基于物化性质对嗜热蛋白的预测

嗜热蛋白在高温下能保持稳定性和活性,是研究蛋白质热稳定性的理想模型,开发一个蛋白质热稳定性识别的方法将对蛋白质工程和蛋白质的设计很有帮助。目前的研究中,氨基酸的组成及其物化性质一直被认为和蛋白质的热稳定性相关。本研究筛选出可靠的数据集,包括915个嗜热蛋白和793个非嗜热蛋白。利用蛋白质氨基酸的物化性质和氨基酸的组成表征嗜热蛋白,将二肽氨基酸组成整合到9组氨基酸物化性质中使蛋白序列公式化。支持向量机5折叠交叉验证表明:当gap=0时,290个特征产生的精度最高,为92.74%。因此说明对于分析蛋白质的热稳定性,所建立的预测模型将是一个很有效的工具。     

Optimal subset selection of primary sequence features using the genetic algorithm for thermophilic proteins identification

A genetic algorithm (GA) coupled with multiple linear regression (MLR) was used to extract useful features from amino acids and g-gap dipeptides for distinguishing between thermophilic and non-thermophilic proteins. The method was trained by a benchmark dataset of 915 thermophilic and 793 non-thermophilic proteins. The method reached an overall accuracy of 95.4 % in a Jackknife test using nine amino acids, 38 0-gap dipeptides and 29 1-gap dipeptides. The accuracy as a function of protein size ranged between 85.8 and 96.9 %. The overall accuracies of three independent tests were 93, 93.4 and 91.8 %. The observed results of detecting thermophilic proteins suggest that the GA-MLR approach described herein should be a powerful method for selecting features that describe thermostabile machines and be an aid in the design of more stable proteins.     

Detecting thermophilic proteins through selecting amino acid and dipeptide composition features

Detecting thermophilic proteins is an important task for designing stable protein engineering in interested temperatures. In this work, we develop a simple but efficient method to classify thermophilic proteins from mesophilic ones using the amino acid and dipeptide compositions. Since most of the amino acid and dipeptide compositions are redundant, we propose a new forward floating selection technique to select only a useful subset of these compositions as features for support vector machine-based classification. We test the proposed method on a benchmark data set of 915 thermophilic and 793 mesophilic proteins. The results show that our method using 28 amino acid and dipeptide compositions achieves an accuracy rate of 93.3% evaluated by the jackknife cross-validation test, which is higher not only than the existing methods but also than using all amino acid and dipeptide compositions.     

Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins

Summary. Thermophilic proteins show substantially higher intrinsic thermal stability than their mesophilic counterparts. Amino acid composition is believed to alter the intrinsic stability of proteins. Several investigations and mutagenesis experiment have been carried out to understand the amino acid composition for the thermostability of proteins. This review presents some generalized features of amino acid composition found in thermophilic proteins, including an increase in residue hydrophobicity, a decrease in uncharged polar residues, an increase in charged residues, an increase in aromatic residues, certain amino acid coupling patterns and amino acid preferences for thermophilic proteins. The differences of amino acids composition between thermophilic and mesophilic proteins are related to some properties of amino acids. These features provide guidelines for engineering mesophilic protein to thermophilic protein. Authors’ addresses: Yuan-Jiang Pan, Institute of Chemical Biology and Pharmaceutical Chemistry, Zhejiang University, Zhejiang University Road 38, Hangzhou 310027, China; Wei-Fen Li, Microbiology Division, College of Animal Science, Zhejiang University, Hangzhou 310029, China     

Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria

One of the well-known observations of proteins from thermophilic bacteria is the bias of the amino acid composition in which charged residues are present in large numbers, and polar residues are scarce. On the other hand, it has been reported that the molecular surfaces of proteins are adapted to their subcellular locations, in terms of the amino acid composition. Thus, it would be reasonable to expect that the differences in the amino acid compositions between proteins of thermophilic and mesophilic bacteria would be much greater on the protein surface than in the interior. We performed systematic comparisons between proteins from thermophilic bacteria and mesophilic bacteria, in terms of the amino acid composition of the protein surface and the interior, as well as the entire amino acid chains, by using sequence information from the genome projects. The biased amino acid composition of thermophilic proteins was confirmed, and the differences from those of mesophilic proteins were most obvious in the compositions of the protein surface. In contrast to the surface composition, the interior composition was not distinctive between the thermophilic and mesophilic proteins. The frequency of the amino acid pairs that are closely located in the space was also analyzed to show the same trend of the single amino acid compositions. Interestingly, extracellular proteins from mesophilic bacteria showed an inverse trend against thermophilic proteins (i.e. a reduced number of charged residues and rich in polar residues). Nuclear proteins from eukaryotes, which are known to be abundant in positive charges, showed different compositions as a whole from the thermophiles. These results suggest that the bias of the amino acid composition of thermophilic proteins is due to the residues on the protein surfaces, which may be constrained by the extreme environment.     

Identification of thermophilic species by the amino acid compositions deduced from their genomes

The global amino acid compositions as deduced from the complete genomic sequences of six thermophilic archaea, two thermophilic bacteria, 17 mesophilic bacteria and two eukaryotic species were analysed by hierarchical clustering and principal components analysis. Both methods showed an influence of several factors on amino acid composition. Although GC content has a dominant effect, thermophilic species can be identified by their global amino acid compositions alone. This study presents a careful statistical analysis of factors that affect amino acid composition and also yielded specific features of the average amino acid composition of thermophilic species. Moreover, we introduce the first example of a 'compositional tree' of species that takes into account not only homologous proteins, but also proteins unique to particular species. We expect this simple yet novel approach to be a useful additional tool for the study of phylogeny at the genome level.     

Amino acid coupling patterns in thermophilic proteins

Structural analysis is useful in elucidating structural features responsible for enhanced thermal stability of proteins. However, due to the rapid increase of sequenced genomic data, there are far more protein sequences than the corresponding three-dimensional (3D) structures. The usual sequence-based amino acid composition analysis provides useful but simplified clues about the amino acid types related to thermal stability of proteins. In this work, we developed a statistical approach to identify the significant amino acid coupling sequence patterns in thermophilic proteins. The amino acid coupling sequence pattern is defined as any 2 types of amino acids separated by 1 or more amino acids. Using this approach, we construct the rho profiles for the coupling patterns. The rho value gives a measure of the relative occurrence of a coupling pattern in thermophiles compared with mesophiles. We found that thermophiles and mesophiles exhibit significant bias in their amino acid coupling patterns. We showed that such bias is mainly due to temperature adaptation instead of species or GC content variations. Though no single outstanding coupling pattern can adequately account for protein thermostability, we can use a group of amino acid coupling patterns having strong statistical significance (p values < 10(-7)) to distinguish between thermophilic and mesophilic proteins. We found a good correlation between the optimal growth temperatures of the genomes and the occurrences of the coupling patterns (the correlation coefficient is 0.89). Furthermore, we can separate the thermophilic proteins from their mesophilic orthologs using the amino acid coupling patterns. These results may be useful in the study of the enhanced stability of proteins from thermophiles-especially when structural information is scarce. Proteins 2005. (c) 2005 Wiley-Liss, Inc.     

Discrimination of mesophilic and thermophilic proteins using machine learning algorithms

Discriminating thermophilic proteins from their mesophilic counterparts is a challenging task and it would help to design stable proteins. In this work, we have systematically analyzed the amino acid compositions of 3075 mesophilic and 1609 thermophilic proteins belonging to 9 and 15 families, respectively. We found that the charged residues Lys, Arg, and Glu as well as the hydrophobic residues, Val and Ile have higher occurrence in thermophiles than mesophiles. Further, we have analyzed the performance of different methods, based on Bayes rules, logistic functions, neural networks, support vector machines, decision trees and so forth for discriminating mesophilic and thermophilic proteins. We found that most of the machine learning techniques discriminate these classes of proteins with similar accuracy. The neural network-based method could discriminate the thermophiles from mesophiles at the five-fold cross-validation accuracy of 89% in a dataset of 4684 proteins. Moreover, this method is tested with 325 mesophiles in Xylella fastidosa and 382 thermophiles in Aquifex aeolicus and it could successfully discriminate them with the accuracy of 91%. These accuracy levels are better than other methods in the literature and we suggest that this method could be effectively used to discriminate mesophilic and thermophilic proteins.     

Search for structural factors responsible for the stability of proteins from thermophilic organisms

Database including 392 homologous pairs of proteins from thermophilic and mesophilic organisms was created. Using this database we have found that proteins from termophilic organisms contain more atom-atom contacts per residue in comparison with mesophilic homologues. Contribution to increase of the number of contacts gives exterior amino acid residues, accessible for the solvent. Amino acid composition of interior, inaccessible for the solvent, and exterior amino acid residues of proteins from thermophilic and mesophilic organisms were analyzed. We have obtained that exterior residues of proteins from thermophilic organisms contain more such amino acid residues as Lys, Arg and Glu and smaller such amino acid residues as Ala, Asp, Asn. Gln, Ser, and Thr in comparison with proteins from mesophilic organisms. Amino acid compositions of interior residues of considered proteins are not different.     

Diversity of thermophilic and non-thermophilic Crenarchaeota at 80 degrees C

A hot spring in the solfataric field of Pisciarelli (Naples-Italy) was analysed for Archaeal diversity. Total DNA was extracted from the environment, archaeal 16S rRNA genes were amplified with Archaea specific primers, and a clone library consisting of 201 clones was established. The clones were grouped in 10 different groups each representing a specific band pattern using restriction fragment length polymorphism (RFLP). Members of all 10 groups were sequenced and phylogenetically analyzed. Surprisingly, a high abundance of clones belonging to non-thermophilic Crenarchaeal clusters were detected together with the thermophilic archaeon Acidianus infernus in this thermophilic environment. Neither Sulfolobus species nor other hyperthermophilic Crenarchaeota were detected in the clone library. The relative abundance of the sequenced clones was confirmed by terminal restriction fragment analyses. Amplification of 16S rRNA genes from Archaea transferred from the surrounding environment was considered negligible because DNA from non-thermophilic Crenarchaeota incubated under conditions similar to the solfatara could not be PCR amplified after 5 min.     

Robustness of predictions of extremely thermally stable proteins in ancient organisms

A number of studies have addressed the environmental temperatures experienced by ancient life. Computational studies using a nonhomogeneous evolution model have estimated ancestral G + C contents of ribosomal RNAs and the amino acid compositions of ancestral proteins, generating hypotheses regarding the mesophilic last universal common ancestor. In contrast, our previous study computationally reconstructed ancestral amino acid sequences of nucleoside diphosphate kinases using a homogeneous model and then empirically resurrected the ancestral proteins. The thermal stabilities of these ancestral proteins were equivalent to or greater than those of extant homologous thermophilic proteins, supporting the thermophilic universal ancestor theory. In this study, we reinferred ancestral sequences using a dataset from which hyperthermophilic sequences were excluded. We also reinferred ancestral sequences using a nonhomogeneous evolution model. The newly reconstructed ancestral proteins are still thermally stable, further supporting the hypothesis that the ancient organisms contained thermally stable proteins and therefore that they were thermophilic.     

Support vector machine for discrimination of thermophilic and mesophilic proteins based on amino acid composition

The identification of the thermostability from the amino acid sequence information would be helpful in computational screening for thermostable proteins. We have developed a method to discriminate thermophilic and mesophilic proteins based on support vector machines. Using self-consistency validation, 5-fold cross-validation and independent testing procedure with other datasets, this module achieved overall accuracy of 94.2%, 90.5% and 92.4%, respectively. The performance of this SVM-based module was better than the classifiers built using alternative machine learning and statistical algorithms including artificial neural networks, Bayesian statistics, and decision trees, when evaluated using these three validation methods. The influence of protein size on prediction accuracy was also addressed.     

A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor

MOTIVATION: Knowledge of how proteomic amino acid composition has changed over time is important for constructing realistic models of protein evolution and increasing our understanding of molecular evolutionary history. The proteomic amino acid composition of the Last Universal Ancestor (LUA) of life is of particular interest, since that might provide insight into the early evolution of proteins and the nature of the LUA itself. RESULTS: We introduce a method to estimate ancestral amino acid composition that is based on expectation-maximization. On simulated data, the approach was found to be very effective in estimating ancestral amino acid composition, with accuracy improving as the number of residues in the dataset was increased. The method was then used to infer the amino acid composition of a set of proteins in the LUA. In general, as compared with the modern protein set, LUA proteins were found to be richer in amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those believed to have been unavailable or scarce. Additionally, we found the inferred amino acid composition of this protein set in the LUA to be more similar to the observed composition of the same set in extant thermophilic species than in extant mesophilic species, supporting the idea that the LUA lived in a thermophilic environment. AVAILABILITY: The program is available at http://compbio.cs.princeton.edu/ancestralaa     

Cloning, nucleotide sequence, and engineered expression of Thermus thermophilus DNA ligase, a homolog of Escherichia coli DNA ligase.

We have cloned and sequenced the gene for DNA ligase from Thermus thermophilus. A comparison of this sequence and those of other ligases reveals significant homology only with that of Escherichia coli. The overall amino acid composition of the thermophilic ligase and the pattern of amino acid substitutions between the two proteins are consistent with compositional biases in other thermophilic enzymes. We have engineered the expression of the T. thermophilus gene in Escherichia coli, and we show that E. coli proteins may be substantially removed from the thermostable ligase by a simple heat precipitation step.     

Patterns of temperature adaptation in proteins from Methanococcus and Bacillus

It has long been known that amino acid substitutions in proteins of organisms living at moderate and high temperatures (mesophiles and thermophiles, respectively) are not all symmetrical; for example, more aligned sites have lysine in mesophiles and arginine in thermophiles than have the opposite pattern. This is generally taken to indicate that certain amino acids are favored over others by selection at different temperatures. Previous comparisons of protein sequences from mesophiles and thermophiles have used relatively small numbers of sequences from a diverse array of species, meaning that only the most common amino acid substitutions could be examined and any taxon-specific patterns would be obscured. Here, we compare a large number of proteins between mesophiles and thermophiles in the archaeal genus Methanococcus and the bacterial genus Bacillus. Each genus exhibits dramatically asymmetrical substitution patterns for many pairs of amino acids. There are several pairs of amino acids for which one amino acid is favored in thermophilic Bacillus and the other is favored in thermophilic Methanococcus; this appears to result from the higher G + C content of the DNA of thermophilic Bacillus, a complication not seen in Methanococcus.     

Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis

A prerequisite for the survival of (micro)organisms at high temperatures is an adaptation of protein stability to extreme environmental conditions. In contrast to soluble proteins, where many factors have already been identified, the mechanisms by which the thermostability of membrane proteins is enhanced are almost unknown. The hydrophobic membrane environment constrains possible stabilizing factors for transmembrane domains, so that a difference might be expected between soluble and membrane proteins. Here we present sequence analysis of predicted transmembrane helices of the genomes from eight thermophilic and 12 mesophilic organisms. A comparison of the amino acid compositions indicates that more polar residues can be found in the transmembrane helices of thermophilic organisms. Particularly, the amino acids aspartic acid and glutamic acid replace the corresponding amides. Cysteine residues are found to be significantly decreased by about 70% in thermophilic membrane domains suggesting a non-specific function of most cysteine residues in transmembrane domains of mesophilic organisms. By a pair-motif analysis of the two sets of transmembrane helices, we found that the small residues glycine and serine contribute more to transmembrane helix-helix interactions in thermophilic organisms. This may result in a tighter packing of the helices allowing more hydrogen bond formation.     

Hydrophobic environment is a key factor for the stability of thermophilic proteins

The stability of thermophilic proteins has been viewed from different perspectives and there is yet no unified principle to understand this stability. It would be valuable to reveal the most important interactions for designing thermostable proteins for such applications as industrial protein engineering. In this work, we have systematically analyzed the importance of various interactions by computing different parameters such as surrounding hydrophobicity, inter‐residue interactions, ion‐pairs and hydrogen bonds. The importance of each interaction has been determined by its predicted relative contribution in thermophiles versus the same contribution in mesophilic homologues based on a dataset of 373 protein families. We predict that hydrophobic environment is the major factor for the stability of thermophilic proteins and found that 80% of thermophilic proteins analyzed showed higher hydrophobicity than their mesophilic counterparts. Ion pairs, hydrogen bonds, and interaction energy are also important and favored in 68%, 50%, and 62% of thermophilic proteins, respectively. Interestingly, thermophilic proteins with decreased hydrophobic environments display a greater number of hydrogen bonds and/or ion pairs. The systematic elimination of mesophilic proteins based on surrounding hydrophobicity, interaction energy, and ion pairs/hydrogen bonds, led to correctly identifying 95% of the thermophilic proteins in our analyses. Our analysis was also applied to another, more refined set of 102 thermophilic–mesophilic pairs, which again identified hydrophobicity as a dominant property in 71% of the thermophilic proteins. Further, the notion of surrounding hydrophobicity, which characterizes the hydrophobic behavior of residues in a protein environment, has been applied to the three‐dimensional structures of elongation factor‐Tu proteins and we found that the thermophilic proteins are enriched with a hydrophobic environment. The results obtained in this work highlight the importance of hydrophobicity as the dominating characteristic in the stability of thermophilic proteins, and we anticipate this will be useful in our attempts to engineering thermostable proteins. © Proteins 2013. © 2012 Wiley Periodicals, Inc.     

A search for structural factors responsible for the stability of proteins from thermophilic organisms

A database was designed to include 392 pairs of homologous proteins from thermophilic and mesophilic organisms. Proteins from thermophilic organisms proved to contain more atom-atom contacts per residue as compared with their mesophilic homologs. Solvent-accessible exterior amino acid residues contribute to the increase in the number of contacts. The amino acid composition was analyzed for internal (solvent-inaccessible) and exterior amino acid residues of thermophilic and mesophilic proteins. The exterior residues of thermophils have higher contents of Lys, Arg, and Glu and lower contents of Ala, Asp, Asn, Gln, Ser, and Thr as compared with mesophilic proteins. Interior protein regions did not differ in amino acid composition.     

氨基酸组成对蛋白质耐热性的影响

为了研究一级结构对蛋白质耐热性的影响,利用软件DNAMAN对16个家族32种蛋白质序列进行了氨基酸含量分析,并统计分析了氨基酸组成对蛋白质耐热性的影响。通过比较同一家族的高低温蛋白质序列及16个家族中所有高温和低温蛋白质序列中氨基酸含量的变化可以推断(从低温到高温)：Ser、Cys．含量降低显著,Arg、Ile、Pro含量升高显著。由此可知高温蛋白质倾向于含有疏水性氨基酸而避免亲水性氨基酸。