Journal of Molecular Biology

Article	Citations
Outside Front Cover	503
Outside Front Cover	292
Outside Front Cover	262
Outside Front Cover	201
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	145
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	142
Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment	126
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	111
Outside Front Cover	106
Intein-based Design Expands Diversity of Selenocysteine Reporters	102
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	98
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	90
Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae	88
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	83
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	83
Biomolecular Condensates as Novel Antiviral Targets	81
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	81
Kinetic Investigation of Resistance to Islatravir Conferred by Mutations in HIV-1 Reverse Transcriptase	80
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	80
Mechanisms of Translation-coupled Quality Control	78
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	77
Transcriptional and Epigenetic Regulation of Gasdermins	74
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	72
Editorial Board	68
Extracellular uncoating of bacteriophage MS2	67

Single-molecule Tracking and Kinetic Analysis in Living Cells and Multicellular Organisms	67
Minireview: What is Known about SUMOylation Among NR4A Family Members?	66
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	65
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	61
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	58
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	58
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	57
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	56
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	55
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	55
In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain	55
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	54
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	54
Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections	54
Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes	53
ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	52
Mechanisms of Gasdermin Recognition by Proteases	52
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	52
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	52
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	52
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	50
HIV-Induced CPSF6 Condensates	47
Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent	47
Outside Front Cover	44
Editorial Board	44
Pyroptosis, and its Role in Central Nervous System Disease	44
Outside Front Cover	44
Editorial Board	43
Editorial Board	42
Outside Front Cover	41
The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	41
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation	40
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	40
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	40
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	39
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	39
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	38
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures	38
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	37
Biosynthesis and Genetic Incorporation of 3,4-Dihydroxy-L-Phenylalanine into Proteins in Escherichia coli	37
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	37
Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator	37
Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement	36
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	36
Distinct Antiretroviral Mechanisms Elicited by a Viral Mutagen	35
Near-Infrared Optogenetic Module for Conditional Protein Splicing	34
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	34
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	34
Chaperone Recycling in Late-Stage Flagellar Assembly	34
AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	33

EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	33
CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature	33
Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	33
Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region	33
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	33
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	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
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	33
AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	33
Outside Front Cover	32
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	32
Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry	32
Editorial Board	32
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	32
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	32
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	32
GMMA Can Stabilize Proteins Across Different Functional Constraints	32
memerna: Sparse RNA folding including coaxial stacking	32
Electrostatics Drive the Molecular Chaperone BiP to Preferentially Bind Oligomerized States of a Client Protein	31
GRAMMCell: Docking-based Cell Modeling Resource	31
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	30
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	30
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	30
The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy	29
Co-Translational Membrane Targeting and Holo-Translocon Docking of Ribosomes Translating the SRP Receptor	29
Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation	29
In vitro Evolution of Uracil Glycosylase Towards DnaKJ and GroEL Binding Evolves Different Misfolded States	28
Editorial Board	28
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	28
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	28
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	28
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	28
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	27
The Evolution of Sequence Specificity in a DNA Binding Protein Family	27
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	27
The Role of LRRK2 in Intracellular Organelle Dynamics	27
Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering	27
ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis	27
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	27
Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation	26
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	26
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	26
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	26
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	26
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	26
Structure of the Borrelia Bacteriophage φBB1 Procapsid	26
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	26
Gasdermin Pore Forming Activities that Promote Inflammation from Living and Dead Cells	26
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	26
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	25
D154Q Mutation does not Alter KRAS Dimerization	25
Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling	25
Anthrax Toxin: Model System for Studying Protein Translocation	25
Saccharomyces cerevisiae Xrs2 Binds DNA Through Its FHA Domain	25
Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition	25
Editorial Board	24
Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins	24
Corrigendum to “Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria” [J. Mol. Biol. 432(14) (2020) 4032–4048]	24
Outside Front Cover	24
Editorial Board	24
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	24
Editorial Board	24
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die	24
Deciphering Long-Range Effects of Mutations: An Integrated Approach Using Elastic Network Models and Protein Structure Networks	24
Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action	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	23
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]	23
Schizophrenia risk candidate protein ZNF804A interacts with STAT2 and influences interferon-mediated gene transcription in mammalian cells	23
Editorial Board	23
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	23
Split Chloramphenicol Acetyl-Transferase Assay Reveals Self-Ubiquitylation-Dependent Regulation of UBE3B	23
Global Analysis of Multi-Mutants to Improve Protein Function	23
The Positively Charged Cluster in the N-terminal Disordered Region may Affect Prion Protein Misfolding: Cryo-EM Structure of Hamster PrP(23–144) Fibrils	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
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	22
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	22
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	22

DeepMS: super-fast peptide identification using end-to-end deep learning method	22
Inflammasomes in T cells	22
Editorial Board	22
Epithelial Pyroptosis in Host Defense	22
NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species	22
Structural Analysis of Mammalian Sialic Acid Esterase	22
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	22
GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design	22
psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	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
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	22
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	22
YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	21
Editorial Board	21
Editorial Board	21
AlphaFold and the amyloid landscape	21
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	21
K-Pro: Kinetics Data on Proteins and Mutants	21
In vivo Architecture of the Polar Organizing Protein Z (PopZ) Meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus	21
Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	21
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	21
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	21
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	21
The Specific Elongation Factor to Selenocysteine Incorporation in Escherichia coli: Unique tRNASec Recognition and its Interactions	21
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances	21
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	21
Outside Front Cover	21
Outside Front Cover	20
The Alarmone (p)ppGpp Regulates Primer Extension by Bacterial Primase	20
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	20
Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis	20
Editorial Board	20
PANDA: PAN Cancer Data Analysis Web Tool	20
Editorial Board	20
Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain	20
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	20
AlphaFold – A Personal Perspective on the Impact of Machine Learning	20
Optogenetic Control of the Canonical Wnt Signaling Pathway During Xenopus laevis Embryonic Development	20
TCREMP: A Bioinformatic Pipeline for Efficient Embedding of T-cell Receptor Sequences from Immune Repertoire and Single-cell Sequencing Data	20
Editorial Board	20
Unexpected Richness of the Bacterial Small RNA World	20
Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution	20
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	20
The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis	20
AmIActive (AIA): A Large-scale QSAR Based Target Fishing and Polypharmacology Predictive Web Tool	20
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	20
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome	19
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	19
Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality	19
Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase	19
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	19
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	19
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	19
Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting	19
Elucidating the Roles of Intrinsically Disordered Proteins in Eukaryotic Transcriptional Regulation with Single-Molecule Imaging	18
Structural Dynamics of Rho GTPases	18
A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread	18
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	18
FTO Suppresses STAT3 Activation and Modulates Proinflammatory Interferon-Stimulated Gene Expression	18
Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function	18
Timing of TolA and TolQ Recruitment at the Septum Depends on the Functionality of the Tol-Pal System	18
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	18
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	18
Outside Front Cover	18
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	17
Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR	17
Magnitude of Ubiquitination Determines the Fate of Epidermal Growth Factor Receptor Upon Ligand Stimulation	17
An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells	17
Structural Basis of Main Proteases of Coronavirus Bound to Bofutrelvir	17
Structural and Mechanistic Insight into CRISPR-Cas9 Inhibition by Anti-CRISPR Protein AcrIIC4	17
Outside Front Cover	17
Biomolecular Condensation of the Human Papillomavirus E2 Master Regulator with p53: Implications in Viral Replication	17
Outside Front Cover	17
Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch	17
Outside Front Cover	17
Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA	17
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]	17
Loss of Residues 119–136, Including the First β-strand of Human Prion Protein, Generates an Aggregation-competent Partially “Open” Form	17
Signal Propagation Within the MCL-1/BIM Protein Complex	17
Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins	17
Editorial Board	17
Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction	17
DciA, the Bacterial Replicative Helicase Loader, Promotes LLPS in the Presence of ssDNA	17
Towards Molecular Understanding of the pH Dependence Characterizing NhaA of Which Structural Fold is Shared by Other Transporters	16
Charge Segregation in the Intrinsically Disordered Region Governs VRN1 and DNA Liquid-like Phase Separation Robustness	16
The Functional Relationship Between RNA Splicing and the Chromatin Landscape	16
Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC	16
A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression	16
SSP: An In Silico Tool for Salmonella Species Serotyping Using the Sequences of O-Antigen Biosynthesis Proteins and H-Antigen Filament Proteins	16
Euchromatin and Heterochromatin: Implications for DNA Accessibility and Transcription	16
Multiply Perturbed Response to Disclose Allosteric Control of Conformational Change: Application to Fluorescent Biosensor Design	16
The UBR Domain of Plant Ubr1 Homolog PRT6 Accommodates Basic and Hydrophobic Amino Termini for Substrate Recognition	16
Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication	16
Channel Gating in Kalium Channelrhodopsin Slow Mutants	16
From embryos to condensates: A developmental biologist’s journey	16