Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
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 …

Causes of evolutionary rate variation among protein sites

J Echave, SJ Spielman, CO Wilke - Nature Reviews Genetics, 2016 - nature.com
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 …

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 …

Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants

S Iqbal, E Pérez-Palma, JB Jespersen… - Proceedings of the …, 2020 - National Acad Sciences
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 …

Biophysics of protein evolution and evolutionary protein biophysics

T Sikosek, HS Chan - Journal of The Royal Society …, 2014 - royalsocietypublishing.org
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 …

Evol and ProDy for bridging protein sequence evolution and structural dynamics

A Bakan, A Dutta, W Mao, Y Liu, C Chennubhotla… - …, 2014 - academic.oup.com
Correlations between sequence evolution and structural dynamics are of utmost importance
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

RA Studer, BH Dessailly, CA Orengo - Biochemical journal, 2013 - portlandpress.com
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 …

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 …

Structure and mutations of SARS-CoV-2 spike protein: a focused overview

R Mehra, KP Kepp - ACS Infectious Diseases, 2021 - ACS Publications
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 …

The 3D mutational constraint on amino acid sites in the human proteome

B Li, DM Roden, JA Capra - Nature communications, 2022 - nature.com
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 …