Intrinsically disordered proteins: an overview

R Trivedi, HA Nagarajaram - International journal of molecular sciences, 2022 - mdpi.com
Many proteins and protein segments cannot attain a single stable three-dimensional
structure under physiological conditions; instead, they adopt multiple interconverting …

Examples of extreme survival: tardigrade genomics and molecular anhydrobiology

K Arakawa - Annual review of animal biosciences, 2022 - annualreviews.org
Tardigrades are ubiquitous meiofauna that are especially renowned for their exceptional
extremotolerance to various adverse environments, including pressure, temperature, and …

New pathways of mutational change in SARS-CoV-2 proteomes involve regions of intrinsic disorder important for virus replication and release

T Tomaszewski, RS DeVries, M Dong… - Evolutionary …, 2020 - journals.sagepub.com
The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic.
Since the first whole-genome sequence was published in January 2020, a growing …

IDPConformerGenerator: a flexible software suite for sampling the conformational space of disordered protein states

JMC Teixeira, ZH Liu, A Namini, J Li… - The Journal of …, 2022 - ACS Publications
The power of structural information for informing biological mechanisms is clear for stable
folded macromolecules, but similar structure–function insight is more difficult to obtain for …

The evolution of temperature and desiccation-related protein families in Tardigrada reveals a complex acquisition of extremotolerance

JF Fleming, D Pisani, K Arakawa - Genome biology and …, 2024 - academic.oup.com
Tardigrada is an ecdysozoan lineage famed for its resilience. Tardigrades can tolerate high
doses of radiation, low-oxygen environments, desiccation, and both high and low …

Evolution of short linear motifs and disordered proteins Topic: yeast as model system to study evolution

AG Sangster, T Zarin, AM Moses - Current Opinion in Genetics & …, 2022 - Elsevier
Evolutionary preservation of protein structure had a major influence on the field of molecular
evolution: changes in individual amino acids that did not disrupt protein folding would either …

CapsNet-MHC predicts peptide-MHC class I binding based on capsule neural networks

M Kalemati, S Darvishi, S Koohi - Communications Biology, 2023 - nature.com
Abstract The Major Histocompatibility Complex (MHC) binds to the derived peptides from
pathogens to present them to killer T cells on the cell surface. Developing computational …

Substitution scoring matrices for proteins‐An overview

R Trivedi, HA Nagarajaram - Protein Science, 2020 - Wiley Online Library
Sequence analysis is the primary and simplest approach to discover structural, functional
and evolutionary details of related proteins. All the alignment based approaches of …

Insights from analyses of low complexity regions with canonical methods for protein sequence comparison

P Jarnot, J Ziemska-Legiecka… - Briefings in …, 2022 - academic.oup.com
Low complexity regions are fragments of protein sequences composed of only a few types of
amino acids. These regions frequently occur in proteins and can play an important role in …

Suppression of aggregate and amyloid formation by a novel intrinsically disordered region in metazoan Hsp110 chaperones

UM Yakubu, KA Morano - Journal of Biological Chemistry, 2021 - ASBMB
Molecular chaperones maintain proteostasis by ensuring the proper folding of polypeptides.
Loss of proteostasis has been linked to numerous neurodegenerative disorders including …