[HTML][HTML] Insertions and deletions in protein evolution and engineering

S Savino, T Desmet, J Franceus - Biotechnology Advances, 2022 - Elsevier
Protein evolution or engineering studies are traditionally focused on amino acid
substitutions and the way these contribute to fitness. Meanwhile, the insertion and deletion …

Efficient and accurate quantitative profiling of alternative splicing patterns of any complexity on a laptop

T Sterne-Weiler, RJ Weatheritt, AJ Best, KCH Ha… - Molecular cell, 2018 - cell.com
Alternative splicing (AS) is a widespread process underlying the generation of transcriptomic
and proteomic diversity and is frequently misregulated in human disease. Accordingly, an …

Regulatory expansion in mammals of multivalent hnRNP assemblies that globally control alternative splicing

S Gueroussov, RJ Weatheritt, D O'Hanlon, ZY Lin… - Cell, 2017 - cell.com
Alternative splicing (AS) patterns have diverged rapidly during vertebrate evolution, yet the
functions of most species-and lineage-specific splicing events are not known. We observe …

Tandem repeats in proteins: prediction algorithms and biological role

M Pellegrini - Frontiers in bioengineering and biotechnology, 2015 - frontiersin.org
Tandem repetitions in protein sequence and structure is a fascinating subject of research
which has been a focus of study since the late 1990s. In this survey, we give an overview on …

Geobacter sulfurreducens Extracellular Multiheme Cytochrome PgcA Facilitates Respiration to Fe(III) Oxides But Not Electrodes

LA Zacharoff, DJ Morrone, DR Bond - Frontiers in Microbiology, 2017 - frontiersin.org
Extracellular cytochromes are hypothesized to facilitate the final steps of electron transfer
between the outer membrane of the metal-reducing bacterium Geobacter sulfurreducens …

Evolutionary tinkering enriches the hierarchical and nested structures in amino acid sequences

Z Zhang, C Liu, Y Zhu, L Peng, W Qiu, Q Tang… - Physical Review …, 2024 - APS
Genetic information often exhibits hierarchical and nested relationships, achieved through
the reuse of repetitive subsequences such as duplicons and transposable elements, a …

Evolution of protein domain repeats in metazoa

A Schüler, E Bornberg-Bauer - Molecular biology and evolution, 2016 - academic.oup.com
Repeats are ubiquitous elements of proteins and they play important roles for cellular
function and during evolution. Repeats are, however, also notoriously difficult to capture …

Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming

V Pugacheva, A Korotkov, E Korotkov - Statistical Applications in …, 2016 - degruyter.com
The aim of this study was to show that amino acid sequences have a latent periodicity with
insertions and deletions of amino acids in unknown positions of the analyzed sequence …

DbStRiPs: Database of structural repeats in proteins

B Chakrabarty, N Parekh - Protein Science, 2022 - Wiley Online Library
Recent interest in repeat proteins has arisen due to stable structural folds, high evolutionary
conservation and repertoire of functions provided by these proteins. However, repeat …

Structural, functional, and evolutionary characteristics of proteins with repeats

EI Deryusheva, AV Machulin, OV Galzitskaya - Molecular Biology, 2021 - Springer
The review summarizes and systematizes the data on the classification, taxonomic
distribution, structural features, and functions of proteins with structural repeats. Modern …