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Journals Methods : a Companion to Metho...

Methods : a Companion to Methods in Enzymology

https://read.qxmd.com/read/38301751/fluorescent-human-rpa-to-track-assembly-dynamics-on-dna
#21
JOURNAL ARTICLE
Vikas Kaushik, Rahul Chadda, Sahiti Kuppa, Nilisha Pokhrel, Abhinav Vayyeti, Scott Grady, Chris Arnatt, Edwin Antony
DNA metabolic processes including replication, repair, recombination, and telomere maintenance occur on single-stranded DNA (ssDNA). In each of these complex processes, dozens of proteins function together on the ssDNA template. However, when double-stranded DNA is unwound, the transiently open ssDNA is protected and coated by the high affinity heterotrimeric ssDNA binding Replication Protein A (RPA). Almost all downstream DNA processes must first remodel/remove RPA or function alongside to access the ssDNA occluded under RPA...
January 30, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38295894/metabolic-insights-from-mass-spectrometry-imaging-of-biofilms-a-perspective-from-model-microorganisms
#22
JOURNAL ARTICLE
Dharmeshkumar Parmar, Joenisse M Rosado-Rosa, Joshua D Shrout, Jonathan V Sweedler
Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence...
January 29, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38295893/nmr-techniques-for-investigating-antimicrobial-peptides-in-model-membranes-and-bacterial-cells
#23
JOURNAL ARTICLE
Marc-Antoine Sani, Sunnia Rajput, David W Keizer, Frances Separovic
AMPs are short, mainly cationic membrane-active peptides found in all living organism. They perform diverse roles including signaling and acting as a line of defense against bacterial infections. AMPs have been extensively investigated as templates to facilitate the development of novel antimicrobial therapeutics. Understanding the interplay between these membrane-active peptides and the lipid membranes is considered to be a significant step in elucidating the specific mechanism of action of AMPs against prokaryotic and eukaryotic cells to aid the development of new therapeutics...
January 29, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38295892/loopsage-an-energy-based-monte-carlo-approach-for-the-loop-extrusion-modeling-of-chromatin
#24
JOURNAL ARTICLE
Sevastianos Korsak, Dariusz Plewczynski
The connection between the patterns observed in 3C-type experiments and the modeling of polymers remains unresolved. This paper presents a simulation pipeline that generates thermodynamic ensembles of 3D structures for topologically associated domain (TAD) regions by loop extrusion model (LEM). The simulations consist of two main components: a stochastic simulation phase, employing a Monte Carlo approach to simulate the binding positions of cohesins, and a dynamical simulation phase, utilizing these cohesins' positions to create 3D structures...
January 29, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38295891/enhancing-antigenic-peptide-discovery-improved-mhc-i-binding-prediction-and-methodology
#25
JOURNAL ARTICLE
Stanisław Giziński, Grzegorz Preibisch, Piotr Kucharski, Michał Tyrolski, Michał Rembalski, Piotr Grzegorczyk, Anna Gambin
The Major Histocompatibility Complex (MHC) is a critical element of the vertebrate cellular immune system, responsible for presenting peptides derived from intracellular proteins. MHC-I presentation is pivotal in the immune response and holds considerable potential in the realms of vaccine development and cancer immunotherapy. This study delves into the limitations of current methods and benchmarks for MHC-I presentation. We introduce a novel benchmark designed to assess generalization properties and the reliability of models on unseen MHC molecules and peptides, with a focus on the Human Leukocyte Antigen (HLA)-a specific subset of MHC genes present in humans...
January 29, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38286333/mfd-gdrug-multimodal-feature-fusion-based-deep-learning-for-gpcr-drug-interaction-prediction
#26
JOURNAL ARTICLE
Xingyue Gu, Junkai Liu, Yue Yu, Pengfeng Xiao, Yijie Ding
The accurate identification of drug-protein interactions (DPIs) is crucial in drug development, especially concerning G protein-coupled receptors (GPCRs), which are vital targets in drug discovery. However, experimental validation of GPCR-drug pairings is costly, prompting the need for accurate predictive methods. To address this, we propose MFD-GDrug, a multimodal deep learning model. Leveraging the ESM pretrained model, we extract protein features and employ a CNN for protein feature representation. For drugs, we integrated multimodal features of drug molecular structures, including three-dimensional features derived from Mol2vec and the topological information of drug graph structures extracted through Graph Convolutional Neural Networks (GCN)...
January 28, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38286332/atomic-force-microscope-kymograph-analysis-a-case-study-of-two-membrane-proteins
#27
JOURNAL ARTICLE
Dylan R Weaver, Katherine G Schaefer, Gavin M King
Kymograph analysis is employed across the biological atomic force microscopy (AFM) community to boost temporal resolution. The method is well suited for revealing protein dynamics at the single molecule level in near-native conditions. Yet, kymograph analysis comes with limitations that depend on several factors including protein geometry and instrumental drift. This work focuses on conformational dynamics of difficult-to-study sparse distributions of membrane proteins. We compare and contrast AFM kymograph analysis for two proteins, one of which (SecDF) exhibits conformational dynamics primarily in the vertical direction (normal to the membrane surface) and the other (Pgp) exhibits a combination of lateral dynamics and vertical motion...
January 28, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38280472/mitds-uncovering-mirna-mrna-interactions-with-deep-learning-for-functional-target-prediction
#28
JOURNAL ARTICLE
Jialin Zhang, Haoran Zhu, Yin Liu, Xiangtao Li
MicroRNAs (miRNAs) are vital in regulating gene expression through binding to specific target sites on messenger RNAs (mRNAs), a process closely tied to cancer pathogenesis. Identifying miRNA functional targets is essential but challenging, due to incomplete genome annotation and an emphasis on known miRNA-mRNA interactions, restricting predictions of unknown ones. To address those challenges, we have developed a deep learning model based on miRNA functional target identification, named miTDS, to investigate miRNA-mRNA interactions...
January 26, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38272245/an-amphiphilic-dansyl-based-multianalyte-sensor-for-the-detection-of-hg-2-ppi-and-tnp-a-three-in-one-chemical-sensor
#29
JOURNAL ARTICLE
Srushti Gadiyaram, M Aakshika Sree, Nancy Sharma, D Amilan Jose
A fluorescent dansyl-based amphiphilic probe, 5-(dimethylamino)-N-hexadecylnaphthalene-1-sulfonamide (DLC), was synthesized and characterized to detect multiple analytes at different sensing environments. In acetonitrile, DLC detects nitro explosives such as trinitrophenol (TNP) and 2,4-dinitrophenol (2,4-DNP) by an emission "on-off" response method, and the detection limits (LOD) were estimated to be as low as 4.3 µM and 17.4 µM, respectively. Amphiphilic long chains of the probe were embedded into lipid bilayers to form nanoscale vesicles DLC...
January 23, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38266951/synthesis-of-functionalized-mesoporous-silica-nanoparticles-for-colorimetric-and-fluorescence-sensing-of-selective-metal-fe-3-ions-in-aqueous-solution
#30
JOURNAL ARTICLE
Madhappan Santhamoorthy, Anandhu Mohan, Kailasam Saravana Mani, Tamiloli Devendhiran, Govindasami Periyasami, Seong-Cheol Kim, Mei-Ching Lin, Keerthika Kumarasamy, Po-Jui Huang, Asif Ali
The fabrication of red fluorescent hybrid mesoporous silica-based nanosensor materials has promised the bioimaging and selective detection of toxic pollutants in aqueous solutions. In this study, we present a hybrid mesoporous silica nanosensor in which the propidium iodide (PI) was used to conveniently integrate into the mesopore walls using bis(trimethoxysilylpropyl silane) precursors. Various characterization techniques including X-ray diffraction (XRD), Fourier-transform infrared (FTIR), N2 adsorption-desorption, zeta potential, particle size analysis, thermogravimetric, and UV-visible analysis were used to analyze the prepared materials...
January 23, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38262485/predicting-drug-drug-interaction-with-graph-mutual-interaction-attention-mechanism
#31
JOURNAL ARTICLE
Xiaoying Yan, Chi Gu, Yuehua Feng, Jiaxin Han
Effective representation of molecules is a crucial step in AI-driven drug design and drug discovery, especially for drug-drug interaction (DDIs) prediction. Previous work usually models the drug information from the drug-related knowledge graph or the single drug molecules, but the interaction information between molecular substructures of drug pair is seldom considered, thus often ignoring the influence of bond information on atom node representation, leading to insufficient drug representation. Moreover, key molecular substructures have significant contribution to the DDIs prediction results...
January 21, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38246229/emulation-of-quantitative-systems-pharmacology-models-to-accelerate-virtual-population-inference-in-immuno-oncology
#32
JOURNAL ARTICLE
Tomasz Pawłowski, Grzegorz Bokota, Georgia Lazarou, Andrzej M Kierzek, Jacek Sroka
Quantitative Systems Pharmacology (QSP) models are increasingly being applied for target discovery and dose selection in immuno-oncology (IO). Typical application involves virtual trial, a simulation of a virtual population of hundreds of model instances with model inputs reflecting individual variability. While the structure of the model and initial parameterisation are based on literature describing the underlying biology, calibration of the virtual population by existing clinical data is frequently required to create tumour and patient population specific model instances...
January 19, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38242384/sensitivity-enhanced-nmr-15-n-r-1-and-r-1%C3%AF-relaxation-experiments-for-the-investigation-of-intrinsically-disordered-proteins-at-high-magnetic-fields
#33
JOURNAL ARTICLE
Tobias Stief, Katharina Vormann, Nils-Alexander Lakomek
NMR relaxation experiments provide residue-specific insights into the structural dynamics of proteins. Here, we present an optimized set of sensitivity-enhanced 15 N R1 and R1ρ relaxation experiments applicable to fully protonated proteins. The NMR pulse sequences are conceptually similar to the set of TROSY-based sequences and their HSQC counterpart (Lakomek et al., J. Biomol. NMR 2012). Instead of the TROSY read-out scheme, a sensitivity-enhanced HSQC read-out scheme is used, with improved and easier optimized water suppression...
January 17, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38237792/dbpboost-a-method-of-classification-of-dna-binding-proteins-based-on-improved-differential-evolution-algorithm-and-feature-extraction
#34
JOURNAL ARTICLE
Ailun Sun, Hongfei Li, Guanghui Dong, Yuming Zhao, Dandan Zhang
DNA-binding proteins are a class of proteins that can interact with DNA molecules through physical and chemical interactions. Their main functions include regulating gene expression, maintaining chromosome structure and stability, and more. DNA-binding proteins play a crucial role in cellular and molecular biology, as they are essential for maintaining normal cellular physiological functions and adapting to environmental changes. The prediction of DNA-binding proteins has been a hot topic in the field of bioinformatics...
January 17, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38228196/lc-ms-ms-platform-based-serum-untargeted-screening-reveals-the-diagnostic-biomarker-panel-and-molecular-mechanism-of-breast-cancer
#35
JOURNAL ARTICLE
Sisi Gong, Qingshui Wang, Jiewei Huang, Rongfu Huang, Shanshan Chen, Xiaojuan Cheng, Lei Liu, Xiaofang Dai, Yameng Zhong, Chunmei Fan, Zhijun Liao
BACKGROUND: Breast cancer (BC), the most common form of malignant cancer affecting women worldwide, was characterized by heterogeneous metabolic disorder and lack of effective biomarkers for diagnosis. The purpose of this study is to search for reliable metabolite biomarkers of BC as well as triple-negative breast cancer (TNBC) using serum metabolomics approach. METHODS: In this study, an untargeted metabolomics technique based on ultra-high performance liquid chromatography combined with mass spectrometry (UHPLC-MS) was utilized to investigate the differences in serum metabolic profile between the BC group (n = 53) and non-BC group (n = 57), as well as between TNBC patients (n = 23) and non-TNBC subjects (n = 30)...
January 14, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38228195/bodipy-based-quinoline-derivative-as-a-highly-hg-2-selective-fluorescent-chemosensor-and-its-potential-applications
#36
JOURNAL ARTICLE
Keerthika Kumarasamy, Tamiloli Devendhiran, Wei-Jyun Chien, Mei-Ching Lin, Selva Kumar Ramasamy, Ji-Jhang Yang
A highly efficient sensor has been successfully developed using quinoline-based BODIPY compounds (8-quinoline-4,4-difluoro-4-boro-3a, 4a-diazaindacene (C1) and 7-hydroxy-8-quinoline-4,4-difluoro-4-boro-3a, 4a-diazindacene (C2) to detect Hg2+ ions. The sensor C1 exhibits remarkable selectivity in detecting Hg2+ with a limit of detection 3.06 × 10-8 mol/L. The developed chemical sensors have shown stability, cost-effectiveness, ease of preparation, and remarkable selectivity towards Hg2+ ions compared to other commonly occurring metal ions...
January 14, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38215898/application-scenario-oriented-molecular-generation-platform-developed-for-drug-discovery
#37
JOURNAL ARTICLE
Lianjun Zheng, Fangjun Shi, Chunwang Peng, Min Xu, Fangda Fan, Yuanpeng Li, Lin Zhang, Jiewen Du, Zonghu Wang, Zhixiong Lin, Yina Sun, Chenglong Deng, Xinli Duan, Lin Wei, Chuanfang Zhao, Lei Fang, Peiyu Zhang, Songling Ma, Lipeng Lai, Mingjun Yang
Design of molecules for candidate compound selection is one of the central challenges in drug discovery due to the complexity of chemical space and requirement of multi-parameter optimization. Here we present an application scenario-oriented platform (ID4Idea) for molecular generation in different scenarios of drug discovery. This platform utilizes both library or rule based and generative based algorithms (VAE, RNN, GAN etc.), in combination with various AI learning types (pre-training, transfer learning, reinforcement learning, and active learning etc...
January 10, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38191006/fluorescent-based-ratiometric-sensors-as-emerging-tools-for-cn-detection-chemical-structures-sensing-mechanisms-and-applications
#38
JOURNAL ARTICLE
Ashwani Kumar, EunHye Jeong, Noh Youngwoo, Pil Seok Chae
Hazardous cyanide anions (CN- ) are increasingly threatening the environment and human health due to their widespread use in industry and many other fields. Over the past three decades, a large number of probes have been reported to sensitively and selectively detect this toxic anion, while a rather limited number of ratiometric fluorescent probes have been developed. The ratiometric probes have significant potential in bio-imaging and biomedical applications because of the ability to detect CN- in a quick, convenient and affordable way...
January 6, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38185227/interpreting-the-effect-of-mutations-to-protein-binding-sites-from-large-scale-genomic-screens
#39
JOURNAL ARTICLE
Sara Jamshidi Parvar, Benjamin A Hall, David Shorthouse
Predicting the functionality of missense mutations is extremely difficult. Large-scale genomic screens are commonly performed to identify mutational correlates or drivers of disease and treatment resistance, but interpretation of how these mutations impact protein function is limited. One such consequence of mutations to a protein is to impact its ability to bind and interact with partners or small molecules such as ATP, thereby modulating its function. Multiple methods exist for predicting the impact of a single mutation on protein-protein binding energy, but it is difficult in the context of a genomic screen to understand if these mutations with large impacts on binding are more common than statistically expected...
January 5, 2024: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/38185226/microbiome-metabolite-quantification-methods-enabling-insights-into-human-health-and-disease
#40
JOURNAL ARTICLE
Jarrod Roach, Rohit Mital, Jacob J Haffner, Nathan Colwell, Randy Coats, Horvey M Palacios, Zongyuan Liu, Joseane L P Godinho, Monica Ness, Thilini Peramuna, Laura-Isobel McCall
Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin...
January 5, 2024: Methods: a Companion to Methods in Enzymology
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