Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …
ability to modify the sequence, and hence the structure and activity, of individual proteins in …
Causes of evolutionary rate variation among protein sites
It has long been recognized that certain sites within a protein, such as sites in the protein
core or catalytic residues in enzymes, are evolutionarily more conserved than other sites …
core or catalytic residues in enzymes, are evolutionarily more conserved than other sites …
Evolutionary biochemistry: revealing the historical and physical causes of protein properties
MJ Harms, JW Thornton - Nature Reviews Genetics, 2013 - nature.com
The repertoire of proteins and nucleic acids in the living world is determined by evolution;
their properties are determined by the laws of physics and chemistry. Explanations of these …
their properties are determined by the laws of physics and chemistry. Explanations of these …
Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants
Interpretation of the colossal number of genetic variants identified from sequencing
applications is one of the major bottlenecks in clinical genetics, with the inference of the …
applications is one of the major bottlenecks in clinical genetics, with the inference of the …
Biophysics of protein evolution and evolutionary protein biophysics
The study of molecular evolution at the level of protein-coding genes often entails comparing
large datasets of sequences to infer their evolutionary relationships. Despite the importance …
large datasets of sequences to infer their evolutionary relationships. Despite the importance …
Evol and ProDy for bridging protein sequence evolution and structural dynamics
Correlations between sequence evolution and structural dynamics are of utmost importance
in understanding the molecular mechanisms of function and their evolution. We have …
in understanding the molecular mechanisms of function and their evolution. We have …
Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes
The present review focuses on the evolution of proteins and the impact of amino acid
mutations on function from a structural perspective. Proteins evolve under the law of natural …
mutations on function from a structural perspective. Proteins evolve under the law of natural …
Osteoarthritis and toll-like receptors: when innate immunity meets chondrocyte apoptosis
G Barreto, M Manninen, K K. Eklund - Biology, 2020 - mdpi.com
Osteoarthritis (OA) has long been viewed as a degenerative disease of cartilage, but
accumulating evidence indicates that inflammation has a critical role in its pathogenesis. In …
accumulating evidence indicates that inflammation has a critical role in its pathogenesis. In …
Structure and mutations of SARS-CoV-2 spike protein: a focused overview
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect
human cells, is the basis for many vaccines and a hotspot of concerning virus evolution …
human cells, is the basis for many vaccines and a hotspot of concerning virus evolution …
The 3D mutational constraint on amino acid sites in the human proteome
Quantification of the tolerance of protein sites to genetic variation has become a cornerstone
of variant interpretation. We hypothesize that the constraint on missense variation at …
of variant interpretation. We hypothesize that the constraint on missense variation at …