scholarly journals EyeSite: a semi-automated database of protein families in the eye

2004 ◽  
Vol 32 (90001) ◽  
pp. 148D-152 ◽  
Author(s):  
D. A. Lee
Keyword(s):  
Protein Families ◽  
Automated Database

Characterization of Venoms of Deinagkistrodon acutus and Bungarus multicinctus Using Proteomics and Peptidomics

2020 ◽  
Vol 17 (3) ◽  
pp. 241-254
Author(s):  
Yaqiong Zhang ◽  
Zhiping Jia ◽  
Yunyang Liu ◽  
Xinwen Zhou ◽  
Yi Kong
Keyword(s):  
Snake Venom ◽  
Protein Families ◽  
Traditional Medicines ◽  
Phospholipases A2 ◽  
Inhibitory Peptides ◽  
Sds Page ◽  
Deinagkistrodon Acutus ◽  
Venom Proteins ◽  
Proteins And Peptides

Background: Deinagkistrodon acutus (D. acutus) and Bungarus multicinctus (B. multicinctus) as traditional medicines have been used for hundreds of years in China. The venoms of these two species have strong toxicity on the victims. Objective: The objective of this study is to reveal the profile of venom proteins and peptides of D. acutus and B. multicinctus. Method: Ultrafiltration, SDS-PAGE coupled with in-gel tryptic digestion and Liquid Chromatography- Electrospray Ionization-Tandem Mass Spectrometry (LC-ESI-MS/MS) were used to characterize proteins and peptides of venoms of D. acutus and B. multicinctus. Results: In the D. acutus venom, 67 proteins (16 protein families) were identified, and snake venom metalloproteinases (SVMPs, 38.0%) and snake venom C-type lectins (snaclecs, 36.7%) were dominated proteins. In the B. multicinctus venom, 47 proteins (15 protein families) were identified, and three-finger toxins (3FTxs, 36.3%) and Kunitz-type Serine Protease Inhibitors (KSPIs, 32.8%) were major components. In addition, both venoms contained small amounts of other proteins, such as Snake Venom Serine Proteinases (SVSPs), Phospholipases A2 (PLA2s), Cysteine-Rich Secreted Proteins (CRISPs), 5'nucleotidases (5'NUCs), Phospholipases B (PLBs), Phosphodiesterases (PDEs), Phospholipase A2 Inhibitors (PLIs), Dipeptidyl Peptidases IV (DPP IVs), L-amino Acid Oxidases (LAAOs) and Angiotensin-Converting Enzymes (ACEs). Each venom also had its unique proteins, Nerve Growth Factors (NGFs) and Hyaluronidases (HYs) in D. acutus, and Cobra Venom Factors (CVFs) in B. multicinctus. In the peptidomics, 1543 and 250 peptides were identified in the venoms of D. acutus and B. multicinctus, respectively. Some peptides showed high similarity with neuropeptides, ACE inhibitory peptides, Bradykinin- Potentiating Peptides (BPPs), LAAOs and movement related peptides. Conclusion: Characterization of venom proteins and peptides of D. acutus and B. multicinctus will be helpful for the treatment of envenomation and drug discovery.

scholarly journals Venom-gland transcriptomic, venomic, and antivenomic profiles of the spine-bellied sea snake (Hydrophis curtus) from the South China Sea

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hong-Yan Zhao ◽  
Lin Wen ◽  
Yu-Feng Miao ◽  
Yu Du ◽  
Yan Sun ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Evolutionary History ◽  
De Novo ◽  
Venom Gland ◽  
The South China Sea ◽  
Protein Families ◽  
The South ◽  
Widespread Species ◽  
China Sea

Abstract Background A comprehensive evaluation of the -omic profiles of venom is important for understanding the potential function and evolution of snake venom. Here, we conducted an integrated multi-omics-analysis to unveil the venom-transcriptomic and venomic profiles in a same group of spine-bellied sea snakes (Hydrophis curtus) from the South China Sea, where the snake is a widespread species and might generate regionally-specific venom potentially harmful to human activities. The capacity of two heterologous antivenoms to immunocapture the H. curtus venom was determined for an in-depth evaluation of their rationality in treatment of H. curtus envenomation. In addition, a phylogenetic analysis by maximum likelihood was used to detect the adaptive molecular evolution of full-length toxin-coding unigenes. Results A total of 90,909,384 pairs of clean reads were generated via Illumina sequencing from a pooled cDNA library of six specimens, and yielding 148,121 unigenes through de novo assembly. Sequence similarity searching harvested 63,845 valid annotations, including 63,789 non-toxin-coding and 56 toxin-coding unigenes belonging to 22 protein families. Three protein families, three-finger toxins (3-FTx), phospholipase A2 (PLA2), and cysteine-rich secretory protein, were detected in the venom proteome. 3-FTx (27.15% in the transcriptome/41.94% in the proteome) and PLA2 (59.71%/49.36%) were identified as the most abundant families in the venom-gland transcriptome and venom proteome. In addition, 24 unigenes from 11 protein families were shown to have experienced positive selection in their evolutionary history, whereas four were relatively conserved throughout evolution. Commercial Naja atra antivenom exhibited a stronger capacity than Bungarus multicinctus antivenom to immunocapture H. curtus venom components, especially short neurotoxins, with the capacity of both antivenoms to immunocapture short neurotoxins being weaker than that for PLA2s. Conclusions Our study clarified the venom-gland transcriptomic and venomic profiles along with the within-group divergence of a H. curtus population from the South China Sea. Adaptive evolution of most venom components driven by natural selection appeared to occur rapidly during evolutionary history. Notably, the utility of commercial N. atra and B. multicinctus antivenoms against H. curtus toxins was not comprehensive; thus, the development of species-specific antivenom is urgently needed.

scholarly journals Bioinformatic and experimental survey of 14-3-3-binding sites

2010 ◽  
Vol 427 (1) ◽  
pp. 69-78 ◽  
Author(s):  
Catherine Johnson ◽  
Sandra Crowther ◽  
Margaret J. Stafford ◽  
David G. Campbell ◽  
Rachel Toth ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Binding Sites ◽  
Histone Deacetylases ◽  
Cognitive Disorders ◽  
Logic Gates ◽  
Protein Families ◽  
Kinase C ◽  
Dependent Protein ◽  
Physiological Demands

More than 200 phosphorylated 14-3-3-binding sites in the literature were analysed to define 14-3-3 specificities, identify relevant protein kinases, and give insights into how cellular 14-3-3/phosphoprotein networks work. Mode I RXX(pS/pT)XP motifs dominate, although the +2 proline residue occurs in less than half, and LX(R/K)SX(pS/pT)XP is prominent in plant 14-3-3-binding sites. Proline at +1 is rarely reported, and such motifs did not stand up to experimental reanalysis of human Ndel1. Instead, we discovered that 14-3-3 interacts with two residues that are phosphorylated by basophilic kinases and located in the DISC1 (disrupted-in-schizophrenia 1)-interacting region of Ndel1 that is implicated in cognitive disorders. These data conform with the general findings that there are different subtypes of 14-3-3-binding sites that overlap with the specificities of different basophilic AGC (protein kinase A/protein kinase G/protein kinase C family) and CaMK (Ca2+/calmodulin-dependent protein kinase) protein kinases, and a 14-3-3 dimer often engages with two tandem phosphorylated sites, which is a configuration with special signalling, mechanical and evolutionary properties. Thus 14-3-3 dimers can be digital logic gates that integrate more than one input to generate an action, and coincidence detectors when the two binding sites are phosphorylated by different protein kinases. Paired sites are generally located within disordered regions and/or straddle either side of functional domains, indicating how 14-3-3 dimers modulate the conformations and/or interactions of their targets. Finally, 14-3-3 proteins bind to members of several multi-protein families. Two 14-3-3-binding sites are conserved across the class IIa histone deacetylases, whereas other protein families display differential regulation by 14-3-3s. We speculate that 14-3-3 dimers may have contributed to the evolution of such families, tailoring regulatory inputs to different physiological demands.

scholarly journals Comparative Genomics of Trace Element Dependence in Biology

2011 ◽  
Vol 286 (27) ◽  
pp. 23623-23629 ◽  
Author(s):  
Yan Zhang ◽  
Vadim N. Gladyshev
Keyword(s):  
Trace Elements ◽  
Comparative Genomics ◽  
Trace Element ◽  
Evolutionary Dynamics ◽  
Protein Families ◽  
Fundamental Properties ◽  
Recent Advances ◽  
Living Organisms ◽  
Zinc Protein

Biological trace elements are needed in small quantities but are used by all living organisms. A growing list of trace element-dependent proteins and trace element utilization pathways highlights the importance of these elements for life. In this minireview, we focus on recent advances in comparative genomics of trace elements and explore the evolutionary dynamics of the dependence of user proteins on these elements. Many zinc protein families evolved representatives that lack this metal, whereas selenocysteine in proteins is dynamically exchanged with cysteine. Several other elements, such as molybdenum and nickel, have a limited number of user protein families, but they are strictly dependent on these metals. Comparative genomics of trace elements provides a foundation for investigating the fundamental properties, functions, and evolutionary dynamics of trace element dependence in biology.

scholarly journals A comparative study of the localization and membrane topology of members of the RIFIN, STEVOR and PfMC-2TM protein families in Plasmodium falciparum-infected erythrocytes

2015 ◽  
Vol 14 (1) ◽  
Author(s):  
Anna Bachmann ◽  
Judith Anna Marie Scholz ◽  
Marthe Janßen ◽  
Mo-Quen Klinkert ◽  
Egbert Tannich ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Comparative Study ◽  
Membrane Topology ◽  
Protein Families
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