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.

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.

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.

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.

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.

Evaluating the stability of disulfide bridges in proteins: a torsional potential energy surface for diethyl disulfide

Disulfide bonds formed by the oxidation of cysteine residues in proteins are the major form of intra- and inter-molecular covalent linkages in the polypeptide chain. To better understand the conformational energetics of this linkage, we have used the MP2(full)/6-31G(d) method to generate a full potential energy surface (PES) for the torsion of the model compound diethyl disulfide (DEDS) around its three critical dihedral angles (χ2, χ3, χ2′). The use of ten degree increments for each of the parameters resulted in a continuous, fine-grained surface. This allowed us to accurately predict the relative stabilities of disulfide bonds in high resolution structures from the Protein Data Bank. The MP2(full) surface showed significant qualitative differences from the PES calculated using the Amber force field. In particular, a different ordering was seen for the relative energies of the local minima. Thus, Amber energies are not reliable for comparison of the relative stabilities of disulfide bonds. Surprisingly, the surface did not show a minimum associated with χ2 − 60°, χ390, χ2′ − 60°. This is due to steric interference between Hα atoms. Despite this, significant populations of disulfides were found to adopt this conformation. In most cases this conformation is associated with an unusual secondary structure motif, the cross-strand disulfide. The relative instability of cross-strand disulfides is of great interest, as they have the potential to act as functional switches in redox processes.

'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.

Balsamin, a novel ribosome-inactivating protein from the seeds of Balsam apple Momordica balsamina

Plant seeds, a rich source of proteins, are considered important for their application as functional ingredients in a food system. A novel ribosome-inactivating protein (RIP), balsamin was purified from the seeds of Balsam apple, Momordica balsamina. Balsamin was purified by ion exchange chromatography on CM Sepharose and gel filtration on superdex-75. It has a molecular weight of 28 kDa as shown by SDS-PAGE analysis. Balsamin inhibits protein synthesis in a rabbit reticulocyte lysate-based cell free translation assay with an IC50 of 90.6 ng ml⁻¹. It has RNA N-glycosidase activity and releases a 400-base long fragment termed the Endo fragment from 28S rRNA in the same manner as does saporin-6 from Saponaria officinalis. The N-terminal sequence analysis of the first 12 amino acids of balsamin revealed that it shares 83% similarity with type I RIP α-MMC from Momordica charantia and 50% similarity with β-MMC (from Momordica charantia), bryodin I (from Bryonia dioica) and luffin a (from Luffa cylindrica). Balsamin was further characterized by mass spectrometry. CD spectroscopic studies indicate that secondary structure of balsamin contains helix (23.5%), β-strand (24.6%), turn (20%) and random coil (31.9%). Thus RIPs activity expressed in vegetables like Momordica sp. advocates its usage in diet.

Solvent induced changes in the conformational state of β-lactoglobulin and the influence of protic ionic liquids

The protic ionic liquids (pILs), triethylammonium acetate, triethylammonium trifluoroacetate, triethylammonium mesylate and trimethylammonium sulfate were used to induce various native and non-native conformational states of the protein β-lactoglobulin (βLG). Changes in the secondary structure of βLG were observed on moving from a high water content to a high pIL content. We examined the stability of various pIL induced states via thermal unfolding and refolding, where it was found that at a given pIL concentration a highly stable non-native conformation was formed. The βLG non-native conformation was characterized by a high α-helical content. Additionally, pIL conditions that promoted amyloid fibril formation were identified and characterized by CD, a Thioflavin T binding assay and transmission electron microscopy (TEM). This work highlights the use of pILs as solvents in the study of protein folding using βLG as a model system.

Structural classification of proteins through amino acid sequence using interval type-2 fuzzy logic system

This paper introduces a new multi-output interval type-2 fuzzy logic system (MOIT2FLS) that is automatically constructed from unsupervised data clustering method and trained using heuristic genetic algorithm for a protein secondary structure classification. Three structure classes are distinguished including helix, strand (sheet) and coil which correspond to three outputs of the MOIT2FLS. Quantitative properties of amino acids are used to characterize the twenty amino acids rather than the widely used computationally expensive binary encoding scheme. Amino acid sequences are parsed into learnable patterns using a local moving window strategy. Three clustering tasks are performed using the adaptive vector quantization method to derive an equal number of initial rules for each type of secondary structure. Genetic algorithm is applied to optimally adjust parameters of the MOIT2FLS with the purpose of maximizing the Q3 measure. Comprehensive experimental results demonstrate the strong superiority of the proposed approach over the traditional methods including Chou-Fasman method, Garnier-Osguthorpe-Robson method, and artificial neural network models.