Amino acid

Summary

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 α-amino acids, from which proteins are composed. Only 22 α-amino acids appear in the genetic code of all life. Amino acids can be classified according to the locations of the core structural functional groups, as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, ionization, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water being the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. It is thought that they played a key role in enabling life on Earth and its emergence. Amino acids are formall

Official source

https://en.wikipedia.org/wiki/Amino_acid

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The formation of supramolecular structures is a central issue in bio- and nanotechnology and therein plays an important role for many novel developments such as biocompatible materials for integrating living cells or coating for implantable sensing devices as well as for designing smart molecular sensor surfaces for miniaturized bioanalytical techniques. The main focus of this thesis is the investigation of polypeptide layers on surfaces, in particular the formation of self-assembled monolayers (SAMs). SAMs made of long hydrocarbon chains or aromatic molecules comprising surface active and other functional groups have been deeply characterized over decades. Surprisingly, peptide SAMs did not meet the same strong interest despite their great potential in several areas. Natural (20) and artificial amino acids with different physical and chemical properties offer a plethora of novel possibilities to design coating of solid surfaces. In fact their combination in simple oligopeptide sequences provides a huge number of molecular components for the formation of SAMs. Control of SAM features such as density, flexibility, adaptability, interface properties, by tailoring the amino acid sequence opens a new route to manifold applications ranging from fundamental research to nano- and biotechnology. In this thesis different and complementary techniques have been used to investigate the self-assembling ability of polypeptides on surfaces with different physical and chemical properties. Infrared spectroscopy and circular dichroism allowed the determination of the peptide secondary structure on surfaces and in solution. Surface plasmon resonance provided the optical thicknesses of peptide SAMs on gold whereas contact angle measurements have been used to characterize their interfacial properties. In the first part of the thesis, a series of hydrophobic peptides (Ac-Cys-Alax-CONH2, x=3-6) have been self assembled on gold via the thiol group present in the cysteine. The main interest was whether these peptides formed densely packed SAMs with a defined secondary structure within the layer and how the properties of such SAMs depended on the length of the polypeptide backbone. The second part concerns the study of the interactions of an amphipathic helical peptide with various functionalized substrates. The aim was to investigate whether a proper design of the peptide could be used to predetermine its secondary structure on the substrate and whether the orientation of the peptide on the surface could be directly controlled via certain parameters of the surrounding medium. Since the hydrophilic residues of the peptide are histidines, a particular effort was spent in characterizing the peptide adsorption on substrates exposing nitrilotriacetic acid (NTA) moieties. Once established that the adsorption process did not alter its helical structure, the peptide was adsorbed on a substrate exposing two different functional groups: NTA, that could interact with the histidine residues, and methyl groups, that could interact with the hydrophobic ones. The goal was to bind the peptide in different orientation to the same substrate, exploiting the particular spatial distribution of its residues. The third part of this thesis concern the formation of nano- and micro-sized fibrils through molecular self-assembly of simple oligopeptides and protected amino acids. Such systems were chosen as models to investigate the role of the different driving forces in the formation of fibrillar structures. The aromatic protecting group being fixed, it could be shown that the protected amino acids formed fibrils with different sizes and morphologies, or did not form fibrils at all, depending on how strongly their side chains interact. The possibility of forming fibrils by using protected amino acids is of major importance not only in bio-related field but also in organic nanotechnology.

EPFL2008

Azide-Containing Hypervalent Iodine Reagents for Biomolecules Functionalization

Raphaël Michel Henri Simonet-Davin

The goal of my PhD was the development of a new method for unselective surface labeling, not substrate-specific, that would give access to direct visualization of any surface interactions.In order to achieve this challenging goal, we wanted to develop a general non-specific method for biomolecule surface modification. With this in mind, azide was especially good due to its biorthogonal post-functionalization potential. Due to the precedence in using hypervalent iodine reagents for azide transfer, they were the perfect entry point to this strategy. However, Zhdankin reagent, known for almost 20 years, turned out to be more hazardous than commonly accepted. After few incidents caused by small detonations, an accident occurred in our lab. At this point, the goal became to synthesize first a fine-tuned family of analogues in order to obtain the best compromise between stability and reactivity. Seventeen analogues were synthesized and complete safety studies as well as reactivity comparison were conducted on the most relevant among them. Two analogues were identified as good substitute for the Zhdankin reagent.Then, this library was applied to our main project: obtain a homogeneous amino acid azidation on protein surface. Co-working with Dr. Daniel Abegg and Anton Shuster, the more efficient compound was determined and reaction conditions were screened for both in vitro and ex vivo reactions. Unexpectedly, the best reagent was not the same for in vitro and ex vivo experiments. Our reagents applied for proteomics experiments uncovered the full potential of this new method. We were able to achieve and excellent surface coverage of proteins, allowing us to access numerous useful applications such as: protein dynamics visualization, quantitative protein-protein binding determination, protein-protein dynamics visualization, protein-antibody active site determination.Investigations on azidation site determination on single amino acids and small peptides, combined with proteomic experiments on native and digested proteins confirmed that our method was not suitable for small substrates. Therefore, precise azidation site determination on each amino acid has been inaccessible so far.In summary, the development and applications of a broader family of fine-tuned azide- containing hypervalent iodine reagents are described. Biomolecule labeling was successfully performed via a new process of unselective surface azidation and post-functionalization with clickable fluorophores, or linkers for enrichment and proteomic applications with mass spectrometry analyses. Therefore, our method has been called Protein Surface Azidation coupled with Mass Spectrometry: ProSurA-MS. The great strength of our method is the non-selectivity of the surface azidation, allowing a "coating" of proteins giving straightforward access to the sequences masked by protein-protein, small molecule-protein or even conformational changes. As this method has been demonstrated to be efficient for any purified protein, cell lysates or even within living cells, we believe that it will be a major contribution to the field of biolabeling.

EPFL2022

Nature-inspired Circular-economy Recycling (NaCRe) for Proteins

Simone Giaveri

Since a few decades our planet has been loaded with billion tons of synthetic polymer-based materials, commonly named plastics. The large scale of plastic production, associated with its limited recyclability, are the driving force for the accumulation of such materials into the environment. Garbage patches, i.e. islands of plastics in the ocean, are striking evidences of this issue. A sustainable handling, that is production and disposal, of synthetic polymer-based materials is one of the greatest challenges that humanity has to face.Proteins and nucleic acids are natural polymers. Arguably, Nature produces an amount of such polymers that is higher with respect to man-made polymers. However, these materials do not accumulate into the environment, that is the approach used by Nature to handle these polymers is sustainable. The secret for its sustainaibility lies on the circularity in the materialsâ use. Indeed, proteins and nucleic acids are sequence-defined polymers that undergo depolymerization to monomers, and recycling into new materials by reassembling the so obtained monomers into arbitrarily different sequences. Organisms digest proteins into amino acids. These monomers are in turn polymerized to produce the protein of need, at the time of the protein synthesis.In this thesis we show that this process is achievable outside living organisms. Indeed, we depolymerized structurally different short peptides, and peptides mixtures into their constitutive amino acids, and recycled such monomers into biotechnologically relevant proteins (green, and red fluorescent proteins), by using an amino acid-free cell-free transcription-translation system. We further applied our methodology to recycle proteins with high relevance in materials engineering such as Î²-lactoglobulin films, used for water filtration, or silk fibroin solutions into green fluorescent protein. We were also successful in recycling mixtures composed of short peptides, and technologically relevant proteins into fluorescent proteins, as well as into bioactive enzymes (catechol 2,3-dioxygenase). Finally, we achieved multiple cycles of recycling (two cycles), and we demonstrated that the strategy can be expanded beyond the set of the twenty proteinogenic amino acids.Presented herein is a nature-inspired approach to recycling of soft materials, where unknown mixtures of polymers are recycled into the polymer of need, by the local community, at the time of recycling. The materials are costantly transformed into different ones, without any external feed, and there is no way to distinguish a new polymer from a recycled one. The strength of this method lies in its compatibility with the principles of circular economy.

EPFL2021