Protein Science

Article	Citations
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An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis	309
Design of an effective small expression tag to enhance GPCR production in E. coli‐based cell‐free and whole cell expression systems	233
Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion‐binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu	161
Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone	147
Issue information	141
Extrinsic and intrinsic factors affect copper‐induced protein precipitation across eukaryotic and prokaryotic proteomes	122
Structure–function mapping and mechanistic insights on the SARS CoV2 Nsp1	118
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	110
Soluble SARS‐CoV‐2 RBD and human ACE2 peptidase domain produced in DrosophilaS2 cells show functions evoking virus–cell interface	103
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix	94
Structural polymorphism and cytotoxicity of brain‐derived β‐amyloid extracts	91
Two residues determine nicotinic acetylcholine receptor requirement for RIC ‐3	84
Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins	83
Structural and functional validation of a highly specific Smurf2 inhibitor	80
Torsional twist of the SARS ‐ CoV and SARS ‐	70
Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains	62
Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers	62
Evolution of affinity between p53 transactivation domain and MDM2 across the animal kingdom demonstrates high plasticity of motif‐mediated interactio	54
Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS‐fold glucosamine‐6‐phosphate deaminases	54
Predicting compatibility between ferredoxins and the Fe protein of nitrogenase using in silico protein modeling	53
Large library docking for novel SARS‐CoV ‐2 main protease non‐covalent and covalent inhibitors	49
CsgA gatekeeper residues control nucleation but not stability of functional amyloid	49

A multi‐pore model of the blood–brain barrier tight junction strands recapitulates the permeability features of wild‐type and mutant claudin‐5	47
Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequenc	46
Similar protein segments shared between domains of different evolutionary lineages	44
Xplor‐NIH: Better parameters and protocols for NMR protein structure determination	41
The peptidyl‐prolyl cis‐trans isomerase, Pin1, is a regulator of the protein kinase C θ ( PKCθ ) catal	41
Torsion angles to map and visualize the conformational space of a protein	41
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase	41
Protein–lipid interplay governs ion channel gating and bioenergetics in human mitochondrial VDAC3	41
Epitope‐directed anti‐SARS‐CoV‐2 scFv engineered against the key spike protein region could block membrane fusion	40
Detergents alter the stability and lipid binding properties of the CD1d immunoreceptor	39
Competing chaperone pathways in α‐synuclein disaggregation and aggregation dynamics	39
An open axial channel of the AAA ClpXP protease enhances degradation of specific classes of protein substrates	38
Biophysical insights into the dimer formation of human Sirtuin 2	37
A novel method for expressing and purifying large quantities of functional and stable human voltage‐gated proton channel (hHv1)	36
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD	35
Fine‐tuned interactions between globular and disordered regions of single‐stranded DNA binding (SSB) protein are required for dynamic condensation under physiological conditions	33
Biophysical characterization of RelA–p52 NF‐κB dimer—A link between the canonical and the non‐canonical NF‐κB pathway	32
Single‐molecule force spectroscopy discovers a dual‐binding mode in the hCG ‐mediated activation of LHCGR	32
MAVISp : A modular structure‐based framework for protein variant effects	32
The subunit composition of the mammalian Mediator complex is not conserved in all vertebrates: Insights from evolutionary plasticity of fish genomes	32
In vitro, cellular and in vivo studies of amyloid oligomers structure and toxicity: Challenges and advances	31
KEGG Syntax for comparison of organisms, organism groups, and viruses by conserved gene repertoires	31
Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B	30
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	30
In and out of the mitochondrial intermembrane space	30
Synonymous and non‐synonymous codon substitutions can alleviate dependence on GroEL for folding	30
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	30
Chemical and temporal manipulation of early steps in protein assembly tunes the structure and intermolecular interactions of protein‐based materials	29
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Analysis of β‐C‐terminal salt bridges in T‐state hemoglobin by trapping tertiary conformations in silica gels	28
A systematic pipeline of protein structure selection for computer‐aided drug discovery: A case study on T790M/L858R mutant EGFR structures	27
Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding	27
Biochemical and structural characterization of meningococcal methylenetetrahydrofolate reductase	27
Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation	26
Unambiguous assignment of kinked‐ β sheets leads to insights into molecular grammar of reversibility in biomolecular condensates	26
Trafficking of the human Na + /H + antiporter NHA2	26
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02	26
Evolution of homo‐oligomerization of methionine S‐adenosyltransferases is replete with structure–function constrains	26
Biophysical investigation of interactions between SARS‐CoV‐2 spike protein and neuropilin‐1	25
Growth hormone receptor antagonists, GHA2 and GHA3, with dual activity against the human and mouse receptor	25
Discovery of broadly‐neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens	25
Phenotypic mutations contribute to protein diversity and shape protein evolution	25
Streptococcus pneumoniae HtrA is a dynamic and monomeric virulence factor capable of forming larger oligomeric complexes	25
PocketOptimizer 2.0: A modular framework for computer‐aided ligand‐binding design	25
ProteinMCP : An agentic AI framework for autonomous protein engineering	24
Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination	24
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway	24
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Mesoscale explorer: Visual exploration of large‐scale molecular models	24

Loop engineering of enzymes to control their immobilization and ultimately fabricate more efficient heterogeneous biocatalysts	23
Integrative visualization of the molecular structure of a cellular microdomain	23
ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families	23
PEG–mCherry interactions beyond classical macromolecular crowding	22
Structure‐based clustering and mutagenesis of bacterial tannases reveals the importance and diversity of active site‐capping domains	22
The oligomeric states of dye‐decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation	22
Molecular basis for different substrate‐binding sites and chaperone functions of the BRICHOS domain	22
Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product‐inhibition mechanism and oxygen gatekeeper	22
Controlled by disorder: Phosphorylation modulates SRSF1 domain availability for spliceosome assembly	22
Ca2+ attenuates nucleation activity of leiomodin	22
Structural features of thyroglobulin linked to protein trafficking	21
Ligand binding Pro ‐miscuity of acylpeptide hydrolase, structural analysis of a detoxifying serine hydrolase	21
A competition smFRET assay to study ligand‐induced conformational changes of the dengue virus protease	21
Cumulative asparagine to aspartate deamidation fails to perturb γD‐crystallin structure and stability	21
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Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation	21
Correction to “The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament”	21
Cryo‐ EM reveals an ensemble of cytochrome P450 reductase conformations in solution	21
The diversity of PET degrading enzymes: A systematic review of sequence, structure, and function	21
Protein degradation of antizyme depends on the N‐terminal degrons	20
Issue information	20
Control of a far‐red/near‐infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin	20
T hermo L ink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning	20
Structure‐guided engineering of protein stability through core hydrophobicity	20
Domain swapping of the C‐terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis	20
Tuning the stator subunit of the flagellar motor with coiled‐coil engineering	19
Construction of a versatile fusion protein for targeted therapy and immunotherapy	19
Protease‐mediated maturation of M‐ PMV reverse transcriptase into a functional heterodimer	19
Photomodulation of the ASIC1a acidic pocket destabilizes the open state	19
The structural heterogeneity of AKT autoinhibition	19
Structural investigations connect the disordered N‐terminal extension of HypB to the activities of HypB and SlyD in E. coli	19
Stabilization versus flexibility: Detergent‐dependent trade‐offs in neurotensin receptor 1 GPCR ensembles	18
In silico peptide self‐assembly reveals the importance of N‐terminal motifs and the inhibition mechanism of the mutation L38M in	18
Project automation in CCP4 Cloud: Enabling customization and high‐throughput efficiency	18
Understanding cell‐penetrating peptide mechanisms using computational electrophysiology simulations	18
Unlocking complexity through neutron scattering: Structure and dynamics of protein–polymer conjugates	18
Phosphorylation of Staphylococcus aureus β‐lactamase, a prerequisite to its sequestration on the cytoplasmic membrane	18
Probing binding and occlusion of substrate in the human creatine transporter‐1 by computation and mutagenesis	18
Issue information	18
An iron–sulfur cluster as a new metal center in a flavodiiron protein	18
The dual‐coding gene SLC35A4 protects against oxidative stress	18
Unveiling the molecular mechanism of Gi protein biased activation at mGlu2–mGlu4 heterodimers through Gaussian accelerated molecular dynam	18
Orthogonal translation with 5‐cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding	18
Modulation of TRPV2 by endogenous and exogenous ligands: A computational study	17
Two‐conformer equilibrium of maltose‐binding protein in the absence of ligand from residual dipolar coupling analysis	17
A conserved motif in Henipavirus P/V/W proteins drives the fibrillation of the W protein from Hendra virus	17
Genetic mutations disrupt the coordinated mode of tyrosinase's intra‐melanosomal domain	17
Computational model predicts function of Rho‐GTPase binding for plexin receptor GAP activity on Rap1b via dynamic allosteric changes	17
Universal paratope–epitope interaction patterns in antibody–antigen structures	17
The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the E. coli L‐asparaginase EcAIII	17
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	16
Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation	16
Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3	16
Lysine acetylation modulates s‐OPA1 GTPase activity and oligomerization in mitochondrial membrane remodeling	16
Cleaved versus Uncleaved: How furin cleavage reshapes the conformational landscape of SARS ‐ CoV ‐	16
Resolving the structure and assembly of the honeybee silk heterotetrameric coiled coil	16
Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity	16
Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations	16
Unveiling catalytic potential and the native role of PETase from Streptomyces sp.	15
KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing	15
Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5T	15
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Issue information	15
Targeting MarA N‐terminal domain dynamics to prevent DNA binding	15
IEDB‐3D 2.0: Structural data analysis within the Immune Epitope Database	15
AggNet: Advancing protein aggregation analysis through deep learning and protein language model	15
Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants	15
Issue information	15
Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125	15
Heterogeneous folding landscapes and predetermined breaking points within a protein family	14
A la carte bioprospecting of substrate‐selective laccases via high‐throughput computational enzyme–substrate interaction profiling	14
Ferritin‐based disruptor nanoparticles: A novel strategy to enhance LDL cholesterol clearance via multivalent inhibition of PCSK9–LDL receptor interaction	14
Investigation of the structure of protein–polymer conjugates in solution reveals the impact of protein deuteration and the size of the polymer on its thermal stability	14
Structure and activity of a bacterial defense‐associated 3′‐5′ exonuclease	14
De novo design of monomeric helical bundles for pH‐controlled membrane lysis	14
Purification and characterization of recombinant human translation initiation factor eIF3	14
CMM—An enhanced platform for interactive validation of metal binding sites	14
The intrinsically disordered protein NUPR1 binds to phospholipids	14
MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2	14

Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns	14
Expanding the genetic code	14
Design of a yeast SUMO tag to eliminate internal translation initiation	14
Employing complementary fractionation‐based N‐terminomics approaches enhances the identification of legumain cleavage events in naïve and inflamed colon tissue	14
Expanding the biocatalytic and oxidative landscape of the old yellow enzyme family	14
Length and saturation of fatty acids in phosphatidylserine determine the rate of lysozyme aggregation simultaneously altering the structure and toxicity of amyloid oligomers and fibrils	14
Kunitz‐type trypsin inhibitor from durian (Durio zibethinus) employs a distinct loop for trypsin inhibition	13
iLight2: A near‐infrared optogenetic tool for gene transcription with low background activation	13
Thermostability and binding properties of single‐chained Fv fragments derived from therapeutic antibodies	13
Residue‐level mapping of crowding effects on protein phase separation	13
Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all‐atom simulations	13
Structures of two LarA ‐like nickel‐pincer nucleotide cofactor‐utilizing enzymes with a single catalytic histidine residue	13
Protein structure accuracy estimation using geometry‐complete perceptron networks	13
Thiol post‐translational modifications modulate allosteric regulation of the OpcA – G6PDH complex	13
Accounting for nonuniformity of bulk‐solvent: A mosaic model	13
A cascade of sulfur transferases delivers sulfur to the sulfur‐oxidizing heterodisulfide reductase‐like complex	13
Structural and dynamic roles of tandem acyl carrier proteins in aryl polyene biosynthesis in carbapenem‐resistant Acinetobacter baumannii	13
Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono‐PEGylated alpha‐1 antitrypsin	13
Human cells for human proteins: Isotope labeling in mammalian cells in suspension for functional NMR studies	13
T3SS effector and regulator discovery by predicting interacting partners of T3SS chaperones in	13
EnAcrPred : A robust ensemble machine learning framework for identifying anti‐ CRISPR proteins	12
Assessing the functional impact of protein binding site definition	12
Structural and biochemical characterization of the C‐terminal region of the human RTEL1 helicase	12
Real‐time FRET assay for monitoring detyrosination by TMCP1 and VASH2	12
Theta‐curves in proteins	12
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Detection of protein symmetry and structural rearrangements using secondary structure elements	12
Global analysis of kinetics reveals the role of secondary nucleation in recombinant spider silk self‐assembly	12
Protein‐tags and their fragments as potent inhibitors of enzymes: Structure of the ternary complex of phosphopantetheine adenylyltransferase from Enterobacter spp. with tag‐peptides	12
Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials	12
LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation	12
Role of associated water in stabilizing human γ‐D crystallin under crowded eye lens conditions	12
Correction to “The structural landscape of the immunoglobulin fold by large‐scale de novo design”	12
A disulfide chaperone knockout facilitates spin labeling and pulse EPR spectroscopy of outer membrane transporters	12
SG‐ML‐PLAP: A structure‐guided machine learning–based scoring function for protein–ligand binding affinity prediction	12
Use of tandem‐affinity chromatography to incorporate nucleotide loading of small GTPases during their purification	12
Issue information	12
Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy	12
Glycopolymers stabilize protein folding and protein–protein interactions via enthalpic interactions	12
Targeting the apical domain of the transferrin receptor: Development of a new protein scaffold for cellular delivery	12
Constant domain polymorphisms influence monoclonal antibody stability and dynamics	12
Issue information	12
An ALS ‐associated mutation in the C‐terminal α‐helix of TDP ‐43 uncouples condensate formation an	12
Active site center redesign increases protein stability preserving catalysis in thioredoxin	12
Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair	11
Deep sequencing combined with high‐throughput screening enables efficient development of a pH‐dependent high‐affinity binding domain targeting HER3	11
pLM ‐Repeat: Exploiting the sequence representations of protein language models for sensitive repeat detection	11
Conformational features and interaction mechanisms of VHH antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction	11
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DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning	11
Site‐directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus	11
Clustering protein functional families at large scale with hierarchical approaches	11
Guanidinylation of the cold shock protein YB‐1: Molecular basis, structural changes and Notch‐3 receptor binding	11
A flexible, allosteric loop regulates protein activity and rewires electrostatics	11
KCD: A prediction web server of knowledge‐based circular dichroism	11
Molecular insight into the specific interactions of the SARS‐Coronavirus‐2 nucleocapsid with RNA and host protein	11
A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase	11
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Optimized genetic code expansion technology for time‐dependent induction of adhesion GPCR‐ligand engagement	11
Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study	11
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Mitigating product inhibition in 2′‐hydroxybiphenyl‐2‐sulfinate desulfinase (DszB) with synthetic glycosylation	11
Revisiting the hydrolysis of ampicillin catalyzed by Temoneira‐1 β‐lactamase, and the effect of Ni(II), Cd(II) and Hg(II)	11
Issue information	11
Exploring the molecular mechanism of cold‐adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network	11
Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi‐enzyme colocalization and environment	11
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The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum	11
Conformational dynamics in insulin receptor kinase reveal a type III allosteric pocket	11
Unperturbed hydration structure involves ADP recognition in the N‐terminal domain of human heat shock protein 90α	11
Discovery of novel, high‐affinity HBV T‐cell epitopes by molecular dynamics‐augmented proteome‐wide screening	11
Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63	11
Post‐translational regulation of human D‐3‐phosphoglycerate dehydrogenase in Alzheimer's disease	11
Differential effects of disulfide bond formation in TEM‐1 versus CTX‐M‐9 β‐lactamase	11
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Ordered ATP hydrolysis in the Hsp90 chaperone is regulated by Aha1 and a conserved post‐translational modification	11
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	11
Ligation of multiple protein domains using orthogonal inteins with non‐native splice junctions	11
Allosteric regulation of L‐lactate dehydrogenase: Beyond effector‐mediated tetramerization	11
Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi	11
Amino acid substitutions at rheostat positions in the Na + /taurocholate cotransporting polypepti	10
Structure‐based insights into the mechanism of [4Fe‐4S]‐dependent sulfur insertase LarE	10
Concentration‐dependent mutational scanning probes the cellular folding landscape of α‐synuclein in yeast	10
Ligand‐driven modulation of chaperone–cochaperone networks shapes proteostasis outcomes	10
The role of phospholipid saturation and composition in α‐synuclein aggregation and toxicity: A dual in vitro and in vivo approach	10
Transient binding facilitates super‐resolution imaging of functional amyloid fibrils on living bacteria	10
Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain	10
Structural and dynamic similarities of nanofibrils and microparticles of engineered spider silk proteins probed by solid‐state NMR spectroscopy	10
VirulentPred 2.0: An improved method for prediction of virulent proteins in bacterial pathogens	10
Phosphate ions modulate enzyme activity and epistatic effects in two clavulanic acid‐resistant β‐lactamase mutants	10
Multivalent interaction induces phase separation and formation of more toxic aggregates of α‐syn in a yeast model of Parkinson's disease	10
Supervised learning of protein variant effects across large‐scale mutagenesis datasets	10
Design of a water‐soluble CD20 antigen with computational epitope scaffolding	10
The PB1 and the ZZ domain of the autophagy receptor p62/SQSTM1 regulate the interaction of p62/SQSTM1 with the autophagosome protein LC3B	10