State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering

P Chaisupa, RC Wright - SLAS technology, 2024 - Elsevier
Genetically encoded biosensors are crucial for enhancing our understanding of how
molecules regulate biological systems. Small molecule biosensors, in particular, help us …

Optimization strategies and advances in the research and development of AAV‐based gene therapy to deliver large transgenes

VV Kolesnik, RF Nurtdinov… - Clinical and …, 2024 - Wiley Online Library
Abstract Adeno‐associated virus (AAV)‐based therapies are recognized as one of the most
potent next‐generation treatments for inherited and genetic diseases. However, several …

BioJava: an open-source framework for bioinformatics in 2012

A Prlić, A Yates, SE Bliven, PW Rose, J Jacobsen… - …, 2012 - academic.oup.com
Motivation: BioJava is an open-source project for processing of biological data in the Java
programming language. We have recently released a new version (3.0. 5), which is a major …

Structure of AP205 coat protein reveals circular permutation in ssRNA bacteriophages

M Shishovs, J Rumnieks, C Diebolder… - Journal of Molecular …, 2016 - Elsevier
AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar
to any other known single-stranded RNA phage. Here, we report an atomic-resolution model …

Cryogenian origin and subsequent diversification of the plant cell-wall enzyme XTH family

N Shinohara, K Nishitani - Plant and Cell Physiology, 2021 - academic.oup.com
All land plants encode large multigene families of xyloglucan endotransglucosylase/
hydrolases (XTHs), plant-specific enzymes that cleave and reconnect plant cell-wall …

An empirical test of convergent evolution in rhodopsins

KA Mackin, RA Roy, DL Theobald - Molecular biology and …, 2014 - academic.oup.com
Rhodopsins are photochemically reactive membrane proteins that covalently bind retinal
chromophores. Type I rhodopsins are found in both prokaryotes and eukaryotic microbes …

Structural and biochemical analyses of concanavalin A circular permutation by jack bean asparaginyl endopeptidase

SG Nonis, J Haywood, JW Schmidberger… - The Plant …, 2021 - academic.oup.com
Over 30 years ago, an intriguing posttranslational modification was found responsible for
creating concanavalin A (conA), a carbohydrate-binding protein from jack bean (Canavalia …

[HTML][HTML] Tandem domain swapping: determinants of multidomain protein misfolding

A Lafita, P Tian, RB Best, A Bateman - Current Opinion in Structural Biology, 2019 - Elsevier
Highlights•Domain swapping refers to the exchange of structural elements between protein
domains.•Experiments show that tandem homologous domains are prone to domain …

[HTML][HTML] Obtaining protein foldability information from computational models of AlphaFold2 and RoseTTAFold

S Liu, K Wu, C Chen - Computational and Structural Biotechnology Journal, 2022 - Elsevier
The recent breakthrough from AlphaFold2 and RoseTTAFold set a profound milestone for
solving the protein folding problem, but they were not explicitly trained to predict protein …

Discovery of natural non-circular permutations in non-coding RNAs

I Eckert, R Friedrich, CE Weinberg… - Nucleic acids …, 2023 - academic.oup.com
Research in the last two decades has increasingly demonstrated that RNA has capabilities
comparable to those of proteins, for example the ability to form intricate 3D structures …