Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

A family of interesting exact solutions of the sine-Gordon equation

By using AKNS [Phys. Rev. Lett. 31 (1973) 125] system and introducing the wave function, a family of interesting exact solutions of the sine-Gordon equation are constructed. These solutions seem to be some soliton, kink, and anti-kink ones respectively for the different choice of the spectrum, whereas due to the interaction between two traveling-waves they have some properties different from usual soliton, kink, and anti-kink solutions.

Fatigue crack-growth rate in ferrite martensite dual-phase steel

An empirical study is made on the fatigue crack growth rate in ferrite-martensite dual-phase (FMDP) steel. Particular attention is given to the effect of ferrite content in the range of 24.2% to 41.5% where good fatigue resistance was found at 33.8%. Variations in ferrite content did not affect the crack growth rate src="http://ars.els-cdn.com/content/image/1-s2.0-016784429190028I-si1.gif" border="0" alt="View the MathML source" title="View the MathML source" width="53" height="18" />when plotted against the effective stress intensity factor range src="http://ars.els-cdn.com/content/image/1-s2.0-016784429190028I-si2.gif" border="0" alt="View the MathML source" title="View the MathML source" width="39" height="14" /> which was assumed to follow a linear relation with the crack tip stress intensity factor range ΔK. A high src="http://ars.els-cdn.com/content/image/1-s2.0-016784429190028I-si4.gif" border="0" alt="View the MathML source" title="View the MathML source" width="39" height="14" /> corresponds to uniformly distributed small size ferrite and martensite. No other appreciable correlation could be ralated to the microstructure morphology of the FMDP steel. The closure stress intensity factor src="http://ars.els-cdn.com/content/image/1-s2.0-016784429190028I-si5.gif" border="0" alt="View the MathML source" title="View the MathML source" width="21" height="13" />, however, is affected by the ferrite content with src="http://ars.els-cdn.com/content/image/1-s2.0-016784429190028I-si6.gif" border="0" alt="View the MathML source" title="View the MathML source" width="64" height="17" /> reaching a maximum value of 0.7. In general, crack growth followed the interphase between the martensite and ferrite.

Dividing the fatigue crack growth process into Stage I and II where the former would be highly sensitive to changes in ΔK and the latter would increase with ΔK depending on the src="http://ars.els-cdn.com/content/image/1-s2.0-016784429190028I-si9.gif" border="0" alt="View the MathML source" title="View the MathML source" width="115" height="18" /> ratio. The same data when correlated with the strain energy density factor range ΔS showed negligible dependence on mean stress or R ratio for Stage I crack growth. A parameter α involving the ratio of ultimate stress to yield stress, percent reduction of area and R is introduced for Stage II crack growth so that the src="http://ars.els-cdn.com/content/image/1-s2.0-016784429190028I-si13.gif" border="0" alt="View the MathML source" title="View the MathML source" width="53" height="18" /> data for different R would collapse onto a single curve with a narrow scatter band when plotted against αΔS.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.