Influence of secondary structure of polyglycine on some conformational properties

Values of four conformational properties, namely unperturbed dimension [r2]0, dipole moment [mu 2], mean squared optical anisotropy [gamma 2], and molar Kerr constant [mK], have been calculated for polyglycine chains allowing several combinations of the secondary structure with the aim of studying the dependence of these magnitudes on the secondary structure of the chain. Two different approaches to the secondary structure have been used. In the first, chains with all their units in a given conformation (random coil, alpha-helix or beta-sheet) are interrupted at several positions by one unit in a different conformation. In the second, chains with varying composition of two conformations alpha-helix/beta-sheet and beta-sheet/random coil were allowed and the results obtained compared with previous work for alpha-helix/random coil chains.     

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure

MOTIVATION: Conformational flexibility is essential to the function of many proteins, e.g. catalytic activity. To assist efforts in determining and exploring the functional properties of a protein, it is desirable to automatically identify regions that are prone to undergo conformational changes. It was recently shown that a probabilistic predictor of continuum secondary structure is more accurate than categorical predictors for structurally ambivalent sequence regions, suggesting that such models are suited to characterize protein flexibility. RESULTS: We develop a computational method for identifying regions that are prone to conformational change directly from the amino acid sequence. The method uses the entropy of the probabilistic output of an 8-class continuum secondary structure predictor. Results for 171 unique amino acid sequences with well-characterized variable structure (identified in the 'Macromolecular movements database') indicate that the method is highly sensitive at identifying flexible protein regions, but false positives remain a problem. The method can be used to explore conformational flexibility of proteins (including hypothetical or synthetic ones) whose structure is yet to be determined experimentally. AVAILABILITY: The predictor, sequence data and supplementary studies are available at http://pprowler.itee.uq.edu.au/sspred/ and are free for academic use.     

Conformational properties of a polyglycine chain with secondary and tertiary structures of lysozyme

Unperturbed dimension mean value of r2(0), dipole moment mean value of mu2, mean squared optical anisotropy mean value of gamma 2 and molar Kerr mean value of mK constant of a polyglycine chain with the secondary and tertiary structures of lysozyme have been calculated and the results compared with polyglycine chains with the same number of repeat units but different conformations including alpha-helix, beta-sheet or random coil. Thus, the influence of secondary and tertiary structures can be investigated. The results obtained show that for mean value of r2 and mean value of gamma 2 this influence is at least of the same order of magnitude as that of the primary structure, and is much greater for mean value of mu 2 and mean value of mK.     

Crystal structure of polyglycine I

An electron diffraction study has been made of oriented polyglycine I (the β modification of polyglycine) and of single crystals grown from solution. The unit cell is very similar to that postulated by Astbu?y (1949). It is monoclinic with parameters a = 9.54 Å, b(chainaxis) = 7.044 Å, c = 3.67 Å and β = 113°. Examination of the possible structures suggests that polyglycine I does not have the familiar antiparallel pleated sheet, but rather the closely related antiparallel rippled sheet structure first described by Pauling &; Corey (1953a).     

SRP-RNA sequence alignment and secondary structure.

The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only base pairs are included for which there is comparative evidence. The structures represent refinements of earlier versions and include a new short helix.     

Optical properties of the polyglycine II helix

The circular dichroism spectrum obtained from a dilute aqueous solution of poly (ala-gly-gly) resembles that described for charged polypeptides such as the salt form of poly glutamic acid. A similar spectrum is found for films cast from aqueous solution where x-ray studies reported elsewhere have indicated a poly-glycinc II conformation. Evidence is presented for a heat induced poly-glycine II to unordered state transition similar to that described for collagen. The interpretation of this, the first observation of the optical properties of a poly-amino acid in the poly glycine II conformation, is further rationalized on the basis of spectra obtained from a number of polypeptides whose conformation approaches that of a 3₁ helix.     

The effect of sequence patterns and local conformational preferences on the structure of collapsed polypeptide

We studied the structure of a polypeptide model by means of the Monte Carlo method. The model chain consisting of two kinds of residues (hydrophobic and hydrophilic) was confined on the (310) hybrid lattice. The residues interacted with the long-range contact potential. The short-range potential was also used by introducing the preferences of conformations corresponding to the helical structure. Simulations of the coil-to-globule collapse were done by an annealing process starting from high-temperature structures and then gradual cooling of the system. The parameters describing the behavior of the system were monitored. It has been found that in a case of a helical pattern -HHPPHPP- the collapsed chains consisted of helical fragments. The resulting structures were formed in such way that the polar residues were located in the outer shell of the molecule since the hydrophobic residues filled the inner part of molecule. The results showed that the proper balance between the magnitude of the potentials used in a model is important and its influence on final structures of molecules was discussed.     

Dependence of microwave effect on the secondary structure of DNA on molecular weight of polynucleotide

The effect of ultralow power pulse-modulated electromagnetic radiation (average power density 60 microW/cm2, carrying frequency 1.05; 2.12; or 2.39 GHz; modulating pulses with frequency 4 Hz) on the secondary structure of DNA was investigated. It was established that the exposure of beta-alanine and formaldehyde containing aqueous DNA solution to electromagnetic radiation had activated the process of DNA despiralization under the action of beta-alanine--formaldehyde reaction product. The effect of electromagnetic radiation on the secondary structure of DNA can be removed by lowering of molecular weight of DNA to 0.46 x 10(6) (at carrying frequency 1.05 GHz), or to 0.25 x 10(3) (at carrying frequency 2.39 GHz).     

Dependence of pepsin conformational states on pH and temperature]

A conformational behaviour of pepsin depending on pH and temperature was studied by circular dichroism, differential UV-spectroscopy, calorimetry and enzymatic hydrolysis kinetics. A subtile conformational transition of the enzyme accompanied by changes in the physico-chemical and enzymatic properties of the protein was observed within the temperature interval of 15--40 degrees and within the pH range of 1,1--5,6. The range of pepsin heat denaturation was studied. A diagram of pepsin conformational states under different values of pH and temperature was built.     

Isoenzyme composition and some properties of pea lipoxygenase]

The isoenzyme composition and some properties of lipoxygenase isolated from the seeds and 10-day old sprouts of pea plant were studied. The enzyme activity assay, using gel- and ion-exchange chromatography, disc-electrophoresis in polyacrylamide gel, etc. revealed that the plant contains two lipoxygenase systems of unsaturated long-chain fatty acids oxidation. The existence of four lipoxygenase isoenzymes whose combination determines the type of lipoxygenase-catalyzed reactions of linoleic acid oxidation, has been confirmed.     

Prediction of protein secondary structure from amino acid sequence

The conformational parametersP _k for each amino acid species (j=1–20) of sequential peptides in proteins are presented as the product ofP _i,k , wherei is the number of the sequential residues in thekth conformational state (k=-helix,-sheet,-turn, or unordered structure). Since the average parameter for ann-residue segment is related to the average probability of finding the segment in the kth state, it becomes a geometric mean of (P _k )_av=(P _i,k ) ^1/n with amino acid residuei increasing from 1 ton. We then used ln(P_k)_av to convert a multiplicative process to a summation, i.e., ln(P _k ) _av =(1/n)P _i,k (i=1 ton) for ease of operation. However, this is unlike the popular Chou-Fasman algorithm, which has the flaw of using the arithmetic mean for relative probabilities. The Chou-Fasman algorithm happens to be close to our calculations in many cases mainly because the difference between theirP _k and our InP _k is nearly constant for about one-half of the 20 amino acids. When stronger conformation formers and breakers exist, the difference become larger and the prediction at the N- and C-terminal-helix or-sheet could differ. If the average conformational parameters of the overlapping segments of any two states are too close for a unique solution, our calculations could lead to a different prediction.     

Isoelectric characteristics and the secondary structure of some nucleic acids

The isoelectric characteristics of some nucleic acid preparations from rat liver have been examined. 10S and 4S RNA species and SV-DNA were found to have isoelectric points of 5.2, 6.0-6.7, and 4.35 respectively. The molecular charge ratios (net negative charge/nucleotide) were calculated. Using SV-DNA as a standard, these isoelectric characteristics and charge ratios have been interpreted as indicating that the 10S and 4S RNAs have 35 and 56% of the molecules involved in secondary structure.     

Cystatin. Amino acid sequence and possible secondary structure.

The amino acid sequence of cystatin, the protein from chicken egg-white that is a tight-binding inhibitor of many cysteine proteinases, is reported. Cystatin is composed of 116 amino acid residues, and the Mr is calculated to be 13 143. No striking similarity to any other known sequence has been detected. The results of computer analysis of the sequence and c.d. spectrometry indicate that the secondary structure includes relatively little alpha-helix (about 20%) and that the remainder is mainly beta-structure.     

Skewed distribution of protein secondary structure contents over the conformational triangle.

A conformational triangle method is presented to analyze the secondary structure contents of 1028 structurally known proteins in the non-redundant data set of the recent 25% PDB_SELECT. The secondary structure contents of each protein are mapped on to a point in the triangle. It was found that the distribution of the 1028 points is strongly skewed in the triangle and about 42% of the whole area is empty, which is called the forbidden area. The detailed border between the allowable and forbidden areas was calculated. The possible explanation of the skewed distribution is discussed. The distributions of the mapping points for enzymes and non-enzymes in this non-redundant data set are compared. It was found that a necessary rather than a sufficient condition for an enzyme molecule is that its coil content must be >/=0.223. It is hoped that the skewed distribution observed here could be used to test the secondary structure and threading predictions.     

Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure

MOTIVATION: Disulfide bonds are primary covalent crosslinks between two cysteine residues in proteins that play critical roles in stabilizing the protein structures and are commonly found in extracy-toplasmatic or secreted proteins. In protein folding prediction, the localization of disulfide bonds can greatly reduce the search in conformational space. Therefore, there is a great need to develop computational methods capable of accurately predicting disulfide connectivity patterns in proteins that could have potentially important applications. RESULTS: We have developed a novel method to predict disulfide connectivity patterns from protein primary sequence, using a support vector regression (SVR) approach based on multiple sequence feature vectors and predicted secondary structure by the PSIPRED program. The results indicate that our method could achieve a prediction accuracy of 74.4% and 77.9%, respectively, when averaged on proteins with two to five disulfide bridges using 4-fold cross-validation, measured on the protein and cysteine pair on a well-defined non-homologous dataset. We assessed the effects of different sequence encoding schemes on the prediction performance of disulfide connectivity. It has been shown that the sequence encoding scheme based on multiple sequence feature vectors coupled with predicted secondary structure can significantly improve the prediction accuracy, thus enabling our method to outperform most of other currently available predictors. Our work provides a complementary approach to the current algorithms that should be useful in computationally assigning disulfide connectivity patterns and helps in the annotation of protein sequences generated by large-scale whole-genome projects. AVAILABILITY: The prediction web server and Supplementary Material are accessible at http://foo.maths.uq.edu.au/~huber/disulfide     

Information on the secondary structure improves the quality of protein sequence alignment

The most popular algorithms employed in the pairwise alignment of protein primary structures (Smith-Watermann (SW) algorithm, FASTA, BLAST, etc.) only analyze the amino acid sequence. The SW algorithm is the most accurate, yielding alignments that agree best with superimpositions of the corresponding spatial structures of proteins. However, even the SW algorithm fails to reproduce the spatial structure alignment when the sequence identity is lower than 30%. The objective of this work was to develop a new and more accurate algorithm taking the secondary structure of proteins into account. The alignments generated by this algorithm and having the maximal weight with the secondary structure considered proved to be more accurate than SW alignments. With sequences having less than 30% identity, the accuracy (i.e., the portion of reproduced positions of a reference alignment obtained by superimposing the protein spatial structures) of the new algorithm is 58 vs. 35% of the SW algorithm. The accuracy of the new algorithm is much the same with secondary structures established experimentally or predicted theoretically. Hence, the algorithm is applicable to proteins with unknown spatial structures. The program is available at ftp://194.149.64.196/STRUSWER/.     

Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA

Using a combination of RNA sequencing and construction of cDNA clones followed by DNA sequencing, we have determined the primary nucleotide sequence of U3 snRNA in Xenopus laevis and Xenopus borealis. This molecule has a length of 219 nucleotides. Alignment of the Xenopus sequences with U3 snRNA sequences from other organisms reveals three evolutionarily conserved blocks. We have probed the secondary structure of U3 snRNA in intact Xenopus laevis nuclei using single-strand specific chemical reagents; primer extension was used to map the positions of chemical modification. The three blocks of conserved sequences fall within single-stranded regions, and are therefore accessible for interaction with other molecules. Models of U3 snRNA function are discussed in light of these data.     

Nucleotide sequence and secondary structure of apple scar skin viroid.

The complete nucleotide sequence of apple scar skin viroid(ASSV) has been established, and a probable secondary structure is proposed. A single-stranded circular ASSV RNA consists of 330 nucleotides and can assume the rodlike conformation with extensive base-pairing characteristic of all the known viroids. ASSV shows low sequence homologies with other viroids and lacks the central conserved region. These indicate that ASSV should be allocated to a separate viroid group. However, homologous sequences with potato spindle tuber viroid(PSTV) in ASSV occur in limited and scattered regions of both viroids. These homologous regions fall within the particular domains in the viroid domain model which has been previously proposed by Keese and Symons(Proc. Natl. Acad. Sci. USA. 82, 4582-4586, 1985).