Journal of Molecular Biology

Article	Citations
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	333
Editorial Board	318
Outside Front Cover	223
Outside Front Cover	153
Outside Front Cover	125
Outside Front Cover	124
Outside Front Cover	117
Extracellular uncoating of bacteriophage MS2	112
Structural and Functional Characterization of Pseudomonas aeruginosa Virulence Factor AaaA, an Autotransporter with Arginine-Specific Aminopeptidase Activity	100
Kinetic Investigation of Resistance to Islatravir Conferred by Mutations in HIV-1 Reverse Transcriptase	95
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	90
Transcriptional and Epigenetic Regulation of Gasdermins	87
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	86
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	86
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	86
Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections	85
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	78
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	75
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	74
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	72
Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae	72
Intein-based Design Expands Diversity of Selenocysteine Reporters	70
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	64
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	63
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	61

NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	61
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	61
Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent	61
Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment	61
HIV-Induced CPSF6 Condensates	58
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	58
Mechanisms of Gasdermin Recognition by Proteases	58
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	58
Single-molecule Tracking and Kinetic Analysis in Living Cells and Multicellular Organisms	58
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	57
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	57
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	54
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	53
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	52
Distinct Cis-acting Elements Combinatorically Mediate Co-localization of mRNAs Encoding for Co-translational Interactors in Cytoplasmic Clusters in S. cerevisiae	51
Biomolecular Condensates as Novel Antiviral Targets	49
Doxorubicin Recognition and Transport by the MATE Multidrug Transporter NorM From Vibrio cholerae	49
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	49
ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	48
Pyroptosis, and its Role in Central Nervous System Disease	48
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	46
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	45
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	45
Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes	45
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	44
Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly	44
Mechanisms of Translation-coupled Quality Control	44
Cryo-EM Observation of AA Amyloid Fibrils in Mouse Model of Systemic AApoAII Amyloidosis	44
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	43
Outside Front Cover	42
Editorial Board	42
Chaperone Recycling in Late-Stage Flagellar Assembly	42
Outside Front Cover	41
Editorial Board	41
Near-Infrared Optogenetic Module for Conditional Protein Splicing	40
Outside Front Cover	40
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	40
CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature	40
EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	38
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	38
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation	38
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	38
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures	37
Evolution of Transcription Factor-containing Superfamilies in Eukaryotes	37
Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry	37
GMMA Can Stabilize Proteins Across Different Functional Constraints	36
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	36
Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	35
Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region	35
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	35

AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	35
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	35
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	34
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	34
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	34
The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	33
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	33
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	33
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	32
RNAsolo 2.0: multimodal database to study RNAs, their structural families and intermolecular interfaces	32
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	32
AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	32
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	32
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	31
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	31
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	31
Editorial Board	31
Editorial Board	31
Biosynthesis and Genetic Incorporation of 3,4-Dihydroxy-L-Phenylalanine into Proteins in Escherichia coli	31
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	31
The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy	30
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	30
D154Q Mutation does not Alter KRAS Dimerization	30
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	30
Deciphering Long-Range Effects of Mutations: An Integrated Approach Using Elastic Network Models and Protein Structure Networks	30
ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis	30
Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling	30
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	29
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	29
TRIM52 Ubiquitin Ligase Acts as a Key Recognition Component of the Mammalian fMet/N-degron Pathway	29
Electrostatics Drive the Molecular Chaperone BiP to Preferentially Bind Oligomerized States of a Client Protein	29
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	29
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	29
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	29
Co-Translational Membrane Targeting and Holo-Translocon Docking of Ribosomes Translating the SRP Receptor	29
Structure of the Borrelia Bacteriophage φBB1 Procapsid	29
The Evolution of Sequence Specificity in a DNA Binding Protein Family	28
Saccharomyces cerevisiae Xrs2 Binds DNA Through Its FHA Domain	28
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	28
Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation	28
Protein Intrinsic Disorder and Adaptation to Extreme Environments: Resilience of Chaos	28
Gasdermin Pore Forming Activities that Promote Inflammation from Living and Dead Cells	28
The Role of LRRK2 in Intracellular Organelle Dynamics	28
memerna: Sparse RNA folding including coaxial stacking	28
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	28
In vitro Evolution of Uracil Glycosylase Towards DnaKJ and GroEL Binding Evolves Different Misfolded States	28
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	27
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	27
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	27
Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation	27
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	27
Anthrax Toxin: Model System for Studying Protein Translocation	27
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	27
Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering	27
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die	26
PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences	26
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	26
GRAMMCell: Docking-based Cell Modeling Resource	26
The Positively Charged Cluster in the N-terminal Disordered Region may Affect Prion Protein Misfolding: Cryo-EM Structure of Hamster PrP(23–144) Fibrils	26
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	26
Editorial Board	26
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	25
Corrigendum to “Conformational Transformation and Selection of Synthetic Prion Strains” [J. Mol. Biol. 413(3) (2011) 527–542]	25
NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species	25
Outside Front Cover	24
Editorial Board	24
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	24
Role of Antitoxin RNA Pseudoknot in Regulating Toxin Activity and Toxin-antitoxin RNP Complex Assembly	24
Editorial Board	24
DeepMS: super-fast peptide identification using end-to-end deep learning method	24
Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?	24
Editorial Board	24
Editorial Board	24
Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic	24
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	23
Structural Analysis of Mammalian Sialic Acid Esterase	23
Global Analysis of Multi-Mutants to Improve Protein Function	23
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	23
Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands	23
Epithelial Pyroptosis in Host Defense	23

Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	23
psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	23
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances	23
Gene Expression Imaging in Hematopoiesis	23
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	23
GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design	23
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	23
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	22
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	22
Editorial Board	22
Editorial Board	22
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	22
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	22
Inflammasomes in T cells	22
Outside Front Cover	22
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	22
Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action	22
Outside Front Cover	22
Editorial Board	22
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	21
Formation Mechanism and Antibacterial Activity of Natural Antimicrobial Lysozyme with Antibiotics Doxycycline and Tigecycline	21
YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	21
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome	21
Elucidating the Roles of Intrinsically Disordered Proteins in Eukaryotic Transcriptional Regulation with Single-Molecule Imaging	21
TCREMP: A Bioinformatic Pipeline for Efficient Embedding of T-cell Receptor Sequences from Immune Repertoire and Single-cell Sequencing Data	21
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	21
Timing of TolA and TolQ Recruitment at the Septum Depends on the Functionality of the Tol-Pal System	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
In vivo Architecture of the Polar Organizing Protein Z (PopZ) Meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus	20
Unexpected Richness of the Bacterial Small RNA World	20
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	20
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	20
Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution	20
The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis	20
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	20
Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality	20
Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function	20
Evolution of Temperature Dependence of TRPM2 Channel Gating and Inactivation in Vertebrates	20
AmIActive (AIA): A Large-scale QSAR Based Target Fishing and Polypharmacology Predictive Web Tool	20
Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis	20
Editorial Board	20
K-Pro: Kinetics Data on Proteins and Mutants	20
Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase	20
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	20
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	20
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	20
Outside Front Cover	19
Outside Front Cover	19
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	19
PANDA: PAN Cancer Data Analysis Web Tool	19
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	19
DciA, the Bacterial Replicative Helicase Loader, Promotes LLPS in the Presence of ssDNA	19
FTO Suppresses STAT3 Activation and Modulates Proinflammatory Interferon-Stimulated Gene Expression	19
Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain	19
Structural Dynamics of Rho GTPases	19
Structural Basis of Main Proteases of Coronavirus Bound to Bofutrelvir	19
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	19
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	19
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	19
The Structure and Function of the Bacterial Osmotically Inducible Protein Y	18
Channel Gating in Kalium Channelrhodopsin Slow Mutants	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
Biomolecular Condensation of the Human Papillomavirus E2 Master Regulator with p53: Implications in Viral Replication	18
Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication	18
Signal Propagation Within the MCL-1/BIM Protein Complex	18
Applications of Genetic Code Expansion in Studying Protein Post-translational Modification	18
Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin	18
Outside Front Cover	18
Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR	18
Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA	18
The Protein Scaffolding Functions of Polyphosphate	18
Mitochondrial tRNA-specific Taurine Modifications Correlate With Ferroptosis-associated Myocardial Injury	18
Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch	18
Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC	18
Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken?	18
Editorial Board	18
A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression	18
PerturbSeq.db: An Integrated Repository for Comprehensive Analysis of Single-cell Perturbation Data	18
Interferon Control of Human Coronavirus Infection and Viral Evasion: Mechanistic Insights and Implications for Antiviral Drug and Vaccine Development	18
A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread	18
Applications of Brain Organoids for Infectious Diseases	17
An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells	17
Multiply Perturbed Response to Disclose Allosteric Control of Conformational Change: Application to Fluorescent Biosensor Design	17
Structural and Mechanistic Insight into CRISPR-Cas9 Inhibition by Anti-CRISPR Protein AcrIIC4	17
Retroviral Vector Technology for Gene Therapy: History, Current Landscape, and Future Prospects	17
Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme	17
From embryos to condensates: A developmental biologist’s journey	17
An Intrinsically Disordered Region of Histone Demethylase KDM5A Activates Catalysis Through Interactions With the Nucleosomal Acidic Patch and DNA	17
Isotopologues of a Metabolic Precursor for Selective N-15 and C-13 Histidine Labeling	17
The Diverse Functions of Small Heat Shock Proteins in the Proteostasis Network	17
SSP: An In Silico Tool for Salmonella Species Serotyping Using the Sequences of O-Antigen Biosynthesis Proteins and H-Antigen Filament Proteins	17
Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins	17
Cryo-EM Structures of Chronic Traumatic Encephalopathy Tau Filaments with PET Ligand Flortaucipir	17
Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction	17
Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation	16