Protein Science

Article	Citations
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Soluble SARS‐CoV‐2 RBD and human ACE2 peptidase domain produced in DrosophilaS2 cells show functions evoking virus–cell interface	329
Similar protein segments shared between domains of different evolutionary lineages	285
Biophysical characterization of RelA–p52 NF‐κB dimer—A link between the canonical and the non‐canonical NF‐κB pathway	184
Structural and functional validation of a highly specific Smurf2 inhibitor	165
Epitope‐directed anti‐SARS‐CoV‐2 scFv engineered against the key spike protein region could block membrane fusion	126
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD	124
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase	120
Structure–function mapping and mechanistic insights on the SARS CoV2 Nsp1	93
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An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis	80
Design of an effective small expression tag to enhance GPCR production in E. coli‐based cell‐free and whole cell expression systems	76
Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion‐binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu	69
Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone	69
Fine‐tuned interactions between globular and disordered regions of single‐stranded DNA binding (SSB) protein are required for dynamic condensation under physiological conditions	65
Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS‐fold glucosamine‐6‐phosphate deaminases	60
Issue information	59
Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins	57
Extrinsic and intrinsic factors affect copper‐induced protein precipitation across eukaryotic and prokaryotic proteomes	51
A novel method for expressing and purifying large quantities of functional and stable human voltage‐gated proton channel (hHv1)	49
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	46
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	45
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	45
Two residues determine nicotinic acetylcholine receptor requirement for RIC ‐3	44

Rapid directed molecular evolution of fluorescent proteins in mammalian cells	40
Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequenc	40
A multi‐pore model of the blood–brain barrier tight junction strands recapitulates the permeability features of wild‐type and mutant claudin‐5	38
Large library docking for novel SARS‐CoV ‐2 main protease non‐covalent and covalent inhibitors	37
Evolution of affinity between p53 transactivation domain and MDM2 across the animal kingdom demonstrates high plasticity of motif‐mediated interactio	36
Torsional twist of the SARS ‐ CoV and SARS ‐	36
Competing chaperone pathways in α‐synuclein disaggregation and aggregation dynamics	34
Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B	32
Structural polymorphism and cytotoxicity of brain‐derived β‐amyloid extracts	31
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	30
Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains	29
Torsion angles to map and visualize the conformational space of a protein	29
CsgA gatekeeper residues control nucleation but not stability of functional amyloid	28
Biophysical insights into the dimer formation of human Sirtuin 2	28
Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers	28
Molecular basis for different substrate‐binding sites and chaperone functions of the BRICHOS domain	27
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix	27
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway	27
Xplor‐NIH: Better parameters and protocols for NMR protein structure determination	27
Cumulative asparagine to aspartate deamidation fails to perturb γD‐crystallin structure and stability	26
Synonymous and non‐synonymous codon substitutions can alleviate dependence on GroEL for folding	26
Structure‐based alteration of tryptophan residues of the multidrug transporter CmABCB1 to assess substrate binding using fluorescence spectroscopy	25
Correction to “The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament”	25
Analysis of β‐C‐terminal salt bridges in T‐state hemoglobin by trapping tertiary conformations in silica gels	25
Chemical and temporal manipulation of early steps in protein assembly tunes the structure and intermolecular interactions of protein‐based materials	25
Ca2+ attenuates nucleation activity of leiomodin	25
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Integrative visualization of the molecular structure of a cellular microdomain	23
Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation	23
The oligomeric states of dye‐decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation	23
Control of a far‐red/near‐infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin	23
Biochemical and structural characterization of meningococcal methylenetetrahydrofolate reductase	23
Growth hormone receptor antagonists, GHA2 and GHA3, with dual activity against the human and mouse receptor	23
Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product‐inhibition mechanism and oxygen gatekeeper	23
A systematic pipeline of protein structure selection for computer‐aided drug discovery: A case study on T790M/L858R mutant EGFR structures	23
A competition smFRET assay to study ligand‐induced conformational changes of the dengue virus protease	23
Structure‐based clustering and mutagenesis of bacterial tannases reveals the importance and diversity of active site‐capping domains	23
Evolution of homo‐oligomerization of methionine S‐adenosyltransferases is replete with structure–function constrains	22
Ligand binding Pro ‐miscuity of acylpeptide hydrolase, structural analysis of a detoxifying serine hydrolase	22
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Controlled by disorder: Phosphorylation modulates SRSF1 domain availability for spliceosome assembly	21
Unambiguous assignment of kinked‐ β sheets leads to insights into molecular grammar of reversibility in biomolecular condensates	21
The diversity of PET degrading enzymes: A systematic review of sequence, structure, and function	21
Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding	20
Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination	20
PocketOptimizer 2.0: A modular framework for computer‐aided ligand‐binding design	20
T hermo L ink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning	20
PEG–mCherry interactions beyond classical macromolecular crowding	20
Phenotypic mutations contribute to protein diversity and shape protein evolution	20

Mesoscale explorer: Visual exploration of large‐scale molecular models	20
Discovery of broadly‐neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens	20
Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation	20
Structural features of thyroglobulin linked to protein trafficking	19
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02	19
Biophysical investigation of interactions between SARS‐CoV‐2 spike protein and neuropilin‐1	19
Resolving the structure and assembly of the honeybee silk heterotetrameric coiled coil	18
Computational model predicts function of Rho‐GTPase binding for plexin receptor GAP activity on Rap1b via dynamic allosteric changes	18
A conserved motif in Henipavirus P/V/W proteins drives the fibrillation of the W protein from Hendra virus	18
Construction of a versatile fusion protein for targeted therapy and immunotherapy	18
Loop engineering of enzymes to control their immobilization and ultimately fabricate more efficient heterogeneous biocatalysts	18
Protein degradation of antizyme depends on the N‐terminal degrons	18
Dimeric assembly of human Suv3 helicase promotes its RNA unwinding function in mitochondrial RNA degradosome for RNA decay	18
An iron–sulfur cluster as a new metal center in a flavodiiron protein	18
Issue information	18
Structure‐guided engineering of protein stability through core hydrophobicity	18
Unlocking complexity through neutron scattering: Structure and dynamics of protein–polymer conjugates	18
Domain swapping of the C‐terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis	18
Photomodulation of the ASIC1a acidic pocket destabilizes the open state	17
Unveiling the molecular mechanism of Gi protein biased activation at mGlu2–mGlu4 heterodimers through Gaussian accelerated molecular dynam	17
Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity	17
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	17
Project automation in CCP4 Cloud: Enabling customization and high‐throughput efficiency	17
Structural investigations connect the disordered N‐terminal extension of HypB to the activities of HypB and SlyD in E. coli	17
Phosphorylation of Staphylococcus aureus β‐lactamase, a prerequisite to its sequestration on the cytoplasmic membrane	17
Programmable protein topology via SpyCatcher‐SpyTag chemistry in one‐pot cell‐free expression system	17
An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase MtLYR3	16
Modulation of TRPV2 by endogenous and exogenous ligands: A computational study	16
The dual‐coding gene SLC35A4 protects against oxidative stress	16
Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations	16
Design principles that protect the proteasome from self‐destruction	16
Lysine acetylation modulates s‐OPA1 GTPase activity and oligomerization in mitochondrial membrane remodeling	16
Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation	16
Partitioning the Hill coefficient into contributions from ligand‐promoted conformational changes and subunit heterogeneity	16
Genetic mutations disrupt the coordinated mode of tyrosinase's intra‐melanosomal domain	16
A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP)	16
Tuning the stator subunit of the flagellar motor with coiled‐coil engineering	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
Probing binding and occlusion of substrate in the human creatine transporter‐1 by computation and mutagenesis	16
The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the E. coli L‐asparaginase EcAIII	15
Issue information	15
Issue information	15
Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5T	15
Ferritin‐based disruptor nanoparticles: A novel strategy to enhance LDL cholesterol clearance via multivalent inhibition of PCSK9–LDL receptor interaction	15
Cleaved versus Uncleaved: How furin cleavage reshapes the conformational landscape of SARS ‐ CoV ‐	15
The Ca2+ response of a smart forisome protein is dependent on polymerization	15
Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants	15
The intrinsically disordered protein NUPR1 binds to phospholipids	15
Orthogonal translation with 5‐cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding	15
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KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing	15
Protein structure accuracy estimation using geometry‐complete perceptron networks	15
Targeting MarA N‐terminal domain dynamics to prevent DNA binding	14
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Issue information	14
Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125	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
Issue information	14
Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways	14
MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2	14
Thermostability and binding properties of single‐chained Fv fragments derived from therapeutic antibodies	13
IEDB‐3D 2.0: Structural data analysis within the Immune Epitope Database	13
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Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono‐PEGylated alpha‐1 antitrypsin	13
Heterogeneous folding landscapes and predetermined breaking points within a protein family	13
AggNet: Advancing protein aggregation analysis through deep learning and protein language model	13
CMM—An enhanced platform for interactive validation of metal binding sites	13
Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns	13
Structure and activity of a bacterial defense‐associated 3′‐5′ exonuclease	13
iLight2: A near‐infrared optogenetic tool for gene transcription with low background activation	13
Structures of two LarA ‐like nickel‐pincer nucleotide cofactor‐utilizing enzymes with a single catalytic histidine residue	13
Expanding the genetic code	13
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	13
De novo design of monomeric helical bundles for pH‐controlled membrane lysis	13
Accounting for nonuniformity of bulk‐solvent: A mosaic model	13
Active site center redesign increases protein stability preserving catalysis in thioredoxin	13
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	13
SG‐ML‐PLAP: A structure‐guided machine learning–based scoring function for protein–ligand binding affinity prediction	13
Structural and dynamic roles of tandem acyl carrier proteins in aryl polyene biosynthesis in carbapenem‐resistant Acinetobacter baumannii	13

A cascade of sulfur transferases delivers sulfur to the sulfur‐oxidizing heterodisulfide reductase‐like complex	13
Global analysis of kinetics reveals the role of secondary nucleation in recombinant spider silk self‐assembly	13
Expanding the biocatalytic and oxidative landscape of the old yellow enzyme family	13
Kunitz‐type trypsin inhibitor from durian (Durio zibethinus) employs a distinct loop for trypsin inhibition	13
Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all‐atom simulations	13
A disulfide chaperone knockout facilitates spin labeling and pulse EPR spectroscopy of outer membrane transporters	12
The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum	12
A flexible, allosteric loop regulates protein activity and rewires electrostatics	12
KCD: A prediction web server of knowledge‐based circular dichroism	12
Correction to “The structural landscape of the immunoglobulin fold by large‐scale de novo design”	12
Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi	12
Revisiting the hydrolysis of ampicillin catalyzed by Temoneira‐1 β‐lactamase, and the effect of Ni(II), Cd(II) and Hg(II)	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
FOXO4 interacts with p53 TAD and CRD and inhibits its binding to DNA	12
Deep sequencing combined with high‐throughput screening enables efficient development of a pH‐dependent high‐affinity binding domain targeting HER3	12
Ligation of multiple protein domains using orthogonal inteins with non‐native splice junctions	12
Issue information	12
Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair	12
Issue information	12
Ordered ATP hydrolysis in the Hsp90 chaperone is regulated by Aha1 and a conserved post‐translational modification	12
Differential effects of disulfide bond formation in TEM‐1 versus CTX‐M‐9 β‐lactamase	12
Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1	12
Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi‐enzyme colocalization and environment	11
Molecular insight into the specific interactions of the SARS‐Coronavirus‐2 nucleocapsid with RNA and host protein	11
Structural and biochemical characterization of the C‐terminal region of the human RTEL1 helicase	11
Theta‐curves in proteins	11
Constant domain polymorphisms influence monoclonal antibody stability and dynamics	11
Structure‐based insights into the mechanism of [4Fe‐4S]‐dependent sulfur insertase LarE	11
Role of associated water in stabilizing human γ‐D crystallin under crowded eye lens conditions	11
Targeting the apical domain of the transferrin receptor: Development of a new protein scaffold for cellular delivery	11
DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning	11
A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase	11
Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials	11
Clustering protein functional families at large scale with hierarchical approaches	11
Site‐directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus	11
Real‐time FRET assay for monitoring detyrosination by TMCP1 and VASH2	11
Allosteric regulation of L‐lactate dehydrogenase: Beyond effector‐mediated tetramerization	11
LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation	11
Assessing the functional impact of protein binding site definition	11
Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy	11
A new strategy to reconcile amyloid cross‐seeding and amyloid prevention in a binary system of α‐synuclein fragmental peptide and hIAPP	11
Exploring the molecular mechanism of cold‐adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network	11
Issue information	11
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Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	11
Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63	10
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Structural adaptability and surface activity of peptides derived from tardigrade proteins	10
Preferential binding of ADP ‐bound mitochondrial HSP70 to the nucleotide exchange factor	10
U‐CIE [/juː ‘siː/]: Color encoding of high‐dimensional data	10
A phase transition modulates the protective function of a tardigrade disordered protein during desiccation	10
Buttressing ligand‐binding pockets in de novo designed NTF2 ‐like domains	10
Amino acid substitutions at rheostat positions in the Na + /taurocholate cotransporting polypepti	10
Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study	10
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A protein fitness predictive framework based on feature combination and intelligent searching	10
Mitigating product inhibition in 2′‐hydroxybiphenyl‐2‐sulfinate desulfinase (DszB) with synthetic glycosylation	10
Guanidinylation of the cold shock protein YB‐1: Molecular basis, structural changes and Notch‐3 receptor binding	10
Unraveling ShuA detergent‐induced colloidal behavior in solution: A comprehensive SEC‐MALS, SAXS, and SANS study	10
Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain	10
Conformational features and interaction mechanisms of VHH antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction	10
Structure–function analysis of cysteine residues in the plasmodium falciparum chitinase, PfCHT1	10
The role of phospholipid saturation and composition in α‐synuclein aggregation and toxicity: A dual in vitro and in vivo approach	10
Optimized genetic code expansion technology for time‐dependent induction of adhesion GPCR‐ligand engagement	10
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Membrane tension‐dependent conformational change of Isoleucine 106 of loop B diminishes water permeability in FaPIP2;1	10
Structural and functional characterization of the cytotoxic protein ledodin, an atypical ribosome‐inactivating protein from shiitake mushroom (Lentinula edodes)	10
Multivalent interaction induces phase separation and formation of more toxic aggregates of α‐syn in a yeast model of Parkinson's disease	10
SPI “sandwich”: Combined SUMO‐Peptide‐Intein expression system and isolation procedure for improved stability and yield of peptides	10
Phosphate ions modulate enzyme activity and epistatic effects in two clavulanic acid‐resistant β‐lactamase mutants	10
Structural insight into the substrate binding of the AMT complex via an inhibitor‐trapped state	10
Issue information	9
AcrDB update: Predicted 3D structures of anti‐CRISPRs in human gut viromes	9
The PB1 and the ZZ domain of the autophagy receptor p62/SQSTM1 regulate the interaction of p62/SQSTM1 with the autophagosome protein LC3B	9
Design of a water‐soluble CD20 antigen with computational epitope scaffolding	9
ExploreTurns : A web tool for the exploration, analysis, and classification of beta turns and structured loops in proteins; application to beta‐bulge and Schellman loops	9
Erratum	9
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Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter jejuni via targeting different sites with different scaffolds	9
Degradation mechanism of AtrA mediated by ClpXP and its application in daptomycin production in Streptomyces roseosporus	9
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Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases	9
Engineering G protein‐coupled receptors for stabilization	9
Heat‐induced structural and chemical changes to a computationally designed miniprotein	9
Structural dynamics and binding of Caenorhabditis elegans lifespan‐extending lipid binding protein‐3 to polyunsaturated fatty acids	9
The structural landscape of the immunoglobulin fold by large‐scale de novo design	9
Enhanced protein extraction and quantification protocol for microsamples: An ultra‐sensitive workflow for low‐volume, low‐concentration total protein lysates	9
Exploring the druggability of the UEV domain of human TSG101 in search for broad‐spectrum antivirals	9
VirulentPred 2.0: An improved method for prediction of virulent proteins in bacterial pathogens	9
Labile assembly of a tardigrade protein induces biostasis	9
Computed cancer interactome explains the effects of somatic mutations in cancers	9
A favorable path to domain separation in the orange carotenoid protein	9
Protein ensemble modeling and analysis with MMMx	9
Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity	9