Nediljko "Ned" Budisa | |
---|---|
![]() Ned in a TU Berlin Laboratory in 2012 | |
Born | |
Nationality | Croatian |
Alma mater | Faculty of Science, University of Zagreb |
Scientific career | |
Fields | Biochemistry, bioorganic chemistry, synthetic biology |
Institutions | University of Manitoba |
Nediljko "Ned" Budisa (Croatian : Nediljko Budiša; born 21 November 1966) is a Croatian biochemist, professor and holder of the Tier 1 Canada Research Chair (CRC) for chemical synthetic biology at the University of Manitoba. As pioneer in the areas of genetic code engineering and chemical synthetic biology (Xenobiology), his research has a wide range of applications in biotechnology and engineering biology in general. Being highly interdisciplinary, it includes bioorganic and medical chemistry, structural biology, biophysics and molecular biotechnology as well as metabolic and biomaterial engineering. He is the author of the only textbook in his research field: “Engineering the genetic code: expanding the amino acid repertoire for the design of novel proteins”. [1]
Ned Budisa earned a High school teacher diploma in Chemistry and Biology in 1990, a B.S. in Molecular Biology and MSc in Biophysics in 1993 from the University of Zagreb. He received a PhD in 1997 from the Technical University of Munich where his thesis advisor was Professor Robert Huber. He also habilitated at the Technical University of Munich in 2005 and worked afterwards as a junior group leader ("Molecular Biotechnology") [2] at the Max Planck Institute for Biochemistry in Munich. Between 2007 and 2010 he was a member of CIPSM in Munich. [3] He was appointed as full professor of biocatalysis at the TU Berlin in 2010 [4] until the end of 2018, when he accepted the Tier 1 CRC position in Chemical Synthetic Biology at the University of Manitoba. [5] Ned Budisa is also a member of the Excellence Cluster ‘Unifying Systems in Catalysis’ (UniSysCat) [6] and keeps adjunct professor status at the TU Berlin. In 2014, he founded the first Berlin iGEM team. [7]
Ned Budisa applies the Selective Pressure Incorporation (SPI) method [8] that enables single and multiple [9] in vivo incorporations of synthetic (i.e. non-canonical) amino acid analogs in proteins, preferably by sense codon reassignment. [10] His methodology allows for fine chemical manipulations of the amino acid side chains, mainly of proline, tryptophan and methionine. These experiments are often assisted with simple metabolic engineering. [11] [12] Ned's research goal is the transfer of various physicochemical properties and bioorthogonal chemistry reactions (chemoselective ligations such as click chemistry) as well as special spectroscopic features (e.g. blue [13] and golden [14] fluorescence or vibration energy transfer [15] ) into the proteins of living cells. In addition, his method allows the delivery of element-specific properties (fluorine, selenium and tellurium) into the biochemistry of life. [16]
Ned Budisa is well known for the establishment of the use of selenium-containing non-canonical amino acids for protein X-ray crystallography [17] and fluorine-containing analogs for 19F NMR-spectroscopy and protein folding studies. [18] He was the first to demonstrate the use of genetic code engineering as a tool for the creation of therapeutic proteins [19] and ribosomally synthesized peptide-drugs. [20] He has succeeded with innovative engineering of biomaterials, in particular photoactivatable mussel-based underwater adhesives. [21] Ned Budisa made seminal contributions to our understanding of the role of methionine oxidation in prion protein aggregation [22] and has discovered the roles of proline side chain conformations (endo-exo isomerism) in translation, folding and stability of proteins. [23] [24]
Together with his co-worker Vladimir Kubyshkin, the new-to-nature hydrophobic [25] polyproline-II helix foldamer was designed. Along with Budisa's previous work on bioexpression using proline analogues, the results of this project contributed to the establishment of the Alanine World hypothesis. [26] It explains why nature chose the genetic code [27] with "only" 20 canonical amino acids for ribosomal protein synthesis. [28]
In 2015, the team led by Ned Budisa reported the successful completion of a long-term evolution experiment that resulted in full, proteome-wide substitution of all 20,899 tryptophan residues with thienopyrrole-alanine in the genetic code of the bacterium Escherichia coli. [29] This is a solid basis for the evolution of life with alternative building blocks, foldamers or biochemistries. [30] At the same time, this approach might be an interesting biosafety technology to evolve biocontained synthetic cells [31] equipped with a "genetic firewall" which prevents their survival outside of man-made unnatural environments. [32] Similar experiments with fluorinated tryptophan analogs [33] as xenobiotic compounds (in collaboration with Beate Koksch from the Free University of Berlin) has led to the discovery of exceptional physiological plasticity in microbial cultures during adaptive laboratory evolution, making them potential environmentally friendly tools for new bioremediation strategies.
Ned Budisa is also actively involved in the debate of possible societal, ethical and philosophical impacts of radical genetic code engineering in the context of synthetic cells and life as well as technologies derived thereof. [34]
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 appear in the genetic code of life.
The genetic code is the set of rules used by living cells to translate information encoded within genetic material into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.
Cysteine is a semiessential proteinogenic amino acid with the formula HOOC−CH(−NH2)−CH2−SH. The thiol side chain in cysteine enables the formation of disulfide bonds, and often participates in enzymatic reactions as a nucleophile. Cysteine is chiral, but both D and L-cysteine are found in nature. L‑Cysteine is a protein monomer in all biota, and D-cysteine acts as a signaling molecule in mammalian nervous systems. Cysteine is named after its discovery in urine, which comes from the urinary bladder or cyst, from Greek κύστη kýsti, "bladder".
Pyrrolysine is an α-amino acid that is used in the biosynthesis of proteins in some methanogenic archaea and bacteria; it is not present in humans. It contains an α-amino group and a carboxylic acid group. Its pyrroline side-chain is similar to that of lysine in being basic and positively charged at neutral pH.
Alanine, or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side chain. Consequently it is classified as a nonpolar, aliphatic α-amino acid. Under biological conditions, it exists in its zwitterionic form with its amine group protonated and its carboxyl group deprotonated. It is non-essential to humans as it can be synthesized metabolically and does not need to be present in the diet. It is encoded by all codons starting with GC.
Synthetic biology (SynBio) is a multidisciplinary field of science that focuses on living systems and organisms, and it applies engineering principles to develop new biological parts, devices, and systems or to redesign existing systems found in nature.
Auxotrophy is the inability of an organism to synthesize a particular organic compound required for its growth. An auxotroph is an organism that displays this characteristic; auxotrophic is the corresponding adjective. Auxotrophy is the opposite of prototrophy, which is characterized by the ability to synthesize all the compounds needed for growth.
Supramolecular chemistry refers to the branch of chemistry concerning chemical systems composed of a discrete number of molecules. The strength of the forces responsible for spatial organization of the system range from weak intermolecular forces, electrostatic charge, or hydrogen bonding to strong covalent bonding, provided that the electronic coupling strength remains small relative to the energy parameters of the component. While traditional chemistry concentrates on the covalent bond, supramolecular chemistry examines the weaker and reversible non-covalent interactions between molecules. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi–pi interactions and electrostatic effects.
Xenobiology (XB) is a subfield of synthetic biology, the study of synthesizing and manipulating biological devices and systems. The name "xenobiology" derives from the Greek word xenos, which means "stranger, alien". Xenobiology is a form of biology that is not (yet) familiar to science and is not found in nature. In practice, it describes novel biological systems and biochemistries that differ from the canonical DNA–RNA-20 amino acid system. For example, instead of DNA or RNA, XB explores nucleic acid analogues, termed xeno nucleic acid (XNA) as information carriers. It also focuses on an expanded genetic code and the incorporation of non-proteinogenic amino acids, or “xeno amino acids” into proteins.
In chemistry, a molecular knot is a mechanically interlocked molecular architecture that is analogous to a macroscopic knot. Naturally-forming molecular knots are found in organic molecules like DNA, RNA, and proteins. It is not certain that naturally occurring knots are evolutionarily advantageous to nucleic acids or proteins, though knotting is thought to play a role in the structure, stability, and function of knotted biological molecules. The mechanism by which knots naturally form in molecules, and the mechanism by which a molecule is stabilized or improved by knotting, is ambiguous. The study of molecular knots involves the formation and applications of both naturally occurring and chemically synthesized molecular knots. Applying chemical topology and knot theory to molecular knots allows biologists to better understand the structures and synthesis of knotted organic molecules.
Chemical biology is a scientific discipline between the fields of chemistry and biology. The discipline involves the application of chemical techniques, analysis, and often small molecules produced through synthetic chemistry, to the study and manipulation of biological systems. Although often confused with biochemistry, which studies the chemistry of biomolecules and regulation of biochemical pathways within and between cells, chemical biology remains distinct by focusing on the application of chemical tools to address biological questions.
Click chemistry is an approach to chemical synthesis that emphasizes efficiency, simplicity, selectivity, and modularity in chemical processes used to join molecular building blocks. It includes both the development and use of "click reactions", a set of simple, biocompatible chemical reactions that meet specific criteria like high yield, fast reaction rates, and minimal byproducts. It was first fully described by K. Barry Sharpless, Hartmuth C. Kolb, and M. G. Finn of The Scripps Research Institute in 2001. In this seminal paper, Sharpless argued that synthetic chemistry could emulate the way nature constructs complex molecules, using efficient reactions to join together simple, non-toxic building blocks.
Directed evolution (DE) is a method used in protein engineering that mimics the process of natural selection to steer proteins or nucleic acids toward a user-defined goal. It consists of subjecting a gene to iterative rounds of mutagenesis, selection and amplification. It can be performed in vivo, or in vitro. Directed evolution is used both for protein engineering as an alternative to rationally designing modified proteins, as well as for experimental evolution studies of fundamental evolutionary principles in a controlled, laboratory environment.
Bioconjugation is a chemical strategy to form a stable covalent link between two molecules, at least one of which is a biomolecule. Methods to conjugate biomolecules are applied in various field, including medicine, diagnostics, biocatalysis and materials. Synthetically modified biomolecules can have diverse functionalities, such as tracking cellular events, revealing enzyme function, determining protein biodistribution, imaging specific biomarkers, and delivering drugs to targeted cells.
An expanded genetic code is an artificially modified genetic code in which one or more specific codons have been re-allocated to encode an amino acid that is not among the 22 common naturally-encoded proteinogenic amino acids.
An alloprotein is a novel synthetic protein containing one or more "non-natural" amino acids. Non-natural in the context means an amino acid either not occurring in nature, or occurring in nature but not naturally occurring within proteins.
Photoactivated peptides are modified natural or synthetic peptides whose functions can be activated or controlled using light. These peptides incorporate light-sensitive elements that allow for precise regulation their biological activity in both space and time. The activation can be either irreversible, as in the case of caged peptides with photocleavable protecting groups, or reversible, utilizing molecular photoswitches like azobenzenes or diarylethenes, and diarylethenes By incorporating these light-responsive components into the peptide structure, peptide properties, functions, and biological activities can be manipulated with high precision. This approach enables targeted activation of peptides in specific areas, making photoactivated peptides valuable tools for applications in cancer therapy, drug delivery, and probing molecular interactions in living cells and in organisms.
An artificial metalloenzyme (ArM) is a designer metalloprotein, not found in nature, which can catalyze desired chemical reactions. Despite fitting into classical enzyme categories, ArMs also have potential in new-to-nature chemical reactivity like catalysing Suzuki coupling, Metathesis etc., which were never reported among natural enzymatic reactions.
Luis Moroder was an Italian peptide chemist, who pioneered research on the interactions between peptide hormones and cell membrane-bound hormone receptors. He later expanded this research to other biological systems of medical relevance such as protein inhibitors, collagens, and synthetic proteins. A hallmark of his research is interdisciplinarity as reflected in his use and development of methods in organic chemistry, biophysics and molecular biology. He was a co-editor of the five-volume Houben-Weyl, Methods of Organic Chemistry, Synthesis of Peptides and Peptidomimetics. From 2008 he was the editor-in-chief of the Journal of Peptide Science, the official journal of the European Peptide Society.
Jason Micklefield is a British Biochemist and a professor in the Department of Chemistry at The University of Manchester. His research involves the discovery, characterisation and engineering of biosynthetic pathways to new bioactive natural products, particularly antibiotics. He is also interested in the discovery, structure, mechanism and engineering of enzymes for synthetic applications, including the integration of enzymes with chemocatalysis for telescoping routes to pharmaceuticals and other valuable products.
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