Zipf’s Law in Proteomics

After completion of the human genome sequencing and determination of its size, there is a great demand for similar information about the human proteome as proteins mediate almost all processes in a cell. To better understand the functionality of proteins, we need the information about their activity that is directly linked to their abundance. However, the situation is not simple here because of the complexity of proteins themselves. This complexity may arise from allelicvariations, alternative splicing of RNA transcripts, and post-translational modifications. All these cellular events create distinct protein molecules, proteoforms/protein species, that modulate a wide variety of biological processes. 

Apparently, by using standard technologies, it has been impossible so far to identify and calculate all protein species/ proteoforms present in a single human cell or in human plasma. The main problem is a huge dynamic range of concentrations, where the number of copies of different protein species in an object lies in the range from one to a billion molecules. One ofquantitative proteomic approaches, a proteomic technique that is mainlyperformed using 2DE or liquid chromatography-tandem mass spectrometry (LC-MS/MS) is expected to offer an alternative solution this problem. Recently, using a shotgun approach, a large amount of information about protein abundance was produced. This information is still not enough as we still need to know how many specific molecules (protein species/ proteoforms) are present in a cell.

Optimizing Urine Processing Protocols for Protein and Metabolite Detection

There is significant interest in studying urine proteins and metabolites as potential biomarkers for clinical diseases. Urine serves as an easily accessible biologic fluid that can be accessed usingnoninvasive methods. Urine is proximate to the bladder wall, and also contains renally-cleared systemic compounds and metabolites. Thus urinary biomarkers may be helpful in distinguishing pathologic versus normal biologic processes for renal, genitourinary, and other medical conditions.

In clinically obtained urine samples, multiple factors may introduce variability and affect the predictive value of urine protein and metabolite data. In general, normal (non-proteinuric) urine has low quantities of protein. Some would argue that 1st morning voids, containing the highest protein concentrations, are helpful for proteomic studies. However, logistically there is an obligate time delay when study participants collect their 1st morning void, and factors such as time at room temperature, ongoing protease activity, or bacterial contamination from urethral microbes may affect data quality. Thus prior studies have suggestedcollecting the 2nd morning or other random “spot” urine. However, it remains unclear if the addition of protease inhibitors or bacteriostatic agents may preserve proteins and metabolites in 1st morning samples and facilitate their use. This is relevant since urinary proteomic studies require maximal concentrations of protein from urine with minimal loss.

Characterization of the Venom Proteome for the Wandering Spider, Ctenus hibernalis (Aranea: Ctenidae)

Spider venoms are a multicomponent mixture of polypeptides that contain a diverse array of structure and function that is used for both the immobilization of prey as well as a defense mechanism. To date, the venom composition of less than 100 of the nearly 40,000 characterized species of spiders has been investigated. Although certain venom protein families are highly conserved across spider taxa, there are several instances of novel taxa-specific venom proteins, such as latrotoxins in Latrodectus, Sphyngomyelinase D in Loxosceles, and μ-ctenitoxin-Pn1a in Phoneutria. Spidervenom has been shown to have several therapeutic applications due to the vastarray of biological functionality such as neurotoxic, antimicrobial, antiparasitic, cytolytic, hemolytic, and antiarrhythmic activities; it is thus likely that undiscovered peptides of novel importance are likely to be found in previously unexplored venoms.

Spiders in the Ctenidae family, a group containing nearly 500 species in 42 genera that range mostly in tropical terrains, is home to the most venomous spider in the world Phoneutrianigriventer, and a nonlethal spider that has become the model species for arachnological studies on evolution and development Cuppienius salei; both of which are South American spiders whose venom has been highly studied.