SuccFind: a novel succinylation sites online prediction tool via enhanced characteristic strategy

Lysine succinylation orchestrates a variety of biological processes. Annotation of succinylation in proteomes is the first-crucial step to decipher physiological roles of succinylation implicated in the pathological processes. In this work, we developed a novel succinylation site online prediction tool, called SuccFind, which is constructed to predict the lysine succinylation sites based on two major categories of characteristics: sequence-derived features and evolutionary-derived information of sequence and via an enhanced feature strategy for further optimizations. The assessment results obtained from cross-validation suggest that SuccFind can provide more instructive guidance for further experimental investigation of protein succinylation.

AVAILABILITY AND IMPLEMENTATION

A user-friendly server is freely available on the web at: http://bioinfo.ncu.edu.cn/SuccFind.aspx.

CONTACT

jdqiu@ncu.edu.cn.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Systematic Analysis of the Genetic Variability That Impacts SUMO Conjugation and Their Involvement in Human Diseases

Protein function has been observed to rely on select essential sites instead of requiring all sites to be indispensable. Small ubiquitin-related modifier (SUMO) conjugation or sumoylation, which is a highly dynamic reversible process and its outcomes are extremely diverse, ranging from changes in localization to altered activity and, in some cases, stability of the modified, has shown to be especially valuable in cellular biology. Motivated by the significance of SUMO conjugation in biological processes, we report here on the first exploratory assessment whether sumoylation related genetic variability impacts protein functions as well as the occurrence of diseases related to SUMO. Here, we defined the SUMOAMVR as sumoylation related amino acid variations that affect sumoylation sites or enzymes involved in the process of connectivity, and categorized four types of potential SUMOAMVRs. We detected that 17.13% of amino acid variations are potential SUMOAMVRs and 4.83% of disease mutations could lead to SUMOAMVR with our system. More interestingly, the statistical analysis demonstrates that the amino acid variations that directly create new potential lysine sumoylation sites are more likely to cause diseases. It can be anticipated that our method can provide more instructive guidance to identify the mechanisms of genetic diseases.

Enzyme-free surface plasmon resonance aptasensor for amplified detection of adenosine via target-triggering strand displacement cycle and Au nanoparticles

Herein, we combine the advantage of aptamer technique with the amplifying effect of an enzyme-free signal-amplification and Au nanoparticles (NPs) to design a sensitive surface plasmon resonance (SPR) aptasensor for detecting small molecules. This detection system consists of aptamer, detection probe (c-DNA1) partially hybridizing to the aptamer strand, Au NPs-linked hairpin DNA (Au-H-DNA1), and thiolated hairpin DNA (H-DNA2) previously immobilized on SPR gold chip. In the absence of target, the H-DNA1 possessing hairpin structure cannot hybridize with H-DNA2 and thereby Au NPs will not be captured on the SPR gold chip surface. Upon addition of target, the detection probe c-DNA1 is forced to dissociate from the c-DNA1/aptamer duplex by the specific recognition of the target to its aptamer. The released c-DNA1 hybridizes with Au-H-DNA1 and opens the hairpin structure, which accelerate the hybridization between Au-H-DNA1 and H-DNA2, leading to the displacement of the c-DNA1 through a branch migration process. The released c-DNA1 then hybridizes with another Au-H-DNA1 probe, and the cycle starts anew, resulting in the continuous immobilization of Au-H-DNA1 probes on the SPR chip, generating a significant change of SPR signal due to the electronic coupling interaction between the localized surface plasma of the Au NPs and the surface plasma wave. With the use of adenosine as a proof-of-principle analyte, this sensing platform can detect adenosine specifically with a detection limit as low as 0.21 pM, providing a simple, sensitive and selective protocol for small target molecules detection.

Label-free colorimetric detection of biothiols utilizing SAM and unmodified Au nanoparticles

Herein, a sensitive and selective sensor for biothiols based on colorimetric assay is reported. S-adenosyl-L-methionine (SAM) could induce the selective aggregation of unmodified gold nanoparticles (AuNPs) by electrostatic interaction. In the presence of biothiols, such as glutathione (GSH), homocysteine (Hcy), and cysteine (Cys), AuNPs prefer to react with thiols of biothiols rather than SAM due to the formation of Au-S bond. Thus, the AuNPs turn from the aggregation to the dispersion state, and the corresponding color variation in the process of anti-aggregation of AuNPs can be used for the quantitative screening of biothiols through UV-vis spectroscopy or by the naked eye. Under optimized conditions, a good linear relationship in the range of 0.4-1.2 µM is obtained for Cys, 0.2-0.9 µM for GSH, and 0.6-3.0 µM for Hcys. The detection limits of this assay for GSH, Cys and Hcys are 35.8 nM, 21.7 nM, and 62.4 nM, respectively. This colorimetric assay exhibits rapid operation (within 5 min), high selectivity and sensitivity towards biothiols with tunable dynamic ranges.

A dual-potential electrochemiluminescence ratiometric approach based on graphene quantum dots and luminol for highly sensitive detection of protein kinase activity

A novel Au NP mediated dual-potential ECL ratiometric approach based on GQDs and luminol for sensitive PKA detection is developed.

Progress and challenges in predicting protein methylation sites

We review the progress in the prediction of protein methylation sites in the past 10 years and discuss the challenges that are faced while developing novel predictors in the future.

Green synthesis of peptide-templated gold nanoclusters as novel fluorescence probes for detecting protein kinase activity

A green method was employed for synthesizing peptide-templated nanoclusters without requiring strong reducing agents. Using synthetic peptide–gold nanoclusters as fluorescence probes, a novel assay for detecting protein kinase is developed.

Target-triggering multiple-cycle amplification strategy for ultrasensitive detection of adenosine based on surface plasma resonance techniques

An ultrasensitive protocol for surface plasma resonance (SPR) detection of adenosine is designed with the aptamer-based target-triggering cascade multiple cycle amplification, and streptavidin-coated Au-NPs (Au NPs-SA) enhancement to enhance the SPR signals. The cascade amplification process consists of the aptamer-based target-triggering nicking enzyme signaling amplification (T-NESA), the nicking enzyme signaling amplification (NESA) and the hybridization chain reaction (HCR), the entire circle amplification process is triggered by the target recognition of adenosine. Upon recognition of the aptamer to target adenosine, DNA s1 is released from the aptamer and then hybridizes with hairpin DNA (HP1). The DNA s1 can be dissociated from HP1 under the reaction of nicking endonuclease to initiate the next hybridization and cleavage process. Moreover, the products of the upstream cycle (T-NESA) (DNA s2 and s3) could act as the "DNA trigger" of the downstream cycle (NESA and HCR) to generate further signal amplification, resulting in the immobilization of abundant Au NPs-SA on the gold substrate, and thus significant SPR enhancement is achieved due to the electronic coupling interaction between the localized surface plasma of Au NPs and the surface plasma wave. This detection method exhibits excellent specificity and sensitivity toward adenosine with a detection limit of 4 fM. The high sensitivity and specificity make this method a great potential for detecting biomolecules with trace amounts in bioanalysis and clinical biomedicine.

PredHydroxy: computational prediction of protein hydroxylation site locations based on the primary structure

Compared to well-known and extensively studied protein phosphorylation, protein hydroxylation attracts much less attention and the molecular mechanism of the hydroxylation is still incompletely understood. And yet annotation of hydroxylation in proteomes is a first-critical step toward decoding protein function and understanding their physiological roles that have been implicated in the pathological processes and providing useful information for the drug designs of various diseases related with hydroxylation. In this work, we present a novel method called PredHydroxy to automate the prediction of the proline and lysine hydroxylation sites based on position weight amino acids composition, 8 high-quality amino acid indices and support vector machines. The PredHydroxy achieved a promising performance with an area under the receiver operating characteristic curve (AUC) of 82.72% and a Matthew's correlation coefficient (MCC) of 69.03% for hydroxyproline as well as an AUC of 87.41% and a MCC of 66.68% for hydroxylysine in jackknife cross-validation. The results obtained from both the cross validation and independent tests suggest that the PredHydroxy might be a powerful and complementary tool for further experimental investigation of protein hydroxylation. Feature analyses demonstrate that hydroxylation and non-hydroxylation have distinct location-specific differences; alpha and turn propensity is of importance for the hydroxylation of proline and lysine residues. A user-friendly server is freely available on the web at: .

Multiplexed electrochemical detection of trypsin and chymotrypsin based on distinguishable signal nanoprobes

In this work, we developed a novel multisignal output for simultaneous detection of multiple proteases by using nanoprobes labeled with distinguishable electrochemical probes. First, biotinylated peptide1 (S1) and biotinylated peptide2 (S2) were associated with biotinylated DNA1 and DNA2 via biotin-streptavidin interaction, forming DNA1-S1 and DNA2-S2, respectively. Two distinguishable signal nanoprobes (DNA1'-Au NPs-Thi and DNA2'-Au NPs-Fc) were prepared by initial assembling DNA1' and DNA2' on the Au NPs surface, respectively, and then carrying corresponding thionine (Thi) and 6-(Ferrocenyl)hexanethiol (Fc). Then, the peptide substrates (DNA1-S1 and DNA2-S2) were immobilized on gold electrode surface through Au-S bonds, and the DNA1'-Au NPs-Thi and DNA2'-Au NPs-Fc were assembled to the peptide-DNA-modified electrode surface via DNA hybridization. The targets of trypsin and chymotrypsin can specifically recognize and cleave peptides with different sequences, releasing DNA1'-Au NPs-Thi and DNA2'-Au NPs-Fc from the electrode surface into solution, thus decreasing the current of Thi and Fc. The decrease in the electrochemical currents of the two signal nanoprobes enables us to simultaneously and quantitatively determine the targets trypsin and chymotrypsin. More importantly, this strategy can be extended easily by designing various proteases-specific peptide substrates and utilizing corresponding electrochemical detectable elements for simultaneous multiplex protease assay in various biosystems.

Enantiomeric separation by microchip electrophoresis using bovine serum albumin conjugated magnetic core-shell Fe3 O4 @Au nanocomposites as stationary phase

In this work, a novel enantioselective MCE was developed employing BSA-conjugated Fe3 O4 @Au nanoparticles (Fe3 O4 @Au NPs) as stationary phase. Fe3 O4 @Au NPs with high magnetic responsively, excellent solubility, and high dispersibility in water were prepared through a sonochemical synthesis strategy. BSA was then immobilized onto the Fe3 O4 @Au NPs surfaces through the well-developed interaction between Au NPs and amine groups of BSA to form Fe3 O4 @Au NPs-BSA conjugates, which were then locally packed into PDMS microchannels with the help of magnets. The resultant Fe3 O4 @Au NPs-BSA conjugates not only have the magnetism of Fe3 O4 NPs that make them easily manipulated by an external magnetic field, but also have the larger surface and excellent biocompatibility of Au shell, which can incorporate much more biomolecules and well maintain their biological activity. In addition, the successful BSA decorations endowed Fe3 O4 @Au NPs-BSA conjugates with pH-tunable water solubility related to the pI of BSA (pI 4.7) and led to enhanced stability against high ionic strength. Compared with the native PDMS microchannel, the modified surfaces exhibited more stable and suppressed electroosmotic mobility, and less nonspecific adsorption toward analytes. Successful separation of chiral amino acids (tryptophan and threonine) and ofloxacin enantiomers demonstrate that the constructed MCE columns own ideal enantioselectivity. The results are expected to open up a new possibility for high-throughput screening of enantiomers with protein targets as well as a new application of magnetic NPs.

PSEA: Kinase-specific prediction and analysis of human phosphorylation substrates

Protein phosphorylation catalysed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of kinase-specific phosphorylation sites and disease-related phosphorylation substrates that have been identified, the desire to explore the regulatory relationship between protein kinases and disease-related phosphorylation substrates is motivated. In this work, we analysed the kinases' characteristic of all disease-related phosphorylation substrates by using our developed Phosphorylation Set Enrichment Analysis (PSEA) method. We evaluated the efficiency of our method with independent test and concluded that our approach is reliable for identifying kinases responsible for phosphorylated substrates. In addition, we found that Mitogen-activated protein kinase (MAPK) and Glycogen synthase kinase (GSK) families are more associated with abnormal phosphorylation. It can be anticipated that our method might be helpful to identify the mechanism of phosphorylation and the relationship between kinase and phosphorylation related diseases. A user-friendly web interface is now freely available at http://bioinfo.ncu.edu.cn/PKPred_Home.aspx.

Highly sensitive electrogenerated chemiluminescence biosensor in profiling protein kinase activity and inhibition using a multifunctional nanoprobe

We presented a novel electrogenerated chemiluminescence (ECL) biosensor for monitoring the activity and inhibition of protein kinases based on signal amplification using enzyme-functionalized Au NPs nanoprobe. In this design, the biotin-DNA labeled glucose oxidase/Au NPs (GOx/Au NPs/DNA-biotin) nanoprobes, prepared by conjugating Au NPs with biotin-DNA and GOx, were bound to the biotinylated anti-phosphoserine labeled phosphorylated peptide modified electrode surface through a biotin-avidin interaction. The GOx assembled on the nanoprobe can catalyze glucose to generate H2O2 in the presence of O2 while the ECL reaction occurred in the luminol ECL biosensor. At a higher concentration of kinase, there are more nanoprobes on the electrode, which gives a higher amount of GOx at the electrode interface and thus higher electrocatalytic efficiency to the luminol ECL reaction. Therefore, the activity of protein kinases can be monitored by ECL with high sensitivity. Protein kinase A (PKA), an important enzyme in regulation of glycogen, sugar, and lipid metabolism in the human body, was used as a model to confirm the present proof-of-concept strategy. The as-proposed biosensor presents high sensitivity, low detection limit of 0.013 U mL(-1), wide linear range (from 0.02 to 40 U mL(-1)), and excellent stability. Moreover, this biosensor can also be used for quantitative analysis of kinase inhibition. On the basis of the inhibitor concentration dependent ECL signal, the half-maximal inhibition value IC50 of ellagic acid, a typical PKA inhibitor, was estimated, which is in agreement with those obtained using the conventional kinase assay. The simple and sensitive biosensor is promising in developing a high-through assay of in vitro kinase activity and inhibitor screening for clinic diagnostic and drug development.

Surface plasmon resonance sensor based on magnetic molecularly imprinted polymers amplification for pesticide recognition

We reported here a method to enhance detection sensitivity in surface plasmon resonance (SPR) spectroscopy integrated with a surface molecular imprinting recognition system and employing magnetic molecular imprinting polymer nanoparticles for amplifying SPR response. The proposed magnetic molecular imprinting polymer was designed by self-polymerization of dopamine on the Fe3O4 NPs surface in weak base aqueous solution in the presence of template chlorpyrifos (CPF). The imprinted Fe3O4@polydopamine nanoparticles (Fe3O4@PDA NPs) were characterized by Fourier transform infrared spectroscopy, UV-vis absorption spectroscopy, and transmission electron microscopy. The biosensor showed a good linear relationship between the SPR angle shift and the chlorpyrifos concentration over a range from 0.001 to 10 μM with a detection limit of 0.76 nM. A significant increase in sensitivity was therefore afforded through the use of imprinted Fe3O4@PDA NPs as an amplifier, and meanwhile, the imprinted Fe3O4@PDA NPs had an excellent recognition capacity to chlorpyrifos over other pesticides. The excellent sensitivity and selectivity and high stability of the designed biosensor make this magnetic imprinted Fe3O4@PDA NP an attractive recognition element for various SPR sensors for detecting pesticide residuals and other environmentally deleterious chemicals.

Simultaneous determination of concanavalin A and peanut agglutinin by dual-color quantum dots

In this work, we designed a novel detection strategy to realize simultaneous determination of multiplex lectin by labeling glucosamine (G1) and galactosamine (G2) with different-colored semiconductor quantum dots (QDs). On the basis of the agglutination of the aminosugar-labeled QDs induced by the exclusive binding between the lectin and sugar on the QDs surfaces, the fluorescence emission of the QDs supernatant after centrifugation decreased with relevant lectin concentration [i.e., when concanavalin A (Con A) exists alone], only green color fluorescence emission from QDs-G1 supernatant decreased, so it is peanut agglutinin (PNA) and red color fluorescence emission from QDs-G2. Moreover, since QDs can be simultaneously excited with multiple fluorescence colors and have a larger Stokes shift than organic fluorophores, when both Con A and PNA are present in the sample, both of the green and red color fluorescence emission from QDs-G1 and QDs-G2 supernatant would decrease, thus realizing the simultaneous determination of Con A and PNA. The detection limits of Con A and PNA are 0.30 and 0.18 nM (3σ), respectively. Furthermore, the present detection method not only can determine the protein/lectins by fluorescence spectral method but also can realize visualization detection by UV lamp illumination. To the best of our knowledge, this is the first report of such analytical method in multiple and simultaneous lectin detection.

DNA-templated Ag nanoclusters as fluorescent probes for sensing and intracellular imaging of hydroxyl radicals

We have developed a simple, rapid and label-free sensor for the essential biological OH radicals based on the fluorescence quenching of DNA-templated Ag nanoclusters (DNA-Ag NCs). The OH radicals generated from the Fenton reagent attack and cleave the DNA template, which disturbs the microenvironments around Ag NCs, resulting in spontaneous aggregation due to the lack of stabilization and further the quenching of the Ag NCs fluorescence. These changes in fluorescence intensity allow sensing of OH radicals with good sensitivity and selectivity under optimal conditions. The sensor can be also applied for quantifying the radical scavenging action of antioxidants. Various characterizations including absorption spectra, fluorescence lifetimes, light scattering (LS) spectra, transmission electron microscopy (TEM), dark field light scattering imaging, and circular dichroism (CD) spectrometry have been employed to illustrate the proposed sensing mechanism. Further investigations demonstrate that the fluorescent probe could penetrate into intact cell membranes to selectively detect intracellular OH radicals induced by the phorbol myristate acetate (PMA) stimulation. These advantageous characteristics make the fluorescent DNA-Ag NCs potentially useful as a new candidate to monitor OH in broad biosystems.

Easy design of colorimetric logic gates based on nonnatural base pairing and controlled assembly of gold nanoparticles

Utilizing the principles of metal-ion-mediated base pairs (C-Ag-C and T-Hg-T), the pH-sensitive conformational transition of C-rich DNA strand, and the ligand-exchange process triggered by DL-dithiothreitol (DTT), a system of colorimetric logic gates (YES, AND, INHIBIT, and XOR) can be rationally constructed based on the aggregation of the DNA-modified Au NPs. The proposed logic operation system is simple, which consists of only T-/C-rich DNA-modified Au NPs, and it is unnecessary to exquisitely design and alter the DNA sequence for different multiple molecular logic operations. The nonnatural base pairing combined with unique optical properties of Au NPs promises great potential in multiplexed ion sensing, molecular-scale computers, and other computational logic devices.

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. In view of this, a high throughput method (DWT_DT), a 2-layer approach by fusing discrete wavelet transform (DWT) and decision-tree algorithm (DT) with physicochemical features, has been developed to predict protein quaternary structures. The 1st layer is to assign a query protein to one of the 10 main quaternary structural attributes. The 2nd layer is to evaluate whether the protein in question is composed of homo- or hetero-oligomers. The overall accuracy by jackknife test for the 1st layer identification was 89.60%. The overall accuracy of the 2nd layer varies from 88.23 to 100%. The results suggest that this newly developed protocol (DWT_DT) is very promising in predicting quaternary structures with complicated composition.

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. Because mass spectrometry-based experimental approaches for identifying ubiquitylation events are costly, time-consuming and biased toward abundant proteins and proteotypic peptides, in silico prediction of ubiquitylation sites is a potentially useful alternative strategy for whole proteome annotation. Because of various limitations, current ubiquitylation site prediction tools were not well designed to comprehensively assess proteomes.

RESULTS

We present a novel tool known as UbiProber, specifically designed for large-scale predictions of both general and species-specific ubiquitylation sites. We collected proteomics data for ubiquitylation from multiple species from several reliable sources and used them to train prediction models by a comprehensive machine-learning approach that integrates the information from key positions and key amino acid residues. Cross-validation tests reveal that UbiProber achieves some improvement over existing tools in predicting species-specific ubiquitylation sites. Moreover, independent tests show that UbiProber improves the areas under receiver operating characteristic curves by ~15% by using the Combined model.

AVAILABILITY

The UbiProber server is freely available on the web at http://bioinfo.ncu.edu.cn/UbiProber.aspx. The software system of UbiProber can be downloaded at the same site.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

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. The in vivo or in vitro experimental identification of palmitoylation sites is both time consuming and expensive. Due to the large volume of protein sequences generated in the post-genomic era, it is extraordinarily important in both basic research and drug discovery to rapidly identify the attributes of a new protein's palmitoylation sites. In this work, a new computational method, WAP-Palm, combining multiple feature extraction, has been developed to predict the palmitoylation sites of proteins. The performance of the WAP-Palm model is measured herein and was found to have a sensitivity of 81.53%, a specificity of 90.45%, an accuracy of 85.99% and a Matthews correlation coefficient of 72.26% in 10-fold cross-validation test. The results obtained from both the cross-validation and independent tests suggest that the WAP-Palm model might facilitate the identification and annotation of protein palmitoylation locations. The online service is available at http://bioinfo.ncu.edu.cn/WAP-Palm.aspx.

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. In this work, we performed a proteome-wide analysis of amino acid variations that could potentially influence protein lysine acetylation characteristics in human variant proteins. Here, we defined the AcetylAAVs as acetylation related amino acid variations that affect acetylation sites or their interacting acetyltransferases, and categorized three types of AcetylAAVs. Using the developed prediction system, named KAcePred, we detected that 50.87% of amino acid variations are potential AcetylAAVs and 12.32% of disease mutations could result in AcetylAAVs. More interestingly, from the statistical analysis, we found that the amino acid variations that directly create new potential lysine acetylation sites have more chance to cause diseases. It can be anticipated that the analysis of AcetylAAVs might be useful to screen important polymorphisms and help to identify the mechanism of genetic diseases. A user-friendly web interface for analysis of AcetylAAVs is now freely available at http://bioinfo.ncu.edu.cn/AcetylAAVs_Home.aspx .

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. The residues around the acetylation sites were selected or excluded based on their entropy values. We incorporated features of amino acid composition information, evolutionary similarity and physicochemical properties to predict lysine acetylation sites. The prediction model achieved an accuracy of 79.84% and a Matthews correlation coefficient of 59.72% using the 10-fold cross-validation on balanced positive and negative samples. A feature analysis showed that all features applied in this method contributed to the acetylation process. A position-specific analysis showed that the features derived from the critical neighboring residues contributed profoundly to the acetylation site determination. The detailed analysis in this paper can help us to understand more of the acetylation mechanism and can provide guidance for the related experimental validation.

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. Three types of encoding algorithms-secondary structure, grouped weight, and autocorrelation function-were applied to mine features from tyrosine sulfation proteins. The prediction model with multiple features achieved an accuracy of 92.89% in 10-fold cross-validation. Feature analysis showed that the coil structure, acidic amino acids, and residue interactions around the tyrosine sulfation sites all contributed to the sulfation site determination. The detailed feature analysis in this work can help us to understand the sulfation mechanism and provide guidance for the related experimental validation. PredSulSite is available as a community resource at http://www.bioinfo.ncu.edu.cn/inquiries_PredSulSite.aspx.