Accurate prediction of species-specific 2-hydroxyisobutyrylation sites based on machine learning frameworks.

Lysine 2-hydroxyisobutyrylation (K) is a newly discovered post-translational modification (PTM) across eukaryotes and prokaryotes in recent years, which plays a significant role in diverse cellular functions. Accurate prediction of K sites is a first-crucial step to decipher its molecular mechanism and urgently needed. In this work, based on a large benchmark datasets in multi-species, a novel online species-specific prediction tool, namely KhibPred, was developed to identify K sites.

Design and synthesis of a vanadate-based ratiometric fluorescent probe for sequential recognition of Cu ions and biothiols.

A novel YVO4:Eu3+@CDs core-shell nanomaterial with two main emission peaks at 405 and 617 nm was synthesized through a simple mixing method, in which the carbon quantum dots (CDs) self-assembled with the YVO4:Eu3+ nanoparticle, due to the high affinity of oxygen-containing groups such as -COOH or -OH of CDs to the metal ions on the surface of YVO4:Eu3+. The red fluorescence of YVO4:Eu3+@CDs located at 617 nm can be quenched by Cu2+ ions efficiently, while the blue emission remains invariable; based on this, we construct a ratio fluorescent probe YVO4:Eu3+@CDs for Cu2+ ion detection, in which the blue emission of CDs is selected as the reference signal, and the red emission of YVO4:Eu3+ acts as an output signal. Furthermore, the addition of biothiol recovers the quenched red fluorescence quickly, which can be completed in 18 minutes.

Curved Fragmented Graphenic Hierarchical Architectures for Extraordinary Charging Capacities.

An approach to assemble hierarchically ordered 3D arrangements of curved graphenic nanofragments for energy storage devices is described. Assembling them into well-defined interconnected macroporous networks, followed by removal of the template, results in spherical macroporous, mesoporous, and microporous carbon microball (3MCM) architectures with controllable features spanning nanometer to micrometer length scales. These structures are ideal porous electrodes and can serve as lithium-ion battery (LIB) anodes as well as capacitive deionization (CDI) devices.

Using support vector machines to identify protein phosphorylation sites in viruses.

Phosphorylation of viral proteins plays important roles in enhancing replication and inhibition of normal host-cell functions. Given its importance in biology, a unique opportunity has arisen to identify viral protein phosphorylation sites. However, experimental methods for identifying phosphorylation sites are resource intensive.

Outcome of patients with bulky IB (≥ 6 cm) cervical squamous cell carcinoma with and without cisplatin-based neoadjuvant chemotherapy.

Objective: To study the surgical morbidity and outcomes of patients with markedly bulky cervical squamous cell carcinoma (≥ 6 cm Cx-SCC) who underwent radical hysterectomy (RH) with and without neoadjuvant chemotherapy (NACT).

Materials And Methods: This retrospective study enrolled patients with International Federation of Gynecology and Obstetrics (FIGO) IB markedly bulky Cx-SCC who were treated with either three courses of weekly single agent cisplatin NACT (50 mg/m2) and subsequent radical hysterectomy (NACT-RH) or direct radical hysterectomy (RH) between 1996 and 2001. A total of 60 patients fulfilled the criteria, including 35 and 25 patients with NsACT-RH and RH, respectively.

Electro-enhanced removal of copper ions from aqueous solutions by capacitive deionization.

This study was performed to determine the feasibility of electrosorptive removal of copper ions from aqueous solutions using a capacitive deionization process. The electrosorptive potential of copper ions was determined using cyclic voltammetry measurements, and copper electrodeposition could be suppressed at a voltage less than 0.8 V.

Optimization of reaction conditions towards multiple types of framework isomers and periodic-increased porosity: luminescence properties and selective CO2 adsorption over N2.

Three new metal-organic frameworks (MOFs) were prepared by solvo(hydro)thermolysis and further characterized as framework isomers. The structural transformation from non-porous to porous MOFs and the purity of these products can be modulated by controlling the reaction temperature. The periodic-increased porosity observed was further confirmed by CO2 adsorption isotherms.

A novel two-dimensional metal-organic supramolecular framework including π-π stacking and hydrogen-bond interactions.

[μ-N,N'-Bis(pyridin-3-yl)benzene-1,4-dicarboxamide-1:2κ(2)N:N']bis{[N,N'-bis(pyridin-3-yl)benzene-1,4-dicarboxamide-κN]diiodidomercury(II)}, [Hg2I4(C18H14N4O2)3], is an S-shaped dinuclear molecule, composed of two HgI2 units and three N,N'-bis(pyridin-3-yl)benzene-1,4-dicarboxamide (L) ligands. The central L ligand is centrosymmetric and coordinated to two Hg(II) cations via two pyridine N atoms, in a syn-syn conformation. The two terminal L ligands are monodentate, with one uncoordinated pyridine N atom, and each adopts a syn-anti conformation.

Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites.

Motivation: Systematic dissection of the ubiquitylation proteome is emerging as an appealing but challenging research topic because of the significant roles ubiquitylation play not only in protein degradation but also in many other cellular functions. High-throughput experimental studies using mass spectrometry have identified many ubiquitylation sites, primarily from eukaryotes. However, the vast majority of ubiquitylation sites remain undiscovered, even in well-studied systems.

The prediction of palmitoylation site locations using a multiple feature extraction method.

As an extremely important and ubiquitous post-translational lipid modification, palmitoylation plays a significant role in a variety of biological and physiological processes. Unlike other lipid modifications, protein palmitoylation and depalmitoylation are highly dynamic and can regulate both protein function and localization. The dynamic nature of palmitoylation is poorly understood because of the limitations in current assay methods.

Proteome-wide analysis of amino acid variations that influence protein lysine acetylation.

Next-generation sequencing (NGS) technologies are yielding ever higher volumes of genetic variation data. Given this large amount of data, it has become both a possibility and a priority to determine what the functional implication of genetic variations is. Considering the essential roles of acetylation in protein functions, it is highly likely that acetylation related genetic variations change protein functions.

[Effects of sodium tanshinone B on the protein expression of NMDAR1 in rat hippocampal subfields following focal ischemia/reperfusion injury].

Unlabelled: OBJECTIVE To observe the changing laws of the protein expression of N-methyl D-aspartate receptor (NMDAR) in rat hippocampal subfields following focal ischemia/reperfusion injury, and to study the effects of sodium tanshinone B (STB) on it, thus exploring the possible mechanism of STB for treating cerebral ischemia.

Methods: The rat model of focal cerebral ischemia/reperfusion injury was established using middle cerebral artery occlusion (MCAO) by reversibly inserting a nylon thread. The Wistar rats were randomly divided into the sham-operation group, the I/R model group, and the low, middle, and high dose STB groups.

Position-specific analysis and prediction for protein lysine acetylation based on multiple features.

Protein lysine acetylation is a type of reversible post-translational modification that plays a vital role in many cellular processes, such as transcriptional regulation, apoptosis and cytokine signaling. To fully decipher the molecular mechanisms of acetylation-related biological processes, an initial but crucial step is the recognition of acetylated substrates and the corresponding acetylation sites. In this study, we developed a position-specific method named PSKAcePred for lysine acetylation prediction based on support vector machines.

Identifying protein quaternary structural attributes by incorporating physicochemical properties into the general form of Chou's PseAAC via discrete wavelet transform.

In vivo, some proteins exist as monomers and others as oligomers. Oligomers can be further classified into homo-oligomers (formed by identical subunits) and hetero-oligomers (formed by different subunits), and they form the structural components of various biological functions, including cooperative effects, allosteric mechanism and ion-channel gating. Therefore, with the avalanche of protein sequences generated in the post-genomic era, it is very important for both basic research and the pharmaceutical industry to acquire the possible knowledge about quaternary structural attributes of their proteins of interest.

A method to distinguish between lysine acetylation and lysine methylation from protein sequences.

Lysine acetylation and methylation are two major post-translational modifications of lysine residues. They play vital roles in both biological and pathological processes. Specific lysine residues in H3 histone protein tails appear to be targeted for either acetylation or methylation.

PMeS: prediction of methylation sites based on enhanced feature encoding scheme.

Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction. Given their important involvement in gene expression, protein methylation and their regulatory enzymes are implicated in a variety of human disease states such as cancer, coronary heart disease and neurodegenerative disorders. Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases.

PredSulSite: prediction of protein tyrosine sulfation sites with multiple features and analysis.

Tyrosine sulfation is a ubiquitous posttranslational modification that regulates extracellular protein-protein interactions, intracellular protein transportation modulation, and protein proteolytic process. However, identifying tyrosine sulfation sites remains a challenge due to the lability of sulfation sequences. In this study, we developed a method called PredSulSite that incorporates protein secondary structure, physicochemical properties of amino acids, and residue sequence order information based on support vector machine to predict sulfotyrosine sites.

PLMLA: prediction of lysine methylation and lysine acetylation by combining multiple features.

Post-translational lysine methylation and acetylation are two major modifications of lysine residues. They play critical roles in various biological processes, especially in gene regulation. Identification of protein methylation and acetylation sites would be a foundation for understanding their modification dynamics and molecular mechanism.

A novel algorithm combining support vector machine with the discrete wavelet transform for the prediction of protein subcellular localization.

Knowing the subcellular localization of proteins within the cell is an important step in elucidating its role in biological processes, its function and its potential as a drug target for disease diagnosis. As the number of complete genomes rapidly increases, accurate and efficient methods that automatically predict the subcellular localizations become more urgent. In the current paper, we developed a novel method that coupled the discrete wavelet transform with support vector machine based on the amino acid polarity to predict the subcellular localizations of prokaryotic and eukaryotic proteins.

2-[4-(4-Methylphenylsulfonyl)piperazin-1-yl]-1-(4,5,6,7-tetrahydrothieno[3,2-c]pyridin-5-yl)ethanone.

In the title thienopyridine derivative, C(20)H(25)N(3)O(3)S(2), the piperazine ring exhibits a chair conformation and the tetra-hydro-pyridine ring exhibits a half-chair conformation. The folded conformation of the mol-ecule is defined by the N-C-C-N torsion angle of -70.20 (2) °.

Predicting homo-oligomers and hetero-oligomers by pseudo-amino acid composition: an approach from discrete wavelet transformation.

Many proteins exist in vivo as oligomers with different quaternary structural attributes rather than as individual chains. These proteins are the structural components of various biological functions, including cooperative effects, allosteric mechanisms and ion-channel gating. With the dramatic increase in the number of protein sequences submitted to the public databank, it is important for both basic research and drug discovery research to acquire the knowledge about possible quaternary structural attributes of their interested proteins in a timely manner.

Identify submitochondria and subchloroplast locations with pseudo amino acid composition: approach from the strategy of discrete wavelet transform feature extraction.

It is very challenging and complicated to predict protein locations at the sub-subcellular level. The key to enhancing the prediction quality for protein sub-subcellular locations is to grasp the core features of a protein that can discriminate among proteins with different subcompartment locations. In this study, a different formulation of pseudoamino acid composition by the approach of discrete wavelet transform feature extraction was developed to predict submitochondria and subchloroplast locations.

Twisting of the DNA-binding surface by a beta-strand-bearing proline modulates DNA gyrase activity.

DNA gyrase is the only topoisomerase capable of introducing (-) supercoils into relaxed DNA. The C-terminal domain of the gyrase A subunit (GyrA-CTD) and the presence of a gyrase-specific 'GyrA-box' motif within this domain are essential for this unique (-) supercoiling activity by allowing gyrase to wrap DNA around itself. Here we report the crystal structure of Xanthomonas campestris GyrA-CTD and provide the first view of a canonical GyrA-box motif.