Multi-output interval type-2 fuzzy logic system for protein secondary structure prediction

A new multi-output interval type-2 fuzzy logic system (MOIT2FLS) is introduced for protein secondary structure prediction in this paper. Three outputs of the MOIT2FLS correspond to three structure classes including helix, strand (sheet) and coil. Quantitative properties of amino acids are employed to characterize twenty amino acids rather than the widely used computationally expensive binary encoding scheme. Three clustering tasks are performed using the adaptive vector quantization method to construct an equal number of initial rules for each type of secondary structure. Genetic algorithm is applied to optimally adjust parameters of the MOIT2FLS. The genetic fitness function is designed based on the Q3 measure. Experimental results demonstrate the dominance of the proposed approach against the traditional methods that are Chou-Fasman method, Garnier-Osguthorpe-Robson method, and artificial neural network models.

Nonribosomal peptide synthetases as technological platforms for the synthesis of highly modified peptied bioeffectors - cyclosporin synthetase as a complex example

Many microbial peptide secondary metabolites possess important medicinal properties, of which the immunosuppressant cyclosporin A is an example. The enormous structural and functional diversity of these low-molecular weight peptides is attributable to their mode of biosynthesis. Peptide secondary metabolites are assembled non-ribosomally by multi-functional enzymes, termed non-ribosomal peptide synthetases. These systems consist of a multi-modular arrangement of the functional domains responsible for the catalysis of the partial reactions of peptide assembly. The extensive homology shared among NRPS systems allows for the generalisation of the knowledge garnered from studies of systems of diverse origins. In this review we shall focus the contemporary knowledge of non-ribosomal peptide biosynthesis on the structure and function of the cyclosporin biosynthetic system, with some emphasis on the re-direction of the biosynthetic potential of this system by combinatorial approaches.

Study of the natriuretic peptide hormone system in plants

In this study, both physiological and cellular effects are elicited by natriuretic peptides (NPs), a novel type of plant hormone. It was found that rat ANP (rANP) influenced stomatal opening movement in Tradescantia sp., where a significant increase in stomatal opening was observed in the presence of 1 µM rANP. Furthermore, this effect is mediated by cGMP, a (putative) second messenger of NPs. Two inhibitors of guanylyl cyclase, LY 83583 and methylene blue, inhibited rANP-induced stomatal opening. In contrast, stomatal opening is induced in a concentration dependent manner by the cell permeant cGMP analogue 8-Br-cGMP. In addition it was found, that like in animals, the secondary structure of rANP is essential for rANP responses. Linearised rANP is biologically inactive. Since ANP elicit plant responses, an attempt was made to isolate NP analogues from plants. A protocol for partially purifying NP from plants was developed. It was found that two fractions eluted from an immunoaffinity chromatography column (0.5 M KCI eluted fraction and 0.75 M KCI eluted fraction) were biologically active. The level of cGMP in response to NPs was also tested. It is suggested that the receptor of NP is specific since only 0.75 M KCI eluted fractions increased cGMP levels in Zea mays root stele tissue. rANP did not elicit an effect on cGMP levels in this tissue and LY 83583 did not affect this response. It is therefore argued that a plant specific biologically active NP system is present in the stele and it is predicted that NPs modulate solute movement in this tissue. NPs also influence K⁺, Na⁺ and H⁺ fluxes in Zea mays root stele. Increase in both K⁺ and Na+ uptake were observed after 30 min., while H⁺ flux shifted immediately toward influx in the presence of both 0.5 and 0.75 KCI eluted fractions. Finally, a model is proposed for the effect of NPs on solute movement and its signalling system in plants.

Equilibrium conformational ensemble of the intrinsically disordered peptide n16N: linking subdomain structures and function in nacre

n16 is a framework protein family associated with biogenic mineral stabilization, thought to operate at three key interfaces in nacre: protein/β-chitin, protein/protein, and protein/CaCO3. The N-terminal half of this protein, n16N, is known to be active in conferring this mineral stabilization and organization. While some details relating to the stabilization and organization of the mineral are known, the molecular mechanisms that underpin these processes are not yet established. To provide these molecular-scale details, here we explore current hypotheses regarding the possible subdomain organization of n16N, as related to these three interfaces in nacre, by combining outcomes of Replica Exchange with Solute Tempering molecular dynamics simulations with NMR experiments, to investigate the conformational ensemble of n16N in solution. We verify that n16N lacks a well-defined secondary structure, both with and without the presence of Ca(2+) ions, as identified from previous experiments. Our data support the presence of three different, functional subdomains within n16N. Our results reveal that tyrosine, chiefly located in the center of the peptide, plays a multifunctional role in stabilizing conformations of n16N, for intrapeptide and possibly interpeptide interactions. Complementary NMR spectroscopy data confirm the participation of tyrosine in this stabilization. The C-terminal half of n16N, lacking in tyrosine and highly charged, shows substantive conformational diversity and is proposed as a likely site for nucleation of calcium carbonate. Finally, dominant structures from our predicted conformational ensemble suggest the presentation of key residues thought to be critical to the selective binding to β-chitin surfaces.

Tuning the mechanical and morphological properties of self-assembled peptide hydrogels via control over the gelation mechanism through regulation of ionic strength and the rate of pH change

Hydrogels formed by the self-assembly of peptides are promising biomaterials. The bioactive and biocompatible molecule Fmoc-FRGDF has been shown to be an efficient hydrogelator via a π-β self-assembly mechanism. Herein, we show that the mechanical properties and morphology of Fmoc-FRGDF hydrogels can be effectively and easily manipulated by tuning both the final ionic strength and the rate of pH change. The increase of ionic strength, and consequent increase in rate of gelation and stiffness, does not interfere with the underlying π-β assembly of this Fmoc-protected peptide. However, by tuning the changing rate of the system's pH through the use of glucono-δ-lactone to form a hydrogel, as opposed to the previously reported HCl methodology, the morphology (nano- and microscale) of the scaffold can be manipulated.

Mining characteristic relations bind to RNA secondary structures

The identification of RNA secondary structures has been among the most exciting recent developments in biology and medical science. It has been recognized that there is an abundance of functional structures with frameshifting, regulation of translation, and splicing functions. However, the inherent signal for secondary structures is weak and generally not straightforward due to complex interleaving substrings. This makes it difficult to explore their potential functions from various structure data. Our approach, based on a collection of predicted RNA secondary structures, allows us to efficiently capture interesting characteristic relations in RNA and bring out the top-ranked rules for specified association groups. Our results not only point to a number of interesting associations and include a brief biological interpretation to them. It assists biologists in sorting out the most significant characteristic structure patterns and predicting structurefunction relationships in RNA.

Structure and properties of biomedical films prepared from aqueous and acidic silk fibroin solutions

Silk fibroin films are promising materials for a range of biomedical applications. To understand the effects of casting solvents on film properties, we used water (W), formic acid (FA), and trifluoroacetic acid (TFA) as solvents. We characterized molecular weight, secondary structure, mechanical properties, and degradation behavior of cast films. Significant degradation of fibroin was observed for TFA-based film compared to W and TA-based films when analyzed by SDS-PAGE. Fibroin degradation resulted in a significant reduction in tensile strength and modulus of TFA-based films. Compared to water, TFA-based films demonstrated lower water solubility (19.6% vs. 62.5% in 12 h) despite having only a marginal increase in their ß-sheet content (26.9% vs. 23.7%). On the other hand, FA-based films with 34.3% ß-sheet were virtually water insoluble. Following solubility treatment, ß-sheet content in FA-based films increased to 50.9%. On exposure to protease XIV, water-annealed FA-based films lost 74% mass in 22 days compared to only 30% mass loss by ethanol annealed FA films. This study demonstrated that a small variation in the ß-sheet percentage and random coil conformations resulted in a significant change in the rates of enzymatic degradation without alteration to their tensile properties. The film surface roughness changed with the extent of enzymatic hydrolysis.

'Forbidden' disulfides : their role as redox switches

Seminal studies by Richardson and Thornton defined the constraints imposed by protein structure on disulfide formation and flagged forbidden regions of primary or secondary structure seemingly incapable of forming disulfide bonds between resident cysteine pairs. With respect to secondary structure, disulfide bonds were not found between cysteine pairs: A. on adjacent beta-stands; B. in a single helix or strand; C. on non-adjacent strands of the same beta-sheet. In primary structure, disulfide bonds were not found between cysteine pairs: D. adjacent in the sequence. In the intervening years it has become apparent that all these forbidden regions are indeed occupied by disulfide-bonded cysteines, albeit rather strained ones. It has been observed that sources of strain in a protein structure, such as residues in forbidden regions of the Ramachandran plot and cis-peptide bonds, are found in functionally important regions of the protein and warrant further investigation. Like the Ramachandran plot, the earlier studies by Richardson and Thornton have identified a fundamental truth in protein stereochemistry: "forbidden" disulfides adopt strained conformations, but there is likely a functional reason for this. Emerging evidence supports a role for forbidden disulfides in redox-regulation of proteins.

Structure and characteristics of milled silk particles

This study examined the structure, thermal property, and ion adsorption of silk particles. The particles were prepared by attritor-bead mill combination, using alkaline (pH10) charge repulsion and surfactant steric repulsion methods. Both methods produced particles with a dominant β-sheet structure, similar to the silk fibre. There was no significant difference in the decomposition temperatures for either the silk fibre or the micro/nano silk particles. An important finding from this study is clear evidence of reduction of amorphous content during the final stage of powdering using the bead mill. As a result, despite reduction in β-sheet crystallites with the progressive milling, the relative β-sheet content actually increased during this process. However, intermolecular forces between the β-sheets reduced significantly and hence the XRD results showed significant reduction in crystallinity in nano silk particles but crystal forming segments remained with β-sheet conformations after milling. The structural change influenced the ion-adsorption property where particle-size reduction resulted in a significant increase in both the rate and volume of HCrO4- adsorption. © 2014 Elsevier B.V.

Mutational interference mapping experiment (MIME) for studying RNA structure and function

RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding.

Testing the transferability of a coarse-grained model to intrinsically disordered proteins

The intermediate-resolution coarse-grained protein model PLUM [T. Bereau and M. Deserno, J. Chem. Phys., 2009, 130, 235106] is used to simulate small systems of intrinsically disordered proteins involved in biomineralisation. With minor adjustments to reduce bias toward stable secondary structure, the model generates conformational ensembles conforming to structural predictions from atomistic simulation. Without additional structural information as input, the model distinguishes regions of the chain by predicted degree of disorder, manifestation of structure, and involvement in chain dimerisation. The model is also able to distinguish dimerisation behaviour between one intrinsically disordered peptide and a closely related mutant. We contrast this against the poor ability of PLUM to model the S1 quartz-binding peptide.

Superhydrophobic electrospun POSS-PMMA copolymer fibres with highly ordered nanofibrillar and surface structures

A POSS-PMMA copolymer has been synthesised by conventional free-radical polymerisation reaction. Uniform electrospun fibres from this copolymer showed a water contact angle as high as 1651 with a sliding angle as low as 61. For the first time, we found that the electrospun fibres had a bundled nanofibril secondary structure with an ordered POSS morphology on the fibre surface.

Protein solubilising and stabilising ionic liquids

We report a family of biocompatible ionic liquids (ILs) which are able to dissolve significant amounts of proteins such as cytochrome c and in which ATR-FTIR spectroscopy results show retention of secondary structure to extreme temperatures.