Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

Flanking signal and mature peptide residues influence signal peptide cleavage

Background

Signal peptides (SPs) mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient peptides is crucial to the medical, food and beverage and biotechnology industries yet our understanding of these peptides remains limited. This paper examines the most common type of signal peptides cleavable by the endoprotease signal peptidase I (SPase I), and the residues flanking the cleavage sites of three groups of signal peptide sequences, namely (i) eukaryotes (Euk) (ii) Gram-positive (Gram+) bacteria, and (iii) Gram-negative (Gram-) bacteria.

Results

In this study, 2352 secretory peptide sequences from a variety of organisms with amino-terminal SPs are extracted from the manually curated SPdb database for analysis based on physicochemical properties such as pI, aliphatic index, GRAVY score, hydrophobicity, net charge and position-specific residue preferences. Our findings show that the three groups share several similarities in general, but they display distinctive features upon examination in terms of their amino acid compositions and frequencies, and various physico-chemical properties. Thus, analysis or prediction of their sequences should be separated and treated as distinct groups.

Conclusion

We conclude that the peptide segment recognized by SPase I extends to the start of the mature protein to a limited extent, upon our survey of the amino acid residues surrounding the cleavage processing site. These flanking residues possibly influence the cleavage processing and contribute to non-canonical cleavage sites. Our findings are applicable in defining more accurate prediction tools for recognition and identification of cleavage site of SPs.

Discovery of proteomic code with mRNA assisted protein folding

The 3x redundancy of the Genetic Code is usually explained as a necessity to increase the mutation-resistance of the genetic information. However recent bioinformatical observations indicate that the redundant Genetic Code contains more biological information than previously known and which is additional to the 64/20 definition of amino acids. It might define the physico-chemical and structural properties of amino acids, the codon boundaries, the amino acid co-locations (interactions) in the coded proteins and the free folding energy of mRNAs. This additional information, which seems to be necessary to determine the 3D structure of coding nucleic acids as well as the coded proteins, is known as the Proteomic Code and mRNA Assisted Protein Folding.

The Proteomic Code: a molecular recognition code for proteins

Background

The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code.

Review

The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and culminating in the recent conceptualization of partial complementary coding of interacting amino acids as well as the theory of the nucleic acid-assisted protein folding.

Methods and conclusions

A novel cloning method for the design and production of specific, high-affinity-reacting proteins (SHARP) is presented. This method is based on the concept of proteomic codes and is suitable for large-scale, industrial production of specifically interacting peptides.

Fine airborne urban particles (PM2.5) sequester lung surfactant and amino acids from human lung lavage

Components of surfactant act as opsonins and enhance phagocytosis of bacteria; whether this process occurs with atmospheric fine particles has not been shown. We have studied the interactions of fine particles (urban PM2.5) and surfactant removed from normal human lungs by lavage, using a surface analysis technique. The aim was to identify which of the chemical components of brochoalveolar lavage (BAL) deposit on the surfaces of urban PM2.5. Deposition of surfactant components on urban PM2.5 surfaces was reported in previous studies, but molecular identification and relative quantification was not possible using simple data analysis. In this study, we were able to identify adsorbed components by applying an appropriate statistical technique, factor analysis. In this study, the most strongly associated mass fragment on PM2.5 surfaces exposed to BAL (and undetected on both untreated samples and saline controls) was di-palmitoyl-phosphatidylcholine, a component of lung surfactant. Amino acids were also strongly associated with BAL-exposed PM2.5 surfaces and not other sample types. Thirteen mass fragments were identified, diagnostic of the amino acids alanine, arginine, asparagine, aspartic acid, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, serine, and valine. This study provides evidence that lung surfactant and amino acids related to opsonin proteins adsorb to nonbiological particle surfaces exposed to human lung lining fluid. Disruption of normal surfactant function, both physical and immunological, is possible but unproven. Further work on this PM-opsonin interaction is recommended.

Amino acid quantitative structure property relationship database: a web-based platform for quantitative investigations of amino acids

Here, we present the AA-QSPR Db (Amino Acid Quantitative Structure Property Relationship Database): a novel, freely available web-resource of data pertaining to amino acids, both engineered and naturally occurring. In addition to presenting fundamental molecular descriptors of size, charge and hydrophobicity, it also includes online visualization tools for users to perform instant, interactive analyses of amino acid sub-sets in which they are interested. The database has been designed with extensible markup language technology to provide a flexible structure, suitable for future development. In addition to providing easy access for queries by external computers, it also offers a user-friendly web-based interface that facilitates human interactions (submission, storage and retrieval of amino acid data) and an associated e-forum that encourages users to question and discuss current and future database contents.