Protein Science

Article	Citations
	4657
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An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis	447
Design of an effective small expression tag to enhance GPCR production in E. coli‐based cell‐free and whole cell expression systems	260
Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion‐binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu	184
Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone	160
Issue information	149
Extrinsic and intrinsic factors affect copper‐induced protein precipitation across eukaryotic and prokaryotic proteomes	135
Structure–function mapping and mechanistic insights on the SARS CoV2 Nsp1	129
Soluble SARS‐CoV‐2 RBD and human ACE2 peptidase domain produced in DrosophilaS2 cells show functions evoking virus–cell interface	126
Structural polymorphism and cytotoxicity of brain‐derived β‐amyloid extracts	108
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase	104
The peptidyl‐prolyl cis‐trans isomerase, Pin1, is a regulator of the protein kinase C θ ( PKCθ ) catal	100
Epitope‐directed anti‐SARS‐CoV‐2 scFv engineered against the key spike protein region could block membrane fusion	97
An open axial channel of the AAA ClpXP protease enhances degradation of specific classes of protein substrates	95
A novel method for expressing and purifying large quantities of functional and stable human voltage‐gated proton channel (hHv1)	84
Fine‐tuned interactions between globular and disordered regions of single‐stranded DNA binding (SSB) protein are required for dynamic condensation under physiological conditions	71
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD	71
Single‐molecule force spectroscopy discovers a dual‐binding mode in the hCG ‐mediated activation of LHCGR	64
The subunit composition of the mammalian Mediator complex is not conserved in all vertebrates: Insights from evolutionary plasticity of fish genomes	59
Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins	58
Structural and functional validation of a highly specific Smurf2 inhibitor	57
Torsional twist of the SARS ‐ CoV and SARS ‐	56
Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains	54
Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers	48

Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS‐fold glucosamine‐6‐phosphate deaminases	46
Predicting compatibility between ferredoxins and the Fe protein of nitrogenase using in silico protein modeling	44
CsgA gatekeeper residues control nucleation but not stability of functional amyloid	43
A multi‐pore model of the blood–brain barrier tight junction strands recapitulates the permeability features of wild‐type and mutant claudin‐5	43
Torsion angles to map and visualize the conformational space of a protein	42
Similar protein segments shared between domains of different evolutionary lineages	42
Two residues determine nicotinic acetylcholine receptor requirement for RIC ‐3	41
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	40
Xplor‐NIH: Better parameters and protocols for NMR protein structure determination	40
Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B	40
Large library docking for novel SARS‐CoV ‐2 main protease non‐covalent and covalent inhibitors	40
Detergents alter the stability and lipid binding properties of the CD1d immunoreceptor	39
Biophysical insights into the dimer formation of human Sirtuin 2	37
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in	36
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MAVISp : A modular structure‐based framework for protein variant effects	34
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	34
Evolution of affinity between p53 transactivation domain and MDM2 across the animal kingdom demonstrates high plasticity of motif‐mediated interactio	34
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	33
Biophysical characterization of RelA–p52 NF‐κB dimer—A link between the canonical and the non‐canonical NF‐κB pathway	33
In vitro, cellular and in vivo studies of amyloid oligomers structure and toxicity: Challenges and advances	33
Small electrical field effects on biological polymers	32
Protein–lipid interplay governs ion channel gating and bioenergetics in human mitochondrial VDAC3	32
The impact of physiological oxidants on triggering amyloid formation of the cell cycle regulator protein p16 INK4A	32
Achieving protease substrate‐specific inhibition by mAb dual functional selections	32
Competing chaperone pathways in α‐synuclein disaggregation and aggregation dynamics	32
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Correction to “Aggregation‐driven expression of liraglutide precursors using engineered mini‐tags in Escherichia coli ”	30
Fusion protein condensate formation via coiled‐coil domains	30
KEGG Syntax for comparison of organisms, organism groups, and viruses by conserved gene repertoires	29
Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequenc	29
In and out of the mitochondrial intermembrane space	29
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Chemical and temporal manipulation of early steps in protein assembly tunes the structure and intermolecular interactions of protein‐based materials	28
Synonymous and non‐synonymous codon substitutions can alleviate dependence on GroEL for folding	28
A systematic pipeline of protein structure selection for computer‐aided drug discovery: A case study on T790M/L858R mutant EGFR structures	27
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Biochemical and structural characterization of meningococcal methylenetetrahydrofolate reductase	26
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway	26
Discovery of broadly‐neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens	26
Unambiguous assignment of kinked‐ β sheets leads to insights into molecular grammar of reversibility in biomolecular condensates	26
Growth hormone receptor antagonists, GHA2 and GHA3, with dual activity against the human and mouse receptor	26
Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation	26
Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding	26
ProteinMCP : An agentic AI framework for autonomous protein engineering	26
Biophysical investigation of interactions between SARS‐CoV‐2 spike protein and neuropilin‐1	26
Trafficking of the human Na + /H + antiporter NHA2	26
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Integrative visualization of the molecular structure of a cellular microdomain	25
ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families	24

A competition smFRET assay to study ligand‐induced conformational changes of the dengue virus protease	24
Molecular basis for different substrate‐binding sites and chaperone functions of the BRICHOS domain	24
Correction to “The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament”	24
Cumulative asparagine to aspartate deamidation fails to perturb γD‐crystallin structure and stability	24
Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product‐inhibition mechanism and oxygen gatekeeper	24
Controlled by disorder: Phosphorylation modulates SRSF1 domain availability for spliceosome assembly	23
Structure‐based clustering and mutagenesis of bacterial tannases reveals the importance and diversity of active site‐capping domains	22
Loop engineering of enzymes to control their immobilization and ultimately fabricate more efficient heterogeneous biocatalysts	22
Control of a far‐red/near‐infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin	22
Ligand binding Pro ‐miscuity of acylpeptide hydrolase, structural analysis of a detoxifying serine hydrolase	22
T hermo L ink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning	22
The oligomeric states of dye‐decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation	22
Cryo‐ EM reveals an ensemble of cytochrome P450 reductase conformations in solution	22
PocketOptimizer 2.0: A modular framework for computer‐aided ligand‐binding design	22
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02	21
Structural features of thyroglobulin linked to protein trafficking	21
Streptococcus pneumoniae HtrA is a dynamic and monomeric virulence factor capable of forming larger oligomeric complexes	21
PEG–mCherry interactions beyond classical macromolecular crowding	21
Mesoscale explorer: Visual exploration of large‐scale molecular models	21
The diversity of PET degrading enzymes: A systematic review of sequence, structure, and function	21
Phenotypic mutations contribute to protein diversity and shape protein evolution	21
Analysis of β‐C‐terminal salt bridges in T‐state hemoglobin by trapping tertiary conformations in silica gels	21
De novo design of proteinaceous binders targeting the LEDGF PWWP domain	20
Computational design of blue melanin by motif‐scaffolding a pentapeptide‐repeat protein	20
Damping amyloid‐associated conformational fluctuations in a protein by an engineered diselenide bridge	20
Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination	20
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Structure‐guided engineering of protein stability through core hydrophobicity	20
Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation	20
Construction of a versatile fusion protein for targeted therapy and immunotherapy	19
The dual‐coding gene SLC35A4 protects against oxidative stress	19
Domain swapping of the C‐terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis	19
Probing binding and occlusion of substrate in the human creatine transporter‐1 by computation and mutagenesis	19
Structural investigations connect the disordered N‐terminal extension of HypB to the activities of HypB and SlyD in E. coli	19
Issue information	19
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	19
Tuning the stator subunit of the flagellar motor with coiled‐coil engineering	18
Stabilization versus flexibility: Detergent‐dependent trade‐offs in neurotensin receptor 1 GPCR ensembles	18
Protease‐mediated maturation of M‐ PMV reverse transcriptase into a functional heterodimer	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
The structural heterogeneity of AKT autoinhibition	18
An iron–sulfur cluster as a new metal center in a flavodiiron protein	18
Photomodulation of the ASIC1a acidic pocket destabilizes the open state	18
Computational model predicts function of Rho‐GTPase binding for plexin receptor GAP activity on Rap1b via dynamic allosteric changes	18
Phosphorylation of Staphylococcus aureus β‐lactamase, a prerequisite to its sequestration on the cytoplasmic membrane	18
Two‐conformer equilibrium of maltose‐binding protein in the absence of ligand from residual dipolar coupling analysis	17
Unveiling the molecular mechanism of Gi protein biased activation at mGlu2–mGlu4 heterodimers through Gaussian accelerated molecular dynam	17
Cleaved versus Uncleaved: How furin cleavage reshapes the conformational landscape of SARS ‐ CoV ‐	17
Orthogonal translation with 5‐cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding	17
Lysine acetylation modulates s‐OPA1 GTPase activity and oligomerization in mitochondrial membrane remodeling	17
In silico peptide self‐assembly reveals the importance of N‐terminal motifs and the inhibition mechanism of the mutation L38M in	17
Issue information	17
Universal paratope–epitope interaction patterns in antibody–antigen structures	17
Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation	17
Unlocking complexity through neutron scattering: Structure and dynamics of protein–polymer conjugates	17
Genetic mutations disrupt the coordinated mode of tyrosinase's intra‐melanosomal domain	17
Project automation in CCP4 Cloud: Enabling customization and high‐throughput efficiency	17
The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the E. coli L‐asparaginase EcAIII	17
Issue information	16
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Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations	16
Unveiling catalytic potential and the native role of PETase from Streptomyces sp.	16
Protein degradation of antizyme depends on the N‐terminal degrons	16
KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing	16
Resolving the structure and assembly of the honeybee silk heterotetrameric coiled coil	16
High‐throughput mutational analysis of F 1 ‐ AT	16
Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity	16
Modulation of TRPV2 by endogenous and exogenous ligands: A computational study	16
A conserved motif in Henipavirus P/V/W proteins drives the fibrillation of the W protein from Hendra virus	16
Understanding cell‐penetrating peptide mechanisms using computational electrophysiology simulations	16
Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants	15
Issue information	15
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
Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5T	15
Employing complementary fractionation‐based N‐terminomics approaches enhances the identification of legumain cleavage events in naïve and inflamed colon tissue	15
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Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125	15
Ferritin‐based disruptor nanoparticles: A novel strategy to enhance LDL cholesterol clearance via multivalent inhibition of PCSK9–LDL receptor interaction	15
An ALS ‐associated mutation in the C‐terminal α‐helix of TDP ‐43 uncouples condensate formation an	14
Heterogeneous folding landscapes and predetermined breaking points within a protein family	14

A la carte bioprospecting of substrate‐selective laccases via high‐throughput computational enzyme–substrate interaction profiling	14
Purification and characterization of recombinant human translation initiation factor eIF3	14
T3SS effector and regulator discovery by predicting interacting partners of T3SS chaperones in	14
A cascade of sulfur transferases delivers sulfur to the sulfur‐oxidizing heterodisulfide reductase‐like complex	14
Active site center redesign increases protein stability preserving catalysis in thioredoxin	14
Expanding the biocatalytic and oxidative landscape of the old yellow enzyme family	14
De novo design of monomeric helical bundles for pH‐controlled membrane lysis	14
Human cells for human proteins: Isotope labeling in mammalian cells in suspension for functional NMR studies	14
Structural and dynamic roles of tandem acyl carrier proteins in aryl polyene biosynthesis in carbapenem‐resistant Acinetobacter baumannii	14
Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all‐atom simulations	14
AggNet: Advancing protein aggregation analysis through deep learning and protein language model	14
Design of a yeast SUMO tag to eliminate internal translation initiation	14
Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns	14
Expanding the genetic code	14
MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2	14
Protein structure accuracy estimation using geometry‐complete perceptron networks	14
Accounting for nonuniformity of bulk‐solvent: A mosaic model	14
Residue‐level mapping of crowding effects on protein phase separation	14
The intrinsically disordered protein NUPR1 binds to phospholipids	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
Global analysis of kinetics reveals the role of secondary nucleation in recombinant spider silk self‐assembly	13
Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono‐PEGylated alpha‐1 antitrypsin	13
iLight2 : A near‐infrared optogenetic tool for gene transcription with low background activation	13
Issue information	13
EnAcrPred : A robust ensemble machine learning framework for identifying anti‐ CRISPR proteins	13
Detection of protein symmetry and structural rearrangements using secondary structure elements	13
IEDB‐3D 2.0: Structural data analysis within the Immune Epitope Database	13
Structures of two LarA ‐like nickel‐pincer nucleotide cofactor‐utilizing enzymes with a single catalytic histidine residue	13
SG‐ML‐PLAP: A structure‐guided machine learning–based scoring function for protein–ligand binding affinity prediction	13
Protein Data Bank Japan: A unified portal for integrating structural and chemical data to explore protein–ligand interactions in PDB and	13
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Thermostability and binding properties of single‐chained Fv fragments derived from therapeutic antibodies	13
Thiol post‐translational modifications modulate allosteric regulation of the OpcA – G6PDH complex	13
Kunitz‐type trypsin inhibitor from durian (Durio zibethinus) employs a distinct loop for trypsin inhibition	13
Targeting MarA N‐terminal domain dynamics to prevent DNA binding	13
CMM—An enhanced platform for interactive validation of metal binding sites	13
AF ‐ CALVADOS : AlphaFold ‐guided simulations of multi‐domain prote	13
A disulfide chaperone knockout facilitates spin labeling and pulse EPR spectroscopy of outer membrane transporters	13
Structural and biochemical characterization of the C‐terminal region of the human RTEL1 helicase	13
Use of tandem‐affinity chromatography to incorporate nucleotide loading of small GTPases during their purification	13
Protein‐tags and their fragments as potent inhibitors of enzymes: Structure of the ternary complex of phosphopantetheine adenylyltransferase from Enterobacter spp. with tag‐peptides	12
LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation	12
A flexible, allosteric loop regulates protein activity and rewires electrostatics	12
Constant domain polymorphisms influence monoclonal antibody stability and dynamics	12
Role of associated water in stabilizing human γ‐D crystallin under crowded eye lens conditions	12
pLM ‐Repeat: Exploiting the sequence representations of protein language models for sensitive repeat detection	12
Conformational dynamics in insulin receptor kinase reveal a type III allosteric pocket	12
KCD: A prediction web server of knowledge‐based circular dichroism	12
Revisiting the hydrolysis of ampicillin catalyzed by Temoneira‐1 β‐lactamase, and the effect of Ni(II), Cd(II) and Hg(II)	12
Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi	12
Differential effects of disulfide bond formation in TEM‐1 versus CTX‐M‐9 β‐lactamase	12
Deep sequencing combined with high‐throughput screening enables efficient development of a pH‐dependent high‐affinity binding domain targeting HER3	12
Correction to “The structural landscape of the immunoglobulin fold by large‐scale de novo design”	12
Real‐time FRET assay for monitoring detyrosination by TMCP1 and VASH2	12
The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum	12
Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi‐enzyme colocalization and environment	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
Assessing the functional impact of protein binding site definition	12
A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase	12
Targeting the apical domain of the transferrin receptor: Development of a new protein scaffold for cellular delivery	12
Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials	12
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Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy	12
Conformational features and interaction mechanisms of VHH antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction	11
Phosphate ions modulate enzyme activity and epistatic effects in two clavulanic acid‐resistant β‐lactamase mutants	11
Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain	11
A protein fitness predictive framework based on feature combination and intelligent searching	11
Force fields matter in DNA pol η mechanistic analysis	11
Site‐directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus	11
Ordered ATP hydrolysis in the Hsp90 chaperone is regulated by Aha1 and a conserved post‐translational modification	11
DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning	11
Theta‐curves in proteins	11
Unperturbed hydration structure involves ADP recognition in the N‐terminal domain of human heat shock protein 90α	11
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Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study	11
The role of phospholipid saturation and composition in α‐synuclein aggregation and toxicity: A dual in vitro and in vivo approach	11
Multivalent interaction induces phase separation and formation of more toxic aggregates of α‐syn in a yeast model of Parkinson's disease	11
Concentration‐dependent mutational scanning probes the cellular folding landscape of α‐synuclein in yeast	11
Issue information	11
Allosteric regulation of L‐lactate dehydrogenase: Beyond effector‐mediated tetramerization	11
RINAMI : Residue‐attributed interpretable neural network for predicting absolute folding free energy by merging structure and sequence information	11
Clustering protein functional families at large scale with hierarchical approaches	11
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Structural and dynamic similarities of nanofibrils and microparticles of engineered spider silk proteins probed by solid‐state NMR spectroscopy	11
Discovery of novel, high‐affinity HBV T‐cell epitopes by molecular dynamics‐augmented proteome‐wide screening	11
Buttressing ligand‐binding pockets in de novo designed NTF2 ‐like domains	11
Transient binding facilitates super‐resolution imaging of functional amyloid fibrils on living bacteria	11
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	11
Glycopolymers stabilize protein folding and protein–protein interactions via enthalpic interactions	11
From extracellular entry to intracellular release: A water‐assisted transport cycle for creatine in SLC6A8	11
Molecular insight into the specific interactions of the SARS‐Coronavirus‐2 nucleocapsid with RNA and host protein	11
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