Journal of Molecular Biology

Article	Citations
Outside Front Cover	490
Outside Front Cover	280
Outside Front Cover	246
Outside Front Cover	196
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	143
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	140
Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment	123
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	121
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	115
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	109
Outside Front Cover	103
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	98
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	93
Intein-based Design Expands Diversity of Selenocysteine Reporters	88
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	85
In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain	83
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	83
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	81
ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	80
Kinetic Investigation of Resistance to Islatravir Conferred by Mutations in HIV-1 Reverse Transcriptase	80
Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent	80
Single-molecule Tracking and Kinetic Analysis in Living Cells and Multicellular Organisms	80
Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae	78
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	77
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	75

Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections	75
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	72
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	71
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	67
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	66
Extracellular uncoating of bacteriophage MS2	65
Biomolecular Condensates as Novel Antiviral Targets	65
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	64
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	62
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	62
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	58
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	57
HIV-Induced CPSF6 Condensates	56
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	55
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	55
Mechanisms of Translation-coupled Quality Control	55
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	55
Mechanisms of Gasdermin Recognition by Proteases	54
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	54
Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases	53
Minireview: What is Known about SUMOylation Among NR4A Family Members?	53
Pyroptosis, and its Role in Central Nervous System Disease	51
Structural and Functional Characterization of Pseudomonas aeruginosa Virulence Factor AaaA, an Autotransporter with Arginine-Specific Aminopeptidase Activity	51
Transcriptional and Epigenetic Regulation of Gasdermins	50
Outside Front Cover	49
Editorial Board	49
Outside Front Cover	49
Editorial Board	49
Editorial Board	48
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures	47
Outside Front Cover	47
AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	45
The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	44
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation	44
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	43
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	43
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	42
Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator	41
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	41
Biosynthesis and Genetic Incorporation of 3,4-Dihydroxy-L-Phenylalanine into Proteins in Escherichia coli	41
Distinct Antiretroviral Mechanisms Elicited by a Viral Mutagen	40
Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement	40
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	40
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	39
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	39
Chaperone Recycling in Late-Stage Flagellar Assembly	39
Small Molecular Inhibitors Block TRPM4 Currents in Prostate Cancer Cells, with Limited Impact on Cancer Hallmark Functions	39
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	37
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	36
Near-Infrared Optogenetic Module for Conditional Protein Splicing	36

Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	36
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	36
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	36
Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry	35
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	35
GMMA Can Stabilize Proteins Across Different Functional Constraints	35
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	34
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	34
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	34
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	33
AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	33
CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature	33
Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region	33
Evolution of Transcription Factor-containing Superfamilies in Eukaryotes	33
Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly	33
EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	32
Electrostatics Drive the Molecular Chaperone BiP to Preferentially Bind Oligomerized States of a Client Protein	32
Outside Front Cover	32
Editorial Board	32
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	32
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	31
Editorial Board	31
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	31
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	31
Deciphering Long-Range Effects of Mutations: An Integrated Approach Using Elastic Network Models and Protein Structure Networks	31
GRAMMCell: Docking-based Cell Modeling Resource	31
ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis	31
Co-Translational Membrane Targeting and Holo-Translocon Docking of Ribosomes Translating the SRP Receptor	31
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	31
memerna: Sparse RNA folding including coaxial stacking	31
Anthrax Toxin: Model System for Studying Protein Translocation	29
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	29
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	29
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	29
In vitro Evolution of Uracil Glycosylase Towards DnaKJ and GroEL Binding Evolves Different Misfolded States	29
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	29
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	29
Gasdermin Pore Forming Activities that Promote Inflammation from Living and Dead Cells	29
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	28
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	28
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	28
Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering	28
Structure of the Borrelia Bacteriophage φBB1 Procapsid	28
D154Q Mutation does not Alter KRAS Dimerization	28
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	28
The Evolution of Sequence Specificity in a DNA Binding Protein Family	27
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	27
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	27
Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling	27
The Role of LRRK2 in Intracellular Organelle Dynamics	27
Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition	26
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	26
Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins	26
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	26
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	26
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die	26
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	26
Editorial Board	25
Saccharomyces cerevisiae Xrs2 Binds DNA Through Its FHA Domain	25
Outside Front Cover	25
Editorial Board	25
Corrigendum to “Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria” [J. Mol. Biol. 432(14) (2020) 4032–4048]	25
Editorial Board	25
Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation	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	24
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	24
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	24
Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?	24
Structural Analysis of Mammalian Sialic Acid Esterase	24
Editorial Board	24
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]	24
Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands	24
GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design	24
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	23
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	23
Global Analysis of Multi-Mutants to Improve Protein Function	23
psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	23
Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic	23
PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences	23

Inflammasomes in T cells	23
Epithelial Pyroptosis in Host Defense	23
Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action	23
Schizophrenia risk candidate protein ZNF804A interacts with STAT2 and influences interferon-mediated gene transcription in mammalian cells	23
AlphaFold and the amyloid landscape	22
Outside Front Cover	22
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	22
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	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
Editorial Board	22
Split Chloramphenicol Acetyl-Transferase Assay Reveals Self-Ubiquitylation-Dependent Regulation of UBE3B	22
Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	22
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	22
High-Resolution Views and Transport Mechanisms of the NKCC1 and KCC Transporters	22
Editorial Board	22
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	22
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	22
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	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
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	21
In vivo Architecture of the Polar Organizing Protein Z (PopZ) Meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus	21
The Alarmone (p)ppGpp Regulates Primer Extension by Bacterial Primase	21
Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function	21
Outside Front Cover	21
Elucidating the Roles of Intrinsically Disordered Proteins in Eukaryotic Transcriptional Regulation with Single-Molecule Imaging	21
YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	21
The Specific Elongation Factor to Selenocysteine Incorporation in Escherichia coli: Unique tRNASec Recognition and its Interactions	21
Editorial Board	21
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	21
K-Pro: Kinetics Data on Proteins and Mutants	21
Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution	21
Editorial Board	21
Unexpected Richness of the Bacterial Small RNA World	21
Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain	21
TCREMP: A Bioinformatic Pipeline for Efficient Embedding of T-cell Receptor Sequences from Immune Repertoire and Single-cell Sequencing Data	20
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	20
Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality	20
Editorial Board	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
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	20
Optogenetic Control of the Canonical Wnt Signaling Pathway During Xenopus laevis Embryonic Development	20
PANDA: PAN Cancer Data Analysis Web Tool	20
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	20
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	20
The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis	20
AlphaFold – A Personal Perspective on the Impact of Machine Learning	20
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	19
FTO Suppresses STAT3 Activation and Modulates Proinflammatory Interferon-Stimulated Gene Expression	19
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome	19
Structural Dynamics of Rho GTPases	19
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	19
Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase	19
Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting	19
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	19
Outside Front Cover	19
Timing of TolA and TolQ Recruitment at the Septum Depends on the Functionality of the Tol-Pal System	19
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
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	19
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	19
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	19
A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread	19
Magnitude of Ubiquitination Determines the Fate of Epidermal Growth Factor Receptor Upon Ligand Stimulation	18
Outside Front Cover	18
Signal Propagation Within the MCL-1/BIM Protein Complex	18
Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins	18
Outside Front Cover	18
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
Structural and Mechanistic Insight into CRISPR-Cas9 Inhibition by Anti-CRISPR Protein AcrIIC4	18
Outside Front Cover	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
Loss of Residues 119–136, Including the First β-strand of Human Prion Protein, Generates an Aggregation-competent Partially “Open” Form	18
DciA, the Bacterial Replicative Helicase Loader, Promotes LLPS in the Presence of ssDNA	18
Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch	18
Outside Front Cover	17
Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction	17
A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression	17
Editorial Board	17
An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells	17
Towards Molecular Understanding of the pH Dependence Characterizing NhaA of Which Structural Fold is Shared by Other Transporters	17
Mitochondrial tRNA-specific Taurine Modifications Correlate With Ferroptosis-associated Myocardial Injury	17
Structural Basis of Main Proteases of Coronavirus Bound to Bofutrelvir	17
The UBR Domain of Plant Ubr1 Homolog PRT6 Accommodates Basic and Hydrophobic Amino Termini for Substrate Recognition	17
Structural Basis for Silicic Acid Uptake by Higher Plants	17
The Diverse Functions of Small Heat Shock Proteins in the Proteostasis Network	16
Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery	16
Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin	16
Cryo-EM Structures of Chronic Traumatic Encephalopathy Tau Filaments with PET Ligand Flortaucipir	16
The Protein Scaffolding Functions of Polyphosphate	16
Sequence determinants of allosteric back-to-front control of the Arf nucleotide switch	16
Channel Gating in Kalium Channelrhodopsin Slow Mutants	16
The Metal-binding Protein Atlas (MbPA): An Integrated Database for Curating Metalloproteins in All Aspects	16
Phage Against the Machine: Discovery and Mechanism of Type V Anti-CRISPRs	16