Journal of Molecular Biology

Article	Citations
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	328
Editorial Board	303
Single-molecule Tracking and Kinetic Analysis in Living Cells and Multicellular Organisms	218
Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes	152
Outside Front Cover	139
Outside Front Cover	120
Outside Front Cover	119
Outside Front Cover	111
Outside Front Cover	111
Structural and Functional Characterization of Pseudomonas aeruginosa Virulence Factor AaaA, an Autotransporter with Arginine-Specific Aminopeptidase Activity	95
Extracellular uncoating of bacteriophage MS2	95
Kinetic Investigation of Resistance to Islatravir Conferred by Mutations in HIV-1 Reverse Transcriptase	89
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	85
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	85
Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections	84
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	84
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	83
ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	77
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	73
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	72
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	71
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	67
Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae	66
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	61
Intein-based Design Expands Diversity of Selenocysteine Reporters	61

Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	61
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	60
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	60
HIV-Induced CPSF6 Condensates	58
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	58
Pyroptosis, and its Role in Central Nervous System Disease	58
Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent	58
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	57
Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment	56
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	56
Biomolecular Condensates as Novel Antiviral Targets	55
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	54
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	52
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	52
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	51
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	48
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	47
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	47
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	45
Mechanisms of Translation-coupled Quality Control	44
Mechanisms of Gasdermin Recognition by Proteases	44
Transcriptional and Epigenetic Regulation of Gasdermins	44
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	44
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	43
Editorial Board	42
Chaperone Recycling in Late-Stage Flagellar Assembly	42
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	42
Editorial Board	41
Outside Front Cover	41
Outside Front Cover	40
CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature	40
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	40
Outside Front Cover	40
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	40
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	39
Near-Infrared Optogenetic Module for Conditional Protein Splicing	38
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	37
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	37
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	37
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation	36
Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly	36
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	36
EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	36
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	35
Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry	35
The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	35
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures	35
Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region	35
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	35
Evolution of Transcription Factor-containing Superfamilies in Eukaryotes	34

GMMA Can Stabilize Proteins Across Different Functional Constraints	34
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	34
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	33
Biosynthesis and Genetic Incorporation of 3,4-Dihydroxy-L-Phenylalanine into Proteins in Escherichia coli	33
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	33
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	32
Cryo-EM Observation of AA Amyloid Fibrils in Mouse Model of Systemic AApoAII Amyloidosis	32
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	32
Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	32
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	32
AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	31
RNAsolo 2.0: multimodal database to study RNAs, their structural families and intermolecular interfaces	31
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	30
Electrostatics Drive the Molecular Chaperone BiP to Preferentially Bind Oligomerized States of a Client Protein	30
Editorial Board	30
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	30
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	30
Editorial Board	30
GRAMMCell: Docking-based Cell Modeling Resource	30
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	30
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	30
Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation	30
AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	30
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	29
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	29
TRIM52 Ubiquitin Ligase Acts as a Key Recognition Component of the Mammalian fMet/N-degron Pathway	29
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	29
Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition	29
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	28
Protein Intrinsic Disorder and Adaptation to Extreme Environments: Resilience of Chaos	28
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	28
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	28
Anthrax Toxin: Model System for Studying Protein Translocation	28
The Evolution of Sequence Specificity in a DNA Binding Protein Family	28
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die	28
D154Q Mutation does not Alter KRAS Dimerization	27
memerna: Sparse RNA folding including coaxial stacking	27
Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation	27
Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling	27
The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy	27
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	27
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	27
The Role of LRRK2 in Intracellular Organelle Dynamics	27
Deciphering Long-Range Effects of Mutations: An Integrated Approach Using Elastic Network Models and Protein Structure Networks	27
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	27
Saccharomyces cerevisiae Xrs2 Binds DNA Through Its FHA Domain	27
In vitro Evolution of Uracil Glycosylase Towards DnaKJ and GroEL Binding Evolves Different Misfolded States	27
Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering	27
Structure of the Borrelia Bacteriophage φBB1 Procapsid	26
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	26
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	26
Co-Translational Membrane Targeting and Holo-Translocon Docking of Ribosomes Translating the SRP Receptor	26
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	26
ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis	25
Editorial Board	25
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	25
Gasdermin Pore Forming Activities that Promote Inflammation from Living and Dead Cells	25
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	25
PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences	25
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	25
The Positively Charged Cluster in the N-terminal Disordered Region may Affect Prion Protein Misfolding: Cryo-EM Structure of Hamster PrP(23–144) Fibrils	25
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	25
psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	24
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	24
Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action	24
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	24
Corrigendum to “Conformational Transformation and Selection of Synthetic Prion Strains” [J. Mol. Biol. 413(3) (2011) 527–542]	24
Gene Expression Imaging in Hematopoiesis	24
NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species	24
Editorial Board	23
Editorial Board	23
Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic	23
Role of Antitoxin RNA Pseudoknot in Regulating Toxin Activity and Toxin-antitoxin RNP Complex Assembly	23
Editorial Board	23
DeepMS: super-fast peptide identification using end-to-end deep learning method	23
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	23
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	23
Editorial Board	23
Outside Front Cover	23
Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?	23

Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands	22
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	22
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	22
Global Analysis of Multi-Mutants to Improve Protein Function	22
GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design	22
Insight into the Conformational Ensembles Formed by U–U and T–T Mismatches in RNA and DNA Duplexes From a Structure-based Survey, NMR, and Molecular Dynamics Simulations	22
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	22
Inflammasomes in T cells	22
Structural Analysis of Mammalian Sialic Acid Esterase	22
Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	22
Epithelial Pyroptosis in Host Defense	22
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	22
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances	22
Outside Front Cover	21
Editorial Board	21
Elucidating the Roles of Intrinsically Disordered Proteins in Eukaryotic Transcriptional Regulation with Single-Molecule Imaging	21
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	21
Editorial Board	21
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	21
Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution	21
Editorial Board	21
Outside Front Cover	21
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	21
AmIActive (AIA): A Large-scale QSAR Based Target Fishing and Polypharmacology Predictive Web Tool	21
Formation Mechanism and Antibacterial Activity of Natural Antimicrobial Lysozyme with Antibiotics Doxycycline and Tigecycline	21
Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis	20
K-Pro: Kinetics Data on Proteins and Mutants	20
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	20
FTO Suppresses STAT3 Activation and Modulates Proinflammatory Interferon-Stimulated Gene Expression	20
Unexpected Richness of the Bacterial Small RNA World	20
Structural Dynamics of the C-terminal X Domain of Nipah and Hendra Viruses Controls the Attachment to the C-terminal Tail of the Nucleocapsid Protein	20
The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis	20
YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	20
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	20
Editorial Board	20
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	20
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome	20
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	20
TCREMP: A Bioinformatic Pipeline for Efficient Embedding of T-cell Receptor Sequences from Immune Repertoire and Single-cell Sequencing Data	20
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	19
In vivo Architecture of the Polar Organizing Protein Z (PopZ) Meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus	19
PANDA: PAN Cancer Data Analysis Web Tool	19
Evolution of Temperature Dependence of TRPM2 Channel Gating and Inactivation in Vertebrates	19
Structural Dynamics of Rho GTPases	19
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	19
Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase	19
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	19
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	19
Outside Front Cover	19
Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain	19
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	19
Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function	19
Timing of TolA and TolQ Recruitment at the Septum Depends on the Functionality of the Tol-Pal System	19
Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality	19
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	19
Outside Front Cover	18
Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken?	18
Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch	18
Outside Front Cover	18
Structural Basis of Main Proteases of Coronavirus Bound to Bofutrelvir	18
Euchromatin and Heterochromatin: Implications for DNA Accessibility and Transcription	18
Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR	18
A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression	18
Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC	18
DciA, the Bacterial Replicative Helicase Loader, Promotes LLPS in the Presence of ssDNA	18
Editorial Board	18
PerturbSeq.db: An Integrated Repository for Comprehensive Analysis of Single-cell Perturbation Data	18
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]	18
Channel Gating in Kalium Channelrhodopsin Slow Mutants	18
Biomolecular Condensation of the Human Papillomavirus E2 Master Regulator with p53: Implications in Viral Replication	18
Mitochondrial tRNA-specific Taurine Modifications Correlate With Ferroptosis-associated Myocardial Injury	18
Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication	18
Outside Front Cover	18
Liquid-liquid Phase Separation in Viral Function	17
Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin	17
Sequence Determinants of Allosteric Back-to-front Control of the Arf Nucleotide Switch	17
Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation	17
Phage Against the Machine: Discovery and Mechanism of Type V Anti-CRISPRs	17
The Functional Relationship Between RNA Splicing and the Chromatin Landscape	17
The Diverse Functions of Small Heat Shock Proteins in the Proteostasis Network	17
Cancer and Autism: How PTEN Mutations Degrade Function at the Membrane and Isoform Expression in the Human Brain	17
Targeting DNA Topoisomerase I for the Treatment of Cancer: Past, Present and Future	17
From embryos to condensates: A developmental biologist’s journey	17
Applications of Brain Organoids for Infectious Diseases	17
Studying the Function of tRNA Modifications: Experimental Challenges and Opportunities	17
The Structure and Function of the Bacterial Osmotically Inducible Protein Y	17
The Metal-binding Protein Atlas (MbPA): An Integrated Database for Curating Metalloproteins in All Aspects	17
Retroviral Vector Technology for Gene Therapy: History, Current Landscape, and Future Prospects	17
Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA	16
Loss of Residues 119–136, Including the First β-strand of Human Prion Protein, Generates an Aggregation-competent Partially “Open” Form	16
Imaging the Cytoplasmic Lives of Single mRNAs	16
Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction	16
Isotopologues of a Metabolic Precursor for Selective N-15 and C-13 Histidine Labeling	16
Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery	16
Cryo-EM Structures of Chronic Traumatic Encephalopathy Tau Filaments with PET Ligand Flortaucipir	16