Protein Science

Article	Citations
Electronegative clusters modulate folding status and RNA binding of unstructured RNA‐binding proteins	1363
Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone	1178
Dimerization of the CNNM extracellular domain	507
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Issue information	323
Structural insights into the unique recognition module between α‐synuclein peptide and nanobody	243
Escherichia coli strains with precise domain deletions in the ribonuclease RNase E can achieve greatly enhanced levels of membrane protein production	211
Structural and functional validation of a highly specific Smurf2 inhibitor	202
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix	189
Issue information	167
Protein salvage and repurposing in evolution: Phospholipase D toxins are stabilized by a remodeled scrap of a membrane association domain	130
ParSe 2.0: A web tool to identify drivers of protein phase separation at the proteome level	121
Binding specificity of type three secretion system effector NleH2 to multi‐cargo chaperone CesT and their phosphorylation	113
Characterization of the SARS‐CoV‐2 E Protein: Sequence, Structure, Viroporin, and Inhibitors	112
Evolutionary analysis of Quinone Reductases 1 and 2 suggests that NQO2 evolved to function as a pseudoenzyme	95
Protection by desiccation‐tolerance proteins probed at the residue level	90
CC+: A searchable database of validated coiled coils in PDB structures and AlphaFold2 models	88
Cover Image	86
Synthetic antibodies block receptor binding and current‐inhibiting effects of α‐cobratoxin from Naja kaouthia	82
Arginine cluster introduction on framework region in anti‐lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops	76
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Structure determination of an unstable macromolecular complex enabled by nanobody‐peptide bridging	68
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In This Issue	58
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How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins	56
Structural studies of intrinsically disordered MLL‐fusion protein AF9 in complex with peptidomimetic inhibitors	56
Reconstitution and characterization of BRAF in complex with 14‐3‐3 and KRAS4B on nanodiscs	54
An ensemble machine learning model generates a focused screening library for the identification of CDK8 inhibitors	52
Characterization of a novel format scFv×VHH single‐chain biparatopic antibody against metal binding protein MtsA	51
Engineering G protein‐coupled receptors for stabilization	50
Native ion mobility‐mass spectrometry reveals the binding mechanisms of anti‐amyloid therapeutic antibodies	50
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD	45
In vitro characterization of the intramelanosomal domain of human recombinant TYRP1 and its oculocutaneous albinism type 3‐related mutant variants	44
Molecular insights into alginate β‐lactoglobulin A multivalencies—The foundation for their amorphous aggregates and coacervation	42
Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS‐fold glucosamine‐6‐phosphate deaminases	40
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Engineered protein G variants for multifunctional antibody‐based assemblies	34
A functional helix shuffled variant of the B domain of Staphylococcus aureus	34
Hijacking of plasminogen by dengue virus: The kringle‐4 and ‐5 domains of plasminogen binds synergistically to the domain I of envelope protein	32
Methods for detecting, building, and improving tryptophan mannosylation in glycoprotein structures	32
A novel method for expressing and purifying large quantities of functional and stable human voltage‐gated proton channel (hHv1)	32
Insights into the flexibility of the domain‐linking loop in actinobacterial coproheme decarboxylase through structures and molecular dynamics simulations	31
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Inline small‐angle X‐ray scattering‐coupled chromatography under extreme hydrostatic pressure	30
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Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes	30
A conserved electrostatic membrane‐binding surface in synaptotagmin‐like proteins revealed using molecular phylogenetic analysis and homology modeling	29
QSAR via multisite λ‐dynamics in the orphaned TSSK1B kinase	29
Diphtheria toxin‐derived, anti‐PD‐1 immunotoxin, a potent and practical tool to selectively deplete PD‐1+ cells	29
Reply to “Intrinsic protein disorder uncouples affinity from binding specificity”	29
Torsion angles to map and visualize the conformational space of a protein	29
Interface engineering of cellobiose dehydrogenase improves interdomain electron transfer	29
Issue Information	28
Engineering minimal tissue inhibitors of metalloproteinase targeting MMPs via gene shuffling and yeast surface display	28
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Issue information	27
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Characterization of an aminotransferase from Acanthamoeba polyphagaMimivirus	24
Allosteric regulatory control in dihydrofolate reductase is revealed by dynamic asymmetry	23
EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components	23
Protein ensemble modeling and analysis with MMMx	22
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CsgA gatekeeper residues control nucleation but not stability of functional amyloid	21
Structural characterization of the Sel1‐like repeat protein LceB from Legionella pneumophila	21
Evaluating the potential of non‐immunosuppressive cyclosporin analogs for targeting Toxoplasma gondii cyclophilin: Insights from structural studies	21
Parkinson's disease‐linked V15A mutation facilitates α‐synuclein aggregation by reducing membrane affinity	21
Probing effects of site‐specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis	21
Development of charybdotoxin Q18F variant as a selective peptide blocker of neuronal BK(α + β4) channel for the treatment of epileptic seizures	20
GGAssembler: Precise and economical design and synthesis of combinatorial mutation libraries	20
Soluble SARS‐CoV‐2 RBD and human ACE2 peptidase domain produced in DrosophilaS2 cells show functions evoking virus–cell interface	19
Selection of a PD‐1 blocking antibody from a novel fully human phage display library	19
Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS‐CoV‐2	19

Probing the effect of glycosaminoglycan depletion on integrin interactions with collagen I fibrils in the native extracellular matrix environment	19
Examining the mechanistic relationship of APC/CCDH1 and its interphase inhibitor EMI1	18
Synthesis and degradation of the cyclic dinucleotide messenger c‐di‐AMP in the hyperthermophilic archaeon Pyrococcus yayanosii	18
Two residues determine nicotinic acetylcholine receptor requirement for RIC‐3	18
An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis	18
Issue information	18
nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological Magnetic Resonance Data Bank	18
Design of an effective small expression tag to enhance GPCR production in E. coli‐based cell‐free and whole cell expression systems	18
Dissecting the general mechanisms of protein cage self‐assembly by coarse‐grained simulations	18
Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins	17
More is simpler: Decomposition of ligand‐binding affinity for proteins being disordered	17
A hierarchical deep learning based approach for multi‐functional enzyme classification	17
Issue information	17
Nucleocapsid proteins from human coronaviruses possess phase separation capabilities and promote FUS pathological aggregation	17
Engineering gain‐of‐function mutants of a WW domain by dynamics and structural analysis	17
Condensation of the β‐cell secretory granule luminal cargoes pro/insulin and ICA512 RESP18 homology domain	17
From a dimer to a monomer: Construction of a chimeric monomeric isocitrate dehydrogenase	17
Issue information	17
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Reevaluation of bromodomain ligands targeting BAZ2A	17
Liquid–liquid phase separation of α‐synuclein is highly sensitive to sequence complexity	16
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	16
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	16
Structure‐based analysis and evolution of a monomerized red‐colored chromoprotein from the Olindias formosa jellyfish	16
Human islet amyloid polypeptide‐induced β‐cell cytotoxicity is linked to formation of α‐sheet structure	16
Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers	15
Exhaustive mutational analysis of severe acute respiratory syndrome coronavirus 2 ORF3a: An essential component in the pathogen's infectivity cycle	15
Structural characterization of an intrinsically disordered protein complex using integrated small‐angle neutron scattering and computing	15
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	15
Tubulin‐binding region alters tau–lipid interactions and changes toxicity of tau fibrils formed in the presence of phosphatidylserine lipids	15
Kinetic isotope effect reveals rate‐limiting step in green‐to‐red photoconvertible fluorescent proteins	15
Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis	15
Structural investigation on SPI‐6–associated Salmonella typhimuriumVirG‐like stress protein that promotes pathogen survival in macrophages	14
Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B	14
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	14
Structural polymorphism and cytotoxicity of brain‐derived β‐amyloid extracts	14
Uncovering the promiscuous activity of IL‐6 proteins: A multi‐dimensional analysis of phylogeny, classification and residue conservation	14
Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery	14
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase	14
Epitope‐directed anti‐SARS‐CoV‐2 scFv engineered against the key spike protein region could block membrane fusion	13
Engineering of IF1‐susceptive bacterial F1‐ATPase	13
Multiplex measurement of protein–peptide dissociation constants using dialysis and mass spectrometry	13
Correction to “Award Winners and Abstracts of the 30th Anniversary Symposium of the Protein Society, Baltimore, MD, July 16–19, 2016”	13
Dynamic interchange between two protonation states is characteristic of active sites of cholinesterases	13
Structural dynamics and binding of Caenorhabditis elegans lifespan‐extending lipid binding protein‐3 to polyunsaturated fatty acids	13
Ion mobility mass spectrometry unveils conformational effects of drug lead EPI‐001 on the intrinsically disordered N‐terminal domain of the androgen receptor	13
Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter jejuni via targeting different sites with different scaffolds	13
Adaptable SEC‐SAXS data collection for higher quality structure analysis in solution	13
The structural landscape of the immunoglobulin fold by large‐scale de novo design	13
Issue information	13
Structure‐based design of a Plasmodium vivax Duffy‐binding protein immunogen focuses the antibody response to functional epitopes	13
Molecular basis of the CYFIP2 and NCKAP1 autism‐linked variants in the WAVE regulatory complex	13
Expanding the family of extracellular chaperones: Identification of human plasma proteins with chaperone activity	13
Big versus small: The impact of aggregate size in disease	13
Evolution of affinity between p53 transactivation domain and MDM2 across the animal kingdom demonstrates high plasticity of motif‐mediated interactions	13
HadBD dehydratase from Mycobacterium tuberculosis fatty acid synthase type II: A singular structure for a unique function	13
A suicidal and extensively disordered luciferase with a bright luminescence	13
Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion‐binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu	13
A novel method for recombinant mammalian‐expressed S‐HBsAg virus‐like particle production for assembly status analysis and improved anti‐HBs serology	13
Computational design of N‐linked glycans for high throughput epitope profiling	13
Protein stability models fail to capture epistatic interactions of double point mutations	12
A crucial active site network of titratable residues guides catalysis and NAD+ binding in human succinic semialdehyde dehydrogenase	12
Heat‐induced structural and chemical changes to a computationally designed miniprotein	12
Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains	12
In situ characterization of amine‐forming enzymes shows altered oligomeric state	12
Exploring the druggability of the UEV domain of human TSG101 in search for broad‐spectrum antivirals	12
QuoteTarget: A sequence‐based transformer protein language model to identify potentially druggable protein targets	12
Ca2+‐induced structural changes and intramolecular interactions in N‐terminal region of diacylglycerol kinase alpha	12
PairK: Pairwise k‐mer alignment for quantifying protein motif conservation in disordered regions	12
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Only kosmotrope anions trigger fibrillization of the recombinant core spidroin eADF4(C16) from Araneus diadematus	12
The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament	12
Large library docking for novel SARS‐CoV‐2 main protease non‐covalent and covalent inhibitors	11
Site‐specific photo‐crosslinking/cleavage for protein–protein interface identification reveals oligomeric assembly of lysosomal‐associated membrane protein type 2A in mammalian cells	11
Heparins mediate the multimer assembly of secreted Noggin	11
A look beyond the QR code of SNARE proteins	11
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Protein structure–function continuum model: Emerging nexuses between specificity, evolution, and structure	11
Exploring protein functions from structural flexibility using CABS‐flex modeling	11
Stabilization of the open conformation οf insulin‐regulated aminopeptidase by a novel substrate‐selective small‐molecule inhibitor	11

Trifluoroethanol and the behavior of a tardigrade desiccation‐tolerance protein	11
Simple mechanisms for the evolution of protein complexity	11
Classifying metal‐binding sites with neural networks	11
The variable domain from dynamin‐related protein 1 promotes liquid–liquid phase separation that enhances its interaction with cardiolipin‐containing membranes	11
Crystal structure of semisynthetic obelin‐v	10
Adenosine triphosphate energy‐independently controls protein homeostasis with unique structure and diverse mechanisms	10
Degradation mechanism of AtrA mediated by ClpXP and its application in daptomycin production in Streptomyces roseosporus	10
New insights into cancer: MDM2 binds to the citrullinating enzyme PADI4	10
The catalytic domain of free or ligand bound histone deacetylase 4 occurs in solution predominantly in closed conformation	10
Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling	10
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Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity	10
Characterization of protein–ligand binding interactions of enoyl‐ACP reductase (FabI) by native MS reveals allosteric effects of coenzymes and the inhibitor triclosan	10
Biophysical insights into the dimer formation of human Sirtuin 2	10
Mining unique cysteine synthetases and computational study on thoroughly eliminating feedback inhibition through tunnel engineering	10
A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins	10
Disulfide‐mediated oligomerization of mutant Cu/Zn‐superoxide dismutase associated with canine degenerative myelopathy	10
Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint	10
Development of artificial photosystems based on designed proteins for mechanistic insights into photosynthesis	10
A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin α‐dependent nuclear localization signals	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
PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education	10
Phosphorylation of cytochrome c at tyrosine 48 finely regulates its binding to the histone chaperone SET/TAF‐Iβ in the nucleus	10
Structure–function mapping and mechanistic insights on the SARS CoV2 Nsp1	10
Issue information	9
Engineering a monobody specific to monomeric Cu/Zn‐superoxide dismutase associated with amyotrophic lateral sclerosis	9
Deciphering CAD: Structure and function of a mega‐enzymatic pyrimidine factory in health and disease	9
BenchmarkingAlphaFoldfor protein complex modeling reveals accuracy determinants	9
AlzDiscovery: A computational tool to identify Alzheimer's disease‐causing missense mutations using protein structure information	9
Allosteric inhibition of TEM‐1 β lactamase: Microsecond molecular dynamics simulations provide mechanistic insights	9
High‐throughput cell‐free screening of eukaryotic membrane protein expression in lipidic mimetics	9
Protective roles of highly conserved motif 1 in tardigrade cytosolic‐abundant heat soluble protein in extreme environments	9
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Taming interleukin‐12: Engineering of bispecific antibody‐based IL‐12 mimetics with biased agonism capacities	9
Erratum	9
Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures	9
Exploring the pH dependence of the SARS‐CoV‐2 complete fusion domain and the role of its unique structural features	9
ArtiaX: An electron tomography toolbox for the interactive handling of sub‐tomograms in UCSF ChimeraX	9
Evaluation of AlphaFold2 structures as docking targets	9
Semi‐synthetic nanobody‐ligand conjugates exhibit tunable signaling properties and enhanced transcriptional outputs at neurokinin receptor‐1	9
Reconstitution and use of highly active human CDK1:Cyclin‐B:CKS1 complexes	9
Diversity in the protective role(s) of the conserved motif 1 from tardigrade cytoplasmic‐abundant heat‐soluble proteins during drying	9
Insights into the low‐temperature adaptation of an enzyme as studied through ancestral sequence reconstruction	9
Similar protein segments shared between domains of different evolutionary lineages	9
Folding of a tandemly knotted protein: Evidence that a polypeptide chain can get out of deep kinetic traps	9
Transition metal cation inhibition of Mycobacterium tuberculosis esterase RV0045C	9
What the protein data bank tells us about the evolutionary conservation of protein conformational diversity	9
Hydrophobicity and molecular mass‐based separation method for autoantibody discovery from mammalian total cellular proteins	9
Doses for X‐ray and electron diffraction: New features in RADDOSE‐3D including intensity decay models	9
Liquid–liquid phase separation of tau: From molecular biophysics to physiology and disease	9
Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins	9
The myth of high‐resolution liquid phase biological electron microscopy	9
Non‐canonical ORFs‐derived protein products in mitochondria: A multifaceted exploration of their functions in health and disease	9
Torsional twist of the SARS‐CoV and SARS‐CoV‐2 SUD‐N and SUD‐M domains	9
Correction to “A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins”	9
RosettaDDGPrediction for high‐throughput mutational scans: From stability to binding	8
DALI shines a light on remote homologs: One hundred discoveries	8
Quantitative detection of amyloid fibrils using fluorescence resonance energy transfer between engineered yellow and cyan proteins	8
AlphaFold2 fails to predict protein fold switching	8
Intrinsic protein disorder and conditional folding in AlphaFoldDB	8
Structural insights into the fusion of annexin A5 and fluorescent proteins generating hundredfold differentiated binding affinities to phosphatidylserine	8
Rapid prediction and analysis of protein intrinsic disorder	8
Data‐driven evaluation of suitable immunogens for improved antibody selection	8
A new l‐arginine oxidase engineered from l‐glutamate oxidase	8
PDBsum extras: SARS‐CoV‐2 and AlphaFold models	8
A suite of pre‐assembled, pET28b‐based Golden Gate vectors for efficient protein engineering and expression	8
Phylogenetic convergence of phase separation and mitotic function in the disordered protein BuGZ	8
Affinity‐stability trade‐off mechanism of residue 35 in framework region 2 of VHH antibodies with β‐hairpin CDR3	8
Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequence properties of protein‐binding zinc fingers	8
Epitope mapping of novel monoclonal antibodies to human angiotensin I‐converting enzyme	8
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	8
The evolution of the antimicrobial peptide database over 18 years: Milestones and new features	8
Fine‐tuned interactions between globular and disordered regions of single‐stranded DNA binding (SSB) protein are required for dynamic condensation under physiological conditions	8
Xplor‐NIH: Better parameters and protocols for NMR protein structure determination	8
A synthetic heavy chain variable domain antibody library (VHL) provides highly functional antibodies with favorable developability	8
Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins	8
Unraveling paralog‐specific Notch signaling through thermodynamics of ternary complex formation and transcriptional activation of chimeric receptors	8
Allosteric links between the hydrophilic N‐terminus and transmembrane core of human Na+/H+ antiporter NHA2	7
Mutational and structural studies of (βα)8‐barrel fold methylene‐tetrahydropterin reductases utilizing a common catalytic mechanism	7
A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction	7
Discovery of periplasmic solute binding proteins with specificity for ketone bodies: β‐hydroxybutyrate binding proteins	7
Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family	7
Canonical or noncanonical? Structural plasticity of serine protease‐binding loops in Kunitz‐STI protease inhibitors	7
Evaluation of acyllysine isostere interactions with the aromatic pocket of the AF9 YEATS domain	7
Adaptive evolution: Eukaryotic enzyme's specificity shift to a bacterial substrate	7
Characterization of βB2‐crystallin tryptophan mutants reveals two different folding states in solution	7
Widespread amyloid aggregates formation by Zika virus proteins and peptides	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
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Characterization of the Escherichia coli pyridoxal 5′‐phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability	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
Phenotypic mutations contribute to protein diversity and shape protein evolution	7
Award Winners/Abstracts from the 36th Annual Symposium of The Protein Society, July 7 – 10, 2022	7
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway	7