Journal of Molecular Biology

Article	Citations
Outside Front Cover	449
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	326
Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections	252
Outside Front Cover	209
Outside Front Cover	203
Outside Front Cover	186
Outside Front Cover	186
Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases	166
Intein-based Design Expands Diversity of Selenocysteine Reporters	137
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	122
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	110
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	108
Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment	108
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	108
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	95
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	93
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	90
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	87
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	87
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	86
In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain	82
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	81
Outside Front Cover	79
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	79
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	78

HIV-Induced CPSF6 Condensates	78
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	77
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	76
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	74
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	74
Co-Translational Folding of the First Transmembrane Domain of ABC-Transporter CFTR is Supported by Assembly with the First Cytosolic Domain	74
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	74
Minireview: What is Known about SUMOylation Among NR4A Family Members?	74
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	73
Mechanisms of Transcription Elongation Factor DSIF (Spt4–Spt5)	69
The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region	66
Transcriptional and Epigenetic Regulation of Gasdermins	66
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	66
Mechanisms of Gasdermin Recognition by Proteases	65
ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	63
The PHY Domain Dimer Interface of Bacteriophytochromes Mediates Cross-talk between Photosensory Modules and Output Domains	61
Mechanisms of Translation-coupled Quality Control	61
Biomolecular Condensates as Novel Antiviral Targets	60
Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae	60
Pyroptosis, and its Role in Central Nervous System Disease	60
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	59
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	58
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	57
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive	57
Outside Front Cover	55
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	55
Editorial Board	54
Outside Front Cover	54
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	54
Editorial Board	52
Editorial Board	52
Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	51
Editorial Board	51
Outside Front Cover	51
Spatial organization of Dps and DNA–Dps complexes	50
Small Molecular Inhibitors Block TRPM4 Currents in Prostate Cancer Cells, with Limited Impact on Cancer Hallmark Functions	49
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	48
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures	48
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	48
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	47
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	47
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	47
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	47
AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	46
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	44
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	44
Biosynthesis and Genetic Incorporation of 3,4-Dihydroxy-L-Phenylalanine into Proteins in Escherichia coli	44
AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	43
Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly	43
Sodium Ions Do Not Stabilize the Selectivity Filter of a Potassium Channel	43

The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	43
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation	43
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	43
Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator	42
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	42
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	41
EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	41
Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement	41
CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature	40
Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry	40
Distinct Antiretroviral Mechanisms Elicited by a Viral Mutagen	40
Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning	39
Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region	39
Solution NMR Structure of Titin N2A Region Ig Domain I83 and Its Interaction with Metal Ions	39
Chaperone Recycling in Late-Stage Flagellar Assembly	39
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	38
Near-Infrared Optogenetic Module for Conditional Protein Splicing	38
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	38
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	38
Evolution of Transcription Factor-containing Superfamilies in Eukaryotes	37
GMMA Can Stabilize Proteins Across Different Functional Constraints	37
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	37
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	36
Outside Front Cover	36
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	35
Editorial Board	35
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	35
Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation	34
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	34
GRAMMCell: Docking-based Cell Modeling Resource	33
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	33
Structure of the Borrelia Bacteriophage φBB1 Procapsid	32
Electrostatics Drive the Molecular Chaperone BiP to Preferentially Bind Oligomerized States of a Client Protein	32
Towards Decoding the Sequence-Based Grammar Governing the Functions of Intrinsically Disordered Protein Regions	32
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	31
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	31
The ER Chaperones BiP and Grp94 Regulate the Formation of Insulin-Like Growth Factor 2 (IGF2) Oligomers	31
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	30
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	30
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	30
The Role of LRRK2 in Intracellular Organelle Dynamics	30
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	30
Editorial Board	29
ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis	29
Co-Translational Membrane Targeting and Holo-Translocon Docking of Ribosomes Translating the SRP Receptor	29
Anthrax Toxin: Model System for Studying Protein Translocation	29
Editorial Board	29
Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation	28
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	28
Gasdermin Pore Forming Activities that Promote Inflammation from Living and Dead Cells	28
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	28
In vitro Evolution of Uracil Glycosylase Towards DnaKJ and GroEL Binding Evolves Different Misfolded States	28
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	28
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	28
D154Q Mutation does not Alter KRAS Dimerization	28
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	27
Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering	27
memerna: Sparse RNA folding including coaxial stacking	27
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	27
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	27
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	27
The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy	27
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	26
The evolution of sequence specificity in a DNA binding protein family	26
Corrigendum to “Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria” [J. Mol. Biol. 432(14) (2020) 4032–4048]	26
Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins	26
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die	26
Editorial Board	26
Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition	26
Outside Front Cover	25
Editorial Board	25
NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species	25
Editorial Board	25
Schizophrenia risk candidate protein ZNF804A interacts with STAT2 and influences interferon-mediated gene transcription in mammalian cells	25
Editorial Board	25
Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?	25
Corrigendum to “Autophosphorylation in the Leucine-Rich Repeat Kinase 2 (LRRK2) GTPase Domain Modified Kinase and GTP-binding Activities” [J. Mol. Biol. 412(1) (2011) 94–110]	25
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	24
High-Resolution Views and Transport Mechanisms of the NKCC1 and KCC Transporters	24
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	24

psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	24
PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences	24
AlphaFold and the amyloid landscape	24
The Positively Charged Cluster in the N-terminal Disordered Region may Affect Prion Protein Misfolding: Cryo-EM Structure of Hamster PrP(23–144) Fibrils	24
ISCA1 Orchestrates ISCA2 and NFU1 in the Maturation of Human Mitochondrial [4Fe-4S] Proteins	24
Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands	24
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	24
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	24
Structural Analysis of Mammalian Sialic Acid Esterase	24
Split Chloramphenicol Acetyl-Transferase Assay Reveals Self-Ubiquitylation-Dependent Regulation of UBE3B	23
Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	23
Degradation of Alzheimer’s Amyloid-β by a Catalytically Inactive Insulin-Degrading Enzyme	23
Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action	23
Editorial Board	23
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	23
Epithelial Pyroptosis in Host Defense	23
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	23
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	23
Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic	23
GPCRchimeraDB: A database of chimeric G protein-coupled receptors (GPCRs) to assist their design	23
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	22
Community-Wide Experimental Evaluation of the PROSS Stability-Design Method	22
Editorial Board	22
Editorial Board	22
In vivo Architecture of the Polar Organizing Protein Z (PopZ) Meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus	22
Inflammasomes in T cells	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
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	22
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	22
Global Analysis of Multi-Mutants to Improve Protein Function	22
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	22
Outside Front Cover	22
Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase	22
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	21
Outside Front Cover	21
AmIActive (AIA): A Large-scale QSAR Based Target Fishing and Polypharmacology Predictive Web Tool	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
Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution	21
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	21
Timing of TolA and TolQ Recruitment at the Septum Depends on the Functionality of the Tol-Pal System	21
K-Pro: Kinetics Data on Proteins and Mutants	21
Editorial Board	21
Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis	20
The Specific Elongation Factor to Selenocysteine Incorporation in Escherichia coli: Unique tRNASec Recognition and its Interactions	20
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	20
The Alarmone (p)ppGpp Regulates Primer Extension by Bacterial Primase	20
AlphaFold – A Personal Perspective on the Impact of Machine Learning	20
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	20
Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting	20
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	20
Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function	20
PANDA: PAN cancer Data Analysis web tool	20
Editorial Board	20
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	20
FTO Suppresses STAT3 Activation and Modulates Proinflammatory Interferon-Stimulated Gene Expression	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
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	20
Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain	19
A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread	19
Structural Dynamics of Rho GTPases	19
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	19
Interferon Control of Human Coronavirus Infection and Viral Evasion: Mechanistic Insights and Implications for Antiviral Drug and Vaccine Development	19
Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken?	19
SSP: An In Silico Tool for Salmonella Species Serotyping Using the Sequences of O-Antigen Biosynthesis Proteins and H-Antigen Filament Proteins	19
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	19
Optogenetic Control of the Canonical Wnt Signaling Pathway During Xenopus laevis Embryonic Development	19
Studying the Function of tRNA Modifications: Experimental Challenges and Opportunities	19
Outside Front Cover	19
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	19
Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality	19
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	19
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
In Silico Approaches for Prediction of Anti-CRISPR Proteins	18
Outside Front Cover	18
Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch	18
Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins	18
Platforms for Personalized Polytherapeutics Discovery in COVID-19	18
DciA, the Bacterial Replicative Helicase Loader, Promotes LLPS in the Presence of ssDNA	18
Magnitude of Ubiquitination Determines the Fate of Epidermal Growth Factor Receptor Upon Ligand Stimulation	18
Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery	18
Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR	18
Signal Propagation Within the MCL-1/BIM Protein Complex	18
Channel Gating in Kalium Channelrhodopsin Slow Mutants	18
An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells	18
Outside Front Cover	18
Biomolecular Condensation of the Human Papillomavirus E2 Master Regulator with p53: Implications in Viral Replication	18
Loss of Residues 119–136, Including the First β-strand of Human Prion Protein, Generates an Aggregation-competent Partially “Open” Form	18
Outside Front Cover	18
Structural and Mechanistic Insight into CRISPR-Cas9 Inhibition by Anti-CRISPR Protein AcrIIC4	18
Evolutionary Conservation of Structural and Functional Coupling between the BRM AT-Hook and Bromodomain	18
Outside Front Cover	18
Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin	17
Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC	17