Protein Science

Article	Citations
	2048
	1425
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	553
Design of an effective small expression tag to enhance GPCR production in E. coli‐based cell‐free and whole cell expression systems	442
Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains	270
Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion‐binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu	257
Structural and functional validation of a highly specific Smurf2 inhibitor	240
Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone	230
Similar protein segments shared between domains of different evolutionary lineages	151
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	139
Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequence properties of protein‐binding zinc fingers	136
Fine‐tuned interactions between globular and disordered regions of single‐stranded DNA binding (SSB) protein are required for dynamic condensation under physiological conditions	134
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	109
Epitope‐directed anti‐SARS‐CoV‐2 scFv engineered against the key spike protein region could block membrane fusion	102
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD	100
Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS‐fold glucosamine‐6‐phosphate deaminases	99
Issue information	82
Structural polymorphism and cytotoxicity of brain‐derived β‐amyloid extracts	82
Evolution of affinity between p53 transactivation domain and MDM2 across the animal kingdom demonstrates high plasticity of motif‐mediated interactions	72
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase	69
Xplor‐NIH: Better parameters and protocols for NMR protein structure determination	68
Biophysical insights into the dimer formation of human Sirtuin 2	65
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix	65
CsgA gatekeeper residues control nucleation but not stability of functional amyloid	60
Biophysical characterization of RelA–p52 NF‐κB dimer—A link between the canonical and the non‐canonical NF‐κB pathway	59

Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B	56
Structure–function mapping and mechanistic insights on the SARS CoV2 Nsp1	50
A novel method for expressing and purifying large quantities of functional and stable human voltage‐gated proton channel (hHv1)	46
Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins	44
Extrinsic and intrinsic factors affect copper‐induced protein precipitation across eukaryotic and prokaryotic proteomes	40
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Torsional twist of the SARS‐CoV and SARS‐CoV‐2 SUD‐N and SUD‐M domains	40
Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers	39
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	39
An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis	38
Two residues determine nicotinic acetylcholine receptor requirement for RIC‐3	37
Soluble SARS‐CoV‐2 RBD and human ACE2 peptidase domain produced in DrosophilaS2 cells show functions evoking virus–cell interface	37
Large library docking for novel SARS‐CoV‐2 main protease non‐covalent and covalent inhibitors	36
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	35
Issue Information	32
Torsion angles to map and visualize the conformational space of a protein	32
Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work	31
Two different kinds of interaction modes of deaminase APOBEC3A with single‐stranded DNA in solution detected by nuclear magnetic resonance	30
Mesoscale explorer: Visual exploration of large‐scale molecular models	30
Inhibition of bacterial FMN transferase: A potential avenue for countering antimicrobial resistance	30
PEG–mCherry interactions beyond classical macromolecular crowding	29
Structure‐based clustering and mutagenesis of bacterial tannases reveals the importance and diversity of active site‐capping domains	29
Structure‐based alteration of tryptophan residues of the multidrug transporter CmABCB1 to assess substrate binding using fluorescence spectroscopy	28
Chemical and temporal manipulation of early steps in protein assembly tunes the structure and intermolecular interactions of protein‐based materials	28
Evolution of homo‐oligomerization of methionine S‐adenosyltransferases is replete with structure–function constrains	28
Loop engineering of enzymes to control their immobilization and ultimately fabricate more efficient heterogeneous biocatalysts	26
Phenotypic mutations contribute to protein diversity and shape protein evolution	25
Ca2+ attenuates nucleation activity of leiomodin	25
Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination	24
PocketOptimizer 2.0: A modular framework for computer‐aided ligand‐binding design	24
Controlled by disorder: Phosphorylation modulates SRSF1 domain availability for spliceosome assembly	24
Control of a far‐red/near‐infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin	24
A competition smFRET assay to study ligand‐induced conformational changes of the dengue virus protease	23
Analysis of β‐C‐terminal salt bridges in T‐state hemoglobin by trapping tertiary conformations in silica gels	23
Discovery of broadly‐neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens	22
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway	22
Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding	22
Molecular basis for different substrate‐binding sites and chaperone functions of the BRICHOS domain	22
Synonymous and non‐synonymous codon substitutions can alleviate dependence on GroEL for folding	22
Biochemical and structural characterization of meningococcal methylenetetrahydrofolate reductase	22
The oligomeric states of dye‐decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation	22
Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation	21
Cumulative asparagine to aspartate deamidation fails to perturb γD‐crystallin structure and stability	21
Correction to “The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament”	21
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ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction	21
Structural features of thyroglobulin linked to protein trafficking	20
Integrative visualization of the molecular structure of a cellular microdomain	20
Issue information	20
Biophysical investigation of interactions between SARS‐CoV‐2 spike protein and neuropilin‐1	20

A systematic pipeline of protein structure selection for computer‐aided drug discovery: A case study on T790M/L858R mutant EGFR structures	20
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02	20
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Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation	20
Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product‐inhibition mechanism and oxygen gatekeeper	20
Resolving the structure and assembly of the honeybee silk heterotetrameric coiled coil	19
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RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D	19
Structural investigations connect the disordered N‐terminal extension of HypB to the activities of HypB and SlyD in E. coli	19
Design principles that protect the proteasome from self‐destruction	19
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
Tuning the stator subunit of the flagellar motor with coiled‐coil engineering	18
Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation	18
Protein degradation of antizyme depends on the N‐terminal degrons	18
Orthogonal translation with 5‐cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding	18
A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP)	18
The dual‐coding gene SLC35A4 protects against oxidative stress	18
Domain swapping of the C‐terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis	18
Photomodulation of the ASIC1a acidic pocket destabilizes the open state	18
Modulation of TRPV2 by endogenous and exogenous ligands: A computational study	17
Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3	17
An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase MtLYR3	17
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	17
Programmable protein topology via SpyCatcher‐SpyTag chemistry in one‐pot cell‐free expression system	17
Dimeric assembly of human Suv3 helicase promotes its RNA unwinding function in mitochondrial RNA degradosome for RNA decay	17
Unlocking complexity through neutron scattering: Structure and dynamics of protein–polymer conjugates	17
Issue information	17
Lysine acetylation modulates s‐OPA1 GTPase activity and oligomerization in mitochondrial membrane remodeling	16
Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations	16
Project automation in CCP4 Cloud: Enabling customization and high‐throughput efficiency	16
Partitioning the Hill coefficient into contributions from ligand‐promoted conformational changes and subunit heterogeneity	16
Construction of a versatile fusion protein for targeted therapy and immunotherapy	16
Computational model predicts function of Rho‐GTPase binding for plexin receptor GAP activity on Rap1b via dynamic allosteric changes	16
An iron–sulfur cluster as a new metal center in a flavodiiron protein	16
Probing binding and occlusion of substrate in the human creatine transporter‐1 by computation and mutagenesis	16
Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity	15
The Ca2+ response of a smart forisome protein is dependent on polymerization	15
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The intrinsically disordered protein NUPR1 binds to phospholipids	15
Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5T	15
Destabilization of polar interactions in the prion protein triggers misfolding and oligomerization	15
Expanding the genetic code	15
Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono‐PEGylated alpha‐1 antitrypsin	15
Accounting for nonuniformity of bulk‐solvent: A mosaic model	14
Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns	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
Heterogeneous folding landscapes and predetermined breaking points within a protein family	14
Targeting MarA N‐terminal domain dynamics to prevent DNA binding	14
iLight2: A near‐infrared optogenetic tool for gene transcription with low background activation	14
KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing	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
MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2	14
Kunitz‐type trypsin inhibitor from durian (Durio zibethinus) employs a distinct loop for trypsin inhibition	14
Design of a yeast SUMO tag to eliminate internal translation initiation	14
Protein structure accuracy estimation using geometry‐complete perceptron networks	14
Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all‐atom simulations	14
A cascade of sulfur transferases delivers sulfur to the sulfur‐oxidizing heterodisulfide reductase‐like complex	14
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	14
Ferritin‐based disruptor nanoparticles: A novel strategy to enhance LDL cholesterol clearance via multivalent inhibition of PCSK9–LDL receptor interaction	14
Issue information	14
Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125	14
Issue information	13
Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways	13
AggNet: Advancing protein aggregation analysis through deep learning and protein language model	13
Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants	13
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Allosteric regulation of L‐lactate dehydrogenase: Beyond effector‐mediated tetramerization	13
SG‐ML‐PLAP: A structure‐guided machine learning–based scoring function for protein–ligand binding affinity prediction	13
Active site center redesign increases protein stability preserving catalysis in thioredoxin	13
Global analysis of kinetics reveals the role of secondary nucleation in recombinant spider silk self‐assembly	13
Deep sequencing combined with high‐throughput screening enables efficient development of a pH‐dependent high‐affinity binding domain targeting HER3	13
Constant domain polymorphisms influence monoclonal antibody stability and dynamics	13
Structure and activity of a bacterial defense‐associated 3′‐5′ exonuclease	13
Issue information	13
IEDB‐3D 2.0: Structural data analysis within the Immune Epitope Database	13
CMM—An enhanced platform for interactive validation of metal binding sites	13

Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy	13
Differential effects of disulfide bond formation in TEM‐1 versus CTX‐M‐9 β‐lactamase	12
DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning	12
Revisiting the hydrolysis of ampicillin catalyzed by Temoneira‐1 β‐lactamase, and the effect of Ni(II), Cd(II) and Hg(II)	12
Ordered ATP hydrolysis in the Hsp90 chaperone is regulated by Aha1 and a conserved post‐translational modification	12
Issue information	12
Clustering protein functional families at large scale with hierarchical approaches	12
The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum	12
A disulfide chaperone knockout facilitates spin labeling and pulse EPR spectroscopy of outer membrane transporters	12
A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase	12
Ligation of multiple protein domains using orthogonal inteins with non‐native splice junctions	12
Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi‐enzyme colocalization and environment	12
Theta‐curves in proteins	12
Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair	12
Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi	12
Assessing the functional impact of protein binding site definition	12
FOXO4 interacts with p53 TAD and CRD and inhibits its binding to DNA	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	11
Molecular insight into the specific interactions of the SARS‐Coronavirus‐2 nucleocapsid with RNA and host protein	11
Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials	11
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Issue information	11
Labile assembly of a tardigrade protein induces biostasis	11
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	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
Exploring the molecular mechanism of cold‐adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network	11
A favorable path to domain separation in the orange carotenoid protein	11
The PB1 and the ZZ domain of the autophagy receptor p62/SQSTM1 regulate the interaction of p62/SQSTM1 with the autophagosome protein LC3B	11
SMOG 2 and OpenSMOG: Extending the limits of structure‐based models	11
LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation	11
Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1	11
KCD: A prediction web server of knowledge‐based circular dichroism	11
Quantitative analyses for effects of neddylation on CRL2VHL substrate ubiquitination and degradation	11
Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63	11
Structure‐based insights into the mechanism of [4Fe‐4S]‐dependent sulfur insertase LarE	11
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
U‐CIE [/juː ‘siː/]: Color encoding of high‐dimensional data	10
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In This Issue	10
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The role of phospholipid saturation and composition in α‐synuclein aggregation and toxicity: A dual in vitro and in vivo approach	10
Optimized genetic code expansion technology for time‐dependent induction of adhesion GPCR‐ligand engagement	10
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Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases	10
Computed cancer interactome explains the effects of somatic mutations in cancers	10
A protein fitness predictive framework based on feature combination and intelligent searching	10
Structural adaptability and surface activity of peptides derived from tardigrade proteins	10
Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis	10
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KEGG mapping tools for uncovering hidden features in biological data	10
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VirulentPred 2.0: An improved method for prediction of virulent proteins in bacterial pathogens	10
Site‐directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus	10
Membrane tension‐dependent conformational change of Isoleucine 106 of loop B diminishes water permeability in FaPIP2;1	10
SPI “sandwich”: Combined SUMO‐Peptide‐Intein expression system and isolation procedure for improved stability and yield of peptides	10
Guanidinylation of the cold shock protein YB‐1: Molecular basis, structural changes and Notch‐3 receptor binding	10
Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study	10
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Conformational features and interaction mechanisms of VHH antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction	10
Preferential binding of ADP‐bound mitochondrial HSP70 to the nucleotide exchange factor GRPEL1 over GRPEL2	10
Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain	10
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Structural and functional characterization of the cytotoxic protein ledodin, an atypical ribosome‐inactivating protein from shiitake mushroom (Lentinula edodes)	10
Mitigating product inhibition in 2′‐hydroxybiphenyl‐2‐sulfinate desulfinase (DszB) with synthetic glycosylation	10
Structure–function analysis of cysteine residues in the plasmodium falciparum chitinase, PfCHT1	10
Reconstitution and use of highly active human CDK1:Cyclin‐B:CKS1 complexes	9
Diphtheria toxin‐derived, anti‐PD‐1 immunotoxin, a potent and practical tool to selectively deplete PD‐1+ cells	9
Engineering minimal tissue inhibitors of metalloproteinase targeting MMPs via gene shuffling and yeast surface display	9
Insights into the low‐temperature adaptation of an enzyme as studied through ancestral sequence reconstruction	9
Erratum	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
Parkinson's disease‐linked V15A mutation facilitates α‐synuclein aggregation by reducing membrane affinity	9
Molecular insights into alginate β‐lactoglobulin A multivalencies—The foundation for their amorphous aggregates and coacervation	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
Simple mechanisms for the evolution of protein complexity	9
Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes	9
Exploring the druggability of the UEV domain of human TSG101 in search for broad‐spectrum antivirals	9
AlphaFold2 fails to predict protein fold switching	9
Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity	9
Issue information	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
Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery	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
Engineering G protein‐coupled receptors for stabilization	9
Examining the mechanistic relationship of APC/CCDH1 and its interphase inhibitor EMI1	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
Degradation mechanism of AtrA mediated by ClpXP and its application in daptomycin production in Streptomyces roseosporus	9
Tethered heme domains in a triheme cytochrome allow for increased electron transport distances	8
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Restoring adapter protein complex 4 function with small molecules: an in silico approach to spastic paraplegia 50	8
Vitamin D and COVID‐19: A review on the role of vitamin D in preventing and reducing the severity of COVID‐19 infection	8
Allostery‐driven changes in dynamics regulate the activation of bacterial copper transcription factor	8