Elucidation of the structure of supramolecular polymorphs in peptide nanofibres using Raman spectroscopy

Peptide fibre formation via molecular self-assembly is a key step in a range of cellular processes and increasingly considered as an approach to produce supramolecular biomaterials. We previously demonstrated the self-assembly of the tripeptide lysine-dityrosine (KYY) as a substrate for the formation of proton-conducting melanin-like materials. Point based Raman scattering is one of several techniques which were used to characterise the secondary structure of the KYY nanofibre but as is often the case with this type of fibre, the spectra are rather complex and in addition there were variations in intensity between samples making interpretation difficult. Using Raman mapping we show that, as a drop of KYY in solution dries, it self-assembles into two different fibre forms and the simpler spectra obtained for each are easier to interpret. The tyrosine amide marker bands, 852 and 828 cm −1, are present in both forms with similar intensities indicating the formation of a similar secondary structure in both forms with some stacking of the tyrosine rings. However, the tyrosine marker bands at 1614 and 1661 cm −1 vary considerably in intensity between the two forms. It is concluded that both forms consist of stacked polypeptide units joined by hydrogen bonds to form structures similar to β-sheet structures in longer peptides. There are other clear differences such the large intensity difference in the lysine side chain band at 1330 cm −1 and the relative intensities of the bands at 982 and 1034 cm −1. These differences are attributed to changes in the conformation of tyrosine side chains causing different electron withdrawing effects on the ring

Biomolecular condensates formed by designer minimalistic peptides

Inspired by the role of intracellular liquid-liquid phase separation (LLPS) in formation of membraneless organelles, there is great interest in developing dynamic compartments formed by LLPS of intrinsically disordered proteins (IDPs) or short peptides. However, the molecular mechanisms underlying the formation of biomolecular condensates have not been fully elucidated, rendering on-demand design of synthetic condensates with tailored physico-chemical functionalities a significant challenge. To address this need, here we design a library of LLPS-promoting peptide building blocks composed of various assembly domains. We show that the LLPS propensity, dynamics, and encapsulation efficiency of compartments can be tuned by changes to the peptide composition. Specifically, with the aid of Raman and NMR spectroscopy, we show that interactions between arginine and aromatic amino acids underlie droplet formation, and that both intra- and intermolecular interactions dictate droplet dynamics. The resulting sequence-structure-function correlation could support the future development of compartments for a variety of applications

Spontaneous aminolytic cyclization and self-assembly of dipeptide methyl esters in water

Dipeptides are known to spontaneously cyclize to diketopiperazines, and in some cases these cyclic dipeptides have been shown to self-assemble to form supramolecular nanostructures. Herein, we demonstrate the in situ cyclization of dipeptide methyl esters in aqueous buffer by intramolecular aminolysis, leading to the formation of diverse supramolecular nanostructures. The chemical nature of the amino acid side chains dictates the supramolecular arrangement and resulting nanoscale architectures. For c[LF], supramolecular gels are formed, and the concentration of starting materials influences the mechanical properties of hydrogels. Moreover, by adding metalloporphyrin to the starting dipeptide ester solution, these become incorporated through cooperative assembly, resulting in the formation of nanofibers able to catalyse the oxidation of organic phenol in water. The approach taken here, which combines the chemically activated assembly with the versatility of short peptides might pave the way for achieving the spontaneous formation of supramolecular order and function using simple building blocks

Polymeric peptide pigments with sequence-encoded properties

Melanins are a family of heterogeneous polymeric pigments that provide ultraviolet (UV) light protection, structural support, coloration, and free radical scavenging. Formed by oxidative oligomerization of catecholic small molecules, the physical properties of melanins are influenced by covalent and noncovalent disorder. We report the use of tyrosine-containing tripeptides as tunable precursors for polymeric pigments. In these structures, phenols are presented in a (supra-)molecular context dictated by the positions of the amino acids in the peptide sequence. Oxidative polymerization can be tuned in a sequence-dependent manner, resulting in peptide sequence–encoded properties such as UV absorbance, morphology, coloration, and electrochemical properties over a considerable range. Short peptides have low barriers to application and can be easily scaled, suggesting near-term applications in cosmetics and biomedicine

Regulation of enzymatic reactions by chemical composition of peptide biomolecular condensates

Abstract Biomolecular condensates are condensed intracellular phases that are formed by liquid-liquid phase separation (LLPS) of proteins, either in the absence or presence of nucleic acids. These condensed phases regulate various biochemical reactions by recruitment of enzymes and substrates. Developments in the field of LLPS facilitated new insights on the regulation of compartmentalized enzymatic reactions. Yet, the influence of condensate chemical composition on enzymatic reactions is still poorly understood. Here, by using peptides as minimalistic condensate building blocks and β-galactosidase as a simple enzymatic model we show that the reaction is restricted in homotypic peptide condensates, while product formation is enhanced in peptide-RNA condensates. Our findings also show that condensate composition affects the recruitment of substrate, the spatial distribution, and the kinetics of the reaction. Thus, these findings can be further employed for the development of microreactors for biotechnological applications

Values of kinetic parameters of CA assembly either in the absence or presence of different chemical chaperones.

a<p>t₅₀ is the time at which the optical density (OD) is equal to one-half the optical density extrapolated at infinite time. The values given were obtained by fitting the data to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060867#pone.0060867.e001" target="_blank">equation 1</a>. The fitting errors are indicated. For linear-fitted curves, the t₅₀ values cannot be calculated but rather estimated to be >40 min, since the maximal t value is 80 min.</p>b<p>The linear polymerization rate is the average increase in optical density per minute for the approximate linear part of the polymerization curve. Two values of assembly rate are indicated for curves with two phases of linear increase.</p

Schematic model for the effect of different chemical chaperones groups on CA stability and assembly.

<p>The presence of polyols or sugars (dark grey circles) induces compactization of CA structure and inhibits the formation of high-order CA structures. In contrast, the presence of the methylamines TMAO, betaine or sarcosine (light grey circles) destabilizes CA structure and thus promoting CA-CA interactions, resulting in the formation of CA cylinders. Structure of HIV-1 CA (151–231) created using PDB 1A8O <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060867#pone.0060867-Gamble1" target="_blank">[52]</a> represents full-length CA protein. The scale bars are 100 nm (left image) and 200 nm (right image).</p

TEM micrographs of mature-like CA particles.

<p>CA particles formed after 1 h incubation in the absence (A) or presence of 0.5 M of sorbitol (B), adonitol (C), meso-erythritol (D), glycerol (E), ethylene glycol (F), maltose (G), arabinose (H), mannose (I) or trehalose (J). CA structures formed after 30 min incubation in the absence (K) or presence of 0.5 M of TMAO (L), betaine (M), sarcosine (N) or choline chloride (O). Scale bar: 200 nm.</p

Dynamic light scattering measurements of CA assemblies.

<p>Assembly of CA was carried out using the same conditions as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060867#pone-0060867-g001" target="_blank">Fig. 1</a>. The hydrodynamic radius (nm) of CA particles was measured after 30 min incubation in the absence (black solid line) or presence of 0.5 M of (<b>A</b>) polyols: sorbitol (grey solid line); adonitol (black dashed line); meso-erythritol (grey dashed line); glycerol (dotted line) or ethylene glycol (dashed-dotted line), 5 min incubation in the absence (black solid line) or presence of (<b>B</b>) sugars: maltose (grey solid line); arabinose (black dashed line); trehalose (grey dashed line) or mannose (dotted line), and 10 min incubation in the absence (black solid line) or presence of (<b>C</b>) methylamines: TMAO (grey solid line); betaine (black dashed line); sarcosine (grey dashed line) or choline chloride (dotted line).</p