Property-based sequence representations do not adequately encode local protein folding information

We examine the informatic characteristics of amino acid representations based on physical properties. We demonstrate that sequences rewritten using contracted alphabets based on physical properties do not encode local folding information well. The best four-character alphabet can only encode approximately 57% of the maximum possible amount of structural information. This result suggests that property-based representations that operate on a local length scale are not likely to be useful in homology searches and fold-recognition exercises.     

Nonradiative energy transfer in oligopeptide chains generated by a monte-cralo mehod including long-range interactions

A Monte-Carlo method including long-range interactions is used to oligopeptide chains in random-coil state. The chains are composed of 4, 9, or 14 repeating units and are labeled with the luminopheres tyrosine or tryptophan. Interactions with a solvent (water) are taken into account in the calculations through modifications of the semiempirical potential-energy functions. The chains represent oligopeptides composed of hydrophobic or hydrophilic amino acid residues. Various properties relavent to the interpretaiton of nonradiative enrgy-transfer experiments, such as the average value of the orientation factor for dipole-dipole interaction of the luminophores, 〈k²〉, the distribution function of the distances between the luminophores f(r_l), the efficiences of energy transfer in the static and dyamic averaging regimes, 〈T〉_s amnd 〈T〉_d, as well as the fluorescence decay I(t) of the donor luminophore in various averaging conditions, are computed. It is shown that, for all chains considered, 〈k²〉 is not vary far form 0.67 and that 〈T〉_s and 〈T〉_d have completely different values. Due to the small extent of correlation between the distances r_l and the mutual orientations of the lumninophores, the decay kinetics 〈I(t)_s corresponding to a static averaging regime can be expressed in terms of distribution functions f(r_l). These results are in agrrement with those obtained previously for the unperturbed chain model.     

The evolution of proteins from random amino acid sequences. I. Evidence from the lengthwise distribution of amino acids in modern protein sequences

Summary We examine in this paper one of the expected consequences of the hypothesis that modern proteins evolved from random heteropeptide sequences. Specifically, we investigate the lengthwise distributions of amino acids in a set of 1,789 protein sequences with little sequence identity using the run test statistic (r _o) of Mood (1940,Ann. Math. Stat. 11, 367–392). The probability density ofr _o for a collection of random sequences has mean=0 and variance=1 [the N(0,1) distribution] and can be used to measure the tendency of amino acids of a given type to cluster together in a sequence relative to that of a random sequence. We implement the run test using binary representations of protein sequences in which the amino acids of interest are assigned a value of 1 and all others a value of 0. We consider individual amino acids and sets of various combinations of them based upon hydrophobicity (4 sets), charge (3 sets), volume (4 sets), and secondary structure propensity (3 sets). We find that any sequence chosen randomly has a 90% or greater chance of having a lengthwise distribution of amino acids that is indistinguishable from the random expectation regardless of amino acid type. We regard this as strong support for the random-origin hypothesis. However, we do observe significant deviations from the random expectation as might be expected after billions years of evolution. Two important global trends are found: (1) Amino acids with a strong α-helix propensity show a strong tendency to cluster whereas those with β-sheet or reverse-turn propensity do not. (2) Clustered rather than evenly distributed patterns tend to be preferred by the individual amino acids and this is particularly so for methionine. Finally, we consider the problem of reconciling the random nature of protein sequences with structurally meaningful periodic “patterns” that can be detected by sliding-window, autocorrelation, and Fourier analyses. Two examples, rhodopsin and bacteriorhodopsin, show that such patterns are a natural feature of random sequences.     

Isolation and characterization of homologues of plant blue-light photoreceptor (cryptochrome) genes from the fern Adiantum capillus-veneris

Many blue-light mediated physiological responses have been studied in the fern Adiantum capillus-veneris. We have isolated genomic clones encoding sequences similar to those encoding blue-light photoreceptors (cryptochromes) in higher plants using the Arabidopsis CRY1 cDNA as a probe, and these positive clones fall into five independent groups. Using RACE procedures, we obtained full-length cDNA sequences for three of these five groups. The deduced amino acid sequences include the photolyase-homologous domain in the N-terminal half, and they also contain a C-terminal extension of about 200 amino acids in length. These structural features indicate that the genes indeed encode Adiantum cryptochromes and represent a small gene family having at least three members. Received: 16 February 1998 / Accepted: 26 April 1998     

犬种布鲁氏菌ZG株单克隆抗体4H3抗原模拟表位的筛选及分析

【背景】目前犬布鲁氏菌病诊断存在一定的困难。【目的】筛选并研究犬种布鲁氏菌单克隆抗体4H3株的特异性抗原表位。【方法】利用噬菌体肽库展示技术,以犬种布鲁氏菌单克隆抗体4H3株作为靶分子,包被酶标板,用12肽随机肽库经过3轮生物淘洗程序进行筛选。经过3轮筛选后,噬菌体产出率从5.00×10^-7增加到9.84×10^-6,假阳性率逐轮降低。从第3轮筛选的阳性克隆中随机挑取14个进行增殖,提取基因组DNA,进行测序分析;并通过iELISA和cELISA检测阳性克隆的亲和性和特异性。【结果】14株阳性单克隆噬菌体共出现3种不同的短肽序列,分别是KMSIRHPIRLPI、ILRRRRKRIIQI和QRIHMRLTTQS;iELISA结果表明3种短肽序列与单克隆抗体的亲和性依次为KMSIRHPIRLPI>ILRRRRKRIIQI>QRIHMRLTTQS;cELISA结果显示短肽KMSIRHPIRLPI和ILRRRRKRIIQI特异性较强。对亲和性较强、特异性较高的2条短肽KMSIRHPIRLPI和ILRRRRKRIIQI展开具体分析,比对分析表...     

Mean-square helical hydrophobic moments in partially ordered proteins

Helical hydrophobic moment ratios, 〈h²〉/〈H²〉, have been evaluated for 34 polypeptides under conditions where the helix content is dictated solely by the short-range interactions operative in aqueous media. The mean-square helical hydrophobic moment is denoted by 〈h²〉, and 〈H²〉 is the averaged of the squared hydrophobicites. This ratio would be one in absence of any correlation in the hydrophobicities of amino acid residues in helices. The 〈h²〉/〈H²〉 tend to be substantially larger than values of the analogous ratio formulated for the mean-square dipole moments of typical synthetic polymers. For 24 of the 34 polypeptide chains considered, 〈h²〉/〈H²〉 is found to be greater than one, indicating a tendency to form helices with amphiphilic character. The ratio is exceptionally large in the case of the δ-hemolysins. It is also large for two other surface-active peptides, for two of the four apolipoproteins examined, and for myohemerythrin. A much smaller 〈h²〉/〈H²〉 is found for melittins. If melittins is to form helices with large 〈h²〉/〈H²〉, the configurational statistics must be governed by effects in addition to those short-range interactions that occur when water is the solvent.     

Molecular Cloning of cDNA That Encodes Chymotrypsin Inhibitor ECI from Erythrina variegata Seeds and Its Expression in Escherichia coli

Synthetic oligonucleotides representing all possible sequences of the N-terminal and internal amino acid sequences of the chymotrypsin inhibitor ECI from Erythrina variegata seeds were used to generate a probe specific for ECI-related sequences by the polymerase chain reaction on the E. variegata genomic DNA. A lambda phage cDNA library constructed from poly(A⁺) RNA from maturing seeds was screened with the ECI gene thus obtained as a probe and characterized by DNA sequencing. The cloned ECI cDNA comprised 737 nucleotides and one open reading frame that encoded a polypeptide chain of 203 amino acids including a signal peptide composed of 24 amino acids. An expression plasmid was designed for export of the recombinant inhibitor into the periplasm. For this purpose, the cDNA fragment encoding matured ECI was ligated into the NcoI and BamHI sites following the pel B signal sequence in the expression vector pET-22b and expressed in Escherichia coli BL21 (DE3). However, this attempt failed as the recombinant inhibitor caused the formation of inclusion bodies in E. coli cells as a heterologous preprotein (SR-ECI), with the pel B upstream leader. SR-ECI was made soluble and renatured by refolding and reoxidation, and subsequently processed with pronase to give rise to recombinant ECI (R-ECI) that had an extra methionine residue attached to the N-terminal amino acid of ECI. Purified R-ECI inhibited chymotrypsin almost as strongly as authentic ECI.     

Biased Usages of Arginines and Lysines in Proteins Are Correlated with Local-Scale Fluctuations of the G + C Content of DNA Sequences

Amino acid residues arginine (R) and lysine (K) have similar physicochemical characteristics and are often mutually substituted during evolution without affecting protein function. Statistical examinations on human proteins show that more R than K residues are used in the proximity of R residues, whereas more K than R are used near K residues. This biased use occurs on both a global and a local scale (shorter than ∼100 residues). Even within a given exon, G + C-rich and A + T-rich short DNA segments preferentially encode R and K, respectively. The biased use of R and K on a local scale is also seen in Saccharomyces cerevisiae and Caenorhabdidtis elegans, which lack global-scale mosaic structures with varying GC%, or isochores. Besides R and K, several amino acids are also used with a positive or negative correlation with the local GC% of third codon bases. The local-, or ``within-gene'-, scale heterogeneity of the DNA sequence may influence the sequence of the encoded protein segment. Received: 2 March 1998 / Accepted: 23 April 1998     

Study of the periodic arrangement of amino acid residues in fiber proteins of bacteriophage T4

The amino acid sequences of some fiber proteins possibly have a periodic structure. This periodicity can be analyzed using the Fourier transform of the mathematical image of the symbol sequence of amino acid residues in proteins. One of several possible methods of Fourier transform has been chosen as optimal for the given study. This optimal Fourier transform has been used to analyze the periodic structures in several fiber proteins of bacteriophage T4. Amino acids from some groups form sequences of alternating elements with a relatively small period (T=15); those from other groups form sequences with other small periods (T=10 and T=8). Relatively large periods of amino acid arrangement, with the entire amino acid sequence of the protein being divided between them into four or six equal parts, is a new finding. The data on protein structural periodicity make it possible to align the amino acid sequences according to the periodic structures of both type. The results obtained agree with the results of previous crystallographic and electron microscopic studies.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 2, 2005, pp. 321–329.Original Russian Text Copyright © 2005 by Simakova, Simakov.     

Studies on the Acid-protease of Paecilomyces varioti BAINIER TPR-220

Some physical and chemical properties were investigated of the crystalline acid-protease from Paecilomyces varioti BAINIER TPR-220. The sedimentation coefficient of the enzyme was calculated to be 2.7 × 10^?13 at 15°C and the molecular weight to be 37,300 by Archibald’s method. The isoelectric point of the enzyme protein was determined to lie at pH 3.8. The enzyme protein was consisted of 340 amino acid residues including only one residue of cysteine but excluding cystine. With the feature of amino acid composition of the protease acidic amino acids dominated over the basic ones.     

Use of a structural alphabet to find compatible folds for amino acid sequences

The structural annotation of proteins with no detectable homologs of known 3D structure identified using sequence‐search methods is a major challenge today. We propose an original method that computes the conditional probabilities for the amino‐acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as “Protein Blocks” (PBs). PBs constitute a library of 16 local structural prototypes that approximate every part of protein backbone structures. It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships. Our method relies on amino acid occurrence matrices, one for each PB, to score global and local threading of query amino acid sequences to protein folds encoded into PB sequences. It does not use any information from residue contacts or sequence‐search methods or explicit incorporation of hydrophobic effect. The performance of the method was assessed with independent test datasets derived from SCOP 1.75A. With a Z‐score cutoff that achieved 95% specificity (i.e., less than 5% false positives), global and local threading showed sensitivity of 64.1% and 34.2%, respectively. We further tested its performance on 57 difficult CASP10 targets that had no known homologs in PDB: 38 compatible templates were identified by our approach and 66% of these hits yielded correctly predicted structures. This method scales‐up well and offers promising perspectives for structural annotations at genomic level. It has been implemented in the form of a web‐server that is freely available at http://www.bo‐protscience.fr/forsa .     

Novel compound heterozygous variants in ARL13B lead to Joubert syndrome

Joubert syndrome (JBTS) is a systematic developmental disorder mainly characterized by a pathognomonic mid-hindbrain malformation. All known JBTS-associated genes encode proteins involved in the function of antenna-like cellular organelle, primary cilium, which plays essential roles in cellular signal transduction and development. Here, we identified four unreported variants in ARL13B in two patients with the classical features of JBTS. ARL13B is a member of the Ras GTPase family and functions in ciliogenesis and cilia-related signaling. The two missense variants in ARL13B harbored the substitutions of amino acids at evolutionarily conserved positions. Using model cell lines, we found that the accumulations of the missense variants in cilia were impaired and the variants showed attenuated functions in ciliogenesis or the trafficking of INPP5E. Overall, these findings expanded the ARL13B pathogenetic variant spectrum of JBTS.     

Identification of non-catalytic conserved regions in xylanases encoded by the xynB and xynD genes of the cellulolytic rumen anaerobe Ruminococcus flavefaciens

xynB is one of at least four genes from the cellulolytic rumen anaerobe Ruminococcus flavefaciens 17 that encode xylanase activity. The xynB gene is predicted to encode a 781-amino acid product starting with a signal peptide, followed by an amino-terminal xylanase domain which is identical at 89% and 78% of residues, respectively, to the amino-terminal xylanase domains of the bifunctional XynD and XynA enzymes from the same organism. Two separate regions within the carboxy-terminal 537 amino acids of XynB also show close similarities with domain B of XynD. These regions show no significant homology with cellulose- or xylan-binding domains from other species, or with any other sequences, and their functions are unknown. In addition a 30 to 32-residue threonine-rich region is present in both XynD and XynB. Codon usage shows a consistent pattern of bias in the three xylanase genes from R. flavefaciens that have been sequenced.     

Identification of Ourmiavirus 30K movement protein amino acid residues involved in symptomatology,viral movement,subcellular localization and tubule formation

Several plant viruses encode movement proteins (MPs) classified in the 30K superfamily. Despite a great functional diversity, alignment analysis of MP sequences belonging to the 30K superfamily revealed the presence of a central core region, including amino acids potentially critical for MP structure and functionality. We performed alanine‐scanning mutagenesis of the Ourmia melon virus (OuMV) MP, and studied the effects of amino acid substitutions on MP properties and virus infection. We identified five OuMV mutants that were impaired in systemic infection in Nicotiana benthamiana and Arabidopsis thaliana, and two mutants showing necrosis and pronounced mosaic symptoms, respectively, in N. benthamiana. Green fluorescent protein fusion constructs (GFP:MP) of movement‐defective MP alleles failed to localize in distinct foci at the cell wall, whereas a GFP fusion with wild‐type MP (GFP:MPwt) mainly co‐localized with plasmodesmata and accumulated at the periphery of epidermal cells. The movement‐defective mutants also failed to produce tubular protrusions in protoplasts isolated from infected leaves, suggesting a link between tubule formation and the ability of OuMV to move. In addition to providing data to support the importance of specific amino acids for OuMV MP functionality, we predict that these conserved residues might be critical for the correct folding and/or function of the MP of other viral species in the 30K superfamily.     

Statistical analysis of the physical properties of the 20 naturally occurring amino acids

In order to describe the conformational and other physical properties of the 20 naturally occurring amino acid residues with a minimum number of parameters, several multivariate statistical analyses were applied to 188 of their physical properties and ten orthogonal properties (factors) were obtained for the 20 amino acids without losing the information contained in the original physical properties. The analysis consisted of three main steps. First, 72 of the physical properties were eliminated from further consideration because they did not pass statistical tests that they follow a normal distribution. Second, the remaining 116 physical properties of the amino acids were classified by a cluster analysis to eliminate duplications of highly correlated physical properties. This led to nine clusters, each of which was characterized by an average characteristic property, namely bulk, two hydrophobicity indices for free amino acids, one hydrophobicity index for amino acid residues in a protein, two types of -structure preference, -helix preference, and two types of bend-structure preference. The physical properties within a given cluster were highly correlated with each other, but the correlation between clusters was low. Third, a factor analysis was applied to the nine average classified properties and 16 additional physical properties to obtain a small number of orthogonal properties (ten factors). Four of these factors arise from the nine characteristic properties, and the remaining six factors were obtained from the 16 physical properties not included in the nine characteristic properties. Finally, most of the 188 physical properties could be expressed as a sum of these ten orthogonal factors, with appropriate weighting factors. Since these factors contain information relating almost all properties of all 20 amino acids, it is possible to estimate the numerical values of a property for one or two amino acids for which experimental data for this property are not available. For example, the estimated values for the Zimm-Bragg parameters at 20°C are 0.66 and 0.92 for proline and cysteine, respectively, computed from the first four factors.     

Strong Correlation Between Statistical Transmembrane Tendency and Experimental Hydrophobicity Scales for Identification of Transmembrane Helices

Direct physical chemistry measurements of the hydrophobicity of amino acids or their derivatives have often been used to estimate the propensity of amino acids to participate in transmembrane helices. In this short note, it is found that there is a very high degree of correlation (r = 0.944–0.965) between an average physical chemistry hydrophobicity scale (an average of scales derived, e.g., from the solubility of amino acid derivatives in organic solvents versus water or their binding to hydrophobic particles) and the statistically based transmembrane tendency scale (derived from the relative abundance of residues in known transmembrane and soluble protein sequences (Zhao and London, Protein Sci 15:1987–2001, 2006)). This correlation indicates that, other than hydrophobicity, amino acid properties/interactions that promote or inhibit transmembrane helix formation in a specific membrane protein largely cancel out when averaged over all transmembrane sequences. In other words, other than hydrophobicity, there are no properties of a specific amino acid residue within a hydrophobic segment that have a strong systematic effect upon transmembrane helix formation independent of the remainder of the sequence in that hydrophobic segment. However, proline is an exception to this rule.     

Systems biology defines the biological significance of redox‐active proteins during cellulose degradation in an aerobic bacterium

Microbial depolymerization of plant cell walls contributes to global carbon balance and is a critical component of renewable energy. The genomes of lignocellulose degrading microorganisms encode diverse classes of carbohydrate modifying enzymes, although currently there is a paucity of knowledge on the role of these proteins in vivo. We report the comprehensive analysis of the cellulose degradation system in the saprophytic bacterium Cellvibrio japonicus. Gene expression profiling of C. japonicus demonstrated that three of the 12 predicted β‐1,4 endoglucanases (cel5A, cel5B, and cel45A) and the sole predicted cellobiohydrolase (cel6A) showed elevated expression during growth on cellulose. Targeted gene disruptions of all 13 predicted cellulase genes showed that only cel5B and cel6A were required for optimal growth on cellulose. Our analysis also identified three additional genes required for cellulose degradation: lpmo10B encodes a lytic polysaccharide monooxygenase (LPMO), while cbp2D and cbp2E encode proteins containing carbohydrate binding modules and predicted cytochrome domains for electron transfer. CjLPMO10B oxidized cellulose and Cbp2D demonstrated spectral properties consistent with redox function. Collectively, this report provides insight into the biological role of LPMOs and redox proteins in cellulose utilization and suggests that C. japonicus utilizes a combination of hydrolytic and oxidative cleavage mechanisms to degrade cellulose.     

A Monte Carlo study of the excluded-volume effect on the amylosic chain conformation

A Monte Carlo procedure was used to determine the effect of excluded volume on the conformational dimensions of amylosic chains. The excluded volume was introduced into the model by assuming that hard spheres, which cannot overlap each other, exist at the center of mass of each glucose unit in the chain sequence. Monte Carlo chains, which were generated to be distributed consistent with the potential energy of nonbonded nearest-neighbor interactions, underwent self-intersections, and the attrition rate in the generation of self-avoiding chains was found to obey an exponential decay law with increasing chain length x. Thus, in order to generate effectively a large number of self-avoiding chains with long sequences, we used the Wall–Erpenbeck s-p method of chain enrichment [F. T. Wall and J. J. Erpenbeck (1959) J. Chem. Phys. 30 , 634–637]. By examination of the radial distribution of the end-to-end distance and the chain-length dependence of the quantity 〈r²〉/xl² (〈r²〉 is the mean square end-to-end distance and l is the virtual bond length), it was found that unperturbed amylosic chains change in overall conformation from a non-Gaussian chain having a helical character to Gaussian as x is increased, whereas perturbed chains do not show Gaussian behavior even at x = 500. For the perturbed chains, 〈r²〉 can be expressed by the equation 〈r²〉 = ax^b in the range of 100 ≤ x ≤ 500, where a and b > 1 are constants. From comparisons of the persistence vectors and perspective drawings of representative unperturbed and perturbed chains, we felt the local conformation of the amylosic chains, i.e., the local helical character, is also affected by the long-range excluded-volume interaction.