Protein Science

Article	Citations
	1525
Structural and functional validation of a highly specific Smurf2 inhibitor	1238
Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone	519
Soluble SARS‐CoV‐2 RBD and human ACE2 peptidase domain produced in DrosophilaS2 cells show functions evoking virus–cell interface	372
Epitope‐directed anti‐SARS‐CoV‐2 scFv engineered against the key spike protein region could block membrane fusion	338
Two residues determine nicotinic acetylcholine receptor requirement for RIC‐3	252
An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis	222
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix	209
Cover Image	204
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	173
Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS‐fold glucosamine‐6‐phosphate deaminases	137
Evolution of affinity between p53 transactivation domain and MDM2 across the animal kingdom demonstrates high plasticity of motif‐mediated interactions	123
Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers	122
	118
Structure–function mapping and mechanistic insights on the SARS CoV2 Nsp1	92
Biophysical insights into the dimer formation of human Sirtuin 2	92
Design of an effective small expression tag to enhance GPCR production in E. coli‐based cell‐free and whole cell expression systems	91
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD	91
A novel method for expressing and purifying large quantities of functional and stable human voltage‐gated proton channel (hHv1)	83
Issue information	74
Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains	73
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	62
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase	60
Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins	58
Torsional twist of the SARS‐CoV and SARS‐CoV‐2 SUD‐N and SUD‐M domains	58

Epitope mapping of novel monoclonal antibodies to human angiotensin I‐converting enzyme	55
Similar protein segments shared between domains of different evolutionary lineages	53
CsgA gatekeeper residues control nucleation but not stability of functional amyloid	53
Biophysical characterization of RelA–p52 NF‐κB dimer—A link between the canonical and the non‐canonical NF‐κB pathway	52
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	46
Fine‐tuned interactions between globular and disordered regions of single‐stranded DNA binding (SSB) protein are required for dynamic condensation under physiological conditions	45
Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequence properties of protein‐binding zinc fingers	44
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	42
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	36
Xplor‐NIH: Better parameters and protocols for NMR protein structure determination	36
Large library docking for novel SARS‐CoV‐2 main protease non‐covalent and covalent inhibitors	35
Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion‐binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu	35
Structural polymorphism and cytotoxicity of brain‐derived β‐amyloid extracts	33
Torsion angles to map and visualize the conformational space of a protein	33
Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B	33
Structure‐based clustering and mutagenesis of bacterial tannases reveals the importance and diversity of active site‐capping domains	32
Cover Image	32
Correction to “The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament”	32
Cumulative asparagine to aspartate deamidation fails to perturb γD‐crystallin structure and stability	32
Structural features of thyroglobulin linked to protein trafficking	32
Synonymous and non‐synonymous codon substitutions can alleviate dependence on GroEL for folding	31
Ca2+ attenuates nucleation activity of leiomodin	30
Issue Information	30
Evolution of homo‐oligomerization of methionine S‐adenosyltransferases is replete with structure–function constrains	30
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02	29
Control of a far‐red/near‐infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin	29
Structure‐based alteration of tryptophan residues of the multidrug transporter CmABCB1 to assess substrate binding using fluorescence spectroscopy	29
Integrative visualization of the molecular structure of a cellular microdomain	28
Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation	28
Cover Image	28
Biophysical investigation of interactions between SARS‐CoV‐2 spike protein and neuropilin‐1	27
A useful epitope tag derived from maltose binding protein	27
Molecular basis for different substrate‐binding sites and chaperone functions of the BRICHOS domain	27
Controlled by disorder: Phosphorylation modulates SRSF1 domain availability for spliceosome assembly	26
Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding	26
Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product‐inhibition mechanism and oxygen gatekeeper	26
PEG–mCherry interactions beyond classical macromolecular crowding	25
Inhibition of bacterial FMN transferase: A potential avenue for countering antimicrobial resistance	25
Phenotypic mutations contribute to protein diversity and shape protein evolution	23
Mesoscale explorer: Visual exploration of large‐scale molecular models	23
Discovery of broadly‐neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens	22
Two different kinds of interaction modes of deaminase APOBEC3A with single‐stranded DNA in solution detected by nuclear magnetic resonance	22
Chemical and temporal manipulation of early steps in protein assembly tunes the structure and intermolecular interactions of protein‐based materials	22
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway	21
Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work	21
Biochemical and structural characterization of meningococcal methylenetetrahydrofolate reductase	21
A competition smFRET assay to study ligand‐induced conformational changes of the dengue virus protease	21
Loop engineering of enzymes to control their immobilization and ultimately fabricate more efficient heterogeneous biocatalysts	21
A systematic pipeline of protein structure selection for computer‐aided drug discovery: A case study on T790M/L858R mutant EGFR structures	20
PocketOptimizer 2.0: A modular framework for computer‐aided ligand‐binding design	20

ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction	20
Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination	20
The oligomeric states of dye‐decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation	20
Design principles that protect the proteasome from self‐destruction	19
Issue information	19
Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation	19
Probing binding and occlusion of substrate in the human creatine transporter‐1 by computation and mutagenesis	19
Tuning the stator subunit of the flagellar motor with coiled‐coil engineering	19
Domain swapping of the C‐terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis	19
Issue information	19
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	19
Dimeric assembly of human Suv3 helicase promotes its RNA unwinding function in mitochondrial RNA degradosome for RNA decay	18
A conserved motif in Henipavirus P/V/W proteins drives the fibrillation of the W protein from Hendra virus	18
Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity	18
An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase MtLYR3	18
Programmable protein topology via SpyCatcher‐SpyTag chemistry in one‐pot cell‐free expression system	18
Orthogonal translation with 5‐cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding	18
Protein degradation of antizyme depends on the N‐terminal degrons	18
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D	18
Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3	18
Construction of a versatile fusion protein for targeted therapy and immunotherapy	17
The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the E. coli L‐asparaginase EcAIII	17
Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase	17
	17
ATP regulates RNA‐driven cold inducible RNA binding protein phase separation	17
Modulation of TRPV2 by endogenous and exogenous ligands: A computational study	17
iLight2: A near‐infrared optogenetic tool for gene transcription with low background activation	17
Partitioning the Hill coefficient into contributions from ligand‐promoted conformational changes and subunit heterogeneity	17
Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations	17
A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP)	17
Photomodulation of the ASIC1a acidic pocket destabilizes the open state	17
Issue information	16
Accounting for nonuniformity of bulk‐solvent: A mosaic model	16
Issue information	16
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	16
Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways	16
Cover Image	16
De novo design of monomeric helical bundles for pH‐controlled membrane lysis	16
Introduction: Biophysics of biomolecular condensates	16
Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5T	15
KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing	15
Issue information	15
Global analysis of kinetics reveals the role of secondary nucleation in recombinant spider silk self‐assembly	15
Thermostability and binding properties of single‐chained Fv fragments derived from therapeutic antibodies	15
Active site center redesign increases protein stability preserving catalysis in thioredoxin	15
The Ca2+ response of a smart forisome protein is dependent on polymerization	15
Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125	15
Targeting MarA N‐terminal domain dynamics to prevent DNA binding	14
Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns	14
Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all‐atom simulations	14
	14
Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants	14
Expanding the genetic code	14
Heterogeneous folding landscapes and predetermined breaking points within a protein family	14
SG‐ML‐PLAP: A structure‐guided machine learning–based scoring function for protein–ligand binding affinity prediction	14
MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2	14
AggNet: Advancing protein aggregation analysis through deep learning and protein language model	14
Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair	13
Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi	13
CMM—An enhanced platform for interactive validation of metal binding sites	13
Design of a yeast SUMO tag to eliminate internal translation initiation	13
Structure and activity of a bacterial defense‐associated 3′‐5′ exonuclease	13
Ferritin‐based disruptor nanoparticles: A novel strategy to enhance LDL cholesterol clearance via multivalent inhibition of PCSK9–LDL receptor interaction	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
Revisiting the hydrolysis of ampicillin catalyzed by Temoneira‐1 β‐lactamase, and the effect of Ni(II), Cd(II) and Hg(II)	13
Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi‐enzyme colocalization and environment	13
Destabilization of polar interactions in the prion protein triggers misfolding and oligomerization	13
IEDB‐3D 2.0: Structural data analysis within the Immune Epitope Database	13
Protein structure accuracy estimation using geometry‐complete perceptron networks	13
A cascade of sulfur transferases delivers sulfur to the sulfur‐oxidizing heterodisulfide reductase‐like complex	13
The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum	13
Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1	13
Differential effects of disulfide bond formation in TEM‐1 versus CTX‐M‐9 β‐lactamase	13
Crystal structure and molecular dynamics of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability	13
Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono‐PEGylated alpha‐1 antitrypsin	13
Kunitz‐type trypsin inhibitor from durian (Durio zibethinus) employs a distinct loop for trypsin inhibition	13
	13
Theta‐curves in proteins	12
Ordered ATP hydrolysis in the Hsp90 chaperone is regulated by Aha1 and a conserved post‐translational modification	12
Issue information	12

FOXO4 interacts with p53 TAD and CRD and inhibits its binding to DNA	12
A disulfide chaperone knockout facilitates spin labeling and pulse EPR spectroscopy of outer membrane transporters	12
Issue information	12
Ligation of multiple protein domains using orthogonal inteins with non‐native splice junctions	12
Exploring the molecular mechanism of cold‐adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network	12
Clustering protein functional families at large scale with hierarchical approaches	12
Structural and biochemical characterization of the C‐terminal region of the human RTEL1 helicase	12
A new strategy to reconcile amyloid cross‐seeding and amyloid prevention in a binary system of α‐synuclein fragmental peptide and hIAPP	12
A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase	12
Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63	11
Cover Image	11
Structure‐based insights into the mechanism of [4Fe‐4S]‐dependent sulfur insertase LarE	11
Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy	11
Constant domain polymorphisms influence monoclonal antibody stability and dynamics	11
Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials	11
A protein fitness predictive framework based on feature combination and intelligent searching	11
Biochemical properties of VGLL4 from Homo sapiens and Tgi from Drosophila melanogaster and possible biological implications	11
Cover Image	11
LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation	11
DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning	11
Molecular insight into the specific interactions of the SARS‐Coronavirus‐2 nucleocapsid with RNA and host protein	11
Cover Image	11
Membrane tension‐dependent conformational change of Isoleucine 106 of loop B diminishes water permeability in FaPIP2;1	11
Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases	11
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	11
KCD: A prediction web server of knowledge‐based circular dichroism	11
Assessing the functional impact of protein binding site definition	11
Structural and functional characterization of the cytotoxic protein ledodin, an atypical ribosome‐inactivating protein from shiitake mushroom (Lentinula edodes)	11
SPI “sandwich”: Combined SUMO‐Peptide‐Intein expression system and isolation procedure for improved stability and yield of peptides	10
Labile assembly of a tardigrade protein induces biostasis	10
Optimized genetic code expansion technology for time‐dependent induction of adhesion GPCR‐ligand engagement	10
Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study	10
Computed cancer interactome explains the effects of somatic mutations in cancers	10
U‐CIE [/juː ‘siː/]: Color encoding of high‐dimensional data	10
Cover Image	10
Structural basis for the stereospecific inhibition of the dual proline/hydroxyproline catabolic enzyme ALDH4A1 by trans‐4‐hydroxy‐L‐proline	10
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, Asx helix caps, bet	10
VirulentPred 2.0: An improved method for prediction of virulent proteins in bacterial pathogens	10
Identification of amyloidogenic proteins in the microbiomes of a rat Parkinson's disease model and wild‐type rats	10
Structural adaptability and surface activity of peptides derived from tardigrade proteins	10
Site‐directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus	10
Structure–function analysis of cysteine residues in the plasmodium falciparum chitinase, PfCHT1	10
Quantitative analyses for effects of neddylation on CRL2VHL substrate ubiquitination and degradation	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
Conformational features and interaction mechanisms of VHH antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction	10
SMOG 2 and OpenSMOG: Extending the limits of structure‐based models	10
A favorable path to domain separation in the orange carotenoid protein	10
Preferential binding of ADP‐bound mitochondrial HSP70 to the nucleotide exchange factor GRPEL1 over GRPEL2	10
	9
	9
Issue information	9
	9
Characterization of protein–ligand binding interactions of enoyl‐ACP reductase (FabI) by native MS reveals allosteric effects of coenzymes and the inhibitor triclosan	9
PairK: Pairwise k‐mer alignment for quantifying protein motif conservation in disordered regions	9
Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery	9
PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education	9
Molecular insights into alginate β‐lactoglobulin A multivalencies—The foundation for their amorphous aggregates and coacervation	9
Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain	9
A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin α‐dependent nuclear localization signals	9
The role of phospholipid saturation and composition in α‐synuclein aggregation and toxicity: A dual in vitro and in vivo approach	9
Engineering G protein‐coupled receptors for stabilization	9
Characterization of an aminotransferase from Acanthamoeba polyphagaMimivirus	9
Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis	9
Site‐specific photo‐crosslinking/cleavage for protein–protein interface identification reveals oligomeric assembly of lysosomal‐associated membrane protein type 2A in mammalian cells	9
Inline small‐angle X‐ray scattering‐coupled chromatography under extreme hydrostatic pressure	9
In This Issue	9
Degradation mechanism of AtrA mediated by ClpXP and its application in daptomycin production in Streptomyces roseosporus	9
Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes	9
The structural landscape of the immunoglobulin fold by large‐scale de novo design	9
Issue information	9
KEGG mapping tools for uncovering hidden features in biological data	9
Parkinson's disease‐linked V15A mutation facilitates α‐synuclein aggregation by reducing membrane affinity	9
Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins	9
Probing effects of site‐specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis	9
Exploring the druggability of the UEV domain of human TSG101 in search for broad‐spectrum antivirals	9
Issue information	9
Structural dynamics and binding of Caenorhabditis elegans lifespan‐extending lipid binding protein‐3 to polyunsaturated fatty acids	8
Protection by desiccation‐tolerance proteins probed at the residue level	8
Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity	8
Dual‐wield NTPases: A novel protein family mined from AlphaFold DB	8
Issue information	8
	8
Ion mobility mass spectrometry unveils conformational effects of drug lead EPI‐001 on the intrinsically disordered N‐terminal domain of the androgen receptor	8
Diphtheria toxin‐derived, anti‐PD‐1 immunotoxin, a potent and practical tool to selectively deplete PD‐1+ cells	8
MRS2 missense variation at Asp216 abrogates inhibitory Mg2+ binding, potentiating cell migration and apoptosis resistance	8
	8
PTM‐Psi: A python package to facilitate the computational investigation of post‐translational modification on p	8
Cover Image	8
Heat‐induced structural and chemical changes to a computationally designed miniprotein	8
Examining the mechanistic relationship of APC/CCDH1 and its interphase inhibitor EMI1	8
ArtiaX: An electron tomography toolbox for the interactive handling of sub‐tomograms in UCSF ChimeraX	8
Restoring adapter protein complex 4 function with small molecules: an in silico approach to spastic paraplegia 50	8
Growth hormone receptor agonists and antagonists: From protein expression and purification to long‐acting formulations	8
Award Winners/Abstracts from the 36th Annual Symposium of The Protein Society, July 7 – 10, 2022	8
Efficient and economic protein labeling for NMR in mammalian expression systems: Application to a preT‐cell and T‐cell receptor protein	8