Biomolecular Function Research Articles

Molecular platforms based on biocompatible photoreactions for photomodulation of biological targets.

Photoirradiation provides a convenient and biocompatible approach for spatiotemporal modulation of biological systems with photoresponsive components. The construction of molecular platforms with a photoresponse to be integrated into biomolecules for photomodulation has been of great research interest in optochemical biology. In this review, we summarize typical molecular platforms that are integratable with biomolecules for photomodulation purposes. We categorize these molecular platforms according to their excitation light source, namely ultraviolet (UV), visible (Vis) or near-infrared (NIR) light. The protype chemistry of these molecular platforms is introduced along with an overview of their most recent applications for spatiotemporal regulation of biomolecular function in living cells or mice models. Challenges and the outlook are also presented. We hope this review paper will contribute to further progress in the development of molecular platforms and their biomedical use.

Aligning biological sequences by exploiting residue conservation and coevolution.

Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e., arranging sequences from different organisms in such a way to identify similar regions, to detect evolutionary relationships between sequences, and to predict biomolecular structure and function. This is typically addressed through profile models, which capture position specificities like conservation in sequences but assume an independent evolution of different positions. Over recent years, it has been well established that coevolution of different amino-acid positions is essential for maintaining three-dimensional structure and function. Modeling approaches based on inverse statistical physics can catch the coevolution signal in sequence ensembles, and they are now widely used in predicting protein structure, protein-protein interactions, and mutational landscapes. Here, we present DCAlign, an efficient alignment algorithm based on an approximate message-passing strategy, which is able to overcome the limitations of profile models, to include coevolution among positions in a general way, and to be therefore universally applicable to protein- and RNA-sequence alignment without the need of using complementary structural information. The potential of DCAlign is carefully explored using well-controlled simulated data, as well as real protein and RNA sequences.

Understanding the Hydrogen-Bonded Clusters of Ammonia (NH3) n (n = 3-6): Insights from the Electronic Structure Theory.

Although it is well known that hydrogen bonds commonly exist in ammonia clusters and play an important role, there are still many challenges in understanding the electronic structure properties of hydrogen bonds. In this paper, the geometric and electronic structure properties of cyclic ammonia clusters are investigated by using first-principles density functional theory (DFT) and the Møller–Plesset perturbation theory (MP2). The calculation results show that the pentamer and hexamer have deviated from the perfect plane, while the trimer and tetramer present planarization that has been confirmed by infrared (IR) spectra. The electronic structure analysis further shows that the covalent properties play a non-negligible role in hydrogen bonding. The results also indicate that the electronic structure facilitates structure planarization. Our work not only provides insight into the role and nature of hydrogen bonds in ammonia clusters but also provides a theoretical basis for frontier science in fields such as atmospheric haze and biomolecular functions.

Divide-and-Conquer Matrisome Protein (DC-MaP) Strategy: An MS-Friendly Approach to Proteomic Matrisome Characterization.

Currently, the extracellular matrix (ECM) is considered a pivotal complex meshwork of macromolecules playing a plethora of biomolecular functions in health and disease beyond its commonly known mechanical role. Only by unraveling its composition can we leverage related tissue engineering and pharmacological efforts. Nevertheless, its unbiased proteomic identification still encounters some limitations mainly due to partial ECM enrichment by precipitation, sequential fractionation using unfriendly-mass spectrometry (MS) detergents, and resuspension with harsh reagents that need to be entirely removed prior to analysis. These methods can be technically challenging and labor-intensive, which affects the reproducibility of ECM identification and induces protein loss. Here, we present a simple new method applicable to tissue fragments of 10 mg and more. The technique has been validated on human ovarian tissue and involves a standardized procedure for sample processing with an MS-compatible detergent and combined centrifugation. This two-step protocol eliminates the need for laborious sample clarification and divides our samples into 2 fractions, soluble and insoluble, successively enriched with matrisome-associated (ECM-interacting) and core matrisome (structural ECM) proteins.

Probing the response of poly (N-isopropylacrylamide) microgels to solutions of various salts using etalons

The Hofmeister series is a qualitative ordering of ions according to their ability to precipitate proteins in aqueous solution and is extremely important to consider when trying to understand materials and biomolecular structure and function. Herein, we utilized optical devices (etalons) composed of poly(N-isopropylacrylamide) (pNIPAm)-co-10% acrylic acid (AAc) or pNIPAm-based microgels to investigate how various salts in the Hofmeister series influenced the microgel hydration state. Etalons were exposed to a series of salts solutions at different concentrations and the position of the peaks in the reflectance spectra monitored using reflectance spectroscopy. As expected, pNIPAm-co-10%AAc microgel-based etalons responded to the presence of ions, although in this case the response to cations deviated from the Hofmeister series. However, when using etalons prepared with pNIPAm-based microgels, the responses followed the Hofmeister series for both cation and anions. Finally, we observed that the sensitivity of etalons prepared with pNIPAm microgels was significantly higher than the response obtained from etalons composed of pNIPAm-co-10%AAc microgels. This was explained by considering the charge on the pNIPAm-co-10%AAc microgels that influences how osmotic and Hofmeister effects impacts hydration state.

Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities

Enzyme orthologs sharing identical primary functions can have different promiscuous activities. While it is possible to mine this natural diversity to obtain useful biocatalysts, generating comparably rich ortholog diversity is difficult, as it is the product of deep evolutionary processes occurring in a multitude of separate species and populations. Here, we take a first step in recapitulating the depth and scale of natural ortholog evolution on laboratory timescales. Using a continuous directed evolution platform called OrthoRep, we rapidly evolve the Thermotoga maritima tryptophan synthase β-subunit (TmTrpB) through multi-mutation pathways in many independent replicates, selecting only on TmTrpB’s primary activity of synthesizing l-tryptophan from indole and l-serine. We find that the resulting sequence-diverse TmTrpB variants span a range of substrate profiles useful in industrial biocatalysis and suggest that the depth and scale of evolution that OrthoRep affords will be generally valuable in enzyme engineering and the evolution of biomolecular functions.

Ultra-high-throughput analysis of functional biomolecules using in vitro selection and bioinformatics.

Functional analysis of biomolecules, including nucleic acids and proteins, is important for understanding biological mechanisms in living cells such as gene expression and metabolism. To analyze diverse biomolecular functions, large-scale screening systems for biomolecules have been developed for various applications such as to improve enzyme activity and identify target binding molecules. One of these systems, the Bead Display system, utilizes emulsion technology and is a powerful tool for rapidly screening functional nucleic acids or proteins in vitro. Furthermore, an analytical pipeline that consists of genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq, gene expression analysis, and bioinformatics was shown to be a robust platform for comprehensively identifying genes regulated by a transcription factor. This review provides an overview of the biomolecular screening methods developed to date.

Surface polarization effects in confined polyelectrolyte solutions

Understanding nanoscale interactions at the interface between two media with different dielectric constants is crucial for controlling many environmental and biological processes, and for improving the efficiency of energy storage devices. In this contributed paper, we show that polarization effects due to such dielectric mismatch remarkably influence the double-layer structure of a polyelectrolyte solution confined between two charged surfaces. Surprisingly, the electrostatic potential across the adsorbed polyelectrolyte double layer at the confining surface is found to decrease with increasing surface charge density, indicative of a negative differential capacitance. Furthermore, in the presence of polarization effects, the electrostatic energy stored in the double-layer structure is enhanced with an increase in the charge amplification, which is the absorption of ions on a like-charged surface. We also find that all of the important double-layer properties, such as charge amplification, energy storage, and differential capacitance, strongly depend on the polyelectrolyte backbone flexibility and the solvent quality. These interesting behaviors are attributed to the interplay between the conformational entropy of the confined polyelectrolytes, the Coulombic interaction between the charged species, and the repulsion from the surfaces with lower dielectric constant.

Transition-Metal-Mediated versus Tetrazine-Triggered Bioorthogonal Release Reactions: Direct Comparison and Combinations Thereof.

Bioorthogonal cleavage reactions are gaining popularity in chemically inducible prodrug activation and in the control of biomolecular functions. Despite similar applications, these reactions were developed and optimized on different substrates and under different experimental conditions. Reported herein is a side-by-side comparison of palladium-, ruthenium- and tetrazine-triggered release reactions, which aims at comparing the reaction kinetics, efficiency and overall advantages and limitations of the methods. In addition, we disclose the possibility of mutual combination of the cleavage reactions. Finally, we compare the efficiency of the bioorthogonal deprotections in cellular experiments, which revealed that among the three methods investigated, the palladium- and the tetrazine-promoted reaction can be used for efficient prodrug activation, but only the tetrazine-triggered reactions proceed efficiently inside cells.

Dynamics-Function Analysis in Catalytic RNA Using NMR Spin Relaxation and Conformationally Restricted Nucleotides.

A full understanding of biomolecular function requires an analysis of both the dynamic properties of the system of interest and the identification of those dynamics that are required for function. We describe NMR methods based on metabolically directed specific isotope labeling for the identification of molecular disorder and/or conformational transitions on the RNA backbone ribose groups. These analyses are complemented by the use of synthetic covalently modified nucleotides constrained to a single sugar pucker, which allow functional assessment of dynamics by selectively removing a minor conformer identified by NMR from the structural ensemble.

Binding of levobupivacaine-loaded gold nanoparticles to human serum albumin: a simulated physiological study.

Techniques such as Fourier transform infrared (FTIR), ultraviolet-visible (UV-vis) spectra, fluorescence, circular dichroism (CD) and spectroscopy were applied to elucidate the formation, structure and physicochemical properties of levobupivacaine-gold nanoparticle (LGN) binding to human serum albumin (HSA). Thermodynamic parameters (ΔG = -2.58 × 104 J·mol-1 , ΔS = -7.80 J·mol-1 ·K-1 , and ΔS = -2.82 × 104 J·mol-1 at 305 K) suggested one weak binding site on HSA, which was governed by van der Waals forces as well as hydrogen bonds. Moreover, the outcomes of UV-vis, CD, FTIR, synchronous and three-dimensional fluorescence suggested that the microenvironment of HSA had been changed with addition of LGN. Based on the results of fluorescence resonance energy transfer, a distance of 2.8 nm between the LGN and HSA was observed. This approach has potential value for illustrating the pharmacodynamics of LGN when in combination with transmembrane transport, biomolecular function effect, and other experiments.

Computational Methods for Predicting DNA Binding Proteins

Background: DNA-binding proteins are very important to many biomolecular functions. The traditional experimental methods are expensive and time-consuming, so, computational methods that can predict whether a protein is a DNA-binding protein or not are very helpful to researchers. Machine learning has been widely used in many research areas. Many researchers have proposed machine learning methods for DNA-binding protein prediction, and this paper highlights their advantages and disadvantages. Objective: There are many computational methods that can predict DNA-binding proteins. Every method uses different features and different classifier algorithms. In this paper, a review of these methods is provided to find out some common procedures that can help researchers to develop more accurate methods. Methods: Firstly, the information stored in the protein sequence and gene sequence is presented. That information is the basis to find out the patterns leading to binding. Then, feature extraction methods and classifier algorithms are discussed. At last, some commonly used benchmark datasets are analysed and evaluated by methods. Conclusion: In this review, we analyzed some popular computational methods to predict DNAbinding protein. From those methods, we highlighted many features necessary to build up an accurate DNA-binding protein classifier. This can also help researchers to build up more useful computational tools. Currently, there are some machine learning methods with good performance in predicting DNAbinding proteins. The performance can be improved by using different kinds of features and classifiers.

Nanoscale Mapping of the Directional Flow Patterns at Liquid-Solid Interfaces

The nanoscale behavior of liquid molecules and solutes along the interface with solids controls many processes such as molecular exchanges, wetting, electrochemistry, nanofluidics, biomolecular function, and lubrication. Experimentally, several techniques can explore the equilibrium molecular arrangement of liquids near the surface of immersed solids but quantifying the nanoscale flow patterns naturally adopted by this interfacial liquid remains a considerable challenge. Here we describe an approach based on atomic force microscopy, and able to quantify the flow direction preferentially adopted by liquids along interfaces with nanoscale precision. The approach, called vortex dissipation microscopy (VDM), uses high-frequency directional oscillations to derive local flow information around each location of the interface probed. VDM effectively derives nanoscale flow charts of the interfacial liquid parallel to a solid and can operate over a broad range of soft and hard interfaces. To illustrate its capabilities, we quantify the dynamics of aqueous solutions containing $\mathrm{K}\mathrm{Cl}$ or ${\mathrm{Mg}\mathrm{Cl}}_{2}$ along the surface of a same graphene oxide flake. We show that dissolved ${\mathrm{K}}^{+}$ ions can move evenly in all directions along the interface whereas ${\mathrm{Mg}}^{2+}$ ions tend to move in registry with the underlying lattice due to enthalpic effects. The results provide in situ nanoscale insights into the ion-specific sieving properties of graphene oxide membranes.

Fabrication of Pd NPs on pectin-modified Fe3O4 NPs: A magnetically retrievable nanocatalyst for efficient C–C and C–N cross coupling reactions and an investigation of its cardiovascular protective effects

The present report represents the synthesis of a novel Pd NPs immobilized over a natural polysaccharide (pectin) coated Fe3O4 magnetic nanocomposite material (Fe3O4@pectin/Pd) for investigating the cardiovascular protective effects. The biomolecular functionalization not only stabilizes the ferrite nanoparticles from agglomeration but also provides an environment for the biogenic reduction of Pd2+ ions. This protocol is a promising breakthrough for the synthesis of a quasi-heterogeneous catalyst, a bridge between heterogeneous and homogeneous medium. The structure, morphology and physicochemical properties of the material were characterized utilizing various analytical techniques like FT-IR, FE-SEM, TEM, VSM, EDX-elemental mapping, ICP, EDX and XPS. The catalyst showed excellent reactivity in C-C and C-N cross coupling reactions via Suzuki and Buchwald-Hartwig reactions respectively. An array of different biphenyls and aryl amines were then procured by reactions of various aryl halides with phenylboronic acid or secondary amines over the catalyst affording good to excellent yields. The catalyst was easily recoverable using an external magnet and thereafter recycled for several trials with insignificant palladium leaching or loss in catalytic performance. To investigate the cardiovascular protective activities of catalyst, the MTT assay was done on Human Aortic Endothelial Cells (HAEC), Human Coronary Artery Endothelial Cells (HCAEC), and Human Pulmonary Artery Endothelial Cells (HPAEC) cell lines. Nanocatalyst-treated cell cutlers significantly (p ≤ 0.01) decreased the caspase-3 activity, and DNA fragmentation. It raised the cell viability and mitochondrial membrane potential in the high concentration of Mitoxantrone-treated HAEC, HCAEC, and HPAEC cells. According to the above findings, nanocatalyst can be administrated as a cardiovascular protective drug for the treatment of cardiovascular diseases after approving in the clinical trial studies in humans.

SLIM: A Short-Linked, Highly Redox-Stable Trityl Label for High-Sensitivity In-Cell EPR Distance Measurements.

The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site‐directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in‐cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide‐functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm, and shows high stability against reduction. Using this label, the guanine‐nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.

SLIM: A Short‐Linked, Highly Redox‐Stable Trityl Label for High‐Sensitivity In‐Cell EPR Distance Measurements

AbstractThe understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site‐directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in‐cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide‐functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm, and shows high stability against reduction. Using this label, the guanine‐nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.

Evidence Based Faktor yang Berhubungan Dengan Kualitas Hidup Pasien PPOK Stabil: A Systematic Review

; amin.fkua@gmail.com 
 Makhfudli 
 Fakultas Keperawatan, Universitas Airlangga; ievut_rz@yahoo.com (koresponden)
 
 ABSTRACT
 
 Background: Low quality of life in chronic obstructive pulmonary disease is crucial because leads to a high risk to reduced activity of daily and mortality. Objective: To identify determine factors that influence with health-related quality of life on stable COPD patients. Method: The database was performed article from Science Direct, CINAHL, Scopus dan PubMed is limited to the last 5 years of publication from 2014 to 2019, full-text article in English. The keywords used ”Health-Related Quality of Life”, “AND”, “Stable”, “AND”, “COPD”. Results: Fourteen articles with 8401 participants were included in the review. Most studies were cross sectional design. COPD Assasment Test (CAT) was to assess health-related quality of life in stable COPD. There was symptoms and exacerbation, functional capacity exercise, psychology, sociodemography, biomolecular, comorbidity, and pulmonary function affecting health-related quality of life on stable COPD patients. Conclusion: Factors might affect with poor HRQOL because the condition of COPD itself which then give an effect to whole body. Suggestion: Health worker need to be aware and control of the complexity of factors influence health-related quality of life to impove outcomes for COPD patients.
 Keywords: health-related quality of life; chronic obstructive pulmonary disease
 
 ABSTRAK
 
 Latar belakang: Kualitas hidup yang rendah pada pasien Penyakit Paru Obstruktif Kronik (PPOK) menjadi penting karena dapat menyebabkan penurunan aktivitas sehari-hari dan kematian. Tujuan: Untuk mengetahui determinan faktor yang dapat mempengaruhi kualitas hidup pasien PPOK yang stabil Metode: Database yang digunakan dalam penelitian ini adalah Science Direct, CINAHL, Scopus dan PubMed terbatas untuk publikasi 5 tahun terakhir dari 2014 hingga 2019, full text article dengan berbahasa Inggris. Kata kunci yang digunakan adalah “”Health-Related Quality of Life”, “AND”, “Stable”, “AND”, “COPD”. Hasil: Systematic review ini menggunakan 14 artikel dengan 8401 responden. Kuesioner yang digunakan dalam studi adalah COPD Assasment Test (CAT). Tanda gejala dan eksaserbasi, kapasitas latihan fungsional, psikologi, sosiodemografi, biomolekul, komorbiditas dan faal paru mempengaruhi kualitas hidup pasien PPOK stabil. Kesimpulan: Banyak faktor yang mungkin memiliki hubungan dengan kualitas hidup pasien buruk karena kondisi penyakit PPOK itu sendiri yang kemudian berdampak pada seluruh tubuh. Saran: Petugas kesehatan perlu menyadari dan mengontrol kompleksnya dari faktor-faktor yang mempengaruhi kualitas hidup pasien PPOK sehingga menjadi membaik.
 Kata kunci: kualitas hidup; penyakit paru obstruktif kronik

Accurate and rapid calculation of hydration free energy and its physical implication for biomolecular functions.

Here we review a new method for calculating a hydration free energy (HFE) of a solute and discuss its physical implication for biomolecular functions in aqueous environments. The solute hydration is decomposed into processes 1 and 2. A cavity matching the geometric characteristics of the solute at the atomic level is created in process 1. Solute-water van der Waals and electrostatic interaction potentials are incorporated in process 2. The angle-dependent integral equation theory combined with our morphometric approach is applied to process 1, and the three-dimensional reference interaction site model theory is employed for process 2. Molecular models are adopted for water. The new method is characterized by the following. Solutes with various sizes including proteins can be treated in the same manner. It is almost as accurate as the molecular dynamics simulation despite its far smaller computational burden. It enables us to handle a solute possessing a significantly large total charge without difficulty. The HFE can be decomposed into a variety of physically insightful, energetic, and entropic components. It is best suited to the elucidation of mechanisms of protein folding, pressure and cold denaturation of a protein, and different types of molecular recognition.

PIANO: A Web Server for Pseudouridine-Site (Ψ) Identification and Functional Annotation.

Known as the “fifth RNA nucleotide”, pseudouridine (Ψ or psi) is the first-discovered and most abundant RNA modification occurring at the Uridine site, and it plays a prominent role in a number of biological processes. Thousands of Ψ sites have been identified within different biological contexts thanks to the advancement in high-throughput sequencing technology; nevertheless, the transcriptome-wide distribution, biomolecular functions, regulatory mechanisms, and disease relevance of pseudouridylation are largely elusive. We report here a web server—PIANO—for pseudouridine site (Ψ) identification and functional annotation. PIANO was built upon a high-accuracy predictor that takes advantage of both conventional sequence features and 42 additional genomic features. When tested on six independent datasets generated from four independent Ψ-profiling technologies (Ψ-seq, RBS-seq, Pseudo-seq, and CeU-seq) as benchmarks, PIANO achieved an average AUC of 0.955 and 0.838 under the full transcript and mature mRNA models, respectively, marking a substantial improvement in accuracy compared to the existing in silico Ψ-site prediction methods, i.e., PPUS (0.713 and 0.707), iRNA-PseU (0.713 and 0.712), and PseUI (0.634 and 0.652). Besides, PIANO web server systematically annotates the predicted Ψ sites with post-transcriptional regulatory mechanisms (miRNA-targets, RBP-binding regions, and splicing sites) in its prediction report to help the users explore potential machinery of Ψ. Moreover, a concise query interface was also built for 4,303 known Ψ sites, which is currently the largest collection of experimentally validated human Ψ sites. The PIANO website is freely accessible at: http://piano.rnamd.com.

Investigations of the underlying mechanisms of HIF-1α and CITED2 binding to TAZ1

The TAZ1 domain of CREB binding protein is crucial for transcriptional regulation and recognizes multiple targets. The interactions between TAZ1 and its specific targets are related to the cellular hypoxic negative feedback regulation. Previous experiments reported that one of the TAZ1 targets, CITED2, is an efficient competitor of another target, HIF-1α. Here, by developing the structure-based models of TAZ1 complexes, we have uncovered the underlying mechanisms of the competitions between the two intrinsic disordered proteins (IDPs) HIF-1α and CITED2 binding to TAZ1. Our results support the experimental hypothesis on the competition mechanisms and the apparent affinity. Furthermore, the simulations locate the dominant position of forming TAZ1-CITED2 complex in both thermodynamics and kinetics. For thermodynamics, TAZ1-CITED2 is the lowest basin located on the free energy surface of binding in the ternary system. For kinetics, the results suggest that CITED2 binds to TAZ1 faster than HIF-1α. In addition, the analysis of contact map and Φ values is important for guiding further experimental studies to understand the biomolecular functions of IDPs.