targets of interest. Traditionally, generation of such libraries employs "early stage" incorporation of unnatural building blocks into the chemically or translationally produced macrocycles. Here, we describe a divergent late-stage approach to such libraries starting from readily available starting material: genetically encoded libraries of peptides. Read More

View Article and Full-Text PDF

Design and Structure-Activity Relationship of a Potent Furin Inhibitor Derived from Influenza Hemagglutinin.

ACS Med Chem Lett 2021 Mar 5;12(3):365-372. Epub 2021 Feb 5.

Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada.

Furin plays an important role in various pathological states, especially in bacterial and viral infections. A detailed understanding of the structural requirements for inhibitors targeting this enzyme is crucial to develop new therapeutic strategies in infectious diseases, including an urgent unmet need for SARS-CoV-2 infection. Previously, we have identified a potent furin inhibitor, peptide Ac-RARRRKKRT- (CF1), based on the highly pathogenic avian influenza hemagglutinin. Read More

View Article and Full-Text PDF

Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa.

Adv Biol (Weinh) 2021 Mar 8;5(3):e2000308. Epub 2021 Feb 8.

MOE Laboratory of Biosystem Homeostasis and Protection and Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.

Protein crosslinks occur endogenously such as modifications by ubiquitin-like proteins for signaling, or exogenously through genetically encoded chemical crosslinkers (GECX) for studying elusive protein-protein interactions. However, it remains challenging to identify these protein crosslinks efficiently at the proteomic scale. Herein, software OpenUaa is developed for identifying protein crosslinks generated by genetically encoded unnatural amino acids and endogenous protein conjugation. Read More

View Article and Full-Text PDF

Genetic Code Expansion of .

Front Bioeng Biotechnol 2021 26;9:594429. Epub 2021 Feb 26.

Department of Life Sciences, Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

has been considered as the most used model bacteria in the majority of studies for several decades. However, a new, faster chassis for synthetic biology is emerging in the form of the fast-growing gram-negative bacterium . Different methodologies, well established in , are currently being adapted for in the hope to enable a much faster platform for general molecular biology studies. Read More

View Article and Full-Text PDF
February 2021

Determination of modification sites and relative quantitation in large protein conjugation via automated data processing.

J Pharm Biomed Anal 2021 May 27;198:113995. Epub 2021 Feb 27.

Analytical Research & Development, Process Research & Development, Merck & Co., Inc., Rahway, NJ 07065, USA. Electronic address:

Protein conjugation is an effective way to impart different functionalities to the original protein. Conjugation using a native protein (a protein that does not contain special unnatural amino acid for conjugation) typically generates complex mixtures mainly due to the presence of multiple chemically similar competing conjugation sites. It is therefore a challenge to identify products, to optimize the reaction conditions, and to synthesize desired molecules. Read More

View Article and Full-Text PDF

Site-specifically wired and oriented glucose dehydrogenase fused to a minimal cytochrome with high glucose sensing sensitivity.

Biosens Bioelectron 2021 May 27;180:113117. Epub 2021 Feb 27.

Departments of Life Sciences, Chemistry and Ilse Katz institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, PoBox 653, Beer-Sheva, 8410501, Israel. Electronic address:

Direct electron transfer based enzymatic biosensors are highly efficient systems where electrons are transferred directly from the enzyme's electroactive site to the electrode. One way of achieving it is by 'wiring' the enzyme to the electrode surface. The wiring of enzymes to electrode surfaces can be reached in many different ways but controlling its orientation towards the electrode surface is still a challenge. Read More

View Article and Full-Text PDF

Chemical modifications of proteins and their applications in metalloenzyme studies.

Synth Syst Biotechnol 2021 Mar 15;6(1):32-49. Epub 2021 Feb 15.

Department of Chemistry, Boston University, Boston, MA, 02215, United States.

Protein chemical modifications are important tools for elucidating chemical and biological functions of proteins. Several strategies have been developed to implement these modifications, including enzymatic tailoring reactions, unnatural amino acid incorporation using the expanded genetic codes, and recognition-driven transformations. These technologies have been applied in metalloenzyme studies, specifically in dissecting their mechanisms, improving their enzymatic activities, and creating artificial enzymes with non-natural activities. Read More

View Article and Full-Text PDF

Synthesis of Unnatural α-Amino Acids via Photoinduced Decatungstate-Catalyzed Giese Reactions of Aldehydes.

Org Lett 2021 Mar 4;23(6):2199-2204. Epub 2021 Mar 4.

State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China.

Synthesis of unnatural amino acids has long been a focus of chemistry research. Here, we present an efficient, general method that furnishes γ-carbonyl α-amino acids via photoinduced decatungstate-catalyzed Giese reactions of readily available aldehydes as radical precursors. This mild, robust method is compatible with a wide array of functional groups and has a broad substrate scope. Read More

View Article and Full-Text PDF

Site-by-site tracking of signal transduction in an azidophenylalanine-labeled bacteriophytochrome with step-scan FTIR spectroscopy.

Phys Chem Chem Phys 2021 Mar;23(9):5615-5628

University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.

Signal propagation in photosensory proteins is a complex and multidimensional event. Unraveling such mechanisms site-specifically in real time is an eligible but a challenging goal. Here, we elucidate the site-specific events in a red-light sensing phytochrome using the unnatural amino acid azidophenylalanine, vibrationally distinguishable from all other protein signals. Read More

View Article and Full-Text PDF

Conversion of Racemic Unnatural Amino Acids to Optically Pure Forms by a Coupled Enzymatic Reaction.

Molecules 2021 Feb 26;26(5). Epub 2021 Feb 26.

Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Korea.

Genetic code expansion (GCE) technology is a useful tool for the site-specific modification of proteins. An unnatural amino acid (UAA) is one of the essential components of this technique, typically required at high concentration (1 mM or higher) in growth medium. The supply of UAAs is an important limitation to the application of GCE technology, as many UAAs are either expansive or commercially unavailable. Read More

View Article and Full-Text PDF
February 2021

A Genetically Encoded Two-Dimensional Infrared Probe for Enzyme Active-Site Dynamics.

Angew Chem Int Ed Engl 2021 Feb 28. Epub 2021 Feb 28.

Institute of Biophysics, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China.

While two-dimensional infrared (2D-IR) spectroscopy is uniquely suitable for monitoring femtosecond (fs) to picosecond (ps) water dynamics around static protein structures, its utility for probing enzyme active-site dynamics is limited due to the lack of site-specific 2D-IR probes. We demonstrate the genetic incorporation of a novel 2D-IR probe, m-azido-L-tyrosine (N3Y) in the active-site of DddK, an iron-dependent enzyme that catalyzes the conversion of dimethylsulfoniopropionate to dimethylsulphide. Our results show that both the oxidation of active-site iron to Fe , and the addition of denaturation reagents, result in significant decrease in enzyme activity and active-site water motion confinement. Read More

View Article and Full-Text PDF
February 2021

Peptidomimetics - An infinite reservoir of metal binding motifs in metabolically stable and biologically active molecules.

J Inorg Biochem 2021 Apr 10;217:111386. Epub 2021 Feb 10.

Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland. Electronic address:

The involvement of metal ions in interactions with therapeutic peptides is inevitable. They are one of the factors able to fine-tune the biological properties of antimicrobial peptides, a promising group of drugs with one large drawback - a problematic metabolic stability. Appropriately chosen, proteolytically stable peptidomimetics seem to be a reasonable solution of the problem, and the use of D-, β-, γ-amino acids, unnatural amino acids, azapeptides, peptoids, cyclopeptides and dehydropeptides is an infinite reservoir of metal binding motifs in metabolically stable, well-designed, biologically active molecules. Read More

View Article and Full-Text PDF

Metabolically stable neurotensin analogs exert potent and long-acting analgesia without hypothermia.

Behav Brain Res 2021 May 17;405:113189. Epub 2021 Feb 17.

Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada. Electronic address:

The endogenous tridecapeptide neurotensin (NT) has emerged as an important inhibitory modulator of pain transmission, exerting its analgesic action through the activation of the G protein-coupled receptors, NTS1 and NTS2. Whereas both NT receptors mediate the analgesic effects of NT, NTS1 activation also produces hypotension and hypothermia, which may represent obstacles for the development of new pain medications. In the present study, we implemented various chemical strategies to improve the metabolic stability of the biologically active fragment NT(8-13) and assessed their NTS1/NTS2 relative binding affinities. Read More

View Article and Full-Text PDF

Development of a High-Affinity Antibody-Binding Peptide for Site-Specific Modification.

ChemMedChem 2021 Feb 17. Epub 2021 Feb 17.

Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan.

Immunoglobulin G (IgG)-binding peptides such as 15-IgBP are convenient tools for the site-specific modification of antibodies and the preparation of homogeneous antibody-drug conjugates. A peptide such as 15-IgBP can be selectively crosslinked to the fragment crystallizable region of human IgG in an affinity-dependent manner via the ϵ-amino group of Lys8. Previously, we found that the peptide 15-Lys8Leu has a high affinity (K =8. Read More

View Article and Full-Text PDF
February 2021

A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition.

Angew Chem Int Ed Engl 2021 Feb 12. Epub 2021 Feb 12.

State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.

Regulation of specific protein function is of great importance for both research and therapeutic development. Many small or large molecules have been developed to control specific protein function, but there is a lack of a universal approach to regulate the function of any given protein. We report a general host-guest molecular recognition approach involving modification of the protein functional surfaces with genetically encoded unnatural amino acids bearing guest side chains that can be specifically recognized by cucurbit[7]uril. Read More

View Article and Full-Text PDF
February 2021

Synthesis and Evaluation of Novel Ring-Strained Noncanonical Amino Acids for Residue-Specific Bioorthogonal Reactions in Living Cells.

Chemistry 2021 Apr 4;27(19):6094-6099. Epub 2021 Mar 4.

European Molecular Biology Laboratory, Meyerhofstr.1, 69117, Heidelberg, Germany.

Bioorthogonal reactions are ideally suited to selectively modify proteins in complex environments, even in vivo. Kinetics and product stability of these reactions are crucial parameters to evaluate their usefulness for specific applications. Strain promoted inverse electron demand Diels-Alder cycloadditions (SPIEDAC) between tetrazines and strained alkenes or alkynes are particularly popular, as they allow ultrafast labeling inside cells. Read More

View Article and Full-Text PDF