Biological Building Blocks Research Articles

Fabrication of PEGylated fibrinogen: a versatile injectable hydrogel biomaterial.

Hydrogels are one of the most versatile biomaterials in use for tissue engineering and regenerative medicine. They are assembled from either natural or synthetic polymers, and their high water content gives these materials practical advantages in numerous biomedical applications. Semisynthetic hydrogels, such as those that combine synthetic and biological building blocks, have the added advantage of controlled bioactivity and material properties. In myocardial regeneration, injectable hydrogels premised on a semisynthetic design are advantageous both as bioactive bulking agents and as a delivery vehicle for controlled release of bioactive factors and/or cardiomyocytes. A new semisynthetic hydrogel based on PEGylated fibrinogen has been developed to address the many requirements of an injectable biomaterial in cardiac restoration. This chapter highlights the fundamental aspects of making this biomimetic hydrogel matrix for cardiac applications.

A naphthalene-containing amino acid enables hydrogelation of a conjugate of nucleobase–saccharide–amino acids

Here we report the first example of a hydrogelator made of a conjugate of nucleobase-saccharide-amino acids by incorporating L-3-(2-naphthyl)-alanine to the conjugate, which illustrates a facile and effective method for generating bioactive and functional hydrogelators from the basic biological building blocks.

Cell Surface Self-Assembly of Hybrid Nanoconjugates via Oligonucleotide Hybridization Induces Apoptosis

Hybrid nanomaterials composed of synthetic and biological building blocks possess high potential for the design of nanomedicines. The use of self-assembling nanomaterials as "bio-mimics" may trigger cellular events and result in new therapeutic effects. Motivated by this rationale, we designed a therapeutic platform that mimics the mechanism of immune effector cells to cross-link surface receptors of target cells and induce apoptosis. This platform was tested against B-cell lymphomas that highly express the surface antigen CD20. Here, two nanoconjugates were synthesized: (1) an anti-CD20 Fab' fragment covalently linked to a single-stranded morpholino oligonucleotide (MORF1), and (2) a linear polymer of N-(2-hydroxypropyl)methacrylamide (HPMA) grafted with multiple copies of the complementary oligonucleotide MORF2. We show that the two conjugates self-assemble via MORF1-MORF2 hybridization at the surface of CD20(+) malignant B-cells, which cross-links CD20 antigens and initiates apoptosis. When tested in a murine model of human non-Hodgkin's lymphoma, the two conjugates, either administered consecutively or as a premixture, eradicated cancer cells and produced long-term survivors. The designed therapeutics contains no small-molecule cytotoxic compounds and is immune-independent, aiming to improve over chemotherapy, radiotherapy and immunotherapy. This therapeutic platform can be applied to cross-link any noninternalizing receptor and potentially treat other diseases.

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control self-assembly and mimicking this process in vitro will bring about major advances in the areas of materials science and nanotechnology. Among the available biological building blocks, peptides have several advantages as they present substantial diversity, their synthesis in large scale is straightforward, and they can easily be modified with biological and chemical entities(1,2). Several classes of designed peptides such as cyclic peptides, amphiphile peptides and peptide-conjugates self-assemble into ordered structures in solution. Homoaromatic dipeptides, are a class of short self-assembled peptides that contain all the molecular information needed to form ordered structures such as nanotubes, spheres and fibrils(3-8). A large variety of these peptides is commercially available. This paper presents a procedure that leads to the formation of ordered structures by the self-assembly of homoaromatic peptides. The protocol requires only commercial reagents and basic laboratory equipment. In addition, the paper describes some of the methods available for the characterization of peptide-based assemblies. These methods include electron and atomic force microscopy and Fourier-Transform Infrared Spectroscopy (FT-IR). Moreover, the manuscript demonstrates the blending of peptides (coassembly) and the formation of a "beads on a string"-like structure by this process.(9) The protocols presented here can be adapted to other classes of peptides or biological building blocks and can potentially lead to the discovery of new peptide-based structures and to better control of their assembly.

Self‐assembly in nature: using the principles of nature to create complex nanobiomaterials

Self-assembly is a ubiquitous process in biology where it plays numerous important roles and underlies the formation of a wide variety of complex biological structures. Over the past two decades, materials scientists have aspired to exploit nature's assembly principles to create artificial materials, with hierarchical structures and tailored properties, for the fabrication of functional devices. Toward this goal, both biological and synthetic building blocks have been subject of extensive research in self-assembly. In fact, molecular self-assembly is becoming increasingly important for the fabrication of biomaterials because it offers a great platform for constructing materials with high level of precision and complexity, integrating order and dynamics, to achieve functions such as stimuli-responsiveness, adaptation, recognition, transport, and catalysis. The importance of peptide self-assembling building blocks has been recognized in the last years, as demonstrated by the literature available on the topic. The simple structure of peptides, as well as their facile synthesis, makes peptides an excellent family of structural units for the bottom-up fabrication of complex nanobiomaterials. Additionally, peptides offer a great diversity of biochemical (specificity, intrinsic bioactivity, biodegradability) and physical (small size, conformation) properties to form self-assembled structures with different molecular configurations. The motivation of this review is to provide an overview on the design principles for peptide self-assembly and to illustrate how these principles have been applied to manipulate their self-assembly across the scales. Applications of self-assembling peptides as nanobiomaterials, including carriers for drug delivery, hydrogels for cell culture and tissue repair are also described.

Nanoscale assemblies and their biomedical applications

Nanoscale assemblies are a unique class of materials, which can be synthesized from inorganic, polymeric or biological building blocks. The multitude of applications of this class of materials ranges from solar and electrical to uses in food, cosmetics and medicine. In this review, we initially highlight characteristic features of polymeric nanoscale assemblies as well as those built from biological units (lipids, nucleic acids and proteins). We give special consideration to protein nanoassemblies found in nature such as ferritin protein cages, bacterial microcompartments and vaults found in eukaryotic cells and designed protein nanoassemblies, such as peptide nanofibres and peptide nanotubes. Next, we focus on biomedical applications of these nanoscale assemblies, such as cell targeting, drug delivery, bioimaging and vaccine development. In the vaccine development section, we report in more detail the use of virus-like particles and self-assembling polypeptide nanoparticles as new vaccine delivery platforms.

206 An artificial active DNA transporter from biological building blocks

The selective transport of molecules across membrane pores is an essential biological process that occurs in all living organisms. Examples include the chaperone of proteins and mRNA in and out the cell nucleus mediated by the nuclear pore complex and the transport of specific molecules across a biological membrane mediated by active and passive transporters. Here, I describe an artificial DNA transporter that is formed by incorporating a DNA carrier element into a biological nanopore imbedded in a lipid bilayer. This device is able to transport specific DNA strands across a biological membrane mediated by a simple reaction mechanism based on DNA strand displacement. Similar to biological secondary active transporters, this system uses an electrochemical potential difference to pump a specific substrate across a biological membrane at a constant transmembrane potential. Our DNA actuator might be used to separate or concentrate nucleic acids, or to vehicle genetic information across the biological membranes.

Photodynamics of Lys+-Trp protein motifs: Hydrogen bonds ensure photostability

Cation-pi interactions such as Lys(+)-Trp, are highly abundant structural motifs in proteins. Both, experimental and theoretical studies of small prototypical gas phase systems, H+Trp, H+Trp x (H2O)n and H+Gly-Trp, indicate such an arrangement as potential hot spot for photodamage and photoinstability. Here, we study the photodynamical properties of a Lys(+)-Trp pair in the protein human serum albumin (HSA) using nonadiabatic mixed time-dependent density functional theory/molecular mechanics simulations (TDDFT/MM). These simulations show that the findings for small protonated Trp complexes are largely transferable to a more complex protein environment. Under partially hydrated ("dry" conditions), when the -NH3+ head group is not fully solvated, photoexcitation of the tryptophan leads indeed to rapid photodissociation of the proximal charged amino group. In contrast, photostability is well maintained under fully solvated conditions when the lysine head group is fully hydrogen-bonded. In this case, photodynamics takes place in a pi-pi* state without interference of fast dissociative sigma*C-N) or sigma*N-H channels. These results highlight the crucial role of hydrogen bonds in ensuring the photostability of essential biological building blocks.

Mass Spectrometry and Proteomics: Principle, Workflow, Challenges and Perspectives

Mass Spectrometry (MS) is a method that can analyze a variety of chemical and biological compounds, from products of chemical synthesis or degradation to biological building blocks and their products, including proteins, nucleic acids, lipids, and glycans. Within the MS field, different specialized fields have emerged. They have been named based on the chemical or biological entities that are analyzed, including: proteomics, lipidomics, glycomics and others. Proteomics analyzes proteins, peptides, aglycans, protein interactions, or posttranslational modifications (PTMs).

(Invited) Hierarchically Assembly of Materials Using Biological Building Blocks

not Available.

ChemInform Abstract: Synthetic Mammalian Gene Networks as a Blueprint for the Design of Interactive Biohybrid Materials

AbstractReview: 83 refs.

Low-frequency Raman scattering of bioinspired self-assembled diphenylalanine nanotubes/microtubes

Low-frequency Raman scattering from self-assembled bioinspired diphenylalanine (FF) nanotubes/microtubes (NTs/MTs) has been observed for the first time. Four double peaks are identified as the three-dimensional localized collective (acoustic phonon) vibrations of FF molecules in the subnanometer crystalline structure (biological building block) forming the FF NTs/MTs. The increased energy separations between two subpeaks caused by the loss of water in the nanochannel cores are due to the enhancement of vibrational couplings between the FF molecules as a result of the reduction of the influence from water on the coupling. The results provide experimental evidence of localized but still weakly coupled vibrations in organic crystalline nanostructures in the low-frequency region.

Synthetic mammalian gene networks as a blueprint for the design of interactive biohybrid materials

Synthetic biology aims at the rational design and construction of devices, systems and organisms with desired functionality based on modular well-characterized biological building blocks. Based on first proof-of-concept studies in bacteria a decade ago, synthetic biology strategies have rapidly entered mammalian cell technology providing novel therapeutic solutions. Here we review how biological building blocks can be rewired to interactive regulatory genetic networks in mammalian cells and how these networks can be transformed into open- and closed-loop control configurations for autonomously managing disease phenotypes. In the second part of this tutorial review we describe how the regulatory biological sensors and switches can be transferred from mammalian cell synthetic biology to materials sciences in order to develop interactive biohybrid materials with similar (therapeutic) functionality as their synthetic biological archetypes. We develop a perspective of how the convergence of synthetic biology with materials sciences might contribute to the development of truly interactive and adaptive materials for autonomous operation in a complex environment.

Emerging biomedical applications of synthetic biology.

Synthetic biology aims to create functional devices, systems and organisms with novel and useful functions on the basis of catalogued and standardized biological building blocks. Although they were initially constructed to elucidate the dynamics of simple processes, designed devices now contribute to the understanding of disease mechanisms, provide novel diagnostic tools, enable economic production of therapeutics and allow the design of novel strategies for the treatment of cancer, immune diseases and metabolic disorders, such as diabetes and gout, as well as a range of infectious diseases. In this Review, we cover the impact and potential of synthetic biology for biomedical applications.

Self‐Assembly of Hexagonal Peptide Microtubes and Their Optical Waveguiding

Self-assembly of biological building blocks including proteins and peptides is attracting increasing attention due to the versatility for bottom-up fabrication, biocompatibility and biodegradability, and a wide range of applications in biology and in nanotechnology. [ 1 ] In the self-assembly process the precise control of supramolecular architectures is achieved through synergistic effects of some weak non-covalent interactions such as hydrogen bonds, electrostatic interaction, π – π stacking, hydrophobic forces, nonspecifi c van der Waals forces, and chiral dipole–dipole interactions. [ 2 ] These weak forces, in particular hydrogen bonds and hydrophobic interactions, are ubiquitous in biological systems. As a whole they govern the molecular selfassembly into superior and ordered structures. By learning from nature, one can purposefully devise and synthesize artifi cial building blocks amenable to self-assembly into superstructures, which are driven by the cooperative interactions of such weak forces. With respect to other biological building blocks, peptides have been of great interest as a strategy in material fabrication owing to their structural simplicity and tunability, functional versatility, cost effectiveness, and widespread applications. As one of the simplest peptide building blocks, diphenylalanine (L-PheL-Phe, FF), a core recognition motif of Alzheimer’s β -amyloid polypeptide, [ 3 ] has been proven to be an exciting candidate towards bottom-up fabrication. FF-based building blocks are able to self-assemble into a variety of nano structures including nanotubes, spheric vesicles, nanofi brils, nanowires, and ordered molecular chains. [ 1c ] These well-defi ned nanostructures can be regarded as an assembly of molecules into supramolecular systems, however, organization of these into crystalline materials with spatial dimensions remains a formidable challenge. We report here that the FF building block is capable of selfassembling into robust hexagonal crystalline microtubes as a result of confi ned organization of nanoscale tubular structures at long range during slow crystallization or aggregation. In biological systems, the oriented organization or alignment of substructures is a common protocol to achieve functions. For

Directed co-assembly of hemeproteins with amphiphilic block copolymers toward functional biomolecular materials

Directed co-assembly of block copolymers and proteins/peptides may lead to hierarchically structured functional biomolecular materials. However, this requires one to synergistically direct multiple self-assembly processes. Retaining proper cofactor binding is essential to utilize many bio-motifs for catalytic reactions and sensing. Here, by using a heme-binding helix bundle peptide-polymer conjugate and a holomyoglobin-polymer conjugate as examples, we show that the simultaneous, macroscopic assembly of heme-binding proteins and diblock copolymers can be achieved in thin films without compromising protein structures, cofactor binding and enzymatic activities. To our knowledge, this is the first example of a protein/cofactor complex formed upon being co-assembled with an amphiphilic block copolymer in thin films. Molecular assemblyvia a combination of biomolecular recognition and polymer phase separation in this fashion will lead to hybrid materials combining properties of both synthetic and biological building blocks.

Protein assemblies by site-specific avidin–biotin interactions

Exploiting self-assembly systems with biological building blocks is of significant interest in the fabrication of advanced biomaterials. We assessed the potential use of site-specific ligand labeling of protein building blocks in designing functional protein self-assemblies by combining site-specifically biotinylated bacterial alkaline phosphatase (as a bidentate or tetradentate ligand unit) and streptavidin (as a tetrameric receptor).

Ionization-loss stimulated Raman spectroscopy for conformational probing of flexible molecules

The approach of studying structural and dynamical properties of flexible molecules is of substantial interest, as it allows decoding the shapes and intrinsic properties of isolated molecular constituents, which have an influence on the selectivity and functionality in biological processes. Combining quantum computation methods with double resonance or infrared hole burning techniques, mainly covering hydride stretch vibrations, recently led to great progress in understanding the structure of a variety of biological building blocks. Measurements of spectra in the lower frequency range, with relatively compact and convenient laser sources, still pose major challenges. For this reason, the method of ionization-loss stimulated Raman spectroscopy (ILSRS) has been developed and applied for monitoring the spectral features of the 2-phenylethanol prototype. The bands observed in the Raman spectra of its two conformers uniquely identify their structures and are in accord with anharmonic results obtained by density functional theory calculations. These findings point to future opportunities for ILSRS as a powerful conformational probe and set new standards for detailed interrogation of structure and intra- and inter-molecular interactions.

ChemInform Abstract: Chemical Complexity—Supramolecular Self‐Assembly of Synthetic and Biological Building Blocks in Water

AbstractReview: 70 refs.

ChemInform Abstract: Self‐Assembly and Application of Diphenylalanine‐Based Nanostructures

AbstractReview: 66 refs.