Protein Science

Article	Citations
Electronegative clusters modulate folding status and RNA binding of unstructured RNA‐binding proteins	978
Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone	881
Dimerization of the CNNM extracellular domain	446
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Issue information	272
Structural insights into the unique recognition module between α‐synuclein peptide and nanobody	215
Escherichia coli strains with precise domain deletions in the ribonuclease RNase E can achieve greatly enhanced levels of membrane protein production	164
Structural and functional validation of a highly specific Smurf2 inhibitor	158
Distinct specificities of the HEMK2 protein methyltransferase in methylation of glutamine and lysine residues	156
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix	142
Issue information	105
Protein salvage and repurposing in evolution: Phospholipase D toxins are stabilized by a remodeled scrap of a membrane association domain	103
Engineered protein G variants for multifunctional antibody‐based assemblies	85
A novel method for expressing and purifying large quantities of functional and stable human voltage‐gated proton channel (hHv1)	82
Insights into the flexibility of the domain‐linking loop in actinobacterial coproheme decarboxylase through structures and molecular dynamics simulations	81
Methods for detecting, building, and improving tryptophan mannosylation in glycoprotein structures	77
Hijacking of plasminogen by dengue virus: The kringle‐4 and ‐5 domains of plasminogen binds synergistically to the domain I of envelope protein	75
A functional helix shuffled variant of the B domain of Staphylococcus aureus	69
Reconstitution and use of highly active human CDK1:Cyclin‐B:CKS1 complexes	68
ParSe 2.0: A web tool to identify drivers of protein phase separation at the proteome level	58
PDBsum extras: SARS‐CoV‐2 and AlphaFold models	56
Binding specificity of type three secretion system effector NleH2 to multi‐cargo chaperone CesT and their phosphorylation	54
CC+: A searchable database of validated coiled coils in PDB structures and AlphaFold2 models	52
Issue information	50
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Synthetic antibodies block receptor binding and current‐inhibiting effects of α‐cobratoxin from Naja kaouthia	47
How enzymes harness highly unfavorable proton transfer reactions	47
Arginine cluster introduction on framework region in anti‐lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops	43
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD	42
Molecular insights into alginate β‐lactoglobulin A multivalencies—The foundation for their amorphous aggregates and coacervation	42
In vitro characterization of the intramelanosomal domain of human recombinant TYRP1 and its oculocutaneous albinism type 3‐related mutant variants	42
Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS‐fold glucosamine‐6‐phosphate deaminases	41
Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes	35
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QSAR via multisite λ‐dynamics in the orphaned TSSK1B kinase	33
Allosteric inhibition of TEM‐1 β lactamase: Microsecond molecular dynamics simulations provide mechanistic insights	33
Reply to “Intrinsic protein disorder uncouples affinity from binding specificity”	33
Interface engineering of cellobiose dehydrogenase improves interdomain electron transfer	32
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	30
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	28
Diphtheria toxin‐derived, anti‐PD‐1 immunotoxin, a potent and practical tool to selectively deplete PD‐1+ cells	28
A conserved electrostatic membrane‐binding surface in synaptotagmin‐like proteins revealed using molecular phylogenetic analysis and homology modeling	27
Structure determination of an unstable macromolecular complex enabled by nanobody‐peptide bridging	26
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An ensemble machine learning model generates a focused screening library for the identification of CDK8 inhibitors	25
How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins	25
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Reconstitution and characterization of BRAF in complex with 14‐3‐3 and KRAS4B on nanodiscs	25
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Structural studies of intrinsically disordered MLL‐fusion protein AF9 in complex with peptidomimetic inhibitors	25
In This Issue	25
Engineering G protein‐coupled receptors for stabilization	23
Characterization of a novel format scFv×VHH single‐chain biparatopic antibody against metal binding protein MtsA	23
Issue information	23
Native ion mobility‐mass spectrometry reveals the binding mechanisms of anti‐amyloid therapeutic antibodies	23
Issue Information	23
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QuoteTarget: A sequence‐based transformer protein language model to identify potentially druggable protein targets	23
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CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	22
Characterization of an aminotransferase from Acanthamoeba polyphagaMimivirus	22
EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components	22
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Transition metal cation inhibition of Mycobacterium tuberculosis esterase RV0045C	22
Protein ensemble modeling and analysis with MMMx	20
Protective roles of highly conserved motif 1 in tardigrade cytosolic‐abundant heat soluble protein in extreme environments	20
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Allosteric regulatory control in dihydrofolate reductase is revealed by dynamic asymmetry	20
Probing effects of site‐specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis	19
Structural characterization of the Sel1‐like repeat protein LceB from Legionella pneumophila	19
CsgA gatekeeper residues control nucleation but not stability of functional amyloid	18
Parkinson's disease‐linked V15A mutation facilitates α‐synuclein aggregation by reducing membrane affinity	18
Evaluating the potential of non‐immunosuppressive cyclosporin analogs for targeting Toxoplasma gondii cyclophilin: Insights from structural studies	17

Examining the mechanistic relationship of APC/CCDH1 and its interphase inhibitor EMI1	17
GGAssembler: Precise and economical design and synthesis of combinatorial mutation libraries	17
An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis	17
Design of an effective small expression tag to enhance GPCR production in E. coli‐based cell‐free and whole cell expression systems	16
nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological Magnetic Resonance Data Bank	16
Only kosmotrope anions trigger fibrillization of the recombinant core spidroin eADF4(C16) from Araneus diadematus	16
Synthesis and degradation of the cyclic dinucleotide messenger c‐di‐AMP in the hyperthermophilic archaeon Pyrococcus yayanosii	16
Issue information	16
Two residues determine nicotinic acetylcholine receptor requirement for RIC‐3	15
A hierarchical deep learning based approach for multi‐functional enzyme classification	15
The Lys 280 → Gln mutation mimicking disease‐linked acetylation of Lys 280 in tau extends the structural core of fibrils and modulates their catalytic properties	15
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What the protein data bank tells us about the evolutionary conservation of protein conformational diversity	15
Condensation of the β‐cell secretory granule luminal cargoes pro/insulin and ICA512 RESP18 homology domain	15
Engineering gain‐of‐function mutants of a WW domain by dynamics and structural analysis	15
Issue information	15
Dissecting the general mechanisms of protein cage self‐assembly by coarse‐grained simulations	15
Reevaluation of bromodomain ligands targeting BAZ2A	15
Epitope mapping of novel monoclonal antibodies to human angiotensin I‐converting enzyme	15
Issue information	15
Hydrophobicity and molecular mass‐based separation method for autoantibody discovery from mammalian total cellular proteins	14
More is simpler: Decomposition of ligand‐binding affinity for proteins being disordered	14
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Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins	14
Nucleocapsid proteins from human coronaviruses possess phase separation capabilities and promote FUS pathological aggregation	14
Inline small‐angle X‐ray scattering‐coupled chromatography under extreme hydrostatic pressure	14
From a dimer to a monomer: Construction of a chimeric monomeric isocitrate dehydrogenase	14
Structure‐based analysis and evolution of a monomerized red‐colored chromoprotein from the Olindias formosa jellyfish	14
Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers	13
A new l‐arginine oxidase engineered from l‐glutamate oxidase	13
Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS‐CoV‐2	13
Kinetic isotope effect reveals rate‐limiting step in green‐to‐red photoconvertible fluorescent proteins	13
Expanding the family of extracellular chaperones: Identification of human plasma proteins with chaperone activity	13
Development of charybdotoxin Q18F variant as a selective peptide blocker of neuronal BK(α + β4) channel for the treatment of epileptic seizures	13
Selection of a PD‐1 blocking antibody from a novel fully human phage display library	13
Structural characterization of an intrinsically disordered protein complex using integrated small‐angle neutron scattering and computing	13
Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis	13
Adaptable SEC‐SAXS data collection for higher quality structure analysis in solution	13
Probing the effect of glycosaminoglycan depletion on integrin interactions with collagen I fibrils in the native extracellular matrix environment	13
Soluble SARS‐CoV‐2 RBD and human ACE2 peptidase domain produced in DrosophilaS2 cells show functions evoking virus–cell interface	13
Exhaustive mutational analysis of severe acute respiratory syndrome coronavirus 2 ORF3a: An essential component in the pathogen's infectivity cycle	13
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	13
Tubulin‐binding region alters tau–lipid interactions and changes toxicity of tau fibrils formed in the presence of phosphatidylserine lipids	13
Human islet amyloid polypeptide‐induced β‐cell cytotoxicity is linked to formation of α‐sheet structure	12
Computational design of N‐linked glycans for high throughput epitope profiling	12
The structural landscape of the immunoglobulin fold by large‐scale de novo design	12
Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter jejuni via targeting different sites with different scaffolds	12
Similar protein segments shared between domains of different evolutionary lineages	12
Unraveling paralog‐specific Notch signaling through thermodynamics of ternary complex formation and transcriptional activation of chimeric receptors	12
Engineering a monobody specific to monomeric Cu/Zn‐superoxide dismutase associated with amyotrophic lateral sclerosis	12
Big versus small: The impact of aggregate size in disease	12
Epitope‐directed anti‐SARS‐CoV‐2 scFv engineered against the key spike protein region could block membrane fusion	12
Engineering of IF1‐susceptive bacterial F1‐ATPase	12
Evolution of affinity between p53 transactivation domain and MDM2 across the animal kingdom demonstrates high plasticity of motif‐mediated interactions	12
HadBD dehydratase from Mycobacterium tuberculosis fatty acid synthase type II: A singular structure for a unique function	11
PairK: Pairwise k‐mer alignment for quantifying protein motif conservation in disordered regions	11
The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament	11
Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains	11
Heat‐induced structural and chemical changes to a computationally designed miniprotein	11
Multiplex measurement of protein–peptide dissociation constants using dialysis and mass spectrometry	11
A crucial active site network of titratable residues guides catalysis and NAD+ binding in human succinic semialdehyde dehydrogenase	11
In situ characterization of amine‐forming enzymes shows altered oligomeric state	11
Phylogenetic convergence of phase separation and mitotic function in the disordered protein BuGZ	11
High‐throughput cell‐free screening of eukaryotic membrane protein expression in lipidic mimetics	11
Protein stability models fail to capture epistatic interactions of double point mutations	11
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Exploring the druggability of the UEV domain of human TSG101 in search for broad‐spectrum antivirals	11
Semi‐synthetic nanobody‐ligand conjugates exhibit tunable signaling properties and enhanced transcriptional outputs at neurokinin receptor‐1	11
Ca2+‐induced structural changes and intramolecular interactions in N‐terminal region of diacylglycerol kinase alpha	11
Structural investigation on SPI‐6–associated Salmonella typhimuriumVirG‐like stress protein that promotes pathogen survival in macrophages	11
Heparins mediate the multimer assembly of secreted Noggin	10
Trifluoroethanol and the behavior of a tardigrade desiccation‐tolerance protein	10
Liquid–liquid phase separation of tau: From molecular biophysics to physiology and disease	10
Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion‐binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu	10
Site‐specific photo‐crosslinking/cleavage for protein–protein interface identification reveals oligomeric assembly of lysosomal‐associated membrane protein type 2A in mammalian cells	10
Simple mechanisms for the evolution of protein complexity	10
Large library docking for novel SARS‐CoV‐2 main protease non‐covalent and covalent inhibitors	10
The variable domain from dynamin‐related protein 1 promotes liquid–liquid phase separation that enhances its interaction with cardiolipin‐containing membranes	10
A look beyond the QR code of SNARE proteins	10
Deciphering CAD: Structure and function of a mega‐enzymatic pyrimidine factory in health and disease	10

Exploring the pH dependence of the SARS‐CoV‐2 complete fusion domain and the role of its unique structural features	10
The return of the rings: Evolutionary convergence of aromatic residues in the intrinsically disordered regions of RNA‐binding proteins for liquid–liquid phase separation	10
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	10
Engineering minimal tissue inhibitors of metalloproteinase targeting MMPs via gene shuffling and yeast surface display	10
Stabilization of the open conformation οf insulin‐regulated aminopeptidase by a novel substrate‐selective small‐molecule inhibitor	10
Exploring protein functions from structural flexibility using CABS‐flex modeling	10
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Xplor‐NIH: Better parameters and protocols for NMR protein structure determination	10
Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery	10
Protein structure–function continuum model: Emerging nexuses between specificity, evolution, and structure	10
Torsion angles to map and visualize the conformational space of a protein	10
Classifying metal‐binding sites with neural networks	10
A novel method for recombinant mammalian‐expressed S‐HBsAg virus‐like particle production for assembly status analysis and improved anti‐HBs serology	9
Crystal structure of semisynthetic obelin‐v	9
Structure‐based design of a Plasmodium vivax Duffy‐binding protein immunogen focuses the antibody response to functional epitopes	9
Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures	9
New insights into cancer: MDM2 binds to the citrullinating enzyme PADI4	9
Molecular basis of the CYFIP2 and NCKAP1 autism‐linked variants in the WAVE regulatory complex	9
A coarse‐grained model for disordered and multi‐domain proteins	9
Biophysical characterization of RelA–p52 NF‐κB dimer—A link between the canonical and the non‐canonical NF‐κB pathway	9
Dynamic interchange between two protonation states is characteristic of active sites of cholinesterases	9
Structural and functional study of Legionella pneumophila effector RavA	9
Uncovering the promiscuous activity of IL‐6 proteins: A multi‐dimensional analysis of phylogeny, classification and residue conservation	9
Rapid prediction and analysis of protein intrinsic disorder	9
DALI shines a light on remote homologs: One hundred discoveries	9
A suicidal and extensively disordered luciferase with a bright luminescence	9
Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B	9
Structural dynamics and binding of Caenorhabditis elegans lifespan‐extending lipid binding protein‐3 to polyunsaturated fatty acids	9
Issue information	9
The myth of high‐resolution liquid phase biological electron microscopy	9
BenchmarkingAlphaFoldfor protein complex modeling reveals accuracy determinants	9
Correction to “Award Winners and Abstracts of the 30th Anniversary Symposium of the Protein Society, Baltimore, MD, July 16–19, 2016”	9
Structural polymorphism and cytotoxicity of brain‐derived β‐amyloid extracts	9
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase	9
Ion mobility mass spectrometry unveils conformational effects of drug lead EPI‐001 on the intrinsically disordered N‐terminal domain of the androgen receptor	9
RosettaDDGPrediction for high‐throughput mutational scans: From stability to binding	9
Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity	9
N‐terminal acetylation modestly enhances phase separation and reduces aggregation of the low‐complexity domain of RNA‐binding protein fused in sarcoma	8
Evolutionary analysis of Quinone Reductases 1 and 2 suggests that NQO2 evolved to function as a pseudoenzyme	8
AlphaFold2 fails to predict protein fold switching	8
Adenosine triphosphate energy‐independently controls protein homeostasis with unique structure and diverse mechanisms	8
Mining unique cysteine synthetases and computational study on thoroughly eliminating feedback inhibition through tunnel engineering	8
A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin α‐dependent nuclear localization signals	8
Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint	8
PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education	8
Disulfide‐mediated oligomerization of mutant Cu/Zn‐superoxide dismutase associated with canine degenerative myelopathy	8
Phosphorylation of cytochrome c at tyrosine 48 finely regulates its binding to the histone chaperone SET/TAF‐Iβ in the nucleus	8
Liquid–liquid phase separation of α‐synuclein is highly sensitive to sequence complexity	8
Doses for X‐ray and electron diffraction: New features in RADDOSE‐3D including intensity decay models	8
Characterization of protein–ligand binding interactions of enoyl‐ACP reductase (FabI) by native MS reveals allosteric effects of coenzymes and the inhibitor triclosan	8
Biophysical insights into the dimer formation of human Sirtuin 2	8
Intrinsic protein disorder and conditional folding in AlphaFoldDB	8
AlzDiscovery: A computational tool to identify Alzheimer's disease‐causing missense mutations using protein structure information	8
Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling	8
A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins	8
The catalytic domain of free or ligand bound histone deacetylase 4 occurs in solution predominantly in closed conformation	8
Development of artificial photosystems based on designed proteins for mechanistic insights into photosynthesis	8
The evolution of the antimicrobial peptide database over 18 years: Milestones and new features	8
Degradation mechanism of AtrA mediated by ClpXP and its application in daptomycin production in Streptomyces roseosporus	8
ArtiaX: An electron tomography toolbox for the interactive handling of sub‐tomograms in UCSF ChimeraX	8
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Canonical or noncanonical? Structural plasticity of serine protease‐binding loops in Kunitz‐STI protease inhibitors	7
Characterization of βB2‐crystallin tryptophan mutants reveals two different folding states in solution	7
Molecular basis for different substrate‐binding sites and chaperone functions of the BRICHOS domain	7
Signal peptide stabilizes folding and inhibits misfolding of serum amyloid A	7
Rheostat functional outcomes occur when substitutions are introduced at nonconserved positions that diverge with speciation	7
Evaluation of acyllysine isostere interactions with the aromatic pocket of the AF9 YEATS domain	7
Phenotypic mutations contribute to protein diversity and shape protein evolution	7
Allosteric links between the hydrophilic N‐terminus and transmembrane core of human Na+/H+ antiporter NHA2	7
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Erratum	7
Structure–function mapping and mechanistic insights on the SARS CoV2 Nsp1	7
Award Winners/Abstracts from the 36th Annual Symposium of The Protein Society, July 7 – 10, 2022	7
Lectin‐anticancer peptide fusion demonstrates a significant cancer‐cell‐selective cytotoxic effect and inspires the production of “clickable” anticancer peptide in Escherichia coli	7
The oligomeric states of dye‐decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation	7
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway	7
Local sequence‐structure relationships in proteins	7
Vitamin D and COVID‐19: A review on the role of vitamin D in preventing and reducing the severity of COVID‐19 infection	7
DbStRiPs: Database of structural repeats in proteins	7
Efficient and economic protein labeling for NMR in mammalian expression systems: Application to a preT‐cell and T‐cell receptor protein	7
Capturing the geometry, function, and evolution of enzymes with 3D templates	7
Correction to “A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins”	7
Evaluation of AlphaFold2 structures as docking targets	7
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Biophysical investigation of interactions between SARS‐CoV‐2 spike protein and neuropilin‐1	7
Structural and functional characterization of Aedes aegypti pupal cuticle protein that controls dengue virus infection	7
Discovery of periplasmic solute binding proteins with specificity for ketone bodies: β‐hydroxybutyrate binding proteins	7
A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction	7
Neutralizing antibodies targeting the SARS‐CoV‐2 receptor binding domain isolated from a naïve human antibody library	7
Characterization of the Escherichia coli pyridoxal 5′‐phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability	7
Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family	7
1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes	7
Characterization of the SARS‐CoV‐2 E Protein: Sequence, Structure, Viroporin, and Inhibitors	7
Protection by desiccation‐tolerance proteins probed at the residue level	7
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