Oligonucleotides, proteins, peptides, and carbohydrates are the best known biopolymers and one doesn’t have to explain how important each is to a number of biological functions. The synthesis of these materials, or segments of them, are important in order to …
Essentially, biomolecule assisted synthesis of inorganic nanoparticles can be divided into two categories. One uses multi-domain protein cages (template) and other relies on the self-assembly of the biomolecules including small peptides, DNA, and denatured protein. Protein templated synthesis of various nanomaterials is relatively well understood as the cages of the biological macromolecules and their specific interaction with inorganic ions ultimately dictate the size and crystallinity of the nanomaterials. On the other hand formation of nanoparticles using protein in the cost of the native structural integrity for the self-assembly is not well understood till date. In the present work we report a protein-assisted synthesis route to prepare highly crystalline 3–5 nm gold nanoparticles, which relies systematic thermal denaturation of a number of proteins and protein mixture from Escherichia coli in absence of any reducing agent. By using UV–vis, circular dichroism spectroscopy, and high-resolution transmission electron microscopy we have explored details of the associated biochemistry of the proteins dictating kinetics, size, and crystallinity of the nanoparticles. The kinetics of nanoparticles formation in this route, which is sigmoidal in nature, has been modelled in a simple scheme of autocatalytic process. Interestingly, the protein-capped as prepared Au nanoparticles are found to serve as effective catalyst to activate the reduction of 4-nitrophenol in the presence of NaBH4. The kinetic data obtained by monitoring the reduction of 4-nitrophenol by UV/vis-spectroscopy revealing the efficient catalytic activity of the nanoparticles have been explained in terms of the Langmuir–Hinshelwood model. The methodology and the details of the protein chemistry presented here may find relevance in the protein-assisted synthesis of inorganic nanostructures in general.
are the most diverse biomolecules on Earth, performing many functions required for life. Protein are biological catalysts, maintaining life by regulating where and when cellular reactions occur. Structural proteins provide internal and external support to protect and maintain cell shape. For example, keratins are an important class of structural proteins found in the hair, skin, nails, and feathers of animals. Motility proteins provide the basis for cellular and whole organism movement, including muscle motor proteins that can move entire animals! Membrane proteins transmit signals during cell-to-cell communication, transport molecules into and out of cells, and protect living organisms by identifying and flagging invaders.
Protein functions are so diverse because of the many unique three-dimensional structures protein polymers form. Despite such variety, proteins also share several specific structural characteristics in their monomers, the . Structural similarities among amino acids make protein synthesis a uniform and regulated process; however, each amino acid contains a unique structural component as well. Specific differences between each amino acid interact to create unique three-dimensional protein structures. Combined, the similarities and differences between amino acids explain how cells can build a diverse pool of proteins from the same set of building blocks.
We report on the development of a bottom-up nanoantenna to enhance the fluorescence intensity in a reduced hot-spot, ready for biological applications. We use self-assembled DNA origami structures as a breadboard where different gold nanoparticle systems consisting of dimers and monomers are positioned with nanometer precision. The dependence of the fluorescence enhancement on nanoparticle size is studied and compared to numerical simulations. A maximum of 100fold intensity enhancement is obtained using 100 nm gold nanoparticles at a gap of 23 nm between the dimer. Additionally, the binding and unbinding of short DNA strands on the hotspot of the nanoantenna is realized, showing the compatibility of this technique with biomolecular assays. The combination of metallic nanoparticles with DNA origami structures with docking points for biological assays paves the way for the development of bottom up inexpensive enhancement chambers for single molecule measurements at high concentrations where processes like DNA sequencing occurs.
Funding by a starting grant (SiMBA) of the European Research Council, the Volkswagen Foundation, and the Center for NanoScience is gratefully acknowledged.
Unlike polysaccharides, polypeptide chains are assembled with a wide variety of amino acids in each polymer. The set of twenty amino acids commonly found in biological proteins is directly responsible for the diversity of protein structures in living cells. Each protein differs in several aspects that determine structure and, therefore, function. A protein may be composed of one or more polypeptide strands. A cell’s genes determine the length of each polypeptide strand, as well as the type and position of each amino acid in the sequence. Together, these factors determine protein structure, which determines the function a protein can perform.
How does protein structure determine function? The three-dimensional shape of each protein is perfectly suited to perform one specific function. For example, aquaporins are channel proteins that form small tunnels through a cell membrane. The internal surface of aquaporin tunnels possesses a specific diameter and polarity. This structure is perfectly designed to transport water molecules but very little else, providing specificity and function. If protein structure changes, so does a protein’s ability to function.
Gold nanoparticles have attracted considerable attention in molecular recognition applications due to their simplicity and versatility, becoming a critical component in the development of nanotechnology-based approaches for in vitro diagnostics assays. Special attention has been paid to the development of assays and biosensing platforms capable of specific identification of nucleic acid sequences that can be integrated into genome screening strategies and identification of sequence polymorphisms associated to relevant phenotypes, or identification of pathogens1. AuNPs have been extensively used because of their ease of synthesis and unique optical properties with their typical bright red color in colloidal solutions associated with the localised surface plasmon resonance band (LSPR). LSPR is dependent on size, composition, shape and inter-particle distance. Another remarkable property is the easiness of chemical functionalization via the use of thiol-ligands that form quasi-covalent bonds between any given biomolecules (used as probe) and the gold surface, such as oligonucleotides2, rendering them suitable for application in bioassays.
We have developed a method based on the change of colour of a solution constituted by AuNPs functionalized with thiol-ssDNA mediated by a modification of the medium dieletric together by recognition of a target. The colour change occurs due to the decrease of the inter-particle distance that results in a red-shift of the typical LSPR and the concomitant change from red to blue. Here, I shall demonstrate the versatility of this system for the development of simple and robust nucleic acid detection assays: i) DNA – pathogen identification, SNP characterisation, mutation detection; ii) RNA without retrotranscription – quantification of gene expression and direct evaluation of fusion genes involved in cancer, miRNA detection; iii) integration in alloys for multi-colour detection.
Funding by FCT/MEC [CIGMH (PEst-OE/SAU/UI0009/2011); PTDC/QUI-QUI/112597/2009; PTDC/CTM-NAN/109877/2009; PTDC/BBB-NAN/1812/2012] is gratefully acknowledged.
Living organisms synthesize almost all proteins using only twenty different amino acids. Polypeptides form a unique three-dimensional structure based on the type and position (sequence) of these amino acids. Within the sequence, amino acid R-groups form chemical interactions that create a specific three-dimensional structure. These R-groups are commonly called “side chains” because they are not involved in the peptide bonds. The R-groups stick out on the side of a polypeptide, freeing them to chemically interact with one another. Side chain interactions form each protein’s specific structure, a structure uniquely capable of performing that protein’s cellular function.
Knowing the importance of protein structure in determining function, how then is protein structure determined? To answer this, we must first ask how only twenty amino acids can create the diversity of proteins we see in living organisms. This diversity is easily explained by the way polypeptides form a sequence. Imagine creating a dipeptide using the twenty common amino acids. Twenty options exist for the first position, and twenty options exist for the second position of this two amino acid peptide. Math calculations tell us that we could synthesize four hundred different dipeptides! For every additional amino acid in a peptide, we multiply this number of options by twenty again. With more than one hundred amino acids in the average sequence, imagine how many different polypeptides may exist in nature!
In addition to increasing variation, each of the twenty common amino acids plays a vital role in the structure and function of proteins in all living organisms. While like plants synthesize all twenty common amino acids, , who obtain energy by eating biomolecules, rely on dietary intake to obtain one or more amino acids. Humans synthesize ten of the twenty common amino acids, but the remaining ten must be obtained through diet. Although all amino acids are necessary for human life, the “” are the ones humans cannot synthesize on their own. Eating protein-rich foods provides these essential amino acids to the cells.