TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins

Background  

Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discriminating between bbtm proteins and other proteins, screening of entire genomes remains troublesome as these molecules only constitute a small fraction of the sequences screened. Therefore, novel methods are still required capable of detecting new families of bbtm protein in diverse genomes.     

Prediction of Golgi Type II membrane proteins based on their transmembrane domains

MOTIVATION: A major issue in cell biology today is how distinct intracellular regions of the cell, like the Golgi Apparatus, maintain their unique composition of proteins and lipids. The cell differentially separates Golgi resident proteins from proteins that move through the organelle to other subcellular destinations. We set out to determine if we could distinguish these two types of transmembrane proteins using computational approaches. RESULTS: A new method has been developed to predict Golgi membrane proteins based on their transmembrane domains. To establish the prediction procedure, we took the hydrophobicity values and frequencies of different residues within the transmembrane domains into consideration. A simple linear discriminant function was developed with a small number of parameters derived from a dataset of Type II transmembrane proteins of known localization. This can discriminate between proteins destined for Golgi apparatus or other locations (post-Golgi) with a success rate of 89.3% or 85.2%, respectively on our redundancy-reduced data sets. AVAILABILITY: See http://microarray.imb.uq.edu.au/golgi/     

Snorkeling preferences foster an amino acid composition bias in transmembrane helices

By analyzing transmembrane (TM) helices in known structures, we find that some polar amino acids are more frequent at the N terminus than at the C terminus. We propose the asymmetry occurs because most polar amino acids are better able to snorkel their polar atoms away from the membrane core at the N terminus than at the C terminus. Two findings lead us to this proposition: (1) side-chain conformations are influenced strongly by the N or C-terminal position of the amino acid in the bilayer, and (2) the favored snorkeling direction of an amino acid correlates well with its N to C-terminal composition bias. Our results suggest that TM helix predictions should incorporate an N to C-terminal composition bias, that rotamer preferences of TM side-chains are position-dependent, and that the ability to snorkel influences the evolutionary selection of amino acids for the helix N and C termini.     

Discrimination of Golgi type II membrane proteins based on their hydropathy profiles and the amino acid propensities of their transmembrane regions

Membrane proteins in the Golgi apparatus play important roles in biological functions, predominantly as catalysts related to post-translational modification of protein oligosaccharides. We succeeded in extracting the characteristics of Golgi type II membrane proteins computationally by comparison with those of Golgi no retention proteins, which are mainly localized in the plasma membrane. Golgi type II membrane proteins were detected by combining hydropathy alignment and a position-specific score matrix of the amino acid propensities around the transmembrane region. We achieved 96.2% sensitivity, 93.5% specificity, and a 0.949 success rate in a self-consistency test. In a 5-fold cross-validation test, 88.0% sensitivity, 85.5% specificity, and a 0.867 success rate were achieved.     

Unique amino acid composition of proteins in halophilic bacteria

The amino acid compositions of proteins from halophilic archaea were compared with those from non-halophilic mesophiles and thermophiles, in terms of the protein surface and interior, on a genome-wide scale. As we previously reported for proteins from thermophiles, a biased amino acid composition also exists in halophiles, in which an abundance of acidic residues was found on the protein surface as compared to the interior. This general feature did not seem to depend on the individual protein structures, but was applicable to all proteins encoded within the entire genome. Unique protein surface compositions are common in both halophiles and thermophiles. Statistical tests have shown that significant surface compositional differences exist among halophiles, non-halophiles, and thermophiles, while the interior composition within each of the three types of organisms does not significantly differ. Although thermophilic proteins have an almost equal abundance of both acidic and basic residues, a large excess of acidic residues in halophilic proteins seems to be compensated by fewer basic residues. Aspartic acid, lysine, asparagine, alanine, and threonine significantly contributed to the compositional differences of halophiles from meso- and thermophiles. Among them, however, only aspartic acid deviated largely from the expected amount estimated from the dinucleotide composition of the genomic DNA sequence of the halophile, which has an extremely high G+C content (68%). Thus, the other residues with large deviations (Lys, Ala, etc.) from their non-halophilic frequencies could have arisen merely as "dragging effects" caused by the compositional shift of the DNA, which would have changed to increase principally the fraction of aspartic acid alone.     

Common amino acid sequence domains among the LEA proteins of higher plants

LEA proteins are late embryogenesis abundant in the seeds of many higher plants and are probably universal in occurrence in plant seeds. LEA mRNAs and proteins can be induced to appear at other stages in the plant's life by desiccation stress and/or treatment with the plant hormone abscisic acid (ABA). A role in protecting plant structures during water loss is likely for these proteins, with ABA functioning in the stress transduction process. Presented here are conserved tracts of amino acid sequence among LEA proteins from several species that may represent domains functionally important in desiccation protection. Curiously, an 11 amino acid sequence motif is found tandemly repeated in a group of LEA proteins of vastly different sizes. Analysis of this motif suggests that it exists as an amphiphilic helix which may serve as the basis for higher order structure.     

The broken-stick model for amino acid composition in proteins

Summary The relative abundances among the amino acids, which are functionally similar to one another, were explained by random partition of a unit interval.     

The novel transmembrane Escherichia coli proteins involved in the amino acid efflux.

A novel gene of Escherichia coli, rhtB, has been characterized. Amplification of this gene provides resistance to homoserine and homoserine lactone. Another E. coli gene, rhtC, provides resistance to threonine. The homologues of RhtB are widely distributed among various eubacteria and archaea, from one to 12 copies of family members that differ in their primary structure were found in the genomes. Most of them are genes that encode hypothetical transmembrane proteins. Experimental data that indicate participation of the rhtB product in the excretion of homoserine have been obtained.     

The amino-terminal 14 amino acids of v-src can functionally replace the extracellular and transmembrane domains of v-erbB.

The retroviral oncogene v-erbB encodes a truncated form of the receptor for epidermal growth factor, an integral membrane protein-tyrosine kinase. By contrast, the oncogene v-src encodes a protein-tyrosine kinase that is a peripheral membrane protein. The morphologies and spectra of cells transformed by these two oncogenes differ. In an effort to identify the functional determinant(s) of these differences, we constructed and tested first deletion mutants of v-erbB and then chimeras between v-src and v-erbB. As reported previously, the absence of any membrane anchorage eliminated transformation by v-erbB. Anchorage of the cytoplasmic kinase domain of v-erbB to membranes with amino-terminal portions of the v-src protein permitted transformation. The phenotype and spectrum of transformation were those expected for v-erbB rather than for v-src. The transforming chimeras lost their biological activity if the signal for myristylation at the amino terminus of v-src was compromised by mutation. Biochemical fractionations revealed a correlation between transforming activity and the association of chimeric gene products with the membrane fraction of the cell. For reasons not yet apparent, the combined presence of membrane anchorage domains of v-src, and the transmembrane domain of v-erbB in the same chimera typically (but not inevitably) impeded transformation. Our results suggest that the specificity of transformation by v-erbB resides in the selection of substrates by the cytoplasmic domain of the gene product. The protein retains access to those substrates even when anchored to the membrane in the manner of a peripheral rather than a transmembrane protein.     

Identify DNA-binding proteins with optimal Chou's amino acid composition

DNA-binding proteins play an important role in most cellular processes, such as gene regulation, recombination, repair, replication, and DNA modification. In this article, an optimal Chou's pseudo amino acid composition (PseAAC) based on physicochemical characters of amino acid is proposed to represent proteins for identifying DNAbinding proteins. Six physicochemical characters of amino acids are utilized to generate the sequence features via the web server PseAAC. The optimal values of two important parameters (correlation factor δ and weighting factor w) about PseAAC are determined to get the appropriate representation of proteins, which ultimately result in better prediction performance. Experimental results on the benchmark datasets using random forest show that our method is really promising to predict DNA-binding proteins and may at least be a useful supplement tool to existing methods.     

Trend of amino acid composition of proteins of different taxa

Archaea, bacteria and eukaryotes represent the main kingdoms of life. Is there any trend for amino acid compositions of proteins found in full genomes of species of different kingdoms? What is the percentage of totally unstructured proteins in various proteomes? We obtained amino acid frequencies for different taxa using 195 known proteomes and all annotated sequences from the Swiss-Prot data base. Investigation of the two data bases (proteomes and Swiss-Prot) shows that the amino acid compositions of proteins differ substantially for different kingdoms of life, and this difference is larger between different proteomes than between different kingdoms of life. Our data demonstrate that there is a surprisingly small selection for the amino acid composition of proteins for higher organisms (eukaryotes) and their viruses in comparison with the "random" frequency following from a uniform usage of codons of the universal genetic code. On the contrary, lower organisms (bacteria and especially archaea) demonstrate an enhanced selection of amino acids. Moreover, according to our estimates, 12%, 3% and 2% of the proteins in eukaryotic, bacterial and archaean proteomes are totally disordered, and long (> 41 residues) disordered segments are found to occur in 16% of arhaean, 20% of eubacterial and 43% of eukaryotic proteins for 19 archaean, 159 bacterial and 17 eukaryotic proteomes, respectively. A correlation between amino acid compositions of proteins of various taxa, show that the highest correlation is observed between eukaryotes and their viruses (the correlation coefficient is 0.98), and bacteria and their viruses (the correlation coefficient is 0.96), while correlation between eukaryotes and archaea is 0.85 only.     

Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition

The successful prediction of protein subcellular localization directly from protein primary sequence is useful to protein function prediction and drug discovery. In this paper, by using the concept of pseudo amino acid composition (PseAAC), the mycobacterial proteins are studied and predicted by support vector machine (SVM) and increment of diversity combined with modified Mahalanobis Discriminant (IDQD). The results of jackknife cross-validation for 450 non-redundant proteins show that the overall predicted successful rates of SVM and IDQD are 82.2% and 79.1%, respectively. Compared with other existing methods, SVM combined with PseAAC display higher accuracies.     

Nitric oxide can modify amino acid residues in proteins.

Nitric oxide derived from sodium nitroprusside binds to the heme moiety of hemoglobin and also modifies some functional groups in the protein. As hemoglobin concentration is increased, globin modification is decreased presumably due to formation of the NO complex with heme. The SH groups of hemoglobin are probably not involved in the formation of the stable product formed by NO. In the presence of inositol hexaphosphate, which binds preferentially in the cleft between the two beta-chains of hemoglobin, formation of one modified derivative was selectively reduced. With hemoglobin specifically blocked on its N-terminal residues, globin modification was also significantly reduced. Carbonic anhydrase, which is blocked at its N-terminus, was also refractory to modification. The results suggest that the N-terminal groups of some proteins can be modified by nitric oxide, perhaps by deamination.     

Prokaryotic squalene-hopene cyclases can be converted to citronellal cyclases by single amino acid exchange

Squalene-hopene cyclases (SHCs) are prokaryotic enzymes that catalyse the cyclisation of the linear precursor squalene to pentacyclic hopene. Recently, we discovered that a SHC cloned from Zymomonas mobilis (ZMO-1548 gene product) has the unique property to cyclise the monoterpenoid citronellal to isopulegol. In this study, we performed saturation mutagenesis of three amino acids of the catalytic centre of ZMO-1548 (F428, F486 and W555), which had been previously identified to interact with enzyme-bound substrate. Replacement of F428 by tyrosine increased hopene formation from squalene, but isopulegol-forming activity was strongly reduced or abolished in all muteins of position 428. W555 was essential for hopene formation; however, three muteins (W555Y, W428F or W555T) revealed enhanced cyclisation efficiency with citronellal. The residue at position 486 turned out to be the most important for isopulegol-forming activity. While the presence of phenylalanine or tyrosine favoured cyclisation activity with squalene, several small and/or hydrophobic residues such as cysteine, alanine or isoleucine and others reduced activity with squalene but greatly enhanced isopulegol formation from citronellal. Replacement of the conserved aromatic residue corresponding to F486 to cysteine in other SHCs cloned from Z. mobilis (ZMO-0872), Alicyclobacillus acidocaldarius (SHC _Aac ), Acetobacter pasteurianus (SHC _Apa ), Streptomyces coelicolor (SHC _Sco ) and Bradyrhizobium japonicum (SHC _Bja ) resulted in more or less strong isopulegol-forming activities from citronellal. In conclusion, many SHCs can be converted to citronellal cyclases by mutagenesis of the active centre thus broadening the applicability of this interesting class of biocatalyst.     

Chronic irradiation with low doses can be characterized by significant biological efficacy

Chromosomal aberrations (ChA) level was analyzed in the onion root meristem after the chronic irradiation with different dose capacities. It was shown that after the chronic irradiation with doses of 0.87 cGy, 2.61 cGy and 4.35 cGy the level of chromosomal aberrations depended on the dose capacity. Its value may also correspond to those which have been induced with accute irradiation. Biological efficacy of chronic irradiation may be from 20 to 1000 time folder in order to compare it with accute irradiation and this value depends on the irradiation regime.