Related papers: Evolution of protein$-$RNA interactions
Many of life's most fascinating phenomena emerge from interactions among many elements--many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts…
Recent years have witnessed the detection of an increasing number of complex organic molecules in interstellar space, some of them being of prebiotic interest. Disentangling the origin of interstellar prebiotic chemistry and its connection…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
While modern physics and biology satisfactorily explain the passage from the Big Bang to the formation of Earth and the first cells to present-day life, respectively, the origins of biochemical life still remain an open question. Since…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Selected ribonucleotide sequences bind well to zwitterionic phospholipid bilayer membranes, though randomized RNAs do not. There are no evident repeated sequences in selected membrane binding RNAs. This implies small and varied motifs…
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…
Even the simplest organisms are too complex to have spontaneously arisen fully-formed, yet precursors to first life must have emerged ab initio from their environment. A watershed event was the appearance of the first entity capable of…
One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs.…
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the…
Previous studies modelled the origin of life and the emergence of photosynthesis on the early Earth-i.e. the origin of plants-in terms of biological heat engines that worked on thermal cycling caused by suspension in convecting water. In…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
Protocells are a type of synthetic cells, which, if engineered to have properties similar to a natural cell, can have immense applications in synthetic biology and bioengineering communities. Proteinoids are one of the leading contenders…
In the present article, we propose a paradigm shift on evolving Artificial Neural Networks (ANNs) towards a new bio-inspired design that is grounded on the structural properties, interactions, and dynamics of protein networks (PNs): the…
In biology, the evolution of increasingly cooperative groups has shaped the history of life. Genes collaborate in the control of cells; cells efficiently divide tasks to produce cohesive multicellular individuals; individual members of…