Peptides and Proteins: the “Protein World”

The peptides/proteins of all living beings on our planet are mostly made up of 19 L-amino acids and glycine, an achiral amino acid. Arising from endogenous and exogenous sources, the seas of the prebiotic Earth could have contained a huge diversity of biomolecules (including amino acids), and precursors of biomolecules. Thus, how were these amino acids selected from the huge number of available amino acids and other molecules? What were the peptides of prebiotic Earth made up of? How were these peptides synthesized? Minerals have been considered for this task, since they can preconcentrate amino acids from dilute solutions, catalyze their polymerization, and even make the chiral selection of them. However, until now, this problem has only been studied in compartmentalized experiments. There are separate experiments showing that minerals preconcentrate amino acids by adsorption or catalyze their polymerization, or separate L-amino acids from D-amino acids. Based on the [GADV]-protein world hypothesis, as well as the relative abundance of amino acids on prebiotic Earth obtained by Zaia, several experiments are suggested. The main goal of these experiments is to show that using minerals it is possible, at least, to obtain peptides whose composition includes a high quantity of L-amino acids and protein amino acids (PAAs). These experiments should be performed using hydrothermal environments and wet/dry cycles. In addition, for hydrothermal environment experiments, it is very important to use one of the suggested artificial seawaters, and for wet/dry environments, it is important to perform the experiments in distilled water and diluted salt solutions. Finally, from these experiments, we suggest that, without an RNA world or even a pre genetic world, a small peptide set could emerge that better resembles modern proteins.

Download Full-text

Bioinformatic resources for the investigation of proteins and proteomes

Peptidomics ◽

10.1515/ped-2015-0009 ◽

2016 ◽

Vol 2 (1) ◽

Cited By ~ 1

Author(s):

Angelo Facchiano

Keyword(s):

Experimental Data ◽

Data Management ◽

Protein Identification ◽

Molecular Mechanisms ◽

Strong Support ◽

Biological Processes ◽

Functional Interpretation ◽

Huge Data ◽

Protein World ◽

Protein Functions

AbstractExperimental techniques in omics sciences need strong support of bioinformatics tools for the data management, analysis and interpretation. Scientific community develops continuously new databases and tools. They make it possible the comparison of new experimental data with the existing ones, to gain new knowledge. Bioinformatics assists proteomics scientists for protein identification from experimental data, management of the huge data produced, investigation of molecular mechanisms of protein functions, their roles in biochemical pathways, and functional interpretation of biological processes. This article introduces the main bioinformatics resources for investigation in the protein world, with references to analyses performed by means of free tools available on the net.

Download Full-text

Rossmann-Like Proteins Function and Evolution Analysis of a Fifth of the Protein World

Biophysical Journal ◽

10.1016/j.bpj.2019.11.1182 ◽

2020 ◽

Vol 118 (3) ◽

pp. 196a

Author(s):

Kirill E. Medvedev ◽

Lisa N. Kinch ◽

Nick V. Grishin

Keyword(s):

Evolution Analysis ◽

Protein World

Download Full-text

Downward causation by information control in micro-organisms

Interface Focus ◽

10.1098/rsfs.2011.0045 ◽

2011 ◽

Vol 2 (1) ◽

pp. 26-41 ◽

Cited By ~ 20

Author(s):

Luc Jaeger ◽

Erin R. Calkins

Keyword(s):

Operating System ◽

Synthetic Biology ◽

Living Systems ◽

Functional Equivalence ◽

Information Control ◽

Top Down ◽

Adaptive Selection ◽

Feedback Information ◽

Protein World ◽

Micro Organisms

The concepts of functional equivalence classes and information control in living systems are useful to characterize downward (or top-down) causation by feedback information control in synthetic biology. Herein, we re-analyse published experiments of microbiology and synthetic biology that demonstrate the existence of several classes of functional equivalence in microbial organisms. Classes of functional equivalence from the bacterial operating system, which processes and controls the information encoded in the genome, can readily be interpreted as strong evidence, if not demonstration, of top-down causation (TDC) by information control. The proposed biological framework reveals how this type of causality is put in action in the cellular operating system. Considerations on TDC by information control and adaptive selection can be useful for synthetic biology by delineating the irreducible set of properties that characterizes living systems. Through a ‘retro-synthetic’ biology approach, these considerations could contribute to identifying the constraints behind the emergence of molecular complexity during the evolution of an ancient RNA/peptide world into a modern DNA/RNA/protein world. In conclusion, we propose TDCs by information control and adaptive selection as the two types of downward causality absolutely necessary for life.

Download Full-text