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MOST ABUNDANT PROTEINS IN THE CELL. "Many of the biochemical and regulatory pathways that make up the life of a cell have been or are now being mapped with exquisite detail and many of the nodes have essential roles. But a wiring diagram does not a cell make. To really understand the relative rates of the various components of these pathways, we need to know about the abundances of the various proteins and their substrates." https://lnkd.in/e9f92vG View in LinkedIn

2ND ASSUMPTION. "Considering the upper limit, it is clear that bacteria dominate the planet in terms of the product of the number of cells (10(30)) multiplied by the number of genes in each genome (10(4), a small overestimate)." https://lnkd.in/eyPrQUq View in LinkedIn

HOW MANY PROTEIN FOLDS there are is a measure of protein family structural diversity and ingenuity. This deck discusses the issues of massive redundancy in curated databanks, problems with definitions, and ways of determining the true number. Another world. https://lnkd.in/emfAhwU View in LinkedIn

COMPLEXITY FROM SIMPLICITY. "The conclusion from all of these coarse-graining approaches is that a reduced alphabet of amino acids is quite capable of producing all protein folds (approx. a few thousand discrete folds) and providing a scaffold capable of supporting all protein functions." https://lnkd.in/eyPrQUq View in LinkedIn

ENZYMES AND SUBSTRATES. "There is an often-surprising size difference between an enzyme and the substrates it works on. For example, in metabolic pathways, the substrates are metabolites which usually have a mass of less than 500 Da while the corresponding enzymes are usually about 100 times heavier." http://book.bionumbers.org/how-big-is-the-average-protein/ View in LinkedIn

VAST NUMBERS. "A typical estimate of the size of sequence space is 20(100) (approx. 10(130)) for a protein of 100 amino acids in which any of the normally occurring 20 amino acids can be found. This number is indeed gigantic but it is likely to be a significant overestimate of the size of protein sequence space." https://lnkd.in/eyPrQUq View in LinkedIn

THE BIG QUESTIONS. "How many protein sequences are there? How many sequences are novel vs. repetitious? How many sequences are characterized at structural and functional levels? Are sequences of prokaryotes, eukaryotes, and viruses different? Is the number of sequence families saturating or is it still expanding rapidly?" https://lnkd.in/evmEhB5 View in LinkedIn

"PROTEIN SEQUENCE SPACE is often viewed as a limitless desert of maladjusted sequences with only a few oases of working sequences linked by narrow pathways. The navigation over this space by natural selection is difficult and could take many different routes thus resulting in organisms with largely different protein compositions." https://lnkd.in/eyPrQUq View in LinkedIn

CURATED PROTEINS. "Now, there are almost 8 million sequences in a nonredundant (NR) database of protein sequences, including the complete genomes of ≈1,800 different species. This large body of data is doubling in size every 28 months." https://lnkd.in/evmEhB5 View in LinkedIn

MANY AVENUES. "Given the existence of many DNA polymerases whose fidelity can vary over a 10,000-fold range, and given the multiple and complex transactions that all require DNA synthesis to maintain genome stability, there are probably many more ways to generate mutant cells that thrive despite reduced DNA synthesis fidelity. Thus, the current list of associations between defective DNA synthesis fidelity and cancer is almost certainly incomplete." http://www.sciencedirect.com/science/article/pii/S1535610803000278 View in LinkedIn