M. Fayez Aziz
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View article: Tracing the Origin of the Genetic Code and Thermostability to Dipeptide Sequences in Proteomes
Tracing the Origin of the Genetic Code and Thermostability to Dipeptide Sequences in Proteomes Open
The safekeeping of the genetic code has been entrusted to interactions between aminoacyl-tRNA synthetases and their cognate tRNA. In a previous phylogenomic study, chronologies of RNA substructures, protein domains and dipeptide sequences …
View article: Tracing the Origin of the Genetic Code to Dipeptide Sequences in Proteomes
Tracing the Origin of the Genetic Code to Dipeptide Sequences in Proteomes Open
The safekeeping of the genetic code has been entrusted, for the most part, to interactions between aminoacyl-tRNA synthetases and their cognate tRNA. In a previous phylogenomic study, chro-nologies of RNA substructures, protein domains and…
View article: Tracing the birth and intrinsic disorder of loops and domains in protein evolution
Tracing the birth and intrinsic disorder of loops and domains in protein evolution Open
View article: On Protein Loops, Prior Molecular States and Common Ancestors of Life
On Protein Loops, Prior Molecular States and Common Ancestors of Life Open
View article: Tracing the birth of structural domains from loops during protein evolution
Tracing the birth of structural domains from loops during protein evolution Open
The structures and functions of proteins are embedded into the loop scaffolds of structural domains. Their origin and evolution remain mysterious. Here, we use a novel graph-theoretical approach to describe how modular and non-modular loop…
View article: Tracing the birth of structural domains from loops during protein evolution
Tracing the birth of structural domains from loops during protein evolution Open
The structures and functions of proteins are embedded into the loop scaffolds of structural domains. Their origin and evolution remain mysterious. Here, we use a novel graph-theoretical approach to describe how modular and non-modular loop…
View article: The origin and language-like evolutionary behavior of proteins and translation
The origin and language-like evolutionary behavior of proteins and translation Open
While the origin and early evolution of proteins and their biosynthetic mechanisms remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organiza…
View article: Recruitment: A Problem of Entangled Temporal Parts
Recruitment: A Problem of Entangled Temporal Parts Open
Recruitment is a pervasive activity of life that is at the center of novelty generation and persistence. Without recruitment, novelties cannot spread and biological systems cannot maintain identity through time. Here we explore the problem…
View article: Evolution of networks of protein domain organization
Evolution of networks of protein domain organization Open
View article: Evolution of Networks of Protein Domain Organization
Evolution of Networks of Protein Domain Organization Open
Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct n…
View article: Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis
Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis Open
Networks describe how parts associate with each other to form integrated systems which often have modular and hierarchical structure. In biology, network growth involves two processes, one that unifies and the other that diversifies. Here,…
View article: The early history and emergence of molecular functions and modular scale-free network behavior
The early history and emergence of molecular functions and modular scale-free network behavior Open
The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold. Here we trace domain history onto a bipartite network of elementary f…