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Recent advances in data collection for Cryo-EM methods Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-03-13 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
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Dynamics, allostery, and stabilities of whole virus particles by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-03-07 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
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A comprehensive survey on protein-ligand binding site prediction Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-03-05 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)
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NMR tools to detect protein allostery Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-03-01 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
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Deep learning in modeling protein complex structures: From contact prediction to end-to-end approaches Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-02-24 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
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Helical reconstruction, again Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-02-23 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
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Post-COVID highlights: Challenges and solutions of artificial intelligence techniques for swift identification of COVID-19 Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-02-15 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
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Machine learning approaches in predicting allosteric sites Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-02-13 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
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Artificial intelligence for drug discovery and development in Alzheimer's disease Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-02-08 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
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Revolutionizing protein–protein interaction prediction with deep learning Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-02-07 Jing Zhang, Jesse Durham
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
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Application of AI in biological age prediction Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-02-03 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
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Structural highlights of macromolecular complexes and assemblies Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-24 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.
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Editorial overview: ‘The amazing power of physics to provide chemical insight into catalysis and regulation’ … something better … Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-23 Emily J. Parker, Christopher J. Schofield
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Editorial overview: Cryogenic electron microscopy (cryoEM) Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-17 Alexis Rohou, Peijun Zhang
Abstract not available
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Editorial overview: Biophysical methods: Multiple structures of proteins underpin their biological functions Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-12 Irina Gutsche, Gaetano T. Montelione
Abstract not available
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Protein dynamics underlying allosteric regulation Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-11 Miro A. Astore, Akshada S. Pradhan, Erik H. Thiede, Sonya M. Hanson
Allostery is the mechanism by which information and control are propagated in biomolecules. It regulates ligand binding, chemical reactions, and conformational changes. An increasing level of experimental resolution and control over allosteric mechanisms promises a deeper understanding of the molecular basis for life and powerful new therapeutics. In this review, we survey the literature for an up-to-date
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Generative AI for graph-based drug design: Recent advances and the way forward Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-09 Vikas Garg
Discovering new promising molecule candidates that could translate into effective drugs is a key scientific pursuit. However, factors such as the vastness and discreteness of the molecular search space pose a formidable technical challenge in this quest. AI-driven generative models can effectively learn from data, and offer hope to streamline drug design. In this article, we review state of the art
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AI for targeted polypharmacology: The next frontier in drug discovery Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-11 Anna Cichońska, Balaguru Ravikumar, Rayees Rahman
In drug discovery, targeted polypharmacology, i.e., targeting multiple molecular targets with a single drug, is redefining therapeutic design to address complex diseases. Pre-selected pharmacological profiles, as exemplified in kinase drugs, promise enhanced efficacy and reduced toxicity. Historically, many of such drugs were discovered serendipitously, limiting predictability and efficacy, but currently
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Overcoming challenges in structural biology with integrative approaches and nanobody-derived technologies Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-11 Miriam Condeminas, Maria J. Macias
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Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-11 Ji Young Lee, Emma Gebauer, Markus A. Seeliger, Ivet Bahar
The eukaryotic protein kinase domain has been a broadly explored target for drug discovery, despite limitations imposed by its high sequence conservation as a shared modular domain and the development of resistance to drugs. One way of addressing those limitations has been to target its potential allosteric sites, shortly called allo-targeting, in conjunction with, or separately from, its conserved
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Applications of cryo-EM in drug development for STING Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-05 Xiao-chen Bai, Xuewu Zhang
STING is a critical adaptor protein in the cGAS-mediated DNA-sensing innate immune pathway. Binding of the second messenger cGAMP generated by cGAS to STING induces the high-order oligomerization and activation of the STING dimer. STING is a promising target for diseases associated with the cGAS/STING pathway such as cancer and autoimmune diseases. Recent applications of cryo-EM to STING have led to
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Combining per-particle cryo-ET and cryo-EM single particle analysis to elucidate heterogeneous DNA-protein organization Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-04 Leon Palao, Kenji Murakami, Yi-Wei Chang
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RNA polymerase II elongation factors use conserved regulatory mechanisms Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-04 Ying Chen, Patrick Cramer
RNA polymerase II (Pol II) transcription is regulated by many elongation factors. Among these factors, TFIIF, PAF-RTF1, ELL and Elongin stimulate mRNA chain elongation by Pol II. Cryo-EM structures of Pol II complexes with these elongation factors now reveal some general principles on how elongation factors bind Pol II and how they stimulate transcription. All four elongation factors contact Pol II
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Allosteric communication and signal transduction in proteins Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-03 Nan Wu, Mauricio Barahona, Sophia N. Yaliraki
Allostery is one of the cornerstones of biological function, as it plays a fundamental role in regulating protein activity. The modelling of allostery has gradually moved from a conformation-based framework, linked to structural changes, to dynamics-based allostery, whereby the effects of ligand binding propagate via signal transduction from the allosteric site to other regions of the protein via inter-residue
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Allosteric drugs: New principles and design approaches Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2024-01-02 Wei-Ven Tee, Igor N. Berezovsky
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Mechanisms of allostery at the viral surface through the eyes of molecular simulation Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-23 Firdaus Samsudin, Lorena Zuzic, Jan K. Marzinek, Peter J. Bond
The outermost surface layer of any virus is formed by either a capsid shell or envelope. Such layers have traditionally been thought of as immovable structures, but it is becoming apparent that they cannot be viewed exclusively as static architectures protecting the viral genome. A limited number of proteins on the virion surface must perform a multitude of functions in order to orchestrate the viral
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Tandem-repeat proteins conformational mechanics are optimized to facilitate functional interactions and complexations Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-21 Carlos Ventura, Anupam Banerjee, Maria Zacharopoulou, Laura S. Itzhaki, Ivet Bahar
The architectures of tandem-repeat proteins are distinct from those of globular proteins. Individual modules, each comprising small structural motifs of 20–40 residues, are arrayed in a quasi one-dimensional fashion to form striking, elongated, horseshoe-like, and superhelical architectures, stabilized solely by short–range interaction. The spring-like shapes of repeat arrays point to elastic modes
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Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-19 Catherine Ghosh, Suhani Nagpal, Victor Muñoz
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Modelling the assembly and flexibility of antibody structures Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-19 Dongjun Guo, Maria Laura De Sciscio, Joseph Chi-Fung Ng, Franca Fraternali
Antibodies are large protein assemblies capable of both specifically recognising antigens and engaging with other proteins and receptors to coordinate immune action. Traditionally, structural studies have been dedicated to antibody variable regions, but efforts to determine and model full-length antibody structures are emerging. Here we review the current knowledge on modelling the structures of antibody
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Multivalency emerges as a common feature of intrinsically disordered protein interactions Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-14 Emily L. Sipko, Garrett F. Chappell, Rebecca B. Berlow
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A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-17 Danielle Maeser, Weijie Zhang, Yingbo Huang, R. Stephanie Huang
Cancer treatment failure is often attributed to tumor heterogeneity, where diverse malignant cell clones exist within a patient. Despite a growing understanding of heterogeneous tumor cells depicted by single-cell RNA sequencing (scRNA-seq), there is still a gap in the translation of such knowledge into treatment strategies tackling the pervasive issue of therapy resistance. In this review, we survey
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Bonds and bytes: The odyssey of structural biology Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-14 S.E. Hoff, M. Zinke, N. Izadi-Pruneyre, M. Bonomi
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of structural biology, no single method comprehensively reveals the behavior of biological systems across various spatiotemporal scales. Instead, we have a versatile toolkit of techniques, each contributing a
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Circadian regulation of physiology by disordered protein-protein interactions Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-13 Lucas B. Sutton, Jennifer M. Hurley
Cellular circadian clocks, the molecular timers that coordinate physiology to the day/night cycle across the domains of life, are widely regulated by disordereddisordered protein interactions. Here, we review the disordered-disordered protein interactions in the circadian clock of Neurospora crassa (N. crassa), a filamentous fungus which is a model organism for clocks in higher eukaryotes. We focus
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Artificial intelligence approaches for molecular representation in drug response prediction Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-13 Cui-Xiang Lin, Yuanfang Guan, Hong-Dong Li
Drug response prediction is essential for drug development and disease treatment. One key question in predicting drug response is the representation of molecules, which has been greatly advanced by artificial intelligence (AI) techniques in recent years. In this review, we first describe different types of representation methods, pinpointing their key principles and discussing their limitations. Thereafter
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Advances and applications of microcrystal electron diffraction (MicroED) Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-11 Alison Haymaker, Brent L. Nannenga
Microcrystal electron diffraction, commonly referred to as MicroED, has become a powerful tool for high-resolution structure determination. The method makes use of cryogenic transmission electron microscopes to collect electron diffraction data from crystals that are several orders of magnitude smaller than those used by other conventional diffraction techniques. MicroED has been used on a variety
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How the ribosome shapes cotranslational protein folding Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-09 Ekaterina Samatova, Anton A. Komar, Marina V. Rodnina
During protein synthesis, the growing nascent peptide chain moves inside the polypeptide exit tunnel of the ribosome from the peptidyl transferase center towards the exit port where it emerges into the cytoplasm. The ribosome defines the unique energy landscape of the pioneering round of protein folding. The spatial confinement and the interactions of the nascent peptide with the tunnel walls facilitate
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Regulation of tau by peptidyl-prolyl isomerases Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-07 Shannon Zhuang, Pijush Chakraborty, Markus Zweckstetter
Tau is an intrinsically disordered protein found abundantly in axons, where it binds to microtubules. Since tau is a central player in the dynamic microtubule network, it is highly regulated by post-translational modifications. Abnormal hyperphosphorylation and aggregation of tau characterize a group of diseases called tauopathies. A specific protein family of cis/trans peptidyl-prolyl isomerases (PPIases)
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Understanding the heterogeneity intrinsic to protein folding Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-02 Sandhya Bhatia, Jayant B. Udgaonkar
Relating the native fold of a protein to its amino acid sequence remains a fundamental problem in biology. While computer algorithms have demonstrated recently their prowess in predicting what structure a particular amino acid sequence will fold to, an understanding of how and why a specific protein fold is achieved remains elusive. A major challenge is to define the role of conformational heterogeneity
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Commonly asked questions about transcriptional activation domains Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-05 Aditya Udupa, Sanjana R. Kotha, Max V. Staller
Eukaryotic transcription factors activate gene expression with their DNA-binding domains and activation domains. DNA-binding domains bind the genome by recognizing structurally related DNA sequences; they are structured, conserved, and predictable from protein sequences. Activation domains recruit chromatin modifiers, coactivator complexes, or basal transcriptional machinery via structurally diverse
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Integrative approaches for characterizing protein dynamics: NMR, CryoEM, and computer simulations Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-12-03 Roman Zadorozhnyi, Angela M. Gronenborn, Tatyana Polenova
Proteins are inherently dynamic and their internal motions are essential for biological function. Protein motions cover a broad range of timescales: 10−14–10 s, spanning from sub-picosecond vibrational motions of atoms via microsecond loop conformational rearrangements to millisecond large amplitude domain reorientations. Observing protein dynamics over all timescales and connecting motions and structure
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Dynamics and interactions of intrinsically disordered proteins Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-30 Munehito Arai, Shunji Suetaka, Koji Ooka
Intrinsically disordered proteins (IDPs) are widespread in eukaryotes and participate in a variety of important cellular processes. Numerous studies using state-of-the-art experimental and theoretical methods have advanced our understanding of IDPs and revealed that disordered regions engage in a large repertoire of intra- and intermolecular interactions through their conformational dynamics, thereby
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Cryo-electron ptychography: Applications and potential in biological characterisation Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-22 Chen Huang, Judy S. Kim, Angus I. Kirkland
There is a clear need for developments in characterisation techniques that provide detailed information about structure–function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field of view remains a challenge, particularly for radiation-sensitive specimens where the signal-to-noise ratio required to maintain structural integrity is limited
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Protein disaggregation machineries in the human cytosol Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-23 Anne Wentink, Rina Rosenzweig
Proteins carry out the vast majority of functions in cells, but can only do so when properly folded. Following stress or mutation, proteins can lose their proper fold, resulting in misfolding, inactivity, and aggregation–posing a threat to cellular health. In order to counteract protein aggregation, cells have evolved a remarkable subset of molecular chaperones, called protein disaggregases, which
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Artificial intelligence-driven antimicrobial peptide discovery Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-21 Paulina Szymczak, Ewa Szczurek
Antimicrobial peptides (AMPs) emerge as promising agents against antimicrobial resistance, providing an alternative to conventional antibiotics. Artificial intelligence (AI) revolutionized AMP discovery through both discrimination and generation approaches. The discriminators aid in the identification of promising candidates by predicting key peptide properties such as activity and toxicity, while
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Automated pipelines for rapid evaluation during cryoEM data acquisition Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-21 Joshua H. Mendez, Eugene Y.D. Chua, Mohammadreza Paraan, Clinton S. Potter, Bridget Carragher
Cryo-electron microscopy (cryoEM) has become a popular method for determining high-resolution structures of biomolecules. However, data processing can be time-consuming, particularly for new researchers entering the field. To improve data quality and increase data collection efficiency, several software packages have been developed for on-the-fly data processing with various degrees of automation.
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Editorial overview: Restructuring drug design and development Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-08 Andrew R. Leach, Alison E. Ondrus
Abstract not available
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Mechanical forces and the 3D genome Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-09 G.V. Shivashankar
Traditionally, the field of genomics has been studied from a biochemical perspective. Besides chemical influences, cells are subject to a variety of mechanical signals from their surrounding tissue microenvironment. These mechanical signals can not only cause changes to a cell's physical structure but can also lead to alterations in their genomes and gene expression programs. Understanding the mechanical
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3D genome organization and beyond! Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-09 Geneviève Almouzni, Juan M. Vaquerizas
Abstract not available
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Topology regulatory elements: From shaping genome architecture to gene regulation Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-04 Liang-Fu Chen, Hannah Katherine Long
The importance of 3D genome topology in the control of gene expression is becoming increasingly apparent, while regulatory mechanisms remain incompletely understood. Several recent studies have identified architectural elements that influence developmental gene expression by shaping locus topology. We refer to these elements as topological regulatory elements (TopoREs) to reflect their dual roles in
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B12-dependent radical SAM enzymes: Ever expanding structural and mechanistic diversity Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-04 Alhosna Benjdia, Olivier Berteau
In the last decade, B12-dependent radical SAM enzymes have emerged as central biocatalysts in the biosynthesis of a myriad of natural products. Notably, these enzymes have been shown to catalyze carbon–carbon bond formation on unactivated carbon atoms leading to unusual methylations. Recently, structural studies have revealed unprecedented insights into the complex chemistry catalyzed by these enzymes
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Structure–function relationships in protein homorepeats Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-02 Carlos A. Elena-Real, Pablo Mier, Nathalie Sibille, Miguel A. Andrade-Navarro, Pau Bernadó
Homorepeats (or polyX), protein segments containing repetitions of the same amino acid, are abundant in proteomes from all kingdoms of life and are involved in crucial biological functions as well as several neurodegenerative and developmental diseases. Mainly inserted in disordered segments of proteins, the structure/function relationships of homorepeats remain largely unexplored. In this review,
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Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-11-01 Mousam Roy, Amnon Horovitz
Characterization of transition and intermediate states of reactions provides insights into their mechanisms and is often achieved through analysis of linear free energy relationships. Such an approach has been used extensively in protein folding studies but less so for analyzing allosteric transitions. Here, we point out analogies in ways to characterize pathways and intermediates in folding and allosteric
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All over or overall – Do we understand allostery? Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-10-27 Hagen Hofmann
Allostery is probably the most important concept in the regulation of cellular processes. Models to explain allostery are plenty. Each sheds light on different aspects but their entirety conveys an ambiguous feeling of comprehension and disappointment. Here, I discuss the most popular allostery models, their roots, similarities, and limitations. All of them are thermodynamic models. Naturally this
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Cell phenotypes can be predicted from propensities of protein conformations Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-10-21 Ruth Nussinov, Yonglan Liu, Wengang Zhang, Hyunbum Jang
Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities of the conformations can be predictors of cell function. The conformational states that the molecules preferentially visit can be viewed as phenotypic determinants, and their mutations work by altering the relative propensities, thus the cell phenotype. Our examples include (i) inactive state variants harboring
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The new epoch of structural insights into radical SAM enzymology Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-10-18 Jake Lachowicz, James Lee, Alia Sagatova, Kristen Jew, Tyler L. Grove
The Radical SAM (RS) superfamily of enzymes catalyzes a wide array of enzymatic reactions. The majority of these enzymes employ an electron from a reduced [4Fe–4S]+1 cluster to facilitate the reductive cleavage of S-adenosyl-l-methionine, thereby producing a highly reactive 5′-deoxyadenosyl radical (5′-dA⋅) and l-methionine. Typically, RS enzymes use this 5′-dA⋅ to extract a hydrogen atom from the
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Recent developments in catalysis and inhibition of the Jumonji histone demethylases Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-10-11 Letitia Sarah, Danica Galonić Fujimori
Histone methylation, one of the most common histone modifications, has fundamental roles in regulating chromatin-based processes. Jumonji histone lysine demethylases (JMJC KDMs) influence regulation of gene transcription through both their demethylation and chromatin scaffolding functions. It has recently been demonstrated that dysregulation of JMJC KDMs contributes to pathogenesis and progression
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Catalysis and structure of nitrogenases Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-10-04 Oliver Einsle
In providing bioavailable nitrogen as building blocks for all classes of biomacromolecules, biological nitrogen fixation is an essential process for all organismic life. Only a single enzyme, nitrogenase, performs this task at ambient conditions and with ATP as an energy source. The assembly of the complex iron-sulfur enzyme nitrogenase and its catalytic mechanism remains a matter of intense study
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Editorial Overview: Protein-nucleic acid Interactions Curr. Opin. Struc. Biol. (IF 6.8) Pub Date : 2023-10-01 James Berger, Karl-Peter Hopfner
Abstract not available