Topics

PubMed Journals Articles About "Incorporating Nearest Neighbor Site Dependence Into Protein Evolution" RSS

03:27 EDT 2nd April 2020 | BioPortfolio

Incorporating Nearest Neighbor Site Dependence Into Protein Evolution PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Incorporating Nearest Neighbor Site Dependence Into Protein Evolution articles that have been published worldwide.

More Information about "Incorporating Nearest Neighbor Site Dependence Into Protein Evolution" on BioPortfolio

We have published hundreds of Incorporating Nearest Neighbor Site Dependence Into Protein Evolution news stories on BioPortfolio along with dozens of Incorporating Nearest Neighbor Site Dependence Into Protein Evolution Clinical Trials and PubMed Articles about Incorporating Nearest Neighbor Site Dependence Into Protein Evolution for you to read. In addition to the medical data, news and clinical trials, BioPortfolio also has a large collection of Incorporating Nearest Neighbor Site Dependence Into Protein Evolution Companies in our database. You can also find out about relevant Incorporating Nearest Neighbor Site Dependence Into Protein Evolution Drugs and Medications on this site too.

Showing "Incorporating Nearest Neighbor Site Dependence into Protein Evolution" PubMed Articles 1–25 of 23,000+

Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models.


Single-Cell Clustering Based on Shared Nearest Neighbor and Graph Partitioning.

Clustering of single-cell RNA sequencing (scRNA-seq) data enables discovering cell subtypes, which is helpful for understanding and analyzing the processes of diseases. Determining the weight of edges is an essential component in graph-based clustering methods. While several graph-based clustering algorithms for scRNA-seq data have been proposed, they are generally based on k-nearest neighbor (KNN) and shared nearest neighbor (SNN) without considering the structure information of graph. Here, to improve the...

Including crystallographic symmetry in quantum-based refinement: Q|R#2.

Three-dimensional structure models refined using low-resolution data from crystallographic or electron cryo-microscopy experiments can benefit from high-quality restraints derived from quantum-chemical methods. However, nonperiodic atom-centered quantum-chemistry codes do not inherently account for nearest-neighbor interactions of crystallographic symmetry-related copies in a satisfactory way. Here, these nearest-neighbor effects have been included in the model by expanding to a super-cell and then truncati...


Unique roles of iron and zinc binding to the yeast Fe-S cluster scaffold assembly protein "Isu1".

Mitochondrial Fe-S cluster biosynthesis is accomplished within yeast utilizing the biophysical attributes of the "Isu1" scaffold assembly protein. As a member of a highly homologous protein family, Isu1 has sequence conservation between orthologs and a conserved ability to assemble [2Fe-2S] clusters. Regardless of species, scaffold orthologs have been shown to exist in both "disordered" and "structured" conformations, a structural architecture that is directly related to conformations utilized during Fe-S c...

Inspector: A lysine succinylation predictor based on edited nearest-neighbor undersampling and adaptive synthetic oversampling.

Lysine succinylation is an important type of protein post-translational modification and plays a key role in regulating protein function and structural changes. The mechanism and function of succinylation have not been clarified. The key to better understanding the precise mechanism and functional role of succinylation is the identification of lysine succinylation sites. However, conventional experimental methods for succinylation identification are often expensive, time-consuming, and labor-intensive. Ther...

Molecular function limits divergent protein evolution on planetary timescales.

Functional conservation is known to constrain protein evolution. Nevertheless, the long-term divergence patterns of proteins maintaining the same molecular function and the possible limits of this divergence have not been explored in detail. We investigate these fundamental questions by characterizing the divergence between ancient protein orthologs with conserved molecular function. Our results demonstrate that the decline of sequence and structural similarities between such orthologs significantly slows d...

Nontrivial topological phases on the stuffed honeycomb lattice.

We report the appearance of nontrivial topological phases in a tight-binding model on the stuffed honeycomb lattice. The model contains nearest neighbor and next nearest neighbor hopping terms coupled with an additional phase depending on the direction of hopping. Chern insulating and semi-metallic phases emerge with the change of hopping parameters. Nonzero Chern numbers characterizing the bands and the existence of topologically protected edge states in the gap between the relevant bands confirm the prese...

EPR of site-directed spin-labeled proteins: A powerful tool to study structural flexibility.

Electron Paramagnetic Resonance is a spectroscopic technique which, in combination with site-directed spin-labeling, provides structural and dynamic information about proteins in conditions similar to those of their physiological environment. The information is sequence-resolved as it is based on probing the local dynamics of a paramagnetic label incorporated as a side chain of a selected amino acid. This technique does not impose a limit on the size of the protein or protein complex, as long as it is amena...

Evolution of Entanglement Spectra under Generic Quantum Dynamics.

We characterize the early stages of the approach to equilibrium in isolated quantum systems through the evolution of the entanglement spectrum. We find that the entanglement spectrum of a subsystem evolves with three distinct timescales. First, on an o(1) timescale, independent of system or subsystem size and the details of the dynamics, the entanglement spectrum develops nearest-neighbor level repulsion. The second timescale sets in when the light cone has traversed the subsystem. Between these two times, ...

Substrate activation of the low-molecular-weight protein tyrosine phosphatase from .

is known to express a low-molecular-weight protein tyrosine phosphatase. This enzyme, denoted as MptpA ( protein tyrosine phosphatase A), is essential for the pathogen to escape the host immune system, and therefore represents a target for the search of anti-tuberculosis drugs. MptpA was shown to undergo a conformational transition during catalysis, leading to the closure of the active site, which is by this means poised to the chemical step of dephosphorylation. Here we show that MptpA is subjected to subs...

Computational and robotic modeling reveal parsimonious combinations of interactions between individuals in schooling fish.

Coordinated motion and collective decision-making in fish schools result from complex interactions by which individuals integrate information about the behavior of their neighbors. However, little is known about how individuals integrate this information to take decisions and control their motion. Here, we combine experiments with computational and robotic approaches to investigate the impact of different strategies for a fish to interact with its neighbors on collective swimming in groups of rummy-nose tet...

Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription.

Deregulated expression of MYC induces a dependence on the NUAK1 kinase, but the molecular mechanisms underlying this dependence have not been fully clarified. Here, we show that NUAK1 is a predominantly nuclear protein that associates with a network of nuclear protein phosphatase 1 (PP1) interactors and that PNUTS, a nuclear regulatory subunit of PP1, is phosphorylated by NUAK1. Both NUAK1 and PNUTS associate with the splicing machinery. Inhibition of NUAK1 abolishes chromatin association of PNUTS, reduces ...

A new protocol for predicting the ligand binding site and mode based on the 3D-RISM/KH theory.

An efficient algorithm to find the binding position and mode of small ligands bound at an active site of protein is proposed based on the spatial distribution function (SDF) obtained from the 3D-RISM/KH theory. The ligand examined includes hydrophobic, acidic, basic molecules, and zwitterions. Eighteen different types of proteins, which serve as targets for those ligands, are selected to examine the robustness of the algorithm. An imaginary atom, referred to as "anchor site", is defined at the center of geo...

Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum-cofactor utilization.

The nitrogenase metalloenzyme family, essential for supplying fixed nitrogen to the biosphere, is one of life's key biogeochemical innovations. The three forms of nitrogenase differ in their metal dependence, each binding either a FeMo-, FeV-, or FeFe-cofactor where the reduction of dinitrogen takes place. The history of nitrogenase metal dependence has been of particular interest due to the possible implication that ancient marine metal availabilities have significantly constrained nitrogenase evolution ov...

Ligand-Binding Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.

Accurate modeling of ligand-binding site structures plays a critical role in structure-based virtual screening. However, the structures of ligand-binding site in most predicted protein models are generally of low quality and in need of refinements. In this work, we present a ligand-binding site structure refinement protocol using molecular dynamics simulation with restraints derived from predicted binding site templates. Our benchmark validation shows great performance when tested against 40 diverse set of ...

FRSite: Protein drug binding site prediction based on faster R-CNN.

Prediction of binding affinity of proteins and small molecules is a key step in drug design, and the location of binding sites is crucial for affinity prediction and molecular docking. In order to improve the accuracy of binding site prediction, a method called FRSite which improves the Faster R-CNN for protein binding site prediction is proposed in this paper. Multi-channel descriptors for proteins are generated to three dimensional (3D) girds and fed into the proposed Region Proposal Network (RPN-3D) netw...

Corrigendum to "Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes" Mol. Phylogenet. Evolut. 133 (2019) 352-361.

Lattice structures and phase behavior of amphiphilic monoglycerol monolayers.

Due to the Angstrom resolution, Grazing incidence X-ray diffraction (GIXD) represents the most important technique for probing the lateral ordering in condensed monolayers at the air/water interface and allows the construction of phase diagrams of amphiphilic monolayers on the basis of two-dimensional lattice structures and tilt directions of the molecules. The high potential of GIXD is demonstrated by the structural characterization of a variety of amphiphilic monoalkanoylglycerol monolayers in Å-scale. T...

Superconductivity in the doped Hubbard model and its interplay with next-nearest hopping '.

The Hubbard model is widely believed to contain the essential ingredients of high-temperature superconductivity. However, proving definitively that the model supports superconductivity is challenging. Here, we report a large-scale density matrix renormalization group study of the lightly doped Hubbard model on four-leg cylinders at hole doping concentration δ = 12.5%. We reveal a delicate interplay between superconductivity and charge density wave and spin density wave orders tunable via next-nearest neigh...

Evolution of mitochondrial protein import - lessons from trypanosomes.

The evolution of mitochondrial protein import and the systems that mediate it marks the boundary between the endosymbiotic ancestor of mitochondria and a true organelle that is under the control of the nucleus. Protein import has been studied in great detail in Saccharomyces cerevisiae. More recently it has also been extensively investigated in the parasitic protozoan Trypanosoma brucei making it arguably the second best studied system. Here I provide a comparative analysis of the protein import complexes o...

Warfarin increases thermal resistance of albumin through stabilization of the protein lobe that includes its binding site.

Protein-drug interaction is of prominent interest in determining the pharmacokinetic and pharmacodynamic consequences on drug delivery. Warfarin is a widely used anticoagulant drug in the treatment of venous thrombosis and pulmonary embolism and is carried in the blood almost exclusively by human serum albumin. The effects of the binding of warfarin to the native state of albumin were characterized by UV-Vis absorption, conventional and synchronous fluorescence, isothermal titration calorimetry, differentia...

Anabolic androgenic steroid dependence is associated with executive dysfunction.

Anabolic androgenic steroid (AAS) dependence is associated with a high prevalence of intra- and interpersonal problems, hence it is central to identify cognitive factors related to the development and maintenance of dependence.

Dependence on e-cigarettes and cigarettes in a cross-sectional study of US adults.

Cigarette smoking often results in nicotine dependence. With use of electronic cigarettes as an alternative source of nicotine, it is important to assess dependence associated with e-cigarette use. This study assesses dependence among current and former adult e-cigarette users on cigarettes and e-cigarettes, compared with dependence on cigarettes.

Length-scale dependence of protein hydration-shell density.

Here we present a computational approach based on molecular dynamics (MD) simulation to study the dependence of the protein hydration-shell density on the size of the protein molecule. The hydration-shell density of eighteen different proteins, differing in size, shape and function (eight of them are antifreeze proteins), is calculated. The results obtained show that an increase in the hydration-shell density, relative to that of the bulk, is observed (in the range of 4-14%) for all studied proteins and tha...

Saturation mutagenesis genome engineering of infective ΦX174 bacteriophage via unamplified oligo pools and golden gate assembly.

Here we present a novel protocol for the construction of saturation single-site-and massive multi-site-mutant libraries of a bacteriophage. We segmented the ΦX174 genome into 14 non-toxic and non-replicative fragments compatible with golden gate assembly. We next used nicking mutagenesis with oligonucleotides prepared from unamplified oligo pools with individual segments as templates to prepare near-comprehensive single-site mutagenesis libraries of genes encoding the F capsid protein (421 amino acids scan...


Quick Search