Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications
Proteins are dynamical entities that undergo a plethora of conformational changes,
accomplishing their biological functions. Molecular dynamics simulation and normal mode …
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 …
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
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 …
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
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 …
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 …
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
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 …
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
Pseudomonas aeruginosa, a widely distributed opportunistic pathogen, is an important
threat to human health for causing serious infections worldwide. Due to its antibiotic …
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 …
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 …
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 …
investigate general protein function. Studying individual members of a protein family is likely …