Protein Science

Article	Citations
	2214
	1472
Design of an effective small expression tag to enhance GPCR production in E. coli‐based cell‐free and whole cell expression systems	463
Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains	276
Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion‐binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu	273
Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone	253
Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequence properties of protein‐binding zinc fingers	243
Fine‐tuned interactions between globular and disordered regions of single‐stranded DNA binding (SSB) protein are required for dynamic condensation under physiological conditions	156
Epitope‐directed anti‐SARS‐CoV‐2 scFv engineered against the key spike protein region could block membrane fusion	153
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD	138
Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS‐fold glucosamine‐6‐phosphate deaminases	136
Issue information	113
Evolution of affinity between p53 transactivation domain and MDM2 across the animal kingdom demonstrates high plasticity of motif‐mediated interactions	108
Biophysical insights into the dimer formation of human Sirtuin 2	106
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase	106
CsgA gatekeeper residues control nucleation but not stability of functional amyloid	85
Biophysical characterization of RelA–p52 NF‐κB dimer—A link between the canonical and the non‐canonical NF‐κB pathway	83
Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B	77
Structure–function mapping and mechanistic insights on the SARS CoV2 Nsp1	74
A novel method for expressing and purifying large quantities of functional and stable human voltage‐gated proton channel (hHv1)	71
Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins	69
Torsional twist of the SARS‐CoV and SARS‐CoV‐2 SUD‐N and SUD‐M domains	66
Cover Image	62
Extrinsic and intrinsic factors affect copper‐induced protein precipitation across eukaryotic and prokaryotic proteomes	61
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	59

An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis	54
Two residues determine nicotinic acetylcholine receptor requirement for RIC‐3	47
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix	46
Similar protein segments shared between domains of different evolutionary lineages	44
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	44
Large library docking for novel SARS‐CoV‐2 main protease non‐covalent and covalent inhibitors	42
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	42
Soluble SARS‐CoV‐2 RBD and human ACE2 peptidase domain produced in DrosophilaS2 cells show functions evoking virus–cell interface	42
Xplor‐NIH: Better parameters and protocols for NMR protein structure determination	42
A multi‐pore model of the blood–brain barrier tight junction strands recapitulates the permeability features of wild‐type and mutant claudin‐5	40
Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers	40
Structural polymorphism and cytotoxicity of brain‐derived β‐amyloid extracts	37
Torsion angles to map and visualize the conformational space of a protein	36
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	33
Structural and functional validation of a highly specific Smurf2 inhibitor	32
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	31
Issue Information	30
Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination	30
Evolution of homo‐oligomerization of methionine S‐adenosyltransferases is replete with structure–function constrains	30
PocketOptimizer 2.0: A modular framework for computer‐aided ligand‐binding design	30
Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product‐inhibition mechanism and oxygen gatekeeper	29
Loop engineering of enzymes to control their immobilization and ultimately fabricate more efficient heterogeneous biocatalysts	28
A systematic pipeline of protein structure selection for computer‐aided drug discovery: A case study on T790M/L858R mutant EGFR structures	28
The oligomeric states of dye‐decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation	27
Growth hormone receptor antagonists, GHA2 and GHA3, with dual activity against the human and mouse receptor	26
Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding	26
Two different kinds of interaction modes of deaminase APOBEC3A with single‐stranded DNA in solution detected by nuclear magnetic resonance	25
ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction	25
Inhibition of bacterial FMN transferase: A potential avenue for countering antimicrobial resistance	24
Cover Image	24
Analysis of β‐C‐terminal salt bridges in T‐state hemoglobin by trapping tertiary conformations in silica gels	24
Structural features of thyroglobulin linked to protein trafficking	23
Cover Image	23
Biochemical and structural characterization of meningococcal methylenetetrahydrofolate reductase	23
Integrative visualization of the molecular structure of a cellular microdomain	23
Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation	22
Biophysical investigation of interactions between SARS‐CoV‐2 spike protein and neuropilin‐1	22
Structure‐based clustering and mutagenesis of bacterial tannases reveals the importance and diversity of active site‐capping domains	22
Mesoscale explorer: Visual exploration of large‐scale molecular models	22
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02	22
Ca2+ attenuates nucleation activity of leiomodin	21
Control of a far‐red/near‐infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin	21
Chemical and temporal manipulation of early steps in protein assembly tunes the structure and intermolecular interactions of protein‐based materials	21
Phenotypic mutations contribute to protein diversity and shape protein evolution	21
Correction to “The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament”	21
Structure‐based alteration of tryptophan residues of the multidrug transporter CmABCB1 to assess substrate binding using fluorescence spectroscopy	21
Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation	21
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	20
Synonymous and non‐synonymous codon substitutions can alleviate dependence on GroEL for folding	20

Discovery of broadly‐neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens	20
A competition smFRET assay to study ligand‐induced conformational changes of the dengue virus protease	20
PEG–mCherry interactions beyond classical macromolecular crowding	20
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway	20
Issue information	20
Cumulative asparagine to aspartate deamidation fails to perturb γD‐crystallin structure and stability	20
Molecular basis for different substrate‐binding sites and chaperone functions of the BRICHOS domain	20
Probing binding and occlusion of substrate in the human creatine transporter‐1 by computation and mutagenesis	19
Dimeric assembly of human Suv3 helicase promotes its RNA unwinding function in mitochondrial RNA degradosome for RNA decay	19
Protein degradation of antizyme depends on the N‐terminal degrons	19
Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity	19
Issue information	18
Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation	18
Orthogonal translation with 5‐cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding	18
Domain swapping of the C‐terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis	18
Programmable protein topology via SpyCatcher‐SpyTag chemistry in one‐pot cell‐free expression system	18
Photomodulation of the ASIC1a acidic pocket destabilizes the open state	18
An iron–sulfur cluster as a new metal center in a flavodiiron protein	18
An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase MtLYR3	18
A conserved motif in Henipavirus P/V/W proteins drives the fibrillation of the W protein from Hendra virus	18
The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the E. coli L‐asparaginase EcAIII	18
Lysine acetylation modulates s‐OPA1 GTPase activity and oligomerization in mitochondrial membrane remodeling	17
Unlocking complexity through neutron scattering: Structure and dynamics of protein–polymer conjugates	17
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	17
Computational model predicts function of Rho‐GTPase binding for plexin receptor GAP activity on Rap1b via dynamic allosteric changes	17
Tuning the stator subunit of the flagellar motor with coiled‐coil engineering	17
The dual‐coding gene SLC35A4 protects against oxidative stress	17
Project automation in CCP4 Cloud: Enabling customization and high‐throughput efficiency	17
Design principles that protect the proteasome from self‐destruction	16
Unveiling the molecular mechanism of Gi protein biased activation at mGlu2–mGlu4 heterodimers through Gaussian accelerated molecular dynam	16
Partitioning the Hill coefficient into contributions from ligand‐promoted conformational changes and subunit heterogeneity	16
A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP)	16
Construction of a versatile fusion protein for targeted therapy and immunotherapy	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
Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations	16
Resolving the structure and assembly of the honeybee silk heterotetrameric coiled coil	16
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	15
Modulation of TRPV2 by endogenous and exogenous ligands: A computational study	15
The Ca2+ response of a smart forisome protein is dependent on polymerization	15
Protein structure accuracy estimation using geometry‐complete perceptron networks	15
The intrinsically disordered protein NUPR1 binds to phospholipids	15
Structural investigations connect the disordered N‐terminal extension of HypB to the activities of HypB and SlyD in E. coli	15
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D	15
Destabilization of polar interactions in the prion protein triggers misfolding and oligomerization	15
Kunitz‐type trypsin inhibitor from durian (Durio zibethinus) employs a distinct loop for trypsin inhibition	15
Genetic mutations disrupt the coordinated mode of tyrosinase's intra‐melanosomal domain	15
	15
Structure and activity of a bacterial defense‐associated 3′‐5′ exonuclease	15
Cover Image	14
Issue information	14
Investigation of the structure of protein–polymer conjugates in solution reveals the impact of protein deuteration and the size of the polymer on its thermal stability	14
Design of a yeast SUMO tag to eliminate internal translation initiation	14
Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125	14
Heterogeneous folding landscapes and predetermined breaking points within a protein family	14
Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants	14
Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5T	14
Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns	14
A cascade of sulfur transferases delivers sulfur to the sulfur‐oxidizing heterodisulfide reductase‐like complex	14
Targeting MarA N‐terminal domain dynamics to prevent DNA binding	14
Ferritin‐based disruptor nanoparticles: A novel strategy to enhance LDL cholesterol clearance via multivalent inhibition of PCSK9–LDL receptor interaction	14
Active site center redesign increases protein stability preserving catalysis in thioredoxin	14
Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all‐atom simulations	14
De novo design of monomeric helical bundles for pH‐controlled membrane lysis	14
Thermostability and binding properties of single‐chained Fv fragments derived from therapeutic antibodies	14
Issue information	14
MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2	14
	13
Issue information	13
SG‐ML‐PLAP: A structure‐guided machine learning–based scoring function for protein–ligand binding affinity prediction	13
Accounting for nonuniformity of bulk‐solvent: A mosaic model	13
Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono‐PEGylated alpha‐1 antitrypsin	13
AggNet: Advancing protein aggregation analysis through deep learning and protein language model	13
Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy	13
Issue information	13
iLight2: A near‐infrared optogenetic tool for gene transcription with low background activation	13
Expanding the genetic code	13
IEDB‐3D 2.0: Structural data analysis within the Immune Epitope Database	13
Allosteric regulation of L‐lactate dehydrogenase: Beyond effector‐mediated tetramerization	13
Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways	13
KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing	13

Global analysis of kinetics reveals the role of secondary nucleation in recombinant spider silk self‐assembly	13
CMM—An enhanced platform for interactive validation of metal binding sites	13
A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase	12
The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum	12
A new strategy to reconcile amyloid cross‐seeding and amyloid prevention in a binary system of α‐synuclein fragmental peptide and hIAPP	12
Ordered ATP hydrolysis in the Hsp90 chaperone is regulated by Aha1 and a conserved post‐translational modification	12
FOXO4 interacts with p53 TAD and CRD and inhibits its binding to DNA	12
Revisiting the hydrolysis of ampicillin catalyzed by Temoneira‐1 β‐lactamase, and the effect of Ni(II), Cd(II) and Hg(II)	12
A disulfide chaperone knockout facilitates spin labeling and pulse EPR spectroscopy of outer membrane transporters	12
Differential effects of disulfide bond formation in TEM‐1 versus CTX‐M‐9 β‐lactamase	12
Ligation of multiple protein domains using orthogonal inteins with non‐native splice junctions	12
LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation	12
Structural and biochemical characterization of the C‐terminal region of the human RTEL1 helicase	12
Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi	12
Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair	12
Assessing the functional impact of protein binding site definition	12
Issue information	12
Clustering protein functional families at large scale with hierarchical approaches	12
Exploring the molecular mechanism of cold‐adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network	11
Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials	11
Molecular insight into the specific interactions of the SARS‐Coronavirus‐2 nucleocapsid with RNA and host protein	11
Protein‐tags and their fragments as potent inhibitors of enzymes: Structure of the ternary complex of phosphopantetheine adenylyltransferase from Enterobacter spp. with tag‐peptides	11
Theta‐curves in proteins	11
Structural and functional characterization of the cytotoxic protein ledodin, an atypical ribosome‐inactivating protein from shiitake mushroom (Lentinula edodes)	11
Design of a water‐soluble CD20 antigen with computational epitope scaffolding	11
Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi‐enzyme colocalization and environment	11
KCD: A prediction web server of knowledge‐based circular dichroism	11
Constant domain polymorphisms influence monoclonal antibody stability and dynamics	11
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	11
Preferential binding of ADP‐bound mitochondrial HSP70 to the nucleotide exchange factor GRPEL1 over GRPEL2	11
DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning	11
Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1	11
Deep sequencing combined with high‐throughput screening enables efficient development of a pH‐dependent high‐affinity binding domain targeting HER3	11
Correction to “The structural landscape of the immunoglobulin fold by large‐scale de novo design”	11
Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63	11
Membrane tension‐dependent conformational change of Isoleucine 106 of loop B diminishes water permeability in FaPIP2;1	10
U‐CIE [/juː ‘siː/]: Color encoding of high‐dimensional data	10
Structural insight into the substrate binding of the AMT complex via an inhibitor‐trapped state	10
The role of phospholipid saturation and composition in α‐synuclein aggregation and toxicity: A dual in vitro and in vivo approach	10
Structural adaptability and surface activity of peptides derived from tardigrade proteins	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
Guanidinylation of the cold shock protein YB‐1: Molecular basis, structural changes and Notch‐3 receptor binding	10
SPI “sandwich”: Combined SUMO‐Peptide‐Intein expression system and isolation procedure for improved stability and yield of peptides	10
Site‐directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus	10
A favorable path to domain separation in the orange carotenoid protein	10
Structure–function analysis of cysteine residues in the plasmodium falciparum chitinase, PfCHT1	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
Multivalent interaction induces phase separation and formation of more toxic aggregates of α‐syn in a yeast model of Parkinson's disease	10
Unraveling ShuA detergent‐induced colloidal behavior in solution: A comprehensive SEC‐MALS, SAXS, and SANS study	10
Cover Image	10
Optimized genetic code expansion technology for time‐dependent induction of adhesion GPCR‐ligand engagement	10
Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases	10
Mitigating product inhibition in 2′‐hydroxybiphenyl‐2‐sulfinate desulfinase (DszB) with synthetic glycosylation	10
	10
Issue information	10
Cover Image	10
Cover Image	10
SMOG 2 and OpenSMOG: Extending the limits of structure‐based models	10
Labile assembly of a tardigrade protein induces biostasis	10
Conformational features and interaction mechanisms of VHH antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction	10
Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain	10
Cover Image	10
Quantitative analyses for effects of neddylation on CRL2VHL substrate ubiquitination and degradation	10
A protein fitness predictive framework based on feature combination and intelligent searching	10
Structure‐based insights into the mechanism of [4Fe‐4S]‐dependent sulfur insertase LarE	10
	9
	9
Parkinson's disease‐linked V15A mutation facilitates α‐synuclein aggregation by reducing membrane affinity	9
Erratum	9
Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity	9
Diphtheria toxin‐derived, anti‐PD‐1 immunotoxin, a potent and practical tool to selectively deplete PD‐1+ cells	9
Protection by desiccation‐tolerance proteins probed at the residue level	9
Predicting interacting hotspots for nanobodies' binding using triplets of residues	9
VirulentPred 2.0: An improved method for prediction of virulent proteins in bacterial pathogens	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
Degradation mechanism of AtrA mediated by ClpXP and its application in daptomycin production in Streptomyces roseosporus	9
Issue information	9
Structural dynamics and binding of Caenorhabditis elegans lifespan‐extending lipid binding protein‐3 to polyunsaturated fatty acids	9
PairK: Pairwise k‐mer alignment for quantifying protein motif conservation in disordered regions	9
Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter jejuni via targeting different sites with different scaffolds	9
Reconstitution and use of highly active human CDK1:Cyclin‐B:CKS1 complexes	9
Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins	9
	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
Characterization of protein–ligand binding interactions of enoyl‐ACP reductase (FabI) by native MS reveals allosteric effects of coenzymes and the inhibitor triclosan	9
Examining the mechanistic relationship of APC/CCDH1 and its interphase inhibitor EMI1	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
Site‐specific photo‐crosslinking/cleavage for protein–protein interface identification reveals oligomeric assembly of lysosomal‐associated membrane protein type 2A in mammalian cells	9
Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes	9
Engineering minimal tissue inhibitors of metalloproteinase targeting MMPs via gene shuffling and yeast surface display	9
In This Issue	9
AlphaFold2 fails to predict protein fold switching	8
Inline small‐angle X‐ray scattering‐coupled chromatography under extreme hydrostatic pressure	8
Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations	8