We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, “How many distinct primary structures of proteins (proteoforms) are created from the 20...
Multiple proteins per spot confirm the necessity of isotopic labeling in large﹕cale quantification of different protein species in a proteome. Many proteins were present in several of the analyzed spots showing the ability of 2〥E㎝S to separate at the protein species level. 2〥E coupled with ...
own little proteomes, complex and highly regulated.” Although some of the most well-known PTMs include phosphorylation of serine, threonine and tyrosine residues of proteins, there are many other important modifications that also are highly regulated and have a crucial function in cell signaling. ...
Proteomics analyses for the global proteins in the brain tissues of different human prion diseases. Proteomics changes of brain tissues have been described in different neurodegenerative diseases including Alzheimer's disease and Parkinson's disease. However, the brain proteomics of human prion disease re...
Protein coding features can emerge de novo in non coding transcripts, resulting in emergence of new protein coding genes. Studies across many species show that a large fraction of evolutionarily novel non-coding RNAs have an antisense overlap with protei
It is commonly assumed that a heterotrophic ancestor of the supergroup Archaeplastida/Plantae engulfed a cyanobacterium that was transformed into a primary plastid; however, it is still unclear how nuclear-encoded proteins initially were imported into th
current evidence demonstratingthat selenium is essential for a healthy pregnancy and that poor selenium status leads to gestationaldisorders. In particular, we focus on the importance of the placental selenoproteome, and the rolethese proteins
In this paper, we analyze how AF2 has improved the structural coverage of membrane proteins compared to earlier years when only experimental structures were available, and high-throughput structure prediction was greatly limited. We also evaluate how AF2 can be used to search for (distant) homologs...
Coverage of the human transmembrane proteome: (A) Structural coverage of TM proteins (from 2000 to 2021) according to their sequence identity to PDB entries and TMAlphaFold (2022) structures based on their quality level; (B) Distribution of TMAlphaFold quality levels on proteins with and without...
In many of these studies, alternative explanations for the formation of soluble misfolded proteins have been ruled out. Most of these studies have characterized the properties only of soluble protein through the use of centrifugation, ruling out influences from insoluble aggregates. Many also controlled...