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EVPsort: An Atlas of Small ncRNA Profiling and Sorting in Extracellular Vesicles and Particles J. Mol. Biol. (IF 5.6) Pub Date : 2024-04-10 Hua-chang Chen, Jing Wang, Robert J. Coffey, James G. Patton, Alissa M. Weaver, Yu Shyr, Qi Liu
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mRNA Decapping Activator Pat1 Is Required for Efficient Yeast Adaptive Transcriptional Responses via the Cell Wall Integrity MAPK Pathway J. Mol. Biol. (IF 5.6) Pub Date : 2024-04-10 Verónica Pulido, Jose M. Rodríguez-Peña, Graciela Alonso, Ana Belén Sanz, Javier Arroyo, Raúl García
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Transcriptomics Studies Reveal Functions of Transglutaminase 2 in Breast Cancer Cells Using Membrane Permeable and Impermeable Inhibitors J. Mol. Biol. (IF 5.6) Pub Date : 2024-04-10 Pietro Ancona, Alessandro Trentini, Anna Terrazzan, Silvia Grassilli, Pauline Navals, Eric W.J. Gates, Valentina Rosta, Carlo Cervellati, Carlo M. Bergamini, Angela Pignatelli, Jeffrey W. Keillor, Cristian Taccioli, Nicoletta Bianchi
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Enricherator: A Bayesian Method for Inferring Regularized Genome-wide Enrichments from Sequencing Count Data J. Mol. Biol. (IF 5.6) Pub Date : 2024-04-05 Jeremy W. Schroeder, P. Lydia Freddolino
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Cryo-EM Structure of Porphyromonas gingivalis RNA Polymerase J. Mol. Biol. (IF 5.6) Pub Date : 2024-04-05 Fan Bu, Xiaoxuan Wang, Mengke Li, Li Ma, Chuan Wang, Yangbo Hu, Zhengguo Cao, Bin Liu
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HIV-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active for Concerted DNA Integration In vitro J. Mol. Biol. (IF 5.6) Pub Date : 2024-04-04 Min Li, Renbin Yang, Xuemin Chen, Huaibin Wang, Rodolfo Ghirlando, Emilios.K. Dimitriadis, Robert Craigie
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LogoMotif: A Comprehensive Database of Transcription Factor Binding Site Profiles in Actinobacteria J. Mol. Biol. (IF 5.6) Pub Date : 2024-04-03 Hannah E. Augustijn, Dimitris Karapliafis, Kristy M.M. Joosten, Sébastien Rigali, Gilles P. van Wezel, Marnix H. Medema
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An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism J. Mol. Biol. (IF 5.6) Pub Date : 2024-04-03 Andrea L. Rocha, Victor Pai, Guy Perkins, Tina Chang, Jiao Ma, Qian Chu, Joan M. Vaughan, Jolene K. Diedrich, Mark H. Ellisman, Alan Saghatelian
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Deciphering the Substrate Specificity Reveals that CRISPR-Cas12a Is a Bifunctional Enzyme with Both Endo- and Exonuclease Activities J. Mol. Biol. (IF 5.6) Pub Date : 2024-04-03 Supreet Bhattacharya, Ankit Agarwal, Kalappa Muniyappa
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RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-30 Holly M. McCann, Caeden D. Meade, Biswajit Banerjee, Petar I. Penev, Loren Dean Williams, Anton S. Petrov
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CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-27 Lingyang Kong, Sang-Jun Park, Wonpil Im
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RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-27 Marcell Szikszai, Marcin Magnus, Siddhant Sanghi, Sachin Kadyan, Nazim Bouatta, Elena Rivas
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CATH 2024: CATH-AlphaFlow Doubles the Number of Structures in CATH and Reveals Nearly 200 New Folds J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-27 Vaishali P. Waman, Nicola Bordin, Rachel Alcraft, Robert Vickerstaff, Clemens Rauer, Qian Chan, Ian Sillitoe, Hazuki Yamamori, Christine Orengo
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The Mechanism of Folding of Human Frataxin in Comparison to the Yeast Homologue – Broad Energy Barriers and the General Properties of the Transition State J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-27 Paola Pietrangeli, Lucia Marcocci, Valeria Pennacchietti, Awa Diop, Mariana Di Felice, Livia Pagano, Francesca Malagrinò, Angelo Toto, Maurizio Brunori, Stefano Gianni
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Elucidation of the Mechanisms of Inter-domain Coupling in the Monomeric State of Enzyme I by High-pressure NMR J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-27 Sergey L. Sedinkin, Julien Roche, Vincenzo Venditti
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NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-24 Abhinav Mittal, Douglas H. Turner, David H. Mathews
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DockThor-VS: A Free Platform for Receptor-Ligand Virtual Screening J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-20 Isabella Alvim Guedes, Matheus Müller Pereira da Silva, Marcelo Galheigo, Eduardo Krempser, Camila Silva de Magalhães, Helio José Correa Barbosa, Laurent Emmanuel Dardenne
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Structural and Functional Characterization of a Gene Cluster Responsible for Deglycosylation of C-glucosyl Flavonoids and Xanthonoids by Deinococcus aerius J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-18 Valentina Furlanetto, Dayanand C. Kalyani, Anja Kostelac, Jolanta Puc, Dietmar Haltrich, B. Martin Hällberg, Christina Divne
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IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-18 Brinda Vallat, Benjamin M. Webb, John D. Westbrook, Thomas D. Goddard, Christian A. Hanke, Andrea Graziadei, Ezra Peisach, Arthur Zalevsky, Jared Sagendorf, Hongsuda Tangmunarunkit, Serban Voinea, Monica Sekharan, Jian Yu, Alexander A.M.J.J. Bonvin, Frank DiMaio, Gerhard Hummer, Jens Meiler, Emad Tajkhorshid, Thomas E. Ferrin, Catherine L. Lawson, Alexander Leitner, Juri Rappsilber, Claus A.M. Seidel
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AHoJ-DB: A PDB-wide Assignment of apo & holo Relationships Based on Individual Protein–Ligand Interactions J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-18 Christos P. Feidakis, Radoslav Krivak, David Hoksza, Marian Novotny
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C-terminal Domain of T4 gene 32 Protein Enables Rapid Filament Reorganization and Dissociation J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-18 Ben A. Cashen, Michael Morse, Ioulia Rouzina, Richard L. Karpel, Mark C. Williams
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TENET: Triple-enhancement based graph neural network for cell-cell interaction network reconstruction from spatial transcriptomics J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-18 Yujian Lee, Yongqi Xu, Peng Gao, Jiaxing Chen
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Folding of Class IIa HDAC Derived Peptides into α-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-16 Monica Chinellato, Stefano Perin, Alberto Carli, Luana Lastella, Barbara Biondi, Giuseppe Borsato, Eros Di Giorgio, Claudio Brancolini, Laura Cendron, Alessandro Angelini
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CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-16 Keeley W. Collins, Matthew M. Copeland, Guillaume Brysbaert, Shoshana J. Wodak, Alexandre M.J.J. Bonvin, Petras J. Kundrotas, Ilya A. Vakser, Marc F. Lensink
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PrimPol Variant V102A with Altered Primase and Polymerase Activities J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-15 Elizaveta O. Boldinova, Andrey G. Baranovskiy, Yulia V. Filina, Regina R. Miftakhova, Yana F. Shamsutdinova, Tahir H. Tahirov, Alena V. Makarova
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Membrane atg8ylation in Canonical and Noncanonical Autophagy J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-12 Vojo Deretic, Thabata Duque, Einar Trosdal, Masroor Paddar, Ruheena Javed, Prithvi Akepati
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ModFOLD9: A Web Server for Independent Estimates of 3D Protein Model Quality J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-11 Liam J. McGuffin, Shuaa M.A. Alharbi
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Leaf Senescence Database v5.0: A Comprehensive Repository for Facilitating Plant Senescence Research J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-09 Yaning Zhao, Yang Zhang, Shichun Li, Shuya Tan, Jie Cao, Hou-Ling Wang, Jingchu Luo, Hongwei Guo, Zhang Zhang, Zhonghai Li
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A Commentary on Multi-omics Data Integration in Systems Vaccinology J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-07 Casey P Shannon, Amy HY Lee, Scott J Tebbutt, Amrit Singh
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Anthrax Toxin: Model System for Studying Protein Translocation J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-07 Bryan A. Krantz
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BeetleAtlas: An Ontogenetic and Tissue-specific Transcriptomic Atlas of the Red Flour Beetle Tribolium castaneum J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-06 David P. Leader, Muhammad T. Naseem, Kenneth V. Halberg
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TPPU_DSF: A Web Application to Calculate Thermodynamic Parameters Using DSF Data J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-06 Pau Martin-Malpartida, Carles Torner, Aurora Martinez, Maria J. Macias
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MVAR: A Mouse Variation Registry J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-06 Bahá El Kassaby, Francisco Castellanos, Matthew Gerring, Govindarajan Kunde-Ramamoorthy, Carol J. Bult
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Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi J. Mol. Biol. (IF 5.6) Pub Date : 2024-03-05 Tianshuo Liu, Anna Marie Pyle
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Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-28 Junjie Xu, Victoria Esser, Katarzyna Gołębiowska-Mendroch, Agnieszka A. Bolembach, Josep Rizo
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The Protein Scaffolding Functions of Polyphosphate J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-27 Jian Guan, Ursula Jakob
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Skp2-Cyclin A Interaction Is Necessary for Mitotic Entry and Maintenance of Diploidy J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-27 Biju Vasavan, Nilanjana Das, Paria Kahnamouei, Chantelle Trombley, Andrew Swan
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The α-crystallin Chaperones Undergo a Quasi-ordered Co-aggregation Process in Response to Saturating Client Interaction J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-23 Adam P. Miller, Susan E. O'Neill, Kirsten J. Lampi, Steve L. Reichow
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Deciphering Cholesterol's Role in PD-L2 Stability: A Distinct Regulatory Mechanism From PD-L1 J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-22 Yu Zhang, Taoran Xiao, Maorong Wen, Lijuan Shen, Lingyu Du, Shukun Wei, Bin Wu, Yang Yu, Shuqing Wang, Bo OuYang
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Interpreting Combinatorial Epigenetic Modifications for Biological Meaning J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-22 Shannon M Lauberth, Tatiana G Kutateladze, Joshua C Black
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Troponin Structural Dynamics in the Native Cardiac Thin Filament Revealed by Cryo Electron Microscopy J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-20 Cristina M. Risi, Betty Belknap, Jennifer Atherton, Isabella Leite Coscarella, Howard D. White, P. Bryant Chase, Jose R. Pinto, Vitold E. Galkin
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RNA Binding Proteins that Mediate LPS-induced Alternative Splicing of the MyD88 Innate Immune Regulator J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-17 Frank Fang Yao Lee, Chelsea Harris, Scott Alper
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Corrigendum to “Novel LRR-ROC Motif That Links the N- and C-terminal Domains in LRRK2 Undergoes an Order–Disorder Transition Upon Activation” [J. Mol. Biol. 435(12) (2023) 1–17] J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-17 Jui-Hung Weng, Chiara R. Trilling, Pallavi Kaila Sharma, Eliza Störmer, Jian Wu, Friedrich W. Herberg, Susan S. Taylor
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E-pRSA: Embeddings improve the prediction of residue Relative Solvent Accessibility in protein sequence J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-15 Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
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Mechanisms of Translation-coupled Quality Control J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-15 Toshifumi Inada, Roland Beckmann
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Loss of Preproinsulin Interaction with Signal Recognition Particle Activates Protein Quality Control, Decreasing mRNA Stability J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-14 Sarah C. Miller, Elena B. Tikhonova, Sarah M. Hernandez, Jannette M. Dufour, Andrey L. Karamyshev
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Short Peptide Amyloids Are a Potential Sequence Pool for the Emergence of Proteins J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-14 Witek Kwiatkowski, Jason Greenwald, Laura Murzakhmetov, Robert C. Robinson, Roland Riek
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Rapid Long-distance Migration of RPA on Single Stranded DNA Occurs Through Intersegmental Transfer Utilizing Multivalent Interactions J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-14 Sushil Pangeni, Gargi Biswas, Vikas Kaushik, Sahiti Kuppa, Olivia Yang, Chang-Ting Lin, Garima Mishra, Yaakov Levy, Edwin Antony, Taekjip Ha
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Molecular insights into aggrephagy: Their cellular functions in the context of neurodegenerative diseases J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-14 Valentín Cóppola Segovia, Fulvio Reggiori
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Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-13 Weihua Ye, Phani Rama Krishna Behra, Karl Dyrhage, Christian Seeger, Joe D. Joiner, Elin Karlsson, Eva Andersson, Celestine N. Chi, Siv G.E. Andersson, Per Jemth
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Synonymous Mutations Can Alter Protein Dimerization Through Localized Interface Misfolding Involving Self-entanglements J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-09 Pham Dang Lan, Daniel Allen Nissley, Ian Sitarik, Quyen V. Vu, Yang Jiang, Philip To, Yingzi Xia, Stephen D. Fried, Mai Suan Li, Edward P. O'Brien
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Photosensory Receptors – Mechanisms and Effects J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-09 Volha U. Chukhutsina, John T.M. Kennis
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Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-08 Charles Christoffer, Kannan Harini, Gupta Archit, Daisuke Kihara
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Cryo-EM Structures of CRAF2/14-3-32 and CRAF2/14-3-32/MEK12 Complexes J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-07 Dirk Dedden, Julius Nitsche, Elisabeth V. Schneider, Maren Thomsen, Daniel Schwarz, Birgitta Leuthner, Ulrich Grädler
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Role of J-domain Proteins in Yeast Physiology and Protein Quality Control J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-07 Carmen Ruger-Herreros, Lucia Svoboda, Axel Mogk, Bernd Bukau
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Chi hotspot Control of RecBCD Helicase-nuclease: Enzymatic Tests Support the Intramolecular Signal-transduction Model J. Mol. Biol. (IF 5.6) Pub Date : 2024-02-07 Susan K. Amundsen, Gerald R. Smith
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