Related papers: Evolution of protein$-$RNA interactions
The issues we attempt to tackle here are what the first peptides did look like when they emerged on the primitive earth, and what simple catalytic activities they fulfilled. We conjecture that the early functional peptides were short (3 to…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
Prion and prion-like molecules are a type of self replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades the molecular dynamics of prions have been characterized both…
The origin of life is shrouded in mystery, with few surviving clues, obscured by evolutionary competition. Previous reviews have touched on the complementary approaches of top-down and bottom-up synthetic biology to augment our…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
The origin of life is often framed primarily as a chemical problem, yet life's defining feature is evolution. Advances in geochemistry, prebiotic chemistry, and molecular biology have produced diverse scenarios for the emergence of genomes,…
Biosystems contain an almost infinite amount of vital important details, which together ensure their life. There are, however, some common structures and reactions in the systems: the homochirality of carbohydrates and proteins, the…
Changes in gene expression occurring during differentiation of human monocytes into dendritic cells were studied at the RNA and protein levels. These studies showed the induction of several gene classes corresponding to various biological…
The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
Despite great advances in our understanding of the formation of the Solar System, the evolution of the Earth, and the chemical basis for life, we are not much closer than the ancient Greeks to an answer of whether life has arisen and…
Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two…
Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…