Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin.
Sign Up to like & getrecommendations! Published in 2017 at "Structure"
DOI: 10.1016/j.str.2017.03.009
Abstract: Although protein design has been used to introduce new functions, designed variants generally only function as well as natural proteins after rounds of laboratory evolution. One possibility for this pattern is that designed mutants frequently… read more here.
Keywords: protein; flexibility; redesigned ubiquitin; conformational heterogeneity ... See more keywords
Conformational Heterogeneity and the Affinity of Substrate Molecular Recognition by Cytochrome P450cam.
Sign Up to like & getrecommendations! Published in 2017 at "Biochemistry"
DOI: 10.1021/acs.biochem.7b00238
Abstract: The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature… read more here.
Keywords: recognition; spectroscopy; molecular recognition; conformational heterogeneity ... See more keywords
Conformational Heterogeneity and DNA Recognition by the Morphogen Bicoid.
Sign Up to like & getrecommendations! Published in 2017 at "Biochemistry"
DOI: 10.1021/acs.biochem.7b00255
Abstract: The morphogenic activity of the Drosophila transcription factor bicoid (Bcd), the first morphogenic protein identified, is controlled by its DNA binding homeodomain. Homeodomains mediate developmental processes in all multicellular organisms, but the Bcd homeodomain appears… read more here.
Keywords: dna; recognition; homeodomain; conformational heterogeneity ... See more keywords
A Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b00630
Abstract: The inherent flexibility and conformational heterogeneity of carbohydrate pose a challenge for its modelling and sampling by existing classical force field. This work quantitatively assesses the quality of four popular carbohydrate force fields ( CHARMM36,GLYCAM06,… read more here.
Keywords: helix coil; conformational heterogeneity; force; force fields ... See more keywords
Conformational Heterogeneity and Interchain Percolation Revealed in an Amorphous Conjugated Polymer
Sign Up to like & getrecommendations! Published in 2022 at "ACS Nano"
DOI: 10.1021/acsnano.2c04794
Abstract: Conjugated polymers are employed in a variety of application areas due to their bright fluorescence and strong biocompatibility. However, understanding the structure of amorphous conjugated polymers on the nanoscale is extremely challenging compared to their… read more here.
Keywords: amorphous conjugated; interchain percolation; conjugated polymer; heterogeneity interchain ... See more keywords
Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms
Sign Up to like & getrecommendations! Published in 2023 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2215371120
Abstract: Significance Despite being identified as the strongest genetic risk factor for Alzheimer’s disease more than 20 years ago, a connection between the biochemical properties of apolipoprotein E (ApoE) and its role in the disease remains… read more here.
Keywords: lipid bound; apolipoprotein extensive; lipid; extensive conformational ... See more keywords
Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes
Sign Up to like & getrecommendations! Published in 2018 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkx1146
Abstract: Abstract Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes… read more here.
Keywords: transcription; dna; bubble dynamics; conformational heterogeneity ... See more keywords
Cysteine-Dependent Conformational Heterogeneity of Shigella flexneri Autotransporter IcsA and Implications of Its Function
Sign Up to like & getrecommendations! Published in 2022 at "Microbiology Spectrum"
DOI: 10.1128/spectrum.03410-22
Abstract: Shigella species are the leading cause of diarrheal-related death globally by causing bacillary dysentery. The surface virulence factor IcsA, which is essential for Shigella pathogenesis, is a unique multifunctional autotransporter that is responsible for cell… read more here.
Keywords: shigella; icsa; cysteine; autotransporter ... See more keywords
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments
Sign Up to like & getrecommendations! Published in 2022 at "RNA"
DOI: 10.1261/rna.078888.121
Abstract: We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like structures and variations thereof. These structures… read more here.
Keywords: dynamics simulations; rna oligonucleotide; heterogeneity ucaauc; ucaauc rna ... See more keywords
DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.965645
Abstract: Single-particle cryo-electron microscopy (cryo-EM) is a technique for biomolecular structure reconstruction from vitrified samples containing many copies of a biomolecular complex (known as single particles) at random unknown 3D orientations and positions. Cryo-EM allows reconstructing… read more here.
Keywords: continuous conformational; cryo; single particle; particle ... See more keywords
Conformational Heterogeneity and Cooperative Effects of Mammalian ALOX15
Sign Up to like & getrecommendations! Published in 2021 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms22063285
Abstract: Arachidonic acid lipoxygenases (ALOXs) have been suggested to function as monomeric enzymes, but more recent data on rabbit ALOX15 indicated that there is a dynamic monomer-dimer equilibrium in aqueous solution. In the presence of an… read more here.
Keywords: heterogeneity cooperative; mammalian alox15; rabbit alox15; cooperative effects ... See more keywords