Journal of Molecular Biology

Article	Citations
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	464
Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections	258
Outside Front Cover	216
Outside Front Cover	188
Outside Front Cover	187
Outside Front Cover	139
Intein-based Design Expands Diversity of Selenocysteine Reporters	129
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	115
Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment	114
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	114
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	112
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	97
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	97
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	93
Outside Front Cover	89
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	89
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	85
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	85
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	82
Minireview: What is Known about SUMOylation Among NR4A Family Members?	81
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	81
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	81
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	80
Mechanisms of Gasdermin Recognition by Proteases	78
Kinetic Investigation of Resistance to Islatravir Conferred by Mutations in HIV-1 Reverse Transcriptase	76

Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	76
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	76
Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent	76
Co-Translational Folding of the First Transmembrane Domain of ABC-Transporter CFTR is Supported by Assembly with the First Cytosolic Domain	75
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	75
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	72
The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region	69
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	67
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	67
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	64
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	63
In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain	63
Transcriptional and Epigenetic Regulation of Gasdermins	61
HIV-Induced CPSF6 Condensates	61
Pyroptosis, and its Role in Central Nervous System Disease	60
Mechanisms of Transcription Elongation Factor DSIF (Spt4–Spt5)	60
ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	59
The PHY Domain Dimer Interface of Bacteriophytochromes Mediates Cross-talk between Photosensory Modules and Output Domains	58
Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae	56
Mechanisms of Translation-coupled Quality Control	55
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	55
Biomolecular Condensates as Novel Antiviral Targets	55
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	54
Outside Front Cover	53
Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases	53
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	53
Arkadia and Ark2C promote substrate ubiquitylation with multiple E2 enzymes	53
Outside Front Cover	51
Editorial Board	50
Editorial Board	49
Editorial Board	49
Editorial Board	49
Outside Front Cover	49
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures	48
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	47
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	47
The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	46
AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	46
AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	45
Sodium Ions Do Not Stabilize the Selectivity Filter of a Potassium Channel	45
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation	45
Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement	44
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	44
Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator	44
Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry	42
CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature	42
Distinct Antiretroviral Mechanisms Elicited by a Viral Mutagen	42
Chaperone Recycling in Late-Stage Flagellar Assembly	42
Solution NMR Structure of Titin N2A Region Ig Domain I83 and Its Interaction with Metal Ions	41
Near-Infrared Optogenetic Module for Conditional Protein Splicing	40

Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region	40
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	40
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	40
Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning	40
Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	39
EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	38
Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly	38
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	38
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	38
Small Molecular Inhibitors Block TRPM4 Currents in Prostate Cancer Cells, with Limited Impact on Cancer Hallmark Functions	37
Biosynthesis and Genetic Incorporation of 3,4-Dihydroxy-L-Phenylalanine into Proteins in Escherichia coli	37
Evolution of Transcription Factor-containing Superfamilies in Eukaryotes	36
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	36
GMMA Can Stabilize Proteins Across Different Functional Constraints	36
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	35
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	34
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	34
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	34
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	34
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	33
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	33
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	33
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	32
Outside Front Cover	32
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	32
Electrostatics Drive the Molecular Chaperone BiP to Preferentially Bind Oligomerized States of a Client Protein	32
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	32
Editorial Board	32
Structure of the Borrelia Bacteriophage φBB1 Procapsid	31
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	31
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	31
The ER Chaperones BiP and Grp94 Regulate the Formation of Insulin-Like Growth Factor 2 (IGF2) Oligomers	31
ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis	30
Editorial Board	30
Editorial Board	30
The Role of LRRK2 in Intracellular Organelle Dynamics	30
Co-Translational Membrane Targeting and Holo-Translocon Docking of Ribosomes Translating the SRP Receptor	30
The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy	30
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	29
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	29
Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation	29
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	29
Gasdermin Pore Forming Activities that Promote Inflammation from Living and Dead Cells	29
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	29
In vitro Evolution of Uracil Glycosylase Towards DnaKJ and GroEL Binding Evolves Different Misfolded States	29
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	28
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	28
memerna: Sparse RNA folding including coaxial stacking	28
Anthrax Toxin: Model System for Studying Protein Translocation	28
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	28
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	27
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	27
Towards Decoding the Sequence-Based Grammar Governing the Functions of Intrinsically Disordered Protein Regions	27
D154Q Mutation does not Alter KRAS Dimerization	27
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	27
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	27
GRAMMCell: Docking-based Cell Modeling Resource	27
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	27
Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation	27
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	26
Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering	26
Editorial Board	26
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	26
Corrigendum to “Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria” [J. Mol. Biol. 432(14) (2020) 4032–4048]	26
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die	26
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	26
Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition	26
Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins	26
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	25
Outside Front Cover	25
Structural Analysis of Mammalian Sialic Acid Esterase	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
Editorial Board	25
Editorial Board	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
Editorial Board	25
Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?	25
Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands	24
Editorial Board	24
Epithelial Pyroptosis in Host Defense	24

Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	24
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	24
psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	24
High-Resolution Views and Transport Mechanisms of the NKCC1 and KCC Transporters	24
Degradation of Alzheimer’s Amyloid-β by a Catalytically Inactive Insulin-Degrading Enzyme	24
AlphaFold and the amyloid landscape	23
Global Analysis of Multi-Mutants to Improve Protein Function	23
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	23
Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action	23
Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic	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
Inflammasomes in T cells	23
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	23
Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	23
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	23
Schizophrenia risk candidate protein ZNF804A interacts with STAT2 and influences interferon-mediated gene transcription in mammalian cells	23
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	22
Community-Wide Experimental Evaluation of the PROSS Stability-Design Method	22
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	22
Editorial Board	22
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	22
Split Chloramphenicol Acetyl-Transferase Assay Reveals Self-Ubiquitylation-Dependent Regulation of UBE3B	22
DeepMS: super-fast peptide identification using end-to-end deep learning method	22
PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences	22
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	22
NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species	22
Timing of TolA and TolQ Recruitment at the Septum Depends on the Functionality of the Tol-Pal System	21
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	21
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	21
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	21
Outside Front Cover	21
K-Pro: Kinetics Data on Proteins and Mutants	21
Editorial Board	21
Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase	21
YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	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
In vivo Architecture of the Polar Organizing Protein Z (PopZ) Meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus	21
Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting	21
Editorial Board	21
The Specific Elongation Factor to Selenocysteine Incorporation in Escherichia coli: Unique tRNASec Recognition and its Interactions	21
The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis	20
Optogenetic Control of the Canonical Wnt Signaling Pathway During Xenopus laevis Embryonic Development	20
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	20
The Alarmone (p)ppGpp Regulates Primer Extension by Bacterial Primase	20
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	20
Editorial Board	20
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	20
Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain	20
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	20
AlphaFold – A Personal Perspective on the Impact of Machine Learning	20
Unexpected Richness of the Bacterial Small RNA World	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
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	19
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	19
PANDA: PAN Cancer Data Analysis Web Tool	19
TCREMP: A Bioinformatic Pipeline for Efficient Embedding of T-cell Receptor Sequences from Immune Repertoire and Single-cell Sequencing Data	19
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	19
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome	19
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	19
FTO Suppresses STAT3 Activation and Modulates Proinflammatory Interferon-Stimulated Gene Expression	19
Interferon Control of Human Coronavirus Infection and Viral Evasion: Mechanistic Insights and Implications for Antiviral Drug and Vaccine Development	19
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	19
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	19
AmIActive (AIA): A Large-scale QSAR Based Target Fishing and Polypharmacology Predictive Web Tool	19
Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis	19
Structural Dynamics of Rho GTPases	19
Biomolecular Condensation of the Human Papillomavirus E2 Master Regulator with p53: Implications in Viral Replication	18
Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR	18
A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread	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
Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery	18
Magnitude of Ubiquitination Determines the Fate of Epidermal Growth Factor Receptor Upon Ligand Stimulation	18
Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken?	18
SSP: An In Silico Tool for Salmonella Species Serotyping Using the Sequences of O-Antigen Biosynthesis Proteins and H-Antigen Filament Proteins	18
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	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
Outside Front Cover	18
An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells	17
Outside Front Cover	17
Towards Molecular Understanding of the pH Dependence Characterizing NhaA of Which Structural Fold is Shared by Other Transporters	17
Editorial Board	17
The UBR Domain of Plant Ubr1 Homolog PRT6 Accommodates Basic and Hydrophobic Amino Termini for Substrate Recognition	17
Signal Propagation Within the MCL-1/BIM Protein Complex	17
Structural Basis of Main Proteases of Coronavirus Bound to Bofutrelvir	17
A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression	17
Structural Basis for Silicic Acid Uptake by Higher Plants	17
DciA, the Bacterial Replicative Helicase Loader, Promotes LLPS in the Presence of ssDNA	17
Outside Front Cover	17
Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC	17
Phage Against the Machine: Discovery and Mechanism of Type V Anti-CRISPRs	17
Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction	17