Towards the Full Realization of 2DE Power

Naryzhny, Stanislav N.

doi:10.3390/proteomes4040033

Cited by 17 publications

(17 citation statements)

References 125 publications

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“…For example, a big pixel size 10 mm × 6.66 mm × 1 mm (a total of 96 sections from a 2D gel 8 cm × 8 cm × 1 mm) was used to analyze HePG2 cells with the achievement of 20,462 proteoforms encoded by 3774 genes [49], and glioblastoma cells with the achievement of 16,012 proteoforms encoded by 4050 genes [50]. A pixel contains all proteoforms with a very similar pI and M r in a given grid area [61,62]. Such a vision of a molecular scanner [60] was not realized until now because even with the available LC-MS techniques, this would be a very complex, time-consuming, and expensive cataloging exercise, but is ultimately necessary if we are aiming to decipher the proteome at the level of proteoforms.…”

Section: Definition Of Spots and Pixelsmentioning

confidence: 99%

Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level

Zhan

et al. 2019

Proteomes

110

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Two-dimensional gel electrophoresis (2DE) is an important and well-established technical platform enabling extensive top-down proteomic analysis. However, the long-held but now largely outdated conventional concepts of 2DE have clearly impacted its application to in-depth investigations of proteomes at the level of protein species/proteoforms. It is time to popularize a new concept of 2DE for proteomics. With the development and enrichment of the proteome concept, any given “protein” is now recognized to consist of a series of proteoforms. Thus, it is the proteoform, rather than the canonical protein, that is the basic unit of a proteome, and each proteoform has a specific isoelectric point (pI) and relative mass (Mr). Accordingly, using 2DE, each proteoform can routinely be resolved and arrayed according to its different pI and Mr. Each detectable spot contains multiple proteoforms derived from the same gene, as well as from different genes. Proteoforms derived from the same gene are distributed into different spots in a 2DE pattern. High-resolution 2DE is thus actually an initial level of separation to address proteome complexity and is effectively a pre-fractionation method prior to analysis using mass spectrometry (MS). Furthermore, stable isotope-labeled 2DE coupled with high-sensitivity liquid chromatography-tandem MS (LC-MS/MS) has tremendous potential for the large-scale detection, identification, and quantification of the proteoforms that constitute proteomes.

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Section: Definition Of Spots and Pixelsmentioning

confidence: 99%

Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level

Zhan

et al. 2019

Proteomes

110

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“…Given the polar nature of the two edges of alpha-sheet, one edge is predicted to be at the outer surface of the capsid’s shell; the other is predicted to be at the inner surface of the shell. Most likely, the negatively charged edge will be at the outer surface to minimize interaction with other intracellular proteins, most of which are negatively charged at neutral pH [ 39 ].…”

Section: Phage Assembly and Dynamic Statesmentioning

confidence: 99%

Nanomedicine and Phage Capsids

Serwer

Wright

2018

Viruses

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Studies of phage capsids have at least three potential interfaces with nanomedicine. First, investigation of phage capsid states potentially will provide therapies targeted to similar states of pathogenic viruses. Recently detected, altered radius-states of phage T3 capsids include those probably related to intermediate states of DNA injection and DNA packaging (dynamic states). We discuss and test the idea that some T3 dynamic states include extensive α-sheet in subunits of the capsid’s shell. Second, dynamic states of pathogenic viral capsids are possible targets of innate immune systems. Specifically, α-sheet-rich innate immune proteins would interfere with dynamic viral states via inter-α-sheet co-assembly. A possible cause of neurodegenerative diseases is excessive activity of these innate immune proteins. Third, some phage capsids appear to have characteristics useful for improved drug delivery vehicles (DDVs). These characteristics include stability, uniformity and a gate-like sub-structure. Gating by DDVs is needed for (1) drug-loading only with gate opened; (2) closed gate-DDV migration through circulatory systems (no drug leakage-generated toxicity); and (3) drug release only at targets. A gate-like sub-structure is the connector ring of double-stranded DNA phage capsids. Targeting to tumors of phage capsid-DDVs can possibly be achieved via the enhanced permeability and retention effect.

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“…Also, we reported the main technical aspects of developing an inventory of human proteoforms that would be visually attractive, clear, and easy to search [27,28]. In our view, this inventory could use the benefits of our methodology [27]. It should be noted that recent publications of other laboratories have confirmed fidelity of our approach [29].…”

Section: Introductionmentioning

confidence: 96%

A database for inventory of proteoform profiles: “2DE‐pattern”

et al. 2020

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The human proteome is composed of a diverse and heterogeneous range of gene products/proteoforms/protein species. Because of the growing amount of information about proteoforms generated by different methods, we need a convenient approach to make an inventory of the data. Here, we present a database of proteoforms that is based on information obtained by separation of proteoforms using 2DE followed by shotgun ESI–LC–MS/MS. The database's principles and structure are described. The database is called “2DE‐pattern” as it contains multiple isoform‐centric patterns of proteoforms separated according to 2DE principles. The database can be freely used at http://2de-pattern.pnpi.nrcki.ru.

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Towards the Full Realization of 2DE Power

Cited by 17 publications

References 125 publications

Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level

Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level

Nanomedicine and Phage Capsids

A database for inventory of proteoform profiles: “2DE‐pattern”

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