Dataset Information

Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks.

ABSTRACT: The metabolic stability is a very important idiosyncracy of proteins that is related to their global flexibility, intramolecular fluctuations, various internal dynamic processes, as well as many marvelous biological functions. Determination of protein's metabolic stability would provide us with useful information for in-depth understanding of the dynamic action mechanisms of proteins. Although several experimental methods have been developed to measure protein's metabolic stability, they are time-consuming and more expensive. Reported in this paper is a computational method, which is featured by (1) integrating various properties of proteins, such as biochemical and physicochemical properties, subcellular locations, network properties and protein complex property, (2) using the mRMR (Maximum Relevance & Minimum Redundancy) principle and the IFS (Incremental Feature Selection) procedure to optimize the prediction engine, and (3) being able to identify proteins among the four types: "short", "medium", "long", and "extra-long" half-life spans. It was revealed through our analysis that the following seven characters played major roles in determining the stability of proteins: (1) KEGG enrichment scores of the protein and its neighbors in network, (2) subcellular locations, (3) polarity, (4) amino acids composition, (5) hydrophobicity, (6) secondary structure propensity, and (7) the number of protein complexes the protein involved. It was observed that there was an intriguing correlation between the predicted metabolic stability of some proteins and the real half-life of the drugs designed to target them. These findings might provide useful insights for designing protein-stability-relevant drugs. The computational method can also be used as a large-scale tool for annotating the metabolic stability for the avalanche of protein sequences generated in the post-genomic age.

SUBMITTER: Huang T

PROVIDER: S-EPMC2881046 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks.

Huang Tao T Shi Xiao-He XH Wang Ping P He Zhisong Z Feng Kai-Yan KY Hu Lele L Kong Xiangyin X Li Yi-Xue YX Cai Yu-Dong YD Chou Kuo-Chen KC

PloS one 20100604 6

The metabolic stability is a very important idiosyncracy of proteins that is related to their global flexibility, intramolecular fluctuations, various internal dynamic processes, as well as many marvelous biological functions. Determination of protein's metabolic stability would provide us with useful information for in-depth understanding of the dynamic action mechanisms of proteins. Although several experimental methods have been developed to measure protein's metabolic stability, they are tim ...[more]

PMID: 20532046

Similar Datasets

Project description:BACKGROUND: Due to the growing amount of biological knowledge that is incorporated into metabolic network models, their analysis has become more and more challenging. Here, we examine the capabilities of the recently introduced chemical organization theory (OT) to ease this task. Considering only network stoichiometry, the theory allows the prediction of all potentially persistent species sets and therewith rigorously relates the structure of a network to its potential dynamics. By this, the phenotypes implied by a metabolic network can be predicted without the need for explicit knowledge of the detailed reaction kinetics. RESULTS: We propose an approach to deal with regulation - and especially inhibitory interactions - in chemical organization theory. One advantage of this approach is that the metabolic network and its regulation are represented in an integrated way as one reaction network. To demonstrate the feasibility of this approach we examine a model by Covert and Palsson (J Biol Chem, 277(31), 2002) of the central metabolism of E. coli that incorporates the regulation of all involved genes. Our method correctly predicts the known growth phenotypes on 16 different substrates. Without specific assumptions, organization theory correctly predicts the lethality of knockout experiments in 101 out of 116 cases. Taking into account the same model specific assumptions as in the regulatory flux balance analysis (rFBA) by Covert and Palsson, the same performance is achieved (106 correctly predicted cases). Two model specific assumptions had to be considered: first, we have to assume that secreted molecules do not influence the regulatory system, and second, that metabolites with increasing concentrations indicate a lethal state. CONCLUSION: The introduced approach to model a metabolic network and its regulation in an integrated way as one reaction network makes organization analysis a universal technique to study the potential behavior of biological network models. Applying multiple methods like OT and rFBA is shown to be valuable to uncover critical assumptions and helps to improve model coherence.

Project description:BackgroundThe computational prediction of mycobacterial proteins' subcellular localization is of key importance for proteome annotation and for the identification of new drug targets and vaccine candidates. Several subcellular localization classifiers have been developed over the past few years, which have comprised both general localization and feature-based classifiers. Here, we have validated the ability of different bioinformatics approaches, through the use of SignalP 2.0, TatP 1.0, LipoP 1.0, Phobius, PA-SUB 2.5, PSORTb v.2.0.4 and Gpos-PLoc, to predict secreted bacterial proteins. These computational tools were compared in terms of sensitivity, specificity and Matthew's correlation coefficient (MCC) using a set of mycobacterial proteins having less than 40% identity, none of which are included in the training data sets of the validated tools and whose subcellular localization have been experimentally confirmed. These proteins belong to the TBpred training data set, a computational tool specifically designed to predict mycobacterial proteins.ResultsA final validation set of 272 mycobacterial proteins was obtained from the initial set of 852 mycobacterial proteins. According to the results of the validation metrics, all tools presented specificity above 0.90, while dispersion sensitivity and MCC values were above 0.22. PA-SUB 2.5 presented the highest values; however, these results might be biased due to the methodology used by this tool. PSORTb v.2.0.4 left 56 proteins out of the classification, while Gpos-PLoc left just one protein out.ConclusionBoth subcellular localization approaches had high predictive specificity and high recognition of true negatives for the tested data set. Among those tools whose predictions are not based on homology searches against SWISS-PROT, Gpos-PLoc was the general localization tool with the best predictive performance, while SignalP 2.0 was the best tool among the ones using a feature-based approach. Even though PA-SUB 2.5 presented the highest metrics, it should be taken into account that this tool was trained using all proteins reported in SWISS-PROT, which includes the protein set tested in this study, either as a BLAST search or as a training model.

Project description:Subcellular locations of proteins are important functional attributes. An effective and efficient subcellular localization predictor is necessary for rapidly and reliably annotating subcellular locations of proteins. Most of existing subcellular localization methods are only used to deal with single-location proteins. Actually, proteins may simultaneously exist at, or move between, two or more different subcellular locations. To better reflect characteristics of multiplex proteins, it is highly desired to develop new methods for dealing with them. In this paper, a new predictor, called Euk-ECC-mPLoc, by introducing a powerful multi-label learning approach which exploits correlations between subcellular locations and hybridizing gene ontology with dipeptide composition information, has been developed that can be used to deal with systems containing both singleplex and multiplex eukaryotic proteins. It can be utilized to identify eukaryotic proteins among the following 22 locations: (1) acrosome, (2) cell membrane, (3) cell wall, (4) centrosome, (5) chloroplast, (6) cyanelle, (7) cytoplasm, (8) cytoskeleton, (9) endoplasmic reticulum, (10) endosome, (11) extracellular, (12) Golgi apparatus, (13) hydrogenosome, (14) lysosome, (15) melanosome, (16) microsome, (17) mitochondrion, (18) nucleus, (19) peroxisome, (20) spindle pole body, (21) synapse, and (22) vacuole. Experimental results on a stringent benchmark dataset of eukaryotic proteins by jackknife cross validation test show that the average success rate and overall success rate obtained by Euk-ECC-mPLoc were 69.70% and 81.54%, respectively, indicating that our approach is quite promising. Particularly, the success rates achieved by Euk-ECC-mPLoc for small subsets were remarkably improved, indicating that it holds a high potential for simulating the development of the area. As a user-friendly web-server, Euk-ECC-mPLoc is freely accessible to the public at the website http://levis.tongji.edu.cn:8080/bioinfo/Euk-ECC-mPLoc/. We believe that Euk-ECC-mPLoc may become a useful high-throughput tool, or at least play a complementary role to the existing predictors in identifying subcellular locations of eukaryotic proteins.

Dataset Information

Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks.

Publications

Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets