Protein Science

Article	Citations
	1706
Cover Image	1301
	532
Structure–function mapping and mechanistic insights on the SARS CoV2 Nsp1	395
Issue information	351
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase	258
Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins	230
Torsional twist of the SARS‐CoV and SARS‐CoV‐2 SUD‐N and SUD‐M domains	222
Biophysical characterization of RelA–p52 NF‐κB dimer—A link between the canonical and the non‐canonical NF‐κB pathway	210
Fine‐tuned interactions between globular and disordered regions of single‐stranded DNA binding (SSB) protein are required for dynamic condensation under physiological conditions	141
Xplor‐NIH: Better parameters and protocols for NMR protein structure determination	127
Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B	127
Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequence properties of protein‐binding zinc fingers	127
Design of an effective small expression tag to enhance GPCR production in E. coli‐based cell‐free and whole cell expression systems	98
Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone	95
Structural and functional validation of a highly specific Smurf2 inhibitor	95
Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion‐binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu	92
Biophysical insights into the dimer formation of human Sirtuin 2	77
Large library docking for novel SARS‐CoV‐2 main protease non‐covalent and covalent inhibitors	74
Torsion angles to map and visualize the conformational space of a protein	65
Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS‐fold glucosamine‐6‐phosphate deaminases	64
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD	63
Evolution of affinity between p53 transactivation domain and MDM2 across the animal kingdom demonstrates high plasticity of motif‐mediated interactions	62
Two residues determine nicotinic acetylcholine receptor requirement for RIC‐3	57
Soluble SARS‐CoV‐2 RBD and human ACE2 peptidase domain produced in DrosophilaS2 cells show functions evoking virus–cell interface	56

An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis	55
Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains	51
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	46
Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers	44
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	44
Epitope‐directed anti‐SARS‐CoV‐2 scFv engineered against the key spike protein region could block membrane fusion	37
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	37
Similar protein segments shared between domains of different evolutionary lineages	37
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	37
Structural polymorphism and cytotoxicity of brain‐derived β‐amyloid extracts	37
CsgA gatekeeper residues control nucleation but not stability of functional amyloid	34
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	34
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix	33
A novel method for expressing and purifying large quantities of functional and stable human voltage‐gated proton channel (hHv1)	33
Cover Image	32
Correction to “The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament”	32
Extrinsic and intrinsic factors affect copper‐induced protein precipitation across eukaryotic and prokaryotic proteomes	32
Structure‐based clustering and mutagenesis of bacterial tannases reveals the importance and diversity of active site‐capping domains	31
Cumulative asparagine to aspartate deamidation fails to perturb γD‐crystallin structure and stability	30
Cover Image	29
Issue Information	29
Controlled by disorder: Phosphorylation modulates SRSF1 domain availability for spliceosome assembly	29
Synonymous and non‐synonymous codon substitutions can alleviate dependence on GroEL for folding	29
PEG–mCherry interactions beyond classical macromolecular crowding	28
ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction	27
Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding	27
Discovery of broadly‐neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens	27
Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work	27
Molecular basis for different substrate‐binding sites and chaperone functions of the BRICHOS domain	27
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway	26
The oligomeric states of dye‐decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation	26
Structural features of thyroglobulin linked to protein trafficking	23
Biophysical investigation of interactions between SARS‐CoV‐2 spike protein and neuropilin‐1	23
Mesoscale explorer: Visual exploration of large‐scale molecular models	23
Structure‐based alteration of tryptophan residues of the multidrug transporter CmABCB1 to assess substrate binding using fluorescence spectroscopy	22
Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation	22
Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product‐inhibition mechanism and oxygen gatekeeper	22
Two different kinds of interaction modes of deaminase APOBEC3A with single‐stranded DNA in solution detected by nuclear magnetic resonance	21
Ca2+ attenuates nucleation activity of leiomodin	21
Integrative visualization of the molecular structure of a cellular microdomain	21
A competition smFRET assay to study ligand‐induced conformational changes of the dengue virus protease	21
Evolution of homo‐oligomerization of methionine S‐adenosyltransferases is replete with structure–function constrains	21
Biochemical and structural characterization of meningococcal methylenetetrahydrofolate reductase	21
Control of a far‐red/near‐infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin	21
Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination	21
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02	20
PocketOptimizer 2.0: A modular framework for computer‐aided ligand‐binding design	20
Chemical and temporal manipulation of early steps in protein assembly tunes the structure and intermolecular interactions of protein‐based materials	20
Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation	20
Phenotypic mutations contribute to protein diversity and shape protein evolution	20

Inhibition of bacterial FMN transferase: A potential avenue for countering antimicrobial resistance	20
Loop engineering of enzymes to control their immobilization and ultimately fabricate more efficient heterogeneous biocatalysts	20
Protein degradation of antizyme depends on the N‐terminal degrons	19
A conserved motif in Henipavirus P/V/W proteins drives the fibrillation of the W protein from Hendra virus	19
Programmable protein topology via SpyCatcher‐SpyTag chemistry in one‐pot cell‐free expression system	19
Issue information	19
Issue information	19
Partitioning the Hill coefficient into contributions from ligand‐promoted conformational changes and subunit heterogeneity	19
A systematic pipeline of protein structure selection for computer‐aided drug discovery: A case study on T790M/L858R mutant EGFR structures	19
An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase MtLYR3	19
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
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Modulation of TRPV2 by endogenous and exogenous ligands: A computational study	18
Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity	18
The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the E. coli L‐asparaginase EcAIII	18
Probing binding and occlusion of substrate in the human creatine transporter‐1 by computation and mutagenesis	18
Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation	18
Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations	18
Orthogonal translation with 5‐cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding	17
A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP)	17
Design principles that protect the proteasome from self‐destruction	17
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	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
Tuning the stator subunit of the flagellar motor with coiled‐coil engineering	17
Issue information	16
Project automation in CCP4 Cloud: Enabling customization and high‐throughput efficiency	16
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D	16
Issue information	16
Unlocking complexity through neutron scattering: Structure and dynamics of protein–polymer conjugates	16
Construction of a versatile fusion protein for targeted therapy and immunotherapy	16
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Lysine acetylation modulates s‐OPA1 GTPase activity and oligomerization in mitochondrial membrane remodeling	16
Dimeric assembly of human Suv3 helicase promotes its RNA unwinding function in mitochondrial RNA degradosome for RNA decay	16
Issue information	15
Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants	15
Design of a yeast SUMO tag to eliminate internal translation initiation	15
Heterogeneous folding landscapes and predetermined breaking points within a protein family	15
SG‐ML‐PLAP: A structure‐guided machine learning–based scoring function for protein–ligand binding affinity prediction	15
MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2	15
Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns	15
IEDB‐3D 2.0: Structural data analysis within the Immune Epitope Database	15
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Targeting MarA N‐terminal domain dynamics to prevent DNA binding	15
De novo design of monomeric helical bundles for pH‐controlled membrane lysis	15
Destabilization of polar interactions in the prion protein triggers misfolding and oligomerization	15
Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono‐PEGylated alpha‐1 antitrypsin	14
Global analysis of kinetics reveals the role of secondary nucleation in recombinant spider silk self‐assembly	14
A cascade of sulfur transferases delivers sulfur to the sulfur‐oxidizing heterodisulfide reductase‐like complex	14
Ferritin‐based disruptor nanoparticles: A novel strategy to enhance LDL cholesterol clearance via multivalent inhibition of PCSK9–LDL receptor interaction	14
Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways	14
Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125	14
KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing	14
iLight2: A near‐infrared optogenetic tool for gene transcription with low background activation	14
Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5T	14
The Ca2+ response of a smart forisome protein is dependent on polymerization	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
Introduction: Biophysics of biomolecular condensates	14
Thermostability and binding properties of single‐chained Fv fragments derived from therapeutic antibodies	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	13
Protein structure accuracy estimation using geometry‐complete perceptron networks	13
CMM—An enhanced platform for interactive validation of metal binding sites	13
Ordered ATP hydrolysis in the Hsp90 chaperone is regulated by Aha1 and a conserved post‐translational modification	13
Revisiting the hydrolysis of ampicillin catalyzed by Temoneira‐1 β‐lactamase, and the effect of Ni(II), Cd(II) and Hg(II)	13
Clustering protein functional families at large scale with hierarchical approaches	13
Kunitz‐type trypsin inhibitor from durian (Durio zibethinus) employs a distinct loop for trypsin inhibition	13
AggNet: Advancing protein aggregation analysis through deep learning and protein language model	13
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Issue information	13
KCD: A prediction web server of knowledge‐based circular dichroism	13
Issue information	13
Accounting for nonuniformity of bulk‐solvent: A mosaic model	13
Structure and activity of a bacterial defense‐associated 3′‐5′ exonuclease	13
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	13
Expanding the genetic code	13
Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials	13
Assessing the functional impact of protein binding site definition	13
Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1	12
Molecular insight into the specific interactions of the SARS‐Coronavirus‐2 nucleocapsid with RNA and host protein	12

Theta‐curves in proteins	12
DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning	12
Differential effects of disulfide bond formation in TEM‐1 versus CTX‐M‐9 β‐lactamase	12
Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair	12
Ligation of multiple protein domains using orthogonal inteins with non‐native splice junctions	12
A disulfide chaperone knockout facilitates spin labeling and pulse EPR spectroscopy of outer membrane transporters	12
A new strategy to reconcile amyloid cross‐seeding and amyloid prevention in a binary system of α‐synuclein fragmental peptide and hIAPP	12
Structural and biochemical characterization of the C‐terminal region of the human RTEL1 helicase	12
Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi‐enzyme colocalization and environment	12
Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi	12
The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum	12
A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase	11
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	11
FOXO4 interacts with p53 TAD and CRD and inhibits its binding to DNA	11
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Labile assembly of a tardigrade protein induces biostasis	11
Structural basis for the stereospecific inhibition of the dual proline/hydroxyproline catabolic enzyme ALDH4A1 by trans‐4‐hydroxy‐L‐proline	11
Membrane tension‐dependent conformational change of Isoleucine 106 of loop B diminishes water permeability in FaPIP2;1	11
Exploring the molecular mechanism of cold‐adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network	11
LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation	11
Preferential binding of ADP‐bound mitochondrial HSP70 to the nucleotide exchange factor GRPEL1 over GRPEL2	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	11
Biochemical properties of VGLL4 from Homo sapiens and Tgi from Drosophila melanogaster and possible biological implications	11
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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
A protein fitness predictive framework based on feature combination and intelligent searching	11
The role of phospholipid saturation and composition in α‐synuclein aggregation and toxicity: A dual in vitro and in vivo approach	11
Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study	11
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Structural and functional characterization of the cytotoxic protein ledodin, an atypical ribosome‐inactivating protein from shiitake mushroom (Lentinula edodes)	10
Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63	10
Structural adaptability and surface activity of peptides derived from tardigrade proteins	10
Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases	10
VirulentPred 2.0: An improved method for prediction of virulent proteins in bacterial pathogens	10
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SMOG 2 and OpenSMOG: Extending the limits of structure‐based models	10
Site‐directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus	10
Structure‐based insights into the mechanism of [4Fe‐4S]‐dependent sulfur insertase LarE	10
SPI “sandwich”: Combined SUMO‐Peptide‐Intein expression system and isolation procedure for improved stability and yield of peptides	10
Computed cancer interactome explains the effects of somatic mutations in cancers	10
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Conformational features and interaction mechanisms of VHH antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction	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
Structure–function analysis of cysteine residues in the plasmodium falciparum chitinase, PfCHT1	10
Optimized genetic code expansion technology for time‐dependent induction of adhesion GPCR‐ligand engagement	10
Identification of amyloidogenic proteins in the microbiomes of a rat Parkinson's disease model and wild‐type rats	10
Issue information	10
U‐CIE [/juː ‘siː/]: Color encoding of high‐dimensional data	10
Reconstitution and use of highly active human CDK1:Cyclin‐B:CKS1 complexes	9
Engineering G protein‐coupled receptors for stabilization	9
Protein ensemble modeling and analysis with MMMx	9
Insights into the low‐temperature adaptation of an enzyme as studied through ancestral sequence reconstruction	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
Structural dynamics and binding of Caenorhabditis elegans lifespan‐extending lipid binding protein‐3 to polyunsaturated fatty acids	9
In This Issue	9
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KEGG mapping tools for uncovering hidden features in biological data	9
Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery	9
Characterization of an aminotransferase from Acanthamoeba polyphagaMimivirus	9
Degradation mechanism of AtrA mediated by ClpXP and its application in daptomycin production in Streptomyces roseosporus	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
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
Erratum	9
Exploring the druggability of the UEV domain of human TSG101 in search for broad‐spectrum antivirals	9
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Issue information	9
Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis	9
A favorable path to domain separation in the orange carotenoid protein	9
Molecular insights into alginate β‐lactoglobulin A multivalencies—The foundation for their amorphous aggregates and coacervation	9
Diphtheria toxin‐derived, anti‐PD‐1 immunotoxin, a potent and practical tool to selectively deplete PD‐1+ cells	9
Examining the mechanistic relationship of APC/CCDH1 and its interphase inhibitor EMI1	9
The structural landscape of the immunoglobulin fold by large‐scale de novo design	9
Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain	9
Heat‐induced structural and chemical changes to a computationally designed miniprotein	9
Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter jejuni via targeting different sites with different scaffolds	9
PairK: Pairwise k‐mer alignment for quantifying protein motif conservation in disordered regions	9
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Issue information	9
Issue information	9
Engineering minimal tissue inhibitors of metalloproteinase targeting MMPs via gene shuffling and yeast surface display	9
Inline small‐angle X‐ray scattering‐coupled chromatography under extreme hydrostatic pressure	9
Protein Data Bank Japan: Improved tools for sequence‐oriented analysis of protein structures	8
Tethered heme domains in a triheme cytochrome allow for increased electron transport distances	8
MRS2 missense variation at Asp216 abrogates inhibitory Mg2+ binding, potentiating cell migration and apoptosis resistance	8
From duplication to fusion: Expanding Dayhoff's model of protein evolution	8
Dual‐wield NTPases: A novel protein family mined from AlphaFold DB	8
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A comparison of antibody–antigen complex sequence‐to‐structure prediction methods and their systematic biases	8
Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance	8
Retromer‐mediated recruitment of the WASH complex involves discrete interactions between VPS35, VPS29, and FAM21	8
Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost	8
A pressure‐jump EPR system to monitor millisecond conformational exchange rates of spin‐labeled proteins	8