Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core

BACKGROUND: Rop is an RNA binding, dimeric, four-helix bundle protein with a well-defined, regular hydrophobic core ideally suited for redesign studies. A family of Rop variants in which the hydrophobic core was systematically redesigned has previously been created and characterized. RESULTS: We present a structural and thermodynamic analysis of Ala2Ile2-6, a variant of Rop with an extensively redesigned hydrophobic core. The structure of Ala2Ile2-6 reveals a completely new fold formed by a conformational "flip" of the two protomers around the dimeric interface. The free-energy profile of Ala2Ile2-6 is also very different from that of wild-type Rop. Ala2Ile2-6 has a higher melting temperature than Rop, but undergoes a slightly smaller free-energy change on unfolding. CONCLUSIONS: The structure of Ala2Ile2-6, along with molecular modeling results, demonstrate the importance of tight packing of core residues and the adoption of favorable core side chain rotamer values in determining helix-helix interactions in the four-helix bundle fold. Structural disorder at the N and C termini of Ala2Ile2-6 provides a basis for the large differences in the enthalpy and entropy of Ala2Ile2-6 folding compared with wildtype Rop.     

Optimising parallel R correlation matrix calculations on gene expression data using MapReduce

Background

High-throughput molecular profiling data has been used to improve clinical decision making by stratifying subjects based on their molecular profiles. Unsupervised clustering algorithms can be used for stratification purposes. However, the current speed of the clustering algorithms cannot meet the requirement of large-scale molecular data due to poor performance of the correlation matrix calculation. With high-throughput sequencing technologies promising to produce even larger datasets per subject, we expect the performance of the state-of-the-art statistical algorithms to be further impacted unless efforts towards optimisation are carried out. MapReduce is a widely used high performance parallel framework that can solve the problem.

Results

In this paper, we evaluate the current parallel modes for correlation calculation methods and introduce an efficient data distribution and parallel calculation algorithm based on MapReduce to optimise the correlation calculation. We studied the performance of our algorithm using two gene expression benchmarks. In the micro-benchmark, our implementation using MapReduce, based on the R package RHIPE, demonstrates a 3.26-5.83 fold increase compared to the default Snowfall and 1.56-1.64 fold increase compared to the basic RHIPE in the Euclidean, Pearson and Spearman correlations. Though vanilla R and the optimised Snowfall outperforms our optimised RHIPE in the micro-benchmark, they do not scale well with the macro-benchmark. In the macro-benchmark the optimised RHIPE performs 2.03-16.56 times faster than vanilla R. Benefiting from the 3.30-5.13 times faster data preparation, the optimised RHIPE performs 1.22-1.71 times faster than the optimised Snowfall. Both the optimised RHIPE and the optimised Snowfall successfully performs the Kendall correlation with TCGA dataset within 7 hours. Both of them conduct more than 30 times faster than the estimated vanilla R.

Conclusions

The performance evaluation found that the new MapReduce algorithm and its implementation in RHIPE outperforms vanilla R and the conventional parallel algorithms implemented in R Snowfall. We propose that MapReduce framework holds great promise for large molecular data analysis, in particular for high-dimensional genomic data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new algorithm as a basis for optimising high-throughput molecular data correlation calculation for Big Data.     

Solution structure of the pro-hormone convertase 1 pro-domain from Mus musculus

The solution structure of the mouse pro-hormone convertase (PC) 1 pro-domain was determined using heteronuclear NMR spectroscopy and is the first structure to be obtained for any of the domains in the convertase family. The ensemble of NMR-derived structures shows a well-ordered core consisting of a four-stranded antiparallel beta-sheet with two alpha-helices packed against one side of this sheet. Sequence homology suggests that the other eukaryotic PC pro-domains will have the same overall fold and most of the residues forming the hydrophobic core of PC1 are highly conserved within the PC family. However, some of the core residues are predicted by homology to be replaced by polar amino acid residues in other PC pro-domains and this may help to explain their marginal stability. Interestingly, the folding topology observed here is also seen for the pro-domain of bacterial subtilisin despite little or no sequence homology. Both the prokaryotic and eukaryotic structures have hydrophobic residues clustered on the solvent-accessible surface of their beta-sheets although the individual residue types differ. In the bacterial case this region is buried at the binding interface with the catalytic domain and, in the eukaryotic PC family, these surface residues are conserved. We therefore propose that the hydrophobic patch in the PC1 pro-domain is involved in the binding interface with its cognate catalytic domain in a similar manner to that seen for the bacterial system. The PC1 pro-domain structure also reveals potential mechanisms for the acid-induced dissociation of the complex between pro- and catalytic domains.     

CONTSOR--a new knowledge-based fold recognition potential, based on side chain orientation and contacts between residue terminal groups

Recognizing the structural similarity without significant sequence identity (fold recognition) is an effective method for protein structure prediction. Previously, we developed a fold recognition potential called SORDIS, which incorporated side chain orientation in relation to hydrophobic core centers, distance of the residues from the protein globule center and secondary structure terms. But this potential does not include terms, based on close contacts between residues. In this paper a new fold recognition potential CONTSOR was presented, which based on SORDIS terms and the term, based on contacts between amino acid terminal groups. The performance of this potential was evaluated on SABmark benchmark for alignment accuracy and on SABmark and Lindahl benchmarks for fold recognition. The results show that CONTSOR has the best performance among other potentials on SABmark benchmark both for alignment accuracy and fold recognition and one of the best performances on Lindahl benchmark. CONTSOR software package is available for download at http://www.lifescience.org.ge/downloads/contsor.zip.     

Structure of chromatin containing extensively acetylated H3 and H4

I have grown HeLa cells in 5 mM sodium n-butyrate leading to extensive in vivo histone acetylation, and have characterized the structure of chromatin containing the modified histones. Nuclear DNA in butyrate-treated cells is digested 5-10 fold more rapidly by DNAase I than the DNA of control cells. Staphylococcal nuclease degrades the two nuclear samples to acid-soluble material with identical rates; this nuclease, however, does excise nucleosomes with extensively acetylated histones from the nucleoprotein chain preferentially. The physical properties of unsheared chromatin and isolated core particles from control and butyrate-treated cells are closely similar, as are the rates of digestion of core particles from the two cell preparations by DNAase I. Determination of the relative susceptibilities of cleavage sites for DNAase I demonstrates that the site 60 bases from the ends of the DNA resistant in control cells, becomes susceptible to the nuclease in core particles containing acetylated histones. Similarly, the 5' terminal phosphate at the end of DNA in core prticles is removed by staphylococcal nuclease 2-3 fold faster in particles containing acetylated histones than in particles from control cells.     

PC‐ORD version 5: A user‐friendly toolbox for ecologists

Recently, version 5 of PC‐ORD, one of the major commercial software packages for multivariate ecological community data analyses, was released. The new version offers a whole range of techniques and methods for analyses of ecological data. It includes modules for different types of ordination and classification, as well as other exploratory techniques such as species‐area curve analysis and indicator species analysis. Data are stored in spreadsheets and can be easily manipulated in various ways. In essence, version 5 of PC‐ORD offers the user a full toolbox for exploration and analysis of ecological data, packed in a user‐friendly environment.     

Systematic engineering of phytochelatin synthesis and arsenic transport for enhanced arsenic accumulation in E. coli

Phytochelatin (PC) is a naturally occurring peptide with high affinity towards arsenic (As). In this article, we demonstrated the systematic engineering of PC‐producing E. coli for As accumulation by addressing different bottlenecks in PC synthesis as well as As transport. Phytochelatin synthase from Schizosaccharomyces pombe (SpPCS) was expressed in E. coli resulting in 18 times higher As accumulation. PC production was further increased by co‐expressing a feedback desensitized γ‐glutamylcysteine synthetase (GshI*), resulting in 30‐fold higher PC levels and additional 2‐fold higher As accumulation. The significantly increased PC levels were exploited further by co‐expressing an arsenic transporter GlpF, leading to an additional 1.5‐fold higher As accumulation. These engineering steps were finally combined in an arsenic efflux deletion E. coli strain to achieve an arsenic accumulation level of 16.8 µmol/g DCW, a 80‐fold improvement when compared to a control strain not producing phytochelatins. Biotechnol. Bioeng. 2010. 105: 780–785. © 2009 Wiley Periodicals, Inc.     

Conserved signature proposed for folding in the lipocalin superfamily

We systematically identify a group of evolutionarily conserved residues proposed for folding in a model beta-barrel superfamily, the lipocalins. The nature of conservation at the structural level is defined and we show that the conserved residues are involved in a network of interactions that form the core of the fold. Exploratory kinetic studies are conducted with a model superfamily member, human serum retinol-binding protein, to examine their role. The present results, coupled with key experimental studies conducted with another lipocalin beta-lactoglobulin, suggest that the evolutionarily conserved regions fold on a faster folding time-scale than the non-conserved regions.     

CORA--topological fingerprints for protein structural families

CORA is a suite of programs for multiply aligning and analyzing protein structural families to identify the consensus positions and capture their most conserved structural characteristics (e.g., residue accessibility, torsional angles, and global geometry as described by inter-residue vectors/contacts). Knowledge of these structurally conserved positions, which are mostly in the core of the fold and of their properties, significantly improves the identification and classification of newly-determined relatives. Information is encoded in a consensus three-dimensional (3D) template and relatives found by a sensitive alignment method, which employs a new scoring scheme based on conserved residue contacts. By encapsulating these critical "core" features, templates perform more reliably in recognizing distant structural relatives than searches with representative structures. Parameters for 3D-template generation and alignment were optimized for each structural class (mainly-alpha, mainly-beta, alpha-beta), using representative superfold families. For all families selected, the templates gave significant improvements in sensitivity and selectivity in recognizing distant structural relatives. Furthermore, since templates contain less than 70% of fold positions and compare fewer positions when aligning structures, scans are at least an order of magnitude faster than scans using selected structures. CORA was subsequently tested on eight other broad structural families from the CATH database. Diagnostics plots are generated automatically and provide qualitative assistance for classifying newly determined relatives. They are demonstrated here by application to the large globin-like fold family. CORA templates for both homologous superfamilies and fold families will be stored in CATH and used to improve the classification and analysis of newly determined structures.     

Optimizing transport protocol parameters for large scale PC cluster and its evaluation with parallel data mining

Recently, PC clusters have come to be studied intensively for large scale parallel computers of the next generation. ATM technology is a strong candidate as a de facto standard of high speed communication networks. Therefore, an ATM-connected PC cluster is a promising platform from the cost/performance point of view, as a future high performance computing environment. Data intensive applications, such as data mining and ad hoc query processing in databases, are considered very important for massively parallel processors, as well as for conventional scientific calculations. Thus, investigating the feasibility of applications on an ATM-connected PC cluster is meaningful. In this paper, an ATM-connected PC cluster consisting of 100 PCs is reported, and characteristics of a transport layer protocol for the PC cluster are evaluated. Point-to-point communication performance is measured and discussed, when a TCP window size parameter is changed. Parallel data mining is implemented and evaluated on the cluster. Retransmission caused by cell loss at the ATM switch is analyzed, and parameters of retransmission mechanism suitable for parallel processing on the large scale PC cluster are clarified. Default TCP protocol cannot provide good performance, since a lot of collisions happen during all-to-all multicasting executed on the large scale PC cluster. Using TCP parameters with the proposed optimization, performance improvement is achieved for parallel data mining on 100 PCs. This revised version was published online in July 2006 with corrections to the Cover Date.     

蛋白质折叠类型分类方法及分类数据库

蛋白质折叠规律研究是生命科学重大前沿课题,折叠分类是蛋白质折叠研究的基础。目前的蛋白质折叠类型分类基本上靠专家完成,不同的库分类并不相同,迫切需要一个建立在统一原理基础上的蛋白质折叠类型数据库。本文以ASTRAL-1.65数据库中序列同源性在25%以下、分辨率小于2.5的蛋白为基础,通过对蛋白质空间结构的观察及折叠类型特征的分析,提出以蛋白质折叠核心为中心、以蛋白质结构拓扑不变性为原则、以蛋白质折叠核心的规则结构片段组成、连接和空间排布为依据的蛋白质折叠类型分类方法,建立了低相似度蛋白质折叠分类数据库——LIFCA,包含259种蛋白质折叠类型。数据库的建立,将为进一步的蛋白质折叠建模及数据挖掘、蛋白质折叠识别、蛋白质折叠结构进化研究奠定基础。     

Phospholipase A2 from rat spleen lymphocytes hydrolyzing arachidonoyl-phospholipids]

Phospholipase A2 activity in the postnuclear supernatant of lymphocytes has been studied by measuring 14C arachidonate released from labelled phosphatidyl ethanolamine (PE) and phosphatidyl choline (PC) as exogenous substrates. The pH optimum was 7.5-9.0 for PE and 9.0 for PC. Phospholipase A2 was not detected in the presence of 2 mM EGTA. It was optimal with the millimolar calcium concentrations and higher towards PE. Preincubation of lymphocytes with 0.5 M ionophore A-23187 was followed by 2.4 fold stimulation of the phospholipase activity. A stimulatory effect was observed after preincubation of cells with 10 micrograms/ml of phytohemagglutinin, lipopolysaccharide, concanavalin A; it decreased as: lipopolysaccharide greater than phytohemagglutinin greater than concanavalin A. The results obtained have suggested the possibility of existence of different forms of phospholipase A2 in the spleen lymphocytes and participation of the enzyme in the early signalling events.     

Interaction of blood coagulation factor Va with phospholipid vesicles examined by using lipophilic photoreagents

Two different lipophilic photoreagents, [3H]adamantane diazirine and 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine (TID), have been utilized to examine the interactions of blood coagulation factor Va with calcium, prothrombin, factor Xa, and, in particular, phospholipid vesicles. With each of these structurally dissimilar reagents, the extent of photolabeling of factor Va was greater when the protein was bound to a membrane surface than when it was free in solution. Specifically, the covalent photoreaction with Vl, the smaller subunit of factor Va, was 2-fold higher in the presence of phosphatidylcholine/phosphatidylserine (PC/PS, 3:1) vesicles, to which factor Va binds, than in the presence of 100% PC vesicles, to which the protein does not bind. However, the magnitude of the PC/PS-dependent photolabeling was much less than has been observed previously with integral membrane proteins. It therefore appears that the binding of factor Va to the membrane surface exposes Vl to the lipid core of the bilayer, but that only a small portion of the Vl polypeptide is exposed to, or embedded in, the bilayer core. Addition of either prothrombin or active-site-blocked factor Xa to PC/PS-bound factor Va had little effect on the photolabeling of Vl with TID, but reduced substantially the covalent labeling of Vh, the larger subunit of factor Va. This indicates that prothrombin and factor Xa each cover nonpolar surfaces on Vh when the macromolecules associate on the PC/PS surface. It therefore seems likely that the formation of the prothrombinase complex involves a direct interaction between Vh and factor Xa and between Vh and prothrombin.(ABSTRACT TRUNCATED AT 250 WORDS)     

Optimizing reduced-space sequence analysis

MOTIVATION: Dynamic programming is the core algorithm of sequence comparison, alignment and linear hidden Markov model (HMM) training. For a pair of sequence lengths m and n, the problem can be solved readily in O(mn)time and O(mn)space. The checkpoint algorithm introduced by Grice et al. (CABIOS, 13, 45--53, 1997) runs in O(Lmn)time and O(Lm(L) square root of n)space, where L is a positive integer determined by m, n, and the amount of available workspace. The algorithm is appropriate for many string comparison problems, including all-paths and single-best-path hidden Markov model training, and is readily parallelizable. The checkpoint algorithm has a diagonal version that can solve the single-best-path alignment problem in O(mn)time and O(m + n)space. RESULTS: In this work, we improve performance by analyzing optimal checkpoint placement. The improved row checkpoint algorithm performs up to one half the computation of the original algorithm. The improved diagonal checkpoint algorithm performs up to 35% fewer computational steps than the original. We modified the SAM hidden Markov modeling package to use the improved row checkpoint algorithm. For a fixed sequence length, the new version is up to 33% faster for all-paths and 56% faster for single-best-path HMM training, depending on sequence length and allocated memory. Over a typical set of protein sequence lengths, the improvement is approximately 10%.     

The histone database: a comprehensive WWW resource for histones and histone fold-containing proteins

The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences are both eukaryotic and archaeal in origin. Several new histone fold-containing proteins have been identified, including Spt7p, and a few false positives have been removed from the earlier version of HDB. Database contents include compilations of post-translational modifications for each of the core and linker histones, as well as genomic information in the form of map loci for the human histone gene complement, with the genetic loci linked to Online Mendelian Inheritance in Man (OMIM). Conflicts between similar sequence entries from a number of source databases are also documented. Newly added to the HDB are multiple sequence alignments in which predicted functions of histone fold amino acid residues are annotated. The database is freely accessible through the WWW at http://genome.nhgri.nih.gov/histones/     

Functional characteristic of PC12 cells with reduced microsomal glutathione transferase 1

Microsomal glutathione transferase 1 (MGST1) possesses glutathione transferase and peroxidase activities and is active in biotransformation of xenobiotics and in defense against oxidative stress. To assess MGST1 role in the development and functioning of PC12 cells, we constructed a cell line with reduced MGST1 (PC12_M). Real-time PCR and immunoblot assays showed MGST1 expression lowered to 60 % and immunocytochemical analyses demonstrated an altered concentration and distribution of the enzyme. PC12_M cells revealed a larger tendency to grow in clusters, weaker adhesion, irregular shape of bodies, short neurite outgrowth and higher percentage of necrotic cells (34 %). The total GSTs activity determined with non-specific substrate CDNB (1-chloro-2,4-dinitrobenzene) decreased by 15-20 %, whereas that with DCNB (2,4-dichloro-1-nitrobenzene), a substrate more specific for cytosolic GSTs, was similar to the one in control cells. This suggests that reduction of MGST1 cannot be compensated by other glutathione transferases. In PC12_M cells the total glutathione content was higher by 15-20 %, whereas the GSSG/GSH ratio was lower than in control cells. Moreover, the laminin-dependent migration rate was much faster in control cells than in PC12_M, suggesting some alterations in the metastatic potential of the line with suppressed MGST1. The amount of MAP kinases (p38, JNK, ERK1/2) was elevated in PC12_M cells but their phosphorylation level declined. Microarray analysis showed changed expression of several genes, which may be linked with differentiation and necrosis of PC12_M cells. Our data suggest that MGST1 could be an important regulator of PC12 cells development and might have significant effects on cell growth and proliferation, probably through altered expression of genes with different biological function.     

Relevance of lipid polar headgroups on boron-mediated changes in membrane physical properties

Using liposomes composed of either brain phosphatidylcholine (PC), or binary mixtures of PC and phosphatidylserine (PS), galactolipids (GL), phosphatidylinositol (PI), cardiolipin (CL), phosphatidic acid (PA), or phosphatidylethanolamine (PE), we investigated the effects of graded amounts of boric acid (B, 0.5-1000 microM) on the following membrane physical properties: (a) surface potential, (b) lipid rearrangement through lateral phase separation, (c) fluidity, and (d) hydration. Incubation of the different populations of vesicles with B was associated with a small, but statistically significant, increase in membrane surface potential in PC, PC:PS, PC:GL, PC:PI, PC:PA, and PC:PE liposomes. B-induced lipid lateral rearrangement through lateral phase separation in PC, PC:PA, and PC:PE liposomes; but had no effects on PC:PS, PC:GL, and PC:PI liposomes. In PC liposomes B affected membrane fluidity at the water-lipid interface without affecting the hydrophobic core of the bilayer. In all the other binary liposomes studied, B increased membrane fluidity in both, the hydrophobic portion of the membrane and in the anionic domains. The above was associated with a decrease in the fluidity of the cationic domains. B (10-1000 microM) decreased membrane hydration regardless the composition of the liposomes. The obtained results demonstrate the ability of B to interact with membranes, and induce changes in membrane physical properties. Importantly, the extent of B-membrane interactions and the consequent effects were dependent on the nature of the lipid molecule; as such, B had greater affinity with lipids containing polyhydroxylated moieties such as GL and PI. These differential interactions may result in different B-induced modulations of membrane-associated processes in cells.     

Effects of substrate composition on the esterification and hydrolysis activity of lysosomal acid sterol ester hydrolase

Lipid microemulsions with various core and surface lipid compositions were prepared by co-sonication of cholesteryl esters, triolein (TO), egg phosphatidylcholine (egg PC), and cholesterol. The heterogeneous emulsion particle mixture was purified by gel filtration and particles with the size and general organization of low density lipoproteins were obtained. These lipid microemulsion particles were used for studies of the cellular metabolism of lipoprotein-derived cholesterol and cholesteryl esters as catalyzed by the enzyme acid sterol ester hydrolase (EC 3.1.1.13). The hydrolysis of cholesteryl oleate (CO) was more than twice and that of cholesteryl linoleate (CL) more than three times faster than the hydrolysis of cholesteryl stearate (CS) over the temperature range 25-39.6 degrees C. Both the synthesis and hydrolysis of cholesteryl esters were insensitive to the physical state of the microemulsion cores. The synthesis of cholesteryl esters by this enzyme was also insensitive to the ratios of cholesterol and egg PC in the microemulsion surface layers. Incorporation of triolein into the microemulsion cholesteryl ester core slightly increased the rate of cholesteryl ester synthesis. A decreasing fatty acyl chain length (C18:0 to C14:0) and an increasing degree of unsaturation (C18:0 to C18:2) enhanced the synthesis rate. It is suggested that the hydrolysis and synthesis of cholesteryl esters in microemulsions (and lipoproteins) take place only in the particle surface layer and that the rate of catalysis is directly dependent on the amount of substrate in this surface layer.