Journals Methods : a Companion to Metho...

Methods : a Companion to Methods in Enzymology
Siqi Chen, Minghui Li, Ivan Semenov
The identification of drug-target interactions (DTI) is a valuable step in the drug discovery and repositioning process. However, traditional laboratory experiments are time-consuming and expensive. Computational methods have streamlined research to determine DTIs. The application of deep learning methods has significantly improved the prediction performance for DTIs. Modern deep learning methods can leverage multiple sources of information, including sequence data that contains biological structural information, and interaction data...
February 29, 2024: Methods: a Companion to Methods in Enzymology
Jiaqi Yao, Heedeok Hong
Elucidating the folding energy landscape of membrane proteins is essential to the understanding of the proteins' stabilizing forces, folding mechanisms, biogenesis, and quality control. This task has not been trivial because the reversible control of folding is inherently difficult for membrane proteins in a lipid bilayer environment. Recently, novel methods have been developed, each of which has a unique strength in investigating specific aspects of membrane protein folding. Among such methods, steric trapping is a versatile strategy allowing a reversible control of membrane protein folding with minimal perturbation of native protein-water and protein-lipid interactions...
February 28, 2024: Methods: a Companion to Methods in Enzymology
Yajie Zhang, Yongqi Tong, Xin Xia, Qingwen Wu, Yansen Su
Molecular optimization, which aims to improve molecular properties by modifying complex molecular structures, is a crucial and challenging task in drug discovery. In recent years, translation models provide a promising way to transform low-property molecules to high-property molecules, which enables molecular optimization to achieve remarkable progress. However, most existing models require matched molecular pairs, which are prone to be limited by the datasets. Although some models do not require matched molecular pairs, their performance is usually sacrificed due to the lack of useful supervising information...
February 21, 2024: Methods: a Companion to Methods in Enzymology
Sahiti Kuppa, Elliot Corless, Colleen Caldwell, Maria Spies, Edwin Antony
Nucleotide excision repair (NER) promotes genomic integrity by removing bulky DNA adducts introduced by external factors such as ultraviolet light. Defects in NER enzymes are associated with pathological conditions such as Xeroderma Pigmentosum, trichothiodystrophy, and Cockayne syndrome. A critical step in NER is the binding of the Xeroderma Pigmentosum group A protein (XPA) to the ss/ds DNA junction. To better capture the dynamics of XPA interactions with DNA during NER we have utilized the fluorescence enhancement through non-canonical amino acids (FEncAA) approach...
February 20, 2024: Methods: a Companion to Methods in Enzymology
Qingsheng Huang, Yin Peng, Yuefeng Peng, Huijuan Lin, Shiqi Deng, Shengzhong Feng, Yanjie Wei
Bivalent Smac mimetics have been shown to possess binding affinity and pro-apoptotic activity similar to or more potent than that of native Smac, a protein dimer able to neutralize the anti-apoptotic activity of an inhibitor of caspase enzymes, XIAP, which endows cancer cells with resistance to anticancer drugs. We design five new bivalent Smac mimetics, which are formed by various linkers tethering two diazabicyclic cores being the IAP binding motifs. We built in silico models of the five mimetics by the TwistDock workflow and evaluated their conformational tendency, which suggests that compound 3, whose linker is n-hexylene, possess the highest binding potency among the five...
February 17, 2024: Methods: a Companion to Methods in Enzymology
Yuyin Le, Haojie Zhu, Chenjing Ye, Jiexiang Lin, Nila Wang, Ting Yang
PURPOSE: The aim of this study is to create and validate a radiomics model based on CT scans, enabling the distinction between pulmonary mucosa-associated lymphoid tissue (MALT) lymphoma and other pulmonary lesion causes. METHODS: Patients diagnosed with primary pulmonary MALT lymphoma and lung infections at Fuzhou Pulmonary Hospital were randomly assigned to either a training group or a validation group. Meanwhile, individuals diagnosed with primary pulmonary MALT lymphoma and lung infections at Fujian Provincial Cancer Hospital were chosen as the external test group...
February 16, 2024: Methods: a Companion to Methods in Enzymology
Damian Tohl, Anh Tran Tam Pham, Jordan Li, Youhong Tang
Urinalysis is a useful test as an indicator of health or disease and as such, is a part of routine health screening. Urinalysis can be undertaken in many ways, one of which is reagent strips used in the general evaluation of health and to aid in the diagnosis and monitoring of kidney disease. To be effective, the test must be performed properly, and the results interpreted correctly. However, different light conditions and colour perception can vary between users leading to ambiguous readings. This has led to camera devices being used to capture and generate the estimated biomarker concentrations, but image colour can be affected by variations in illumination and inbuilt image processing...
February 15, 2024: Methods: a Companion to Methods in Enzymology
Zixuan E, Guanyu Qiao, Guohua Wang, Yang Li
MOTIVATION: Drug-target interaction prediction is an important area of research to predict whether there is an interaction between a drug molecule and its target protein. It plays a critical role in drug discovery and development by facilitating the identification of potential drug candidates and expediting the overall process. Given the time-consuming, expensive, and high-risk nature of traditional drug discovery methods, the prediction of drug-target interactions has become an indispensable tool...
February 14, 2024: Methods: a Companion to Methods in Enzymology
Li Li, Alain Wuethrich
No abstract text is available yet for this article.
February 12, 2024: Methods: a Companion to Methods in Enzymology
Charles P Collier, Dima Bolmatov, James G Elkins, John Katsaras
Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. In this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes...
February 6, 2024: Methods: a Companion to Methods in Enzymology
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
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
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
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
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
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
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
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
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
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
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