Understanding the role of non‐Watson‐Crick base pairs in DNA–protein recognition: Structural and energetic aspects using crystallographic database analysis and quantum chemical calculation
Sign Up to like & getrecommendations! Published in 2022 at "Biopolymers"
DOI: 10.1002/bip.23492
Abstract: Specific recognition of DNA base sequences by proteins is vital for life‐cycles of all organisms. In a large number of crystal structures of protein–DNA complexes, DNA conformation significantly deviates from the canonical B‐DNA structure. A… read more here.
Keywords: dna; base pairs; canonical base; non canonical ... See more keywords
Protein–DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data
Sign Up to like & getrecommendations! Published in 2022 at "PROTEOMICS"
DOI: 10.1002/pmic.202100197
Abstract: With the development of artificial intelligence (AI) technologies and the availability of large amounts of biological data, computational methods for proteomics have undergone a developmental process from traditional machine learning to deep learning. This review… read more here.
Keywords: intelligence; machine; artificial intelligence; rna interactions ... See more keywords
Molecular characterization of hexokinase (HK) in Haemaphysalis longicornis and evaluation of HK protein- and DNA-based vaccines against adult ticks.
Sign Up to like & getrecommendations! Published in 2023 at "Pest management science"
DOI: 10.1002/ps.7346
Abstract: BACKGROUND Haemaphysalis longicornis is an obligate hematophagous ectoparasite, which transmits various pathogens to humans, livestock, and wild animals. Hexokinase (HK) is a key regulatory enzyme of the glycolytic pathway in the organisms. However, little is… read more here.
Keywords: dna; protein dna; protein; haemaphysalis longicornis ... See more keywords
Studying Protein-DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1126-5_11
Abstract: Protein hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) can be used to study interactions of proteins with various ligands, to describe the effects of mutations, or to reveal structural responses of proteins to different… read more here.
Keywords: protein; mass spectrometry; dna; protein dna ... See more keywords
Optical Tweezers to Investigate the Structure and Energetics of Single-Stranded DNA-Binding Protein-DNA Complexes.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1290-3_17
Abstract: Optical tweezers enable the isolation and mechanical manipulation of individual nucleoprotein complexes. Here, we describe how to use this technique to interrogate the mechanical properties of individual protein-DNA complexes and extract information about their overall… read more here.
Keywords: optical tweezers; investigate structure; dna; protein dna ... See more keywords
The Use of the Chromatin Immunoprecipitation Technique for In Vivo Identification of Plant Protein-DNA Interactions.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7871-7_23
Abstract: Two-hybrid systems allow for the identification of proteins that physically interact in the context of biological processes. In the cases where these proteins interact with DNA it is essential to define their binding properties with… read more here.
Keywords: identification; protein dna; chromatin immunoprecipitation; dna ... See more keywords
Chromatin Immunoprecipitation for Identification of Protein-DNA Interactions in Human Cells.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7871-7_24
Abstract: Chromatin immunoprecipitation (ChIP) is a powerful technique allowing for investigation of protein-DNA interactions in living cells. Here, we provide a detailed step-by-step protocol for ChIP and highlight important considerations, challenges and pitfalls often encountered in… read more here.
Keywords: protein dna; dna interactions; chromatin immunoprecipitation; chip ... See more keywords
DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers.
Sign Up to like & getrecommendations! Published in 2017 at "Cell reports"
DOI: 10.1016/j.celrep.2017.09.035
Abstract: Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has… read more here.
Keywords: protein; protein dna; dms seq; dna interactions ... See more keywords
Reversible assembly of protein-DNA nanostructures triggered by mediated electron transfer
Sign Up to like & getrecommendations! Published in 2017 at "Electrochimica Acta"
DOI: 10.1016/j.electacta.2017.02.075
Abstract: Abstract Stable protein-DNA nanostructures have been assembled by reconstitution of the multi-ligand binding flavoprotein dodecin on top of flavin-terminated dsDNA monolayers on gold electrodes. These structures could be disassembled by electrochemical flavin reduction via mediated… read more here.
Keywords: electron transfer; protein dna; dna nanostructures;
Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.
Sign Up to like & getrecommendations! Published in 2020 at "Structure"
DOI: 10.1016/j.str.2020.04.009
Abstract: The redesign of a macromolecular binding interface and corresponding alteration of recognition specificity is a challenging endeavor that remains recalcitrant to computational approaches. This is particularly true for the redesign of DNA binding specificity, which… read more here.
Keywords: recognition; protein dna; thermostability; specificity ... See more keywords
Effect of Drying Methods on Protein and DNA Conformation Changes in Lactobacillus rhamnosus GG Cells by Fourier Transform Infrared Spectroscopy.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of agricultural and food chemistry"
DOI: 10.1021/acs.jafc.6b05508
Abstract: Microencapsulation protects cells against environmental stress encountered during the production of probiotics, which are used as live microbial food ingredients. Freeze-drying and spray-drying are used in the preparation of powdered microencapsulated probiotics. This study examines… read more here.
Keywords: lactobacillus rhamnosus; protein dna; rhamnosus cells; spectroscopy ... See more keywords