Diversity in sequences, post-translational modifications and expected pharmacological activities of toxins from four Conus species revealed by the combination of cutting-edge proteomics, transcriptomics and bioinformatics

Toxicon ◽  
2017 ◽  
Vol 130 ◽  
pp. 116-125 ◽  
Author(s):  
Michel Degueldre ◽  
Marion Verdenaud ◽  
Garikoitz Legarda ◽  
Rebeca Minambres ◽  
Sheila Zuniga ◽  
...  
2011 ◽  
Vol 21 (5) ◽  
pp. 283-292 ◽  
Author(s):  
K. Adam Bohnert ◽  
Kathleen L. Gould

2011 ◽  
Vol 33 (5) ◽  
pp. 10-13
Author(s):  
Xueli Zhang ◽  
Fuchu He

Proteomics is kind of ‘big science’, just like genomics. Whereas genomics looks globally at the underlying DNA sequence of an entire organism, proteomics is the study of the total complement of proteins. There are more proteins than genes as a result of alternative splicing of genes and post-translational modifications such as glycosylation or phosphorylation. Proteomics therefore offers an exhaustive approach to inspecting the inner workings of cells, tissues and organism, and has huge potential for broadening our understanding of the most complex of protein expression, functions and interactions. That is why proteomics has drawn so much attention from researchers in life sciences and has propelled the rapid development of cutting-edge biotechnology in the 21st Century1. In this article, we give a taste of proteomics research in China.


Author(s):  
J. Temple Black

The output of the ultramicrotomy process with its high strain levels is dependent upon the input, ie., the nature of the material being machined. Apart from the geometrical constraints offered by the rake and clearance faces of the tool, each material is free to deform in whatever manner necessary to satisfy its material structure and interatomic constraints. Noncrystalline materials appear to survive the process undamaged when observed in the TEM. As has been demonstrated however microtomed plastics do in fact suffer damage to the top and bottom surfaces of the section regardless of the sharpness of the cutting edge or the tool material. The energy required to seperate the section from the block is not easily propogated through the section because the material is amorphous in nature and has no preferred crystalline planes upon which defects can move large distances to relieve the applied stress. Thus, the cutting stresses are supported elastically in the internal or bulk and plastically in the surfaces. The elastic strain can be recovered while the plastic strain is not reversible and will remain in the section after cutting is complete.


2020 ◽  
Vol 477 (7) ◽  
pp. 1219-1225 ◽  
Author(s):  
Nikolai N. Sluchanko

Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that ‘read’ the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273–1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.


2020 ◽  
Vol 64 (1) ◽  
pp. 97-110
Author(s):  
Christian Sibbersen ◽  
Mogens Johannsen

Abstract In living systems, nucleophilic amino acid residues are prone to non-enzymatic post-translational modification by electrophiles. α-Dicarbonyl compounds are a special type of electrophiles that can react irreversibly with lysine, arginine, and cysteine residues via complex mechanisms to form post-translational modifications known as advanced glycation end-products (AGEs). Glyoxal, methylglyoxal, and 3-deoxyglucosone are the major endogenous dicarbonyls, with methylglyoxal being the most well-studied. There are several routes that lead to the formation of dicarbonyl compounds, most originating from glucose and glucose metabolism, such as the non-enzymatic decomposition of glycolytic intermediates and fructosyl amines. Although dicarbonyls are removed continuously mainly via the glyoxalase system, several conditions lead to an increase in dicarbonyl concentration and thereby AGE formation. AGEs have been implicated in diabetes and aging-related diseases, and for this reason the elucidation of their structure as well as protein targets is of great interest. Though the dicarbonyls and reactive protein side chains are of relatively simple nature, the structures of the adducts as well as their mechanism of formation are not that trivial. Furthermore, detection of sites of modification can be demanding and current best practices rely on either direct mass spectrometry or various methods of enrichment based on antibodies or click chemistry followed by mass spectrometry. Future research into the structure of these adducts and protein targets of dicarbonyl compounds may improve the understanding of how the mechanisms of diabetes and aging-related physiological damage occur.


2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.


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