Terms Of Protein Structure Research Articles

A new gene for autosomal dominant facial palsy/migraine identified in a family by whole exome sequencing.

Facial palsy manifests as unilateral or bilateral weakness and inability to move some of the facial muscles. The aetiology may be different including idiopathic, trauma, infections or brain tumours or it can be associated with chronic neurological diseases. For instance, in recurrent migraine, an increased risk of idiopathic facial palsy (often unilateral) has been observed. Migraine is a neurovascular disorder characterized by mild to severe intensity of headaches, often associated with neuro-ophthalmological symptoms. A family is reported where five members were affected by facial palsy associated with other clinical features including migraine, diplopia, facial swelling, eye conjunctivitis following a vertical transmission. Whole exome sequencing was performed in three members (two affected and one healthy) in order to identify potential variants causative of their phenotype. A missense variant c.304G>A was found leading to the p.(Ala102Thr) substitution in the TRPM8 gene, previously related to migraine by genome wide association studies. This variant was classified as deleterious by several predictor tools, and the mutant residue was predicted to alter the protein structure in terms of flexibility and interactions with the surrounding residues. These findings suggest that TRPM8 could be a new causative gene further linking migraine and recurrent facial palsy.

Revisiting the Ramachandran plot based on statistical analysis of static and dynamic characteristics of protein structures

Ramachandran plots, which describe protein structures by plotting the dihedral angle pairs of the backbone on a two-dimensional plane, have played an important role in structural biology over the past few decades. However, despite continued discovery of new protein structures to date, the Ramachandran plot is still constructed by only a small number of data points, and further it cannot reflect the steric information of proteins. Here, we investigated the secondary structure of proteins in terms of static and dynamic characteristics. As for static feature, the Ramachandran plot was revisited for the dataset consisting of 9,148 non-redundant high-resolution protein structures released in the protein data bank until April 1, 2022. By calculating amino acid propensities, it was found that the proportion of secondary structures with respect to residue depth is directly related to their hydrophobicity. As for dynamic feature, normal mode analysis (NMA) based on an elastic network model (ENM) was carried out for the dataset using our KOSMOS web server (http://bioengineering.skku.ac.kr/kosmos/). All ENM-based NMA results were stored in the KOSMOS database, allowing researchers to use them in various ways. In this process, it was commonly found that high B-factors appeared at the edge of the alpha helix region, which was elucidated by introducing residue depth. In addition, by investigating the change in dihedral angle, it was possible to quantitatively survey the contribution of structural change of protein on the Ramachandran plot. In conclusion, our statistical analysis of protein characteristics will provide insight into a range of protein structural studies.

Elucidation of rheological properties of frozen non-fermented dough with different thawing treatments: The view from protein structure and water mobility

The objective of this study was to elucidate the rheology differences between the dough with different thawing methods in terms of protein structure and water mobility. The frozen dough samples were thawed by three methods: refrigerator (4 °C), proofer (25 °C, 85% RH), and microwave (1000W), respectively. Results showed that the rheological properties of doughs produced by refrigerator and proofer-thawing were closer to untreated dough than that produced by microwave thawing. Contrastingly, microwave-thawing produced doughs with a harder and less elastic texture. Besides, refrigerator and microwave thawing tended to have highest and lowest percentage of large polymeric proteins (LPP), respectively. A significant decrease in the proportion of α-helices, accompanied with the increased β-sheets and random coils was obtained from the microwave thawing group (P＜0.05). Furthermore, microwave-thawing had the biggest impact on water mobility and distribution, followed by proofer and refrigerator-thawing. The refrigerator-thawing produced dough samples with a more intact inner structure, indicating less damage and impact on the quality of dough.

Characterization of flesh firmness and ease of separation in the fermentation of sea bass in terms of protein structure, texture, and muscle tissue structural changes

This study aims to investigate the reasons for the firmness of fish flesh and the easy separation of fish flesh after curing and fermentation processing of fermented sea bass (FSB) under pressure (approximately 0.02 kg/cm2). Herein, we analyzed fish texture, protein structure, and muscle tissue structure. Results suggest that from the RW (fresh sea bass) to the FS6 (sea bass spontaneously fermented at 6–8 °C for 6 day) processing stage, the increase in hardness and chewiness resulted in firm FSB flesh. The space between the FSB muscle fibers increased and holes appeared in the muscle fiber structure of the FSB. After curing and fermentation of FSB, the stable β-sheet content in the secondary structure of fish meat protein was reduced from 17.1 % to 0 % and converted to an unstable β-turn structure (increased from 36.5 % to 69.5 %). The decrease in the collagen content of the FSB flesh resulted in unstable fish tissue structure. In addition, the FSB myofibrils broke down. Pressure and curing dehydration play a key role in the firmness and easy separation of FSB meat. This study provides a reference for high-value utilization of fermented fish.

Characterization of the p.L145F and p.S135N Mutations in SOD1: Impact on the Metabolism of Fibroblasts Derived from Amyotrophic Lateral Sclerosis Patients.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the loss of the upper and lower motor neurons (MNs). About 10% of patients have a family history (familial, fALS); however, most patients seem to develop the sporadic form of the disease (sALS). SOD1 (Cu/Zn superoxide dismutase-1) is the first studied gene among the ones related to ALS. Mutant SOD1 can adopt multiple misfolded conformation, lose the correct coordination of metal binding, decrease structural stability, and form aggregates. For all these reasons, it is complicated to characterize the conformational alterations of the ALS-associated mutant SOD1, and how they relate to toxicity. In this work, we performed a multilayered study on fibroblasts derived from two ALS patients, namely SOD1L145F and SOD1S135N, carrying the p.L145F and the p.S135N missense variants, respectively. The patients showed diverse symptoms and disease progression in accordance with our bioinformatic analysis, which predicted the different effects of the two mutations in terms of protein structure. Interestingly, both mutations had an effect on the fibroblast energy metabolisms. However, while the SOD1L145F fibroblasts still relied more on oxidative phosphorylation, the SOD1S135N fibroblasts showed a metabolic shift toward glycolysis. Our study suggests that SOD1 mutations might lead to alterations in the energy metabolism.

ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures.

An accurate estimation of the quality of protein model structures typifies as a cornerstone in protein structure prediction regimes. Despite the recent groundbreaking success in the field of protein structure prediction, there are certain prospects for the improvement in model quality estimation at multiple stages of protein structure prediction and thus, to further push the prediction accuracy. Here, a novel approach, named ProFitFun, for assessing the quality of protein models is proposed by harnessing the sequence and structural features of experimental protein structures in terms of the preferences of backbone dihedral angles and relative surface accessibility of their amino acid residues at the tripeptide level. The proposed approach leverages upon the backbone dihedral angle and surface accessibility preferences of the residues by accounting for its N-terminal and C-terminal neighbors in the protein structure. These preferences are used to evaluate protein structures through a machine learning approach and tested on an extensive dataset of diverse proteins. The approach was extensively validated on a large test dataset (n = 25005) of protein structures, comprising 23661 models of 82 non-homologous proteins and 1344 non-homologous experimental structures. In addition, an external dataset of 40000 models of 200 non-homologous proteins was also used for the validation of the proposed method. Both datasets were further used for benchmarking the proposed method with four different state-of-the-art methods for protein structure quality assessment. In the benchmarking, the proposed method outperformed some state-of-the-art methods in terms of Spearman's and Pearson's correlation coefficients, average GDT-TS loss, sum of z-scores and average absolute difference of predictions over corresponding observed values. The high accuracy of the proposed approach promises a potential use of the sequence and structural features in computational protein design. http://github.com/KYZ-LSB/ProTerS-FitFun. Supplementary data are available at Bioinformatics online.

Physicochemical and functional characterization of MYL-1501D, a proposed biosimilar to insulin glargine.

Insulin glargine is a long-acting analogue of human insulin that has been used to manage hyperglycemia in patients with diabetes mellitus (DM) for nearly 20 years. Insulin glargine has a relatively constant concentration-time profile that mimics basal levels of insulin and allows for once-daily administration. MYL-1501D is a biosimilar insulin glargine designed to offer greater access of insulin glargine to patients, with comparable efficacy and safety to the marketed reference product. We conducted a comprehensive panel of studies based on a formal analysis of critical quality attributes to characterize the structural and functional properties of MYL-1501D and reference insulin glargine products available in the United States and European Union. MYL-1501D was comprehensively shown to have high similarity to the reference products in terms of protein structure, metabolic activity (both in vitro cell-based assays and in vivo rabbit bioassays), and in vitro cell-based assays for mitogenic activity. The structural analyses demonstrated that the primary protein sequence was identical, and secondary and tertiary structures are similar between the proposed biosimilar and the reference products. Insulin receptor binding affinity and phosphorylation studies also established analytical similarity. MYL-1501D demonstrated high similarity in different metabolic assays of glucose uptake, adipogenesis activity, and inhibition of stimulated lipolysis. Rabbit bioassay studies showed MYL-1501D and EU-approved insulin glargine are highly similar to US-licensed insulin glargine. These product quality studies show high similarity between MYL-1501D and licensed or approved insulin glargine products and suggest the potential of MYL-1501D as an alternative cost-effective treatment option for patients and clinicians.

Disclosing Allostery Through Protein Contact Networks.

Proteins are located in the twilight zone between chemistry and biology, where a peculiar kind of complexity starts. Proteins are the smallest 'devices' showing a sensible adaptation to their environment by the production of appropriate behavior when facing a specific stimulus. This fact qualifies (from the 'effector' side) proteins as nanomachines working as catalysts, motors, or switches. However (from the sensor side), the need to single out the 'specific stimulus' out of thermal noise qualifies proteins as information processing devices. Allostery corresponds to the modification of the configuration (in a broad sense) of the protein molecule in response to a specific stimulus in a non-strictly local way, thereby connecting the sensor and effector sides of the nanomachine. This is why the 'disclosing' of allostery phenomenon is at the very heart of protein function; in this chapter, we will demonstrate how a network-based representation of protein structure in terms of nodes (aminoacid residues) and edges (effective contacts between residues) is the natural language for getting rid of allosteric phenomena and, more in general, of protein structure/function relationships.

The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer

ABSTRACT Macroautophagy/autophagy is a cellular process to recycle damaged cellular components, and its modulation can be exploited for disease treatments. A key autophagy player is the ubiquitin-like protein MAP1LC3B/LC3B. Mutations and changes in MAP1LC3B expression occur in cancer samples. However, the investigation of the effects of these mutations on MAP1LC3B protein structure is still missing. Despite many LC3B structures that have been solved, a comprehensive study, including dynamics, has not yet been undertaken. To address this knowledge gap, we assessed nine physical models for biomolecular simulations for their capabilities to describe the structural ensemble of MAP1LC3B. With the resulting MAP1LC3B structural ensembles, we characterized the impact of 26 missense mutations from pan-cancer studies with different approaches, and we experimentally validated our prediction for six variants using cellular assays. Our findings shed light on damaging or neutral mutations in MAP1LC3B, providing an atlas of its modifications in cancer. In particular, P32Q mutation was found detrimental for protein stability with a propensity to aggregation. In a broader context, our framework can be applied to assess the pathogenicity of protein mutations or to prioritize variants for experimental studies, allowing to comprehensively account for different aspects that mutational events alter in terms of protein structure and function. Abbreviations: ATG: autophagy-related; Cα: alpha carbon; CG: coarse-grained; CHARMM: Chemistry at Harvard macromolecular mechanics; CONAN: contact analysis; FUNDC1: FUN14 domain containing 1; FYCO1: FYVE and coiled-coil domain containing 1; GABARAP: GABA type A receptor-associated protein; GROMACS: Groningen machine for chemical simulations; HP: hydrophobic pocket; LIR: LC3 interacting region; MAP1LC3B/LC3B microtubule associated protein 1 light chain 3 B; MD: molecular dynamics; OPTN: optineurin; OSF: open software foundation; PE: phosphatidylethanolamine, PLEKHM1: pleckstrin homology domain-containing family M 1; PSN: protein structure network; PTM: post-translational modification; SA: structural alphabet; SLiM: short linear motif; SQSTM1/p62: sequestosome 1; WT: wild-type.

Effects of a Low-Pass Filter on the Classification of Protein Electron-Density Maps in Terms of Structural Polymorphism using Manifold Learning: A Simulation Study for Cryo-Electron Microscopy Experiments

Analyzing the structure of proteins in terms of their structural polymorphism has been recently performed using their two-dimensional electron-density maps obtained through cryo-electron microscopy...

Investigation of the clinical significance and prospective molecular mechanisms of cystatin genes in patients with hepatitis B virus‑related hepatocellular carcinoma.

The present study aimed to investigate the clinical significance and prospective molecular mechanism of cystatin (CST) genes in patients with hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). The role of CST genes in the molecular mechanism of HCC was revealed through bioinformatics analysis. The clinical significance of CST genes was investigated using GSE14520-derived data from patients with HBV-related HCC. Gene set enrichment analysis (GSEA) was used to identify pathways in which the CST genes were enriched, as well as the association between these pathways and HCC. The expression levels of CST1, CST2, CST5, CSTA and CSTB genes were higher in HCC tissue compared with in normal tissue; conversely, CST3 and CST7 were reduced in HCC tissue. Subsequent receiver operating characteristic analysis of the CST genes demonstrated that CST7 and CSTB genes may function as potential diagnostic markers for HCC. Furthermore, the expression levels of CST6 and CST7 were strongly associated with recurrence-free survival and overall survival of patients with HBV-related HCC. GSEA of the CST genes revealed that CST7 was significantly enriched in tumor evasion and tolerogenicity, cancer progenitors, liver cancer late recurrence, liver cancer progression and several liver cancer subclasses. In addition, CST genes demonstrated homology in terms of protein structure and were revealed to be strongly co-expressed. The present findings suggested that CST7 and CSTB genes may serve as potential prognostic and diagnostic biomarkers for HCC.

The species-spanning family of LPX-motif harbouring effector proteins

The delivery of effector proteins into infected eukaryotic cells represents a key virulence feature of many microbial pathogens in order to derail essential cellular processes and effectively counter the host defence system. Although bacterial effectors are truly numerous and exhibit a wide range of biochemical activities, commonalities in terms of protein structure and function shared by many bacterial pathogens exist. Recent progress has shed light on a species-spanning family of bacterial effectors containing an LPX repeat motif as a subtype of the leucine-rich repeat superfamily, partially combined with a novel E3 ubiquitin ligase domain. This review highlights the immunomodulatory effects of LPX effector proteins, with particular emphasis on the exploitation of the host ubiquitin system.

Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.).

The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. Molecular characterization of these proteins has been performed in certain plants, but they are still not characterized in Triticum aestivum (bread wheat). Herein, we identified 34 TaCaCA superfamily proteins, which were classified into TaCAX, TaCCX, TaNCL, and TaMHX protein families based on their structural organization and evolutionary relation with earlier reported proteins. Since the T. aestivum comprises an allohexaploid genome, TaCaCA genes were derived from each A, B, and D subgenome and homeologous chromosome (HC), except chromosome-group 1. Majority of genes were derived from more than one HCs in each family that were considered as homeologous genes (HGs) due to their high similarity with each other. These HGs showed comparable gene and protein structures in terms of exon/intron organization and domain architecture. Majority of TaCaCA proteins comprised two Na_Ca_ex domains. However, TaNCLs consisted of an additional EF-hand domain with calcium binding motifs. Each TaCaCA protein family consisted of about 10 transmembrane and two α-repeat regions with specifically conserved signature motifs except TaNCL, which had single α-repeat. Variable expression of most of the TaCaCA genes during various developmental stages suggested their specified role in development. However, constitutively high expression of a few genes like TaCAX1-A and TaNCL1-B indicated their role throughout the plant growth and development. The modulated expression of certain genes during biotic (fungal infections) and abiotic stresses (heat, drought, salt) suggested their role in stress response. Majority of TaCCX and TaNCL family genes were found highly affected during various abiotic stresses. However, the role of individual gene needs to be established. The present study unfolded the opportunity for detail functional characterization of TaCaCA proteins and their utilization in future crop improvement programs.

Elastin structure and its involvement in skin photoageing

Skin aging is a complex process that may be caused by factors that are intrinsic and extrinsic to the body. Ultraviolet (UV) radiation represents one of the main sources of skin damage over the years and characterizes a process known as photoaging. Among the changes that affect cutaneous tissue with age, the loss of elastic properties caused by changes in elastin production, increased degradation and/or processing produces a substantial impact on tissue esthetics and health. The occurrence of solar elastosis is one of the main markers of cutaneous photoaging and is characterized by disorganized and non-functional deposition of elastic fibers. The occurrence of UV radiation-induced alternative splicing of the elastin gene, which leads to inadequate synthesis of the proteins required for the correct assembly of elastic fibers, is a potential explanation for this phenomenon. Innovative studies have been fundamental for the elucidation of rarely explored photoaging mechanisms and have enabled the identification of effective therapeutic alternatives such as cosmetic products. This review addresses cutaneous photoaging and the changes that affect elastin in this process.

Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs).

The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains, and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought, and salt) stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat.

New horizons in the enzymatic production of biodiesel using neoteric solvents

Globally, tougher legislation in greenhouse gases emissions is prompting the hunt for more sustainable and competitive strategies to synthesize biodiesel. Although enzyme-catalyzed processes are considered as a more environmentally-friendly option, there are still challenges to be approached like the replacement of traditional solvents due to their well-known disadvantages such as their volatility, toxicity or carcinogenic character. Thus, the emergence of neoteric solvents such as perfluorocarbons, liquid polymers, ionic liquids, deep eutectic solvents or supercritical fluids has opened up new opportunities to reach truly green processes. Nonetheless, literature analysis reveals the scarcity of research works, which are exclusively restricted to the last three types of solvents. One of the critical points to take into account refers to the performance of enzymes in this kind of milieu, as this environment may be deleterious in terms of protein structure, leading to enzyme deactivation. Therefore, the final purpose of this review paper is to identify the current trends of research in the field of neoteric solvents applied to enzyme-catalyzed synthesis of biodiesel and to shed light on the possible existing gaps.

Hierarchically clustered HMM for protein sequence motif extraction with variable length

Protein sequence motifs extraction is an important field of bioinformatics since its relevance to the structural analysis. Two major problems are related to this field: (1) searching the motifs within the same protein family; and (2) assuming a window size for the motifs search. This work proposes the Hierarchically Clustered Hidden Markov Model (HC-HMM) approach, which represents the behavior and structure of proteins in terms of a Hidden Markov Model chain and hierarchically clusters each chain by minimizing distance between two given chains’ structure and behavior. It is well known that HMM can be utilized for clustering, however, methods for clustering on Hidden Markov Models themselves are rarely studied. In this paper, we developed a hierarchical clustering based algorithm for HMMs to discover protein sequence motifs that transcend family boundaries with no assumption on the length of the motif. This paper carefully examines the effectiveness of this approach for motif extraction on 2593 proteins that share no more than 25% sequence identity. Many interesting motifs are generated. Three example motifs generated by the HC-HMM approach are analyzed and visualized with their tertiary structure. We believe the proposed method provides a unique protein sequence motif extraction strategy. The related data mining fields using Hidden Markova Model may also benefit from this clustering on HMM themselves approach.

Protein structure modeling for CASP10 by multiple layers of global optimization

In the template-based modeling (TBM) category of CASP10 experiment, we introduced a new protocol called protein modeling system (PMS) to generate accurate protein structures in terms of side-chains as well as backbone trace. In the new protocol, a global optimization algorithm, called conformational space annealing (CSA), is applied to the three layers of TBM procedure: multiple sequence-structure alignment, 3D chain building, and side-chain re-modeling. For 3D chain building, we developed a new energy function which includes new distance restraint terms of Lorentzian type (derived from multiple templates), and new energy terms that combine (physical) energy terms such as dynamic fragment assembly (DFA) energy, DFIRE statistical potential energy, hydrogen bonding term, etc. These physical energy terms are expected to guide the structure modeling especially for loop regions where no template structures are available. In addition, we developed a new quality assessment method based on random forest machine learning algorithm to screen templates, multiple alignments, and final models. For TBM targets of CASP10, we find that, due to the combination of three stages of CSA global optimizations and quality assessment, the modeling accuracy of PMS improves at each additional stage of the protocol. It is especially noteworthy that the side-chains of the final PMS models are far more accurate than the models in the intermediate steps.

Structure and dynamics of an imidazoline nitroxide side chain with strongly hindered internal motion in proteins

A disulfide-linked imidazoline nitroxide side chain (V1) has a similar and highly constrained internal motion at diverse topological sites in a protein, unlike that for the disulfide-linked pyrroline nitroxide side chain (R1) widely used in site directed spin labeling EPR. Crystal structures of V1 at two positions in a helix of T4 Lysozyme and quantum mechanical calculations suggest the source of the constraints as intra-side chain interactions of the disulfide sulfur atoms with both the protein backbone and the 3-nitrogen in the imidazoline ring. These interactions apparently limit the conformation of the side chain to one of only three possible rotamers, two of which are observed in the crystal structure. An inter-spin distance measurement in frozen solution using double electron–electron resonance (DEER) gives a value essentially identical to that determined from the crystal structure of the protein containing two copies of V1, indicating that lattice forces do not dictate the rotamers observed. Collectively, the results suggest the possibility of predetermining a unique rotamer of V1 in helical structures. In general, the reduced rotameric space of V1 compared to R1 should simplify interpretation of inter-spin distance information in terms of protein structure, while the highly constrained internal motion is expected to extend the dynamic range for characterizing large amplitude nanosecond backbone fluctuations.

Structural and Functional Characterization of K339T Substitution Identified in the PB2 Subunit Cap-binding Pocket of Influenza A Virus

Influenza virus RNA-dependent RNA polymerase is a heterotrimer composed of PA, PB1, and PB2 subunits. RNA-dependent RNA polymerase is required for both transcription and replication of influenza viral RNA taking place in the nucleus of infected cells. A "cap-snatching" mechanism is used to generate a 5'-capped primer for transcription in which the cap-binding domain of PB2 (PB2cap) captures the 5' cap of the host pre-mRNA. Our statistical analysis of PB2 sequences showed that residue Lys(339) located in the cap-binding pocket of H5N1 PB2cap was gradually replaced by Thr(339) over the past decade. To understand the role of this amino acid polymorphism, we solved the crystal structures of PB2cap with or without a pre-mRNA cap analog, m(7)GTP, in the presence of Lys(339) or Thr(339). The structures showed that Lys(339) contributes to binding the γ-phosphate group of m(7)GTP, and the replacement of Lys(339) by Thr eliminates this interaction. Isothermal titration calorimetry analysis showed that Thr(339) attenuated the PB2cap cap binding activity in vitro compared with Lys(339). Further functional studies confirmed that Thr(339)-PB2-containing ribonucleoprotein complex has a reduced influenza polymerase activity and RNA synthesis activity, and a reconstituted H5N1 virus containing the Thr(339) substitution exhibited a lower virulence to mice but more active replication in Madin-Darby canine kidney cells. The K339T substitution in the cap-binding pocket of PB2 modulates the polymerase activity and virulence by regulating the cap binding activity. It is informative to track variations in the cap-binding pocket of PB2 in surveillance of the evolution and spread of influenza virus.