Using microalgae in the circular economy to valorise anaerobic digestate::Challenges and Opportunities

Managing organic waste streams is a major challenge for the agricultural industry. Anaerobic digestion (AD) of organicwastes is a preferred option in the waste management hierarchy, as this processcangenerate renewableenergy, reduce emissions from wastestorage, andproduce fertiliser material.However, Nitrate Vulnerable Zone legislation and seasonal restrictions can limit the use of digestate on agricultural land. In this paper we demonstrate the potential of cultivating microalgae on digestate as a feedstock, either directlyafter dilution, or indirectlyfromeffluent remaining after biofertiliser extraction. Resultant microalgal biomass can then be used to produce livestock feed, biofuel or for higher value bio-products. The approach could mitigate for possible regional excesses, and substitute conventional high-impactproducts with bio-resources, enhancing sustainability withinacircular economy. Recycling nutrients from digestate with algal technology is at an early stage. We present and discuss challenges and opportunities associated with developing this new technology

A tensegrity model for hydrogen bond networks in proteins

Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger − covalent bonds connecting the atoms in the molecular skeleton or weaker forces like the so-called hydrophobic interactions. It has been demonstrated that the latter operate independently from hydrogen bonds. Each category of interaction must, if the protein is to have a stable structure, balance out. The hypothesis here is that the entire hydrogen bond network is in balance without any compensating contributions from other types of interaction. For sidechain-sidechain, sidechain-backbone and backbone-backbone hydrogen bonds in proteins, tensegrity balance (“closure”) is required over the entire length of the polypeptide chain that defines individually folding units in globular proteins (“domains”) as well as within the repeating elements in fibrous proteins that consist of extended chain structures. There is no closure to be found in extended structures that do not have repeating elements. This suggests an explanation as to why globular domains, as well as the repeat units in fibrous proteins, have to have a defined number of residues. Apart from networks of sidechain-sidechain hydrogen bonds there are certain key points at which this closure is achieved in the sidechain-backbone hydrogen bonds and these are associated with demarcation points at the start or end of stretches of secondary structure. Together, these three categories of hydrogen bond achieve the closure that is necessary for the stability of globular protein domains as well as repeating elements in fibrous proteins

Why twenty amino acid residue types suffice(d) to support all living systems.

It is well known that proteins are built up from an alphabet of 20 different amino acid types. These suffice to enable the protein to fold into its operative form relevant to its required functional roles. For carrying out these allotted functions, there may in some cases be a need for post-translational modifications and it has been established that an additional three types of amino acid have at some point been recruited into this process. But it still remains the case that the 20 residue types referred to are the major building blocks in all terrestrial proteins, and probably "universally". Given this fact, it is surprising that no satisfactory answer has been given to the two questions: "why 20?" and "why just these 20?". Furthermore, a suggestion is made as to how these 20 map to the codon repertoire which in principle has the capacity to cater for 64 different residue types. Attempts are made in this paper to answer these questions by employing a combination of quantum chemical and chemoinformatic tools which are applied to the standard 20 amino acid types as well as 3 "non-standard" types found in nature, a set of fictitious but feasible analog structures designed to test the need for greater coverage of function space and the collection of candidate alternative structures found either on meteorites or in experiments designed to reconstruct pre-life scenarios

Location and nature of the residues important for ligand recognition in G-protein coupled receptors

The overall structure of the biogenic amine subclass of the G-protein-coupled receptors, and of their ligand binding sites, is discussed with the aim of highlighting the major structural features of these receptors that are responsible for ligand recognition. A comparison is made between biogenic amine receptors, peptide receptors of the rhodopsin class, and the secretin receptors which all have peptide ligands. The question of where the peptide ligands bind, whether at extracellular sites or within the transmembrane helix bundle, is discussed. The suitability of the rhodopsin crystal structure as a template for construction of homology models is discussed and it is concluded that there are many reasons why a caution should be issued against using it uncritically

Comparison of Algorithms for Prediction of Protein Structural Features from Evolutionary Data.

Proteins have many functions and predicting these is still one of the major challenges in theoretical biophysics and bioinformatics. Foremost amongst these functions is the need to fold correctly thereby allowing the other genetically dictated tasks that the protein has to carry out to proceed efficiently. In this work, some earlier algorithms for predicting protein domain folds are revisited and they are compared with more recently developed methods. In dealing with intractable problems such as fold prediction, when different algorithms show convergence onto the same result there is every reason to take all algorithms into account such that a consensus result can be arrived at. In this work it is shown that the application of different algorithms in protein structure prediction leads to results that do not converge as such but rather they collude in a striking and useful way that has never been considered before

On dating stages in prebiotic chemical evolution

Abstract The notion that RNA must have had a unique and decisive role in the development of life needs hardly be questioned. However, the chemical complexity and other properties of RNA, such as high solubility in water and vulnerability to degradation, make it improbable that RNA could have had an early presence in the development of life on Earth or on any comparable telluric planet. Rather, the task of origin of life research must surely be to identify those chemical processes which could have taken place on Earth that could accumulate the complexity and rich molecular information content needed to sustain primitive life, and ultimately give rise to RNA. A collection of likely chemical precursors to modern biomolecules is listed here together with calculations of their molecular complexity. These complexity scores are then used to propose an ordering, on a timescale, of when they might have appeared on Earth. These pre-RNA living systems would have flourished during the first~0.3 Gyrs after the start of the Archaean era (~4.2 Gyr ago). If there ever was an "RNA-world" it could have started after that initial period (~3.9 Gyrs ago), later to be complemented with the appearance of duplex DNA at about~3.6 Gyrs ago, some time before the earliest known stromatolites (~3.4 Gyr)

Selection of cutoff ranges for KOL.

<p>The abscissa of each data point indicates the center of the range, all ranges have a width of ± 0.05 on the KOL scale. The measurements were made at cutoff distances 6Å (KOL06) and 10Å (KOL10). The total number of hits is shown in red.</p

Full results for all methods for the protein 1a4v (item 1 in Table 2).

<p>Full results for all methods for the protein 1a4v (item 1 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150769#pone.0150769.t002" target="_blank">Table 2</a>).</p

The preferred conformation of dipeptides in the context of biosynthesis

Globular proteins are folded polypeptide structures comprising stretches of secondary structures (helical (alpha- or 3(10) helix type), polyproline helix or beta-strands) interspersed by regions of less well-ordered structure ("random coil"). Protein fold prediction is a very active field impacting inte alia on protein engineering and misfolding studies. Apart from the many studies of protein refolding from the denatured state, there has been considerable interest in studying the initial formation of peptides during biosynthesis, when there are at the outset only a few residues in the emerging polypeptide. Although there have been many studies employing quantum chemical methods of the conformation of dipeptides, these have mostly been carried out in the gas phase or simulated water. None of these conditions really apply in the interior confines of the ribosome. In the present work, we are concerned with the conformation of dipeptides in this low dielectric environment. Furthermore, only the residue types glycine and alanine have been studied by previous authors, but we extend this repertoire to include leucine and isoleucine, position isomers which have very different structural propensities

Contact distance plots for the nonredundant set of 10 proteins for CMA, KOL, VRN, P2P and SVB (text colours here correspond to the colours in the figures).

<p>The identities of the proteins for each plot are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150769#pone.0150769.t002" target="_blank">Table 2</a> - column 1: PDB I.d., column 2: working name for the protein, column3: figure number.</p