Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications

Z Liang, GM Verkhivker, G Hu - Briefings in bioinformatics, 2020 - academic.oup.com
Proteins are dynamical entities that undergo a plethora of conformational changes,
accomplishing their biological functions. Molecular dynamics simulation and normal mode …

[HTML][HTML] Co-evolution techniques are resha** the way we do structural bioinformatics

S de Oliveira, C Deane - F1000Research, 2017 - ncbi.nlm.nih.gov
Co-evolution techniques were originally conceived to assist in protein structure prediction by
inferring pairs of residues that share spatial proximity. However, the functional relationships …

Synergistic enhanced rolling circle amplification based on mutS and radical polymerization for single-point mutation DNA detection

S Lee, J You, I Baek, H Park, K Jang, C Park… - Biosensors and …, 2022 - Elsevier
The detection of nucleic acids in biofluids is essential for changing the paradigm of disease
diagnosis. As there are very few nucleic acids present in human biofluids, a high sensitivity …

Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS

SJ LeBlanc, JW Gauer, P Hao, BC Case… - Nucleic acids …, 2018 - academic.oup.com
MutS homologs identify base-pairing errors made in DNA during replication and initiate their
repair. In the presence of adenosine triphosphate, MutS induces DNA bending upon …

Navigating the complexity of p53-DNA binding: implications for cancer therapy

KM Thayer, S Stetson, F Caballero, C Chiu… - Biophysical Reviews, 2024 - Springer
The tumor suppressor protein p53, a transcription factor playing a key role in cancer
prevention, interacts with DNA as its primary means of determining cell fate in the event of …

Highly sensitive and selective detection of single-nucleotide polymorphisms using gold nanoparticle MutS enzymes and a micro cantilever resonator

C Park, J Kang, I Baek, J You, K Jang, S Na - Talanta, 2019 - Elsevier
Mutant DNAs are important markers useful for the diagnosis of human disease. Single-
nucleotide polymorphisms (SNPs) represent the most common types of DNA mutations. As …

Pseudomonas aeruginosa Presents Multiple Vital Changes in Its Proteome in the Presence of 3-Hydroxyphenylacetic Acid, a Promising Antimicrobial Agent

OO Ozdemir, F Soyer - ACS omega, 2020 - ACS Publications
Pseudomonas aeruginosa, a widely distributed opportunistic pathogen, is an important
threat to human health for causing serious infections worldwide. Due to its antibiotic …

Mutagenic Activation of Glutathione Peroxidase-4: Approaches toward Rational Design of Allosteric Drugs

C Ma, DJ Chung, D Abramson, DR Langley… - ACS …, 2022 - ACS Publications
Glutathione peroxidase 4 (GPX4) reduces lipid hydroperoxides in lipid membranes,
effectively inhibiting iron-dependent cell death or ferroptosis. The upregulation of the …

From quantum chemistry to networks in biology: a graph spectral approach to protein structure analyses

V Gadiyaram, S Vishveshwara… - Journal of Chemical …, 2019 - ACS Publications
In this perspective article, we present a multidisciplinary approach for characterizing protein
structure networks. We first place our approach in its historical context and describe the …

General strategies for using amino acid sequence data to guide biochemical investigation of protein function

EN Kennedy, CA Foster, SA Barr… - Biochemical Society …, 2022 - portlandpress.com
The rapid increase of '-omics' data warrants the reconsideration of experimental strategies to
investigate general protein function. Studying individual members of a protein family is likely …