Transmembrane Regions Of Membrane Proteins Research Articles

Analysis of dihedral angle preferences for alanine and glycine residues in alpha and beta transmembrane regions

For the past 50 years, the Ramachandran map has been used effectively to study the protein structure and folding. However, though extensive analysis has been done on dihedral angle preferences of residues in globular proteins, related studies and reports of membrane proteins are limited. It is of interest to explore the conformational preferences of residues in transmembrane regions of membrane proteins which are involved in several important and diverse biological processes. Hence, in the present work, a systematic comparative computational analysis has been made on dihedral angle preferences of alanine and glycine in alpha and beta transmembrane regions (the two major classes of transmembrane proteins) with the aid of the Ramachandran map. Further, the conformational preferences of residues in transmembrane regions were compared with the non-transmembrane regions. We have extracted cation-pi interacting residues present in transmembrane regions and explored the dihedral angle preferences. From our observations, we reveal the higher percentage of occurrences of glycine in alpha and beta transmembrane regions than other hydrophobic residues. Further, we noted a clear shift in ψ-angle preferences of glycine residues from negative bins in alpha transmembrane regions to positive bins in beta transmembrane regions. Also, cation-pi interacting residues in beta transmembrane regions avoid preferring ψ-angles in the range of −59° to −30°. In this article, we insist that the studies on preferences of dihedral angles in transmembrane regions, thorough understanding of structure and folding of transmembrane proteins, can lead to modeling of novel transmembrane regions towards designing membrane proteins.

Predicting protein-protein binding sites in membrane proteins

BackgroundMany integral membrane proteins, like their non-membrane counterparts, form either transient or permanent multi-subunit complexes in order to carry out their biochemical function. Computational methods that provide structural details of these interactions are needed since, despite their importance, relatively few structures of membrane protein complexes are available.ResultsWe present a method for predicting which residues are in protein-protein binding sites within the transmembrane regions of membrane proteins. The method uses a Random Forest classifier trained on residue type distributions and evolutionary conservation for individual surface residues, followed by spatial averaging of the residue scores. The prediction accuracy achieved for membrane proteins is comparable to that for non-membrane proteins. Also, like previous results for non-membrane proteins, the accuracy is significantly higher for residues distant from the binding site boundary. Furthermore, a predictor trained on non-membrane proteins was found to yield poor accuracy on membrane proteins, as expected from the different distribution of surface residue types between the two classes of proteins. Thus, although the same procedure can be used to predict binding sites in membrane and non-membrane proteins, separate predictors trained on each class of proteins are required. Finally, the contribution of each residue property to the overall prediction accuracy is analyzed and prediction examples are discussed.ConclusionGiven a membrane protein structure and a multiple alignment of related sequences, the presented method gives a prioritized list of which surface residues participate in intramembrane protein-protein interactions. The method has potential applications in guiding the experimental verification of membrane protein interactions, structure-based drug discovery, and also in constraining the search space for computational methods, such as protein docking or threading, that predict membrane protein complex structures.

Branched‐chain amino acid metabolism in higher plants

Valine, leucine and isoleucine contain short branched carbohydrate residues responsible for their classification as branched‐chain amino acids (BCAA). Among the proteinogenic amino acids, BCAA show the highest hydrophobicity and are accordingly the major constituents of transmembrane regions of membrane proteins. BCAA cannot be synthesized by humans and thus belong to the essential amino acids. In contrast, plants are able to synthesize these amino acids de novo and are an important source for these compounds in the human diet. However, BCAA cannot only be synthesized in plants, leucine and probably also valine and isoleucine can also be degraded. Many enzymes operating in turnover are found in mitochondria, while some catabolizing activities are located in peroxisomes. The breakdown of BCAA is physically separated from their biosynthesis in chloroplasts. Additionally, in the order of the Capparales, enzymes of the leucine metabolism seem to be evolutionary related to or may even participate in the methionine chain elongation pathway, the early part of the biosynthesis of aliphatic glucosinolates. In summary, in higher plants a complex network of pathways interferes with the homeostasis of Val, Leu and Ile.