Detailed protein sequence alignment based on Spectral Similarity Score (SSS)

BACKGROUND: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. RESULTS: Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases share close biological properties and structural similarities but do not give high scores with character based alignments. Detailed comparison established close similarities between subsequences that do not have any significant character identity. We compared their known 3D structures to establish that the algorithm is able to pick subsequences that are not considered similar by character based matching algorithms but share structural similarities. Similarly many subsequences with low character identity were picked between xyna-theau and xyna-clotm F/10 xylanases. Comparison of 3D structures of the subsequences confirmed the claim of similarity in structure. CONCLUSION: An algorithm is developed which is inspired by successful application of spectral similarity applied to music sequences. The method captures subsequences that do not align by traditional character based alignment tools but give rise to similar secondary and tertiary structures. The Spectral Similarity Score (SSS) is an extension to the conventional similarity methods and results indicate that it holds a strong potential for analysis of various biological sequences and structural variations in proteins

Proteome-wide measurement of non-canonical bacterial mistranslation by quantitative mass spectrometry of protein modifications.

The genetic code is virtually universal in biology and was likely established before the advent of cellular life. The extent to which mistranslation occurs is poorly understood and presents a fundamental question in basic research and production of recombinant proteins. Here we used shotgun proteomics combined with unbiased protein modification analysis to quantitatively analyze in vivo mistranslation in an E. coli strain with a defect in the editing mechanism of leucyl-tRNA synthetase. We detected the misincorporation of a non-proteinogenic amino acid norvaline on 10% of all measured leucine residues under microaerobic conditions and revealed preferential deployment of a tRNA(Leu)(CAG) isoacceptor during norvaline misincorporation. The strain with the norvalylated proteome demonstrated a substantial reduction in cell fitness under both prolonged aerobic and microaerobic cultivation. Unlike norvaline, isoleucine did not substitute for leucine even under harsh error-prone conditions. Our study introduces shotgun proteomics as a powerful tool in quantitative analysis of mistranslation

Protein Structure

Since the dawn of recorded history, and probably even before, men and women have been grasping at the mechanisms by which they themselves exist. Only relatively recently, did this grasp yield anything of substance, and only within the last several decades did the proteins play a pivotal role in this existence. In this expose on the topic of protein structure some of the current issues in this scientific field are discussed. The aim is that a non-expert can gain some appreciation for the intricacies involved, and in the current state of affairs. The expert meanwhile, we hope, can gain a deeper understanding of the topic

14-3-3 Protein Rad24 and its Effect on Mid1 Localization and Contractile Acto- Myosin Ring Assembly During Cytokinesis in S. pombe

In animal and yeast cells, cell division (cytokinesis) is facilitated by the formation of a contractile acto-myosin ring (CAR). Proper CAR formation and constriction is heavily reliant on the temporal regulation, phosphorylation, and localization of key proteins. In the fission yeast S. pombe, Mid1 is an important dimeric CAR scaffolding protein that connects the contractile apparatus to the plasma membrane at the right place and time during cytokinesis. Mid1 is confined to both the nucleus and protein assemblies called nodes during interphase, and transitions to the cell cortex at mitotic entry as nodes mature and coalesce into the CAR. Rad24 is a 14-3-3 protein involved in cell cycle checkpoints known to interact with CAR proteins and some of their regulators. 14-3-3 proteins bind to a conserved consensus phosphorylation motif, RXXpS, which is targeted by Sid2 and other NDR-kinases. The Septation Initiation Network (SIN) is a conserved signaling pathway to facilitate separation of two new daughter cells. Sid2, the terminal kinase of the SIN, has numerous targets in the CAR, including Mid1. Removal of Rad24 has distinct consequences on the timing of major cytokinetic events