Monkeypox: A comprehensive review on mutation, transmission, pathophysiology, and therapeutics.

Monkeypox virus (MPXV) is the causative agent of the monkeypox (Mpox) disease, belongs to the Orthopoxvirus genus of the Poxviridae family. Due to the recent re-emergence of Mpox in 2024, this is the second time when the World Health Organization (WHO) declared Mpox as a Public Health Emergency of International Concern (PHEIC). This review intends to offer an in-depth analysis of Mpox, including its key characteristics, epidemiological, mutation, pathophysiology, transmission, and therapeutics.

Scalable Analysis of Dipole Moment Fluctuations for Characterizing Intermolecular Interactions and Structural Stability.

Accurately predicting protein-ligand interactions is essential in computational molecular biochemistry and in silico drug development. Monitoring changes in molecular dipole moments through molecular dynamics simulations provides valuable insights into dipole-dipole interactions, which are critical for understanding protein structure stability and predicting protein-ligand binding affinity. In this study, we propose a novel method to monitor changes in the interangle between dipole vectors of residue molecules within proteins and ligand molecules, aiming to evaluate the strength and consistency of interactions within the complex.

Efficient Super-Resolution Method for Targets Observed by Satellite SAR.

This study presents an efficient super-resolution (SR) method for targets observed by satellite synthetic aperture radar (SAR). First, a small target image is extracted from a large-scale SAR image and undergoes proper preprocessing. The preprocessing step is adaptively designed depending on the types of movements of targets.

Comparative molecular dynamics study on the features of binding and non-binding modes of retinoic acid in cellular retinol-binding protein (I).

Retinoids play crucial roles in various biological processes by interacting with their carrier proteins such as cellular retinol-binding protein (CRBP). Understanding the molecular interactions between retinoids and CRBP enables their pharmacological and biomedical applications. Experimentally, CRBP(I) does not bind to retinoic acid, but when arginine is introduced into 108th residue instead of glutamine (Q108R), it binds to retinoic acid.

Analysis of protein-protein interface with incorporating low-frequency molecular interactions in molecular dynamics simulation.

Protein-protein interactions are vital for various biological processes such as immune reaction, signal transduction, and viral infection. Molecular Dynamics (MD) simulation is a powerful tool for analyzing non-covalent interactions between two protein molecules. In general, MD simulation studies on the protein-protein interface have focused on the analysis of major and frequent molecular interactions.

Cell disruption and lipid extraction from Chlorella species for biorefinery applications: Recent advances.

Chlorella is a promising microalga for CO-neutral biorefinery that co-produces drop-in biofuels and multiple biochemicals. Cell disruption and selective lipid extraction steps are major technical bottlenecks in biorefinement because of the inherent robustness and complexity of algal cell walls. This review focuses on the state-of-the-art achievements in cell disruption and lipid extraction methods for Chlorella species within the last five years.

Super-Resolution Procedure for Target Responses in KOMPSAT-5 Images.

Recently, target analysis using satellite SAR images has received much attention in the area of satellite SAR remote sensing. Because the spatial resolution of the target response in the satellite SAR image is a main factor that has a large effect on target analysis performances, the improvement of the spatial resolution of target response is required to enhance the target analysis capability. However, the spatial resolution is already determined in the satellite SAR system design process.

Residue interaction network and molecular dynamics simulation study on the binding of S239D/I332E Fc variant with enhanced affinity to FcγRIIIa receptor.

Engineering of Fc has been adapted as an efficient method for enhanced or reduced affinity towards Fc receptors in the development of therapeutic antibodies. S239D/I332E mutation of Fc induces approximately two logs greater affinity to the FcγRIIIa receptor and has been extensively employed in various Fc engineering studies. It is known that the mutation gives rise to the formation of salt bridges between the mutated residues of Fc and FcγRIIIa, but the overall effect of the mutation in the binding interface of the Fc-FcγRIIIa complex is still unclear.

Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions.

The Protein Data Bank (PDB) file format developed at Brookhaven National Laboratory is the most popular file format to store biological data and is widely supported by many software programs for the editing and visualization of macromolecular structures. Unfortunately, many of these structures have variety of issues ranging from missing side chains and/or atoms to alternate locations (rotamers). To fix these flaws, one has to learn a new program, compile modules, and install libraries.

Effect of molecular properties of the protein-ligand complex on the prediction accuracy of AutoDock.

Molecular docking approach has been extensively used to predict the ligand's binding conformation in the binding pocket of protein. However, its prediction accuracy is still limited and highly dependent on target protein-ligand complexes. In this study, we investigated the effects of ligand torsion number, ligand hydrophobicity, and binding-site hydrophobicity on the prediction accuracy of Autodock, a popular molecular docking tool, combinatorially as well as respectively.

Author Correction: In Silico Characterization of the Binding Modes of Surfactants with Bovine Serum Albumin.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Combinatorial Effect of Ligand and Ligand-Binding Site Hydrophobicities on Binding Affinity.

Computational methods to study protein-ligand interactions at a molecular level have been successful to a certain extent in predicting the pose, atomic interactions, and so forth, but poor efficiency in estimating a protein-ligand binding affinity is still a crucial problem to be solved. Analyzing the protein-ligand interactions quantitatively is one primary concern for understanding. Qualitative analysis of these interactions may lead to better insights about protein-ligand interactions.

In Silico Characterization of the Binding Modes of Surfactants with Bovine Serum Albumin.

The binding interactions of the surfactants: anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB), non-ionic octyl glucoside (OG), and zwitterionic 3-[Hexadecyl(dimethyl)ammonio]-1-propanesulfonate (HPS), with bovine serum albumin (BSA) were investigated by computer simulation. The results disclosed that the surfactants bound stably between hydrophobic subdomain IIA and IIIA where tryptophan-213 residue, an important intrinsic fluorophore in BSA is housed. The interactions of the surfactants with the BSA were electrostatic and hydrophobic interactions.

RiSLnet: Rapid identification of smart mutant libraries using protein structure network. Application to thermal stability enhancement.

A key point of protein stability engineering is to identify specific target residues whose mutations can stabilize the protein structure without negatively affecting the function or activity of the protein. Here, we propose a method called RiSLnet (Rapid identification of Smart mutant Library using residue network) to identify such residues by combining network analysis for protein residue interactions, identification of conserved residues, and evaluation of relative solvent accessibility. To validate its performance, the method was applied to four proteins, that is, T4 lysozyme, ribonuclease H, barnase, and cold shock protein B.

Comparative Analysis of TM and Cytoplasmic β-barrel Conformations Using Joint Descriptor.

Macroscopic descriptors have become valuable as coarse-grained features of complex proteins and are complementary to microscopic descriptors. Proteins macroscopic geometric features provide effective clues in the quantification of distant similarity and close dissimilarity searches for structural comparisons. In this study, we performed a systematic comparison of β-barrels, one of the important classes of protein folds in various transmembrane (TM) proteins against cytoplasmic barrels to estimate the conformational features using a joint-based descriptor.

Exploring the differences and similarities between urea and thermally driven denaturation of bovine serum albumin: intermolecular forces and solvation preferences.

The interactions of bovine serum albumin (BSA) with urea/water were investigated by computer simulation. It was revealed that the BSA-hydrophobic residues in urea solutions favored contact with urea more than with water. Energy decomposition analysis showed that van der Waals energy was the dominant driving force behind urea affinity for hydrophobic residues, whereas coulombic attraction was largely responsible for water affinity for these residues.

Engineering an aldehyde dehydrogenase toward its substrates, 3-hydroxypropanal and NAD, for enhancing the production of 3-hydroxypropionic acid.

3-Hydroxypropionic acid (3-HP) can be produced via the biological route involving two enzymatic reactions: dehydration of glycerol to 3-hydroxypropanal (3-HPA) and then oxidation to 3-HP. However, commercial production of 3-HP using recombinant microorganisms has been hampered with several problems, some of which are associated with the toxicity of 3-HPA and the efficiency of NAD regeneration. We engineered α-ketoglutaric semialdehyde dehydrogenase (KGSADH) from Azospirillum brasilense for the second reaction to address these issues.

Measuring the Conformational Distance of GPCR-related Proteins Using a Joint-based Descriptor.

Joint-based descriptor is a new level of macroscopic descriptor for protein structure using joints of secondary structures as a basic element. Here, we propose how the joint-based descriptor can be applied to examine the conformational distances or differences of transmembrane (TM) proteins. Specifically, we performed three independent studies that measured the global and conformational distances between GPCR A family and its related structures.

Simultaneously Enhancing the Stability and Catalytic Activity of Multimeric Lysine Decarboxylase CadA by Engineering Interface Regions for Enzymatic Production of Cadaverine at High Concentration of Lysine.

Cadaverine (1,5-diaminopentane) is a major source of many industrial polyamides such as nylon and chelating agents. Currently, cadaverine is produced by the microbial fermentation of glucose to lysine, which is then decarboxylated by lysine decarboxylase (CadA). However, utilizing CadA for cadaverine production causes enzyme instability.

Joint-based description of protein structure: its application to the geometric characterization of membrane proteins.

A macroscopic description of a protein structure allows an understanding of the protein conformations in a more simplistic manner. Here, a new macroscopic approach that utilizes the joints of the protein secondary structures as a basic descriptor for the protein structure is proposed and applied to study the arrangement of secondary structures in helical membrane proteins. Two types of dihedral angle, Ω and λ, were defined based on the joint points of the transmembrane (TM) helices and loops, and employed to analyze 103 non-homologous membrane proteins with 3 to 14 TM helices.

Separation efficiency of free-solution conjugated electrophoresis with drag-tags incorporating a synthetic amino acid.

DNA sequencing or separation by conventional capillary electrophoresis with a polymer matrix has some inherent drawbacks, such as the expense of polymer matrix and limitations in sequencing read length. As DNA fragments have a linear charge-to-friction ratio in free solution, DNA fragments cannot be separated by size. However, size-based separation of DNA is possible in free-solution conjugate electrophoresis (FSCE) if a "drag-tag" is attached to DNA fragments because the tag breaks the linear charge-to-friction scaling.

Stable isotopic labeling-based quantitative targeted glycomics (i-QTaG).

Mass spectrometry (MS) analysis combined with stable isotopic labeling is a promising method for the relative quantification of aberrant glycosylation in diseases and disorders. We developed a stable isotopic labeling-based quantitative targeted glycomics (i-QTaG) technique for the comparative and quantitative analysis of total N-glycans using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We established the analytical procedure with the chemical derivatizations (i.

Identification of novel cupredoxin homologs using overlapped conserved residues based approach.

Cupredoxin-like proteins are mainly copper-binding proteins that conserve a typical rigid Greek-key arrangement consisting of an eight-stranded β-sandwich, even though they share as little as 10-15% sequence similarity. The electron transport function of the Cupredoxins is critical for respiration and photosynthesis, and the proteins have therapeutic potential. Despite their crucial biological functions, the identification of the distant Cupredoxin homologs has been a difficult task due to their low sequence identity.

Redesigning the type II' β-turn in green fluorescent protein to type I': implications for folding kinetics and stability.

Both Type I' and Type II' β-turns have the same sense of the β-turn twist that is compatible with the β-sheet twist. They occur predominantly in two residue β-hairpins, but the occurrence of Type I' β-turns is two times higher than Type II' β-turns. This suggests that Type I' β-turns may be more stable than Type II' β-turns, and Type I' β-turn sequence and structure can be more favorable for protein folding than Type II' β-turns.

Identification of an ideal-like fingerprint for a protein fold using overlapped conserved residues based approach.

Design of an efficient fingerprint that detects homologous proteins at distant sequence identity has been a great challenge. This paper proposes a strategy to extract an ideal-like fingerprint with high specificity and sensitivity from a group of sequences related to a fold. The approach is devised based on the assumptions that the critical residues for a protein fold may be conserved in three aspects, i.