Local Amino Acid Composition Research Articles

Ligand-Binding Sites in Vanilloid-Subtype TRP Channels.

Vanilloid-subfamily TRP channels TRPV1-6 play important roles in various physiological processes and are implicated in numerous human diseases. Advances in structural biology, particularly the “resolution revolution” in cryo-EM, have led to breakthroughs in molecular characterization of TRPV channels. Structures with continuously improving resolution uncover atomic details of TRPV channel interactions with small molecules and protein-binding partners. Here, we provide a classification of structurally characterized binding sites in TRPV channels and discuss the progress that has been made by structural biology combined with mutagenesis, functional recordings, and molecular dynamics simulations toward understanding of the molecular mechanisms of ligand action. Given the similarity in structural architecture of TRP channels, 16 unique sites identified in TRPV channels may be shared between TRP channel subfamilies, although the chemical identity of a particular ligand will likely depend on the local amino-acid composition. The characterized binding sites and molecular mechanisms of ligand action create a diversity of druggable targets to aid in the design of new molecules for tuning TRP channel function in disease conditions.

Proteome-scale relationships between local amino acid composition and protein fates and functions.

Proteins with low-complexity domains continue to emerge as key players in both normal and pathological cellular processes. Although low-complexity domains are often grouped into a single class, individual low-complexity domains can differ substantially with respect to amino acid composition. These differences may strongly influence the physical properties, cellular regulation, and molecular functions of low-complexity domains. Therefore, we developed a bioinformatic approach to explore relationships between amino acid composition, protein metabolism, and protein function. We find that local compositional enrichment within protein sequences is associated with differences in translation efficiency, abundance, half-life, protein-protein interaction promiscuity, subcellular localization, and molecular functions of proteins on a proteome-wide scale. However, local enrichment of related amino acids is sometimes associated with opposite effects on protein regulation and function, highlighting the importance of distinguishing between different types of low-complexity domains. Furthermore, many of these effects are discernible at amino acid compositions below those required for classification as low-complexity or statistically-biased by traditional methods and in the absence of homopolymeric amino acid repeats, indicating that thresholds employed by classical methods may not reflect biologically relevant criteria. Application of our analyses to composition-driven processes, such as the formation of membraneless organelles, reveals distinct composition profiles even for closely related organelles. Collectively, these results provide a unique perspective and detailed insights into relationships between amino acid composition, protein metabolism, and protein functions.

Arginine metabolism of Arabidopsis thaliana is modulated by Heterodera schachtii infection

The plant-parasitic cyst nematodeHeterodera schachtiiinduces syncytial feeding structures in the roots of host plants. These syncytia provide all required nutrients, water and solutes to the parasites. Previous studies on the composition of primary metabolites in syncytia revealed significantly increased amino acid levels. However, mainly due to technical limitations, little is known about the role of arginine in plant-nematode interactions. This free amino acid plays a central role in the plant primary metabolism and serves as substrate for metabolites involved in plant stress responses. Thus, in the present work, expression of genes coding for the enzymes of arginine metabolism were studied in nematode-induced syncytia compared to non-infected control roots ofArabidopsis thaliana. Further, amiRNA lines were constructed and T-DNA lines were isolated to test their effects on nematode development. While the silencing of genes involved in arginine synthesis increased nematode development, most T-DNA lines did not show any significant difference from the wild type. Amino acid analyses of syncytia showed that they accumulate high arginine levels. In addition, manipulating arginine cycling had a global effect on the local amino acid composition in syncytia as well as on the systemic amino acid levels in roots and shoots.

BiasViz: visualization of amino acid biased regions in protein alignments

About a third of all protein sequences have at least one composition biased region (CBR). Such regions might act as linkers between protein domains but often confer specific binding to various molecules; therefore, their characterization in terms of their boundaries and over-represented residues is important. Analysis of CBRs in a particular sequence can be time consuming if several types of biases have to be explored and their position visualized. Assessment of the significance of the detected CBRs can be approached by comparison to homologous protein sequences. To assist this procedure, we have developed BiasViz, a tool that allows to graphically studying local amino acid composition in protein sequences of a multiple sequence alignment.

Constraints acting on the exon positions of the splice site sequences and local amino acid composition of the protein.

The exon positions located at the 5' and 3' splice sites are involved in two functions: in the accurate removal of introns from the nuclear pre-messenger RNAs and in coding for amino acids. Therefore, at least two constraints will act on the exon positions: the splicing constraint and the protein constraint. In the present study we investigate the effect of those constraints on a set of splice sites extracted from GenBank. The consensus matrices computed for each intron location in the reading frame present striking differences at the exon positions of the 5' splice sites. The results obtained can not be explained by the action of a single constraint but rather by the competition between the splicing and protein constraints. Out of eight sites corresponding to codons located in the vicinity of the intron, three present an amino acid distribution that differs greatly from the average amino acid composition of the proteins. Each of these three sites can be characterized by specific amino acids. Results show that the splicing constraint has an effect on the local amino acid composition of the protein as long as the function of the protein is not disrupted.

Metallo-enzyme catalysis: the entatic state

The best of all possible homogeneous catalysts must have carefully designed coordination spheres such that their acid/base or redox ground state properties are correctly tuned for the optimum expression of function, and such that the sites retain sufficient mobility to allow the catalyst atoms to pass easily along the reaction coordinates. Biological evolution has had the opportunity to generate such catalysts through the use of advantageous mutations. The coordination sphere in metallo-enzymes is controlled by the local amino acid composition, the fold energy of the protein and the use of a variety of synthesised special ligands. The question arises as to how near to perfection have the metallo-protein catalysts become. Specially and specifically strained coordination centres of many metallo-enzymes in their ground states have already been identified and called ‘entatic’. We shall show that biological evolution has done a remarkable series of special syntheses, and that indeed the resultant coordination compounds can be described as very well designed for catalytic purposes, with respect to both structure and mobility. They may fall just short of perfection in that metallo-proteins are not simple catalysts but must perform one or two other functions.