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Journals Current Opinion in Structural ...

Current Opinion in Structural Biology

https://read.qxmd.com/read/38537534/chromatin-compaction-by-polycomb-group-proteins-revisited
#1
REVIEW
Michael Uckelmann, Chen Davidovich
The chromatin compaction activity of Polycomb group proteins has traditionally been considered essential for transcriptional repression. However, there is very little information on how Polycomb group proteins compact chromatin at the molecular level and no causal link between the compactness of chromatin and transcriptional repression. Recently, a more complete picture of Polycomb-dependent chromatin architecture has started to emerge, owing to advanced methods for imaging and chromosome conformation capture...
March 26, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38537533/metamorphic-proteins-and-how-to-find-them
#2
REVIEW
Lauren L Porter, Irina Artsimovitch, César A Ramírez-Sarmiento
In the last two decades, our existing notion that most foldable proteins have a unique native state has been challenged by the discovery of metamorphic proteins, which reversibly interconvert between multiple, sometimes highly dissimilar, native states. As the number of known metamorphic proteins increases, several computational and experimental strategies have emerged for gaining insights about their refolding processes and identifying unknown metamorphic proteins amongst the known proteome. In this review, we describe the current advances in biophysically and functionally ascertaining the structural interconversions of metamorphic proteins and how coevolution can be harnessed to identify novel metamorphic proteins from sequence information...
March 26, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38531188/modern-approaches-to-improving-phase-contrast-electron-microscopy
#3
REVIEW
Jeremy J Axelrod, Jessie T Zhang, Petar N Petrov, Robert M Glaeser, Holger Müller
Although defocus can be used to generate partial phase contrast in transmission electron microscope images, cryo-electron microscopy (cryo-EM) can be further improved by the development of phase plates which increase contrast by applying a phase shift to the unscattered part of the electron beam. Many approaches have been investigated, including the ponderomotive interaction between light and electrons. We review the recent successes achieved with this method in high-resolution, single-particle cryo-EM. We also review the status of using pulsed or near-field enhanced laser light as alternatives, along with approaches that use scanning transmission electron microscopy (STEM) with a segmented detector rather than a phase plate...
March 25, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38484552/recent-advances-in-data-collection-for-cryo-em-methods
#4
REVIEW
Anchi Cheng, Yue Yu
Methods of transmission electron microscopy (TEM) are typically used to resolve structures of vitrified biological specimens using both single particle analysis (SPA) and tomographic methods and use both conventional as well as scanning transmission modes of data collection. Automation of data collection for each method has been developed to different levels of convenience for the users. Automation of methods using the conventional TEM mode has progressed the furthest. Beam-image shift strategies first used in data collection for SPA were shown to be equally valuable for cryo-electron tomography (cryo-ET)...
March 13, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38458088/dynamics-allostery-and-stabilities-of-whole-virus-particles-by-amide-hydrogen-deuterium-exchange-mass-spectrometry-hdxms
#5
REVIEW
Varun Venkatakrishnan, Sean M Braet, Ganesh S Anand
X-ray crystallography and cryo-electron microscopy have enabled the determination of structures of numerous viruses at high resolution and have greatly advanced the field of structural virology. These structures represent only a subset of snapshot end-state conformations, without describing all conformational transitions that virus particles undergo. Allostery plays a critical role in relaying the effects of varied perturbations both on the surface through environmental changes and protein (receptor/antibody) interactions into the genomic core of the virus...
March 7, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38447285/a-comprehensive-survey-on-protein-ligand-binding-site-prediction
#6
REVIEW
Ying Xia, Xiaoyong Pan, Hong-Bin Shen
Protein-ligand binding site prediction is critical for protein function annotation and drug discovery. Biological experiments are time-consuming and require significant equipment, materials, and labor resources. Developing accurate and efficient computational methods for protein-ligand interaction prediction is essential. Here, we summarize the key challenges associated with ligand binding site (LBS) prediction and introduce recently published methods from their input features, computational algorithms, and ligand types...
March 5, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38432063/navigating-the-complexities-of-multi-domain-protein-folding
#7
REVIEW
Nandakumar Rajasekaran, Christian M Kaiser
Proteome complexity has expanded tremendously over evolutionary time, enabling biological diversification. Much of this complexity is achieved by combining a limited set of structural units into long polypeptides. This widely used evolutionary strategy poses challenges for folding of the resulting multi-domain proteins. As a consequence, their folding differs from that of small single-domain proteins, which generally fold quickly and reversibly. Co-translational processes and chaperone interactions are important aspects of multi-domain protein folding...
March 2, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38428364/nmr-tools-to-detect-protein-allostery
#8
REVIEW
Olivia Gampp, Harindranath Kadavath, Roland Riek
Allostery is a fundamental mechanism of cellular homeostasis by intra-protein communication between distinct functional sites. It is an internal process of proteins to steer interactions not only with each other but also with other biomolecules such as ligands, lipids, and nucleic acids. In addition, allosteric regulation is particularly important in enzymatic activities. A major challenge in structural and molecular biology today is unraveling allosteric sites in proteins, to elucidate the detailed mechanism of allostery and the development of allosteric drugs...
February 29, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38417184/editorial-overview-folding-and-binding-2024
#9
EDITORIAL
H Jane Dyson, Peter E Wright
No abstract text is available yet for this article.
February 27, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38402744/deep-learning-in-modeling-protein-complex-structures-from-contact-prediction-to-end-to-end-approaches
#10
REVIEW
Peicong Lin, Hao Li, Sheng-You Huang
Protein-protein interactions play crucial roles in many biological processes. Traditionally, protein complex structures are normally built by protein-protein docking. With the rapid development of artificial intelligence and its great success in monomer protein structure prediction, deep learning has widely been applied to modeling protein-protein complex structures through inter-protein contact prediction and end-to-end approaches in the past few years. This article reviews the recent advances of deep-learning-based approaches in modeling protein-protein complex structures as well as their advantages and limitations...
February 24, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38401399/helical-reconstruction-again
#11
REVIEW
Edward H Egelman
Many protein and nucleoprotein complexes exist as helical polymers. As a result, much effort has been invested in developing methods for using electron microscopy to determine the structure of these assemblies. With the revolution in cryo-electron microscopy (cryo-EM), it has now become routine to reach a near-atomic level of resolution for these structures, and it is the exception when this is not possible. However, the greatest challenge is frequently determining the correct symmetry. This review focuses on why this can be so difficult and the current absence of a better approach than trial-and-error...
February 23, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38364679/post-covid-highlights-challenges-and-solutions-of-artificial-intelligence-techniques-for-swift-identification-of-covid-19
#12
REVIEW
Yingying Fang, Xiaodan Xing, Shiyi Wang, Simon Walsh, Guang Yang
Since the onset of the COVID-19 pandemic in 2019, there has been a concerted effort to develop cost-effective, non-invasive, and rapid AI-based tools. These tools were intended to alleviate the burden on healthcare systems, control the rapid spread of the virus, and enhance intervention outcomes, all in response to this unprecedented global crisis. As we transition into a post-COVID era, we retrospectively evaluate these proposed studies and offer a review of the techniques employed in AI diagnostic models, with a focus on the solutions proposed for different challenges...
February 15, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38354652/machine-learning-approaches-in-predicting-allosteric-sites
#13
REVIEW
Francho Nerín-Fonz, Zoe Cournia
Allosteric regulation is a fundamental biological mechanism that can control critical cellular processes via allosteric modulator binding to protein distal functional sites. The advantages of allosteric modulators over orthosteric ones have sparked the development of numerous computational approaches, such as the identification of allosteric binding sites, to facilitate allosteric drug discovery. Building on the success of machine learning (ML) models for solving complex problems in biology and chemistry, several ML models for predicting allosteric sites have been developed...
February 13, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38335558/artificial-intelligence-for-drug-discovery-and-development-in-alzheimer-s-disease
#14
REVIEW
Yunguang Qiu, Feixiong Cheng
The complex molecular mechanism and pathophysiology of Alzheimer's disease (AD) limits the development of effective therapeutics or prevention strategies. Artificial Intelligence (AI)-guided drug discovery combined with genetics/multi-omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) analysis contributes to the understanding of the pathophysiology and precision medicine of the disease, including AD and AD-related dementia. In this review, we summarize the AI-driven methodologies for AD-agnostic drug discovery and development, including de novo drug design, virtual screening, and prediction of drug-target interactions, all of which have shown potentials...
February 8, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38330793/revolutionizing-protein-protein-interaction-prediction-with-deep-learning
#15
REVIEW
Jing Zhang, Jesse Durham, Qian Cong
Protein-protein interactions (PPIs) are pivotal for driving diverse biological processes, and any disturbance in these interactions can lead to disease. Thus, the study of PPIs has been a central focus in biology. Recent developments in deep learning methods, coupled with the vast genomic sequence data, have significantly boosted the accuracy of predicting protein structures and modeling protein complexes, approaching levels comparable to experimental techniques. Herein, we review the latest advances in the computational methods for modeling 3D protein complexes and the prediction of protein interaction partners, emphasizing the application of deep learning methods deriving from coevolution analysis...
February 7, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38310737/application-of-ai-in-biological-age-prediction
#16
REVIEW
Dawei Meng, Shiqiang Zhang, Yuanfang Huang, Kehang Mao, Jing-Dong J Han
The development of anti-aging interventions requires quantitative measurement of biological age. Machine learning models, known as "aging clocks," are built by leveraging diverse aging biomarkers that vary across lifespan to predict biological age. In addition to traditional aging clocks harnessing epigenetic signatures derived from bulk samples, emerging technologies allow the biological age estimating at single-cell level to dissect cellular diversity in aging tissues. Moreover, imaging-based aging clocks are increasingly employed with the advantage of non-invasive measurement, making it suitable for large-scale human cohort studies...
February 3, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38271778/structural-highlights-of-macromolecular-complexes-and-assemblies
#17
REVIEW
Brinda Vallat, Helen M Berman
The structures of macromolecular assemblies have given us deep insights into cellular processes and have profoundly impacted biological research and drug discovery. We highlight the structures of macromolecular assemblies that have been modeled using integrative and computational methods and describe how open access to these structures from structural archives has empowered the research community. The arsenal of experimental and computational methods for structure determination ensures a future where whole organelles and cells can be modeled...
January 24, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38266470/editorial-overview-the-amazing-power-of-physics-to-provide-chemical-insight-into-catalysis-and-regulation-%C3%A2-something-better-%C3%A2
#18
EDITORIAL
Emily J Parker, Christopher J Schofield
No abstract text is available yet for this article.
January 23, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38237366/editorial-overview-cryogenic-electron-microscopy-cryoem
#19
EDITORIAL
Alexis Rohou, Peijun Zhang
No abstract text is available yet for this article.
January 17, 2024: Current Opinion in Structural Biology
https://read.qxmd.com/read/38217897/editorial-overview-biophysical-methods-multiple-structures-of-proteins-underpin-their-biological-functions
#20
EDITORIAL
Irina Gutsche, Gaetano T Montelione
No abstract text is available yet for this article.
January 12, 2024: Current Opinion in Structural Biology
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