Genomes and Genes
Summary: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
- Min W, Bruhn C, Grigaravicius P, Zhou Z, Li F, Krüger A, et al. Poly(ADP-ribose) binding to Chk1 at stalled replication forks is required for S-phase checkpoint activation. Nat Commun. 2013;4:2993 pubmed publisher..Collectively, we disclose a previously unrecognized mechanism of the S-phase checkpoint by PAR metabolism that modulates Chk1 activity at the replication fork. ..
- Foster T, Geoghegan J, Ganesh V, Hook M. Adhesion, invasion and evasion: the many functions of the surface proteins of Staphylococcus aureus. Nat Rev Microbiol. 2014;12:49-62 pubmed publisher..Thus, cell wall-anchored proteins are essential virulence factors for the survival of S. aureus in the commensal state and during invasive infections, and targeting them with vaccines could combat S. aureus infections. ..
- Beyer T, Weiss A, Khomchuk Y, Huang K, Ogunjimi A, Varelas X, et al. Switch enhancers interpret TGF-? and Hippo signaling to control cell fate in human embryonic stem cells. Cell Rep. 2013;5:1611-24 pubmed publisher..These studies define switch-enhancer elements and provide a framework to understand how cellular context dictates interpretation of the same morphogen signal in development. ..
- Li X, Wang X, Zhang X, Zhao M, Tsang W, Zhang Y, et al. Genetically encoded fluorescent probe to visualize intracellular phosphatidylinositol 3,5-bisphosphate localization and dynamics. Proc Natl Acad Sci U S A. 2013;110:21165-70 pubmed publisher..Our development of a PI(3,5)P2-specific probe may facilitate studies of both intracellular signal transduction and membrane trafficking in the endosomes and lysosomes. ..
- Loose M, Mitchison T. The bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns. Nat Cell Biol. 2014;16:38-46 pubmed publisher..Our findings provide a model for the initial steps of bacterial cell division and illustrate how dynamic polymers can self-organize into large-scale structures. ..
- Cedano Prieto D, Cheng Y, Chang C, Yu J, Takada Y, Takada Y. Direct integrin binding to insulin-like growth factor-2 through the C-domain is required for insulin-like growth factor receptor type 1 (IGF1R) signaling. PLoS ONE. 2017;12:e0184285 pubmed publisher..The present study defines the role of the C-domain in integrin binding and signaling. ..
- Ivanova I, Much C, Di Giacomo M, Azzi C, Morgan M, Moreira P, et al. The RNA m6A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence. Mol Cell. 2017;67:1059-1067.e4 pubmed publisher..In summary, the m6A-reader YTHDF2 is an intrinsic determinant of mammalian oocyte competence and early zygotic development. ..
- Nagao R, Suzuki T, Dohmae N, Shen J, Tomo T. Functional role of Lys residues of Psb31 in electrostatic interactions with diatom photosystem II. FEBS Lett. 2017;591:3259-3264 pubmed publisher..These results provide evidence that some Lys residues of Psb31 are responsible for electrostatic interactions with PSII. ..
- Klein M, Schmidt S, Wadhwani P, Bürck J, Reichert J, Afonin S, et al. Lactam-Stapled Cell-Penetrating Peptides: Cell Uptake and Membrane Binding Properties. J Med Chem. 2017;60:8071-8082 pubmed publisher..The other systems (DRIM, WWSP, KFGF) did not improve, however. The data suggest that cell uptake of amphipathic CPPs correlates with their adopted ?-helix content in membranes rather than their helicity in solution. ..
- Kumar A, Basu D, Satpati P. Structure-Based Energetics of Stop Codon Recognition by Eukaryotic Release Factor. J Chem Inf Model. 2017;57:2321-2328 pubmed publisher..Our work provides a clue to how eRF1 discriminates between cognate and near-cognate codons during protein synthesis. ..
- Singh N, Riley T, Baker S, Borrman T, Weng Z, Baker B. Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes. J Immunol. 2017;199:2203-2213 pubmed publisher..We demonstrate how these same principles can also explain amino acid preferences in immunogenic epitopes and highlight opportunities for structural considerations in predictive immunology. ..
- Stine J, Ahl G, Schlenker C, Rusnac D, Briknarová K. The Interaction between the Third Type III Domain from Fibronectin and Anastellin Involves ?-Strand Exchange. Biochemistry. 2017;56:4667-4675 pubmed publisher..3FN3 adopts a compact globular fold in solution, and to interact with anastellin in a manner consistent with our data, it has to open up and expose a ?-strand edge that is not accessible in the context of the folded domain...
- Wang R, Du Z, Bai Z, Liang Z. The interaction between endogenous 30S ribosomal subunit protein S11 and Cucumber mosaic virus LS2b protein affects viral replication, infection and gene silencing suppressor activity. PLoS ONE. 2017;12:e0182459 pubmed publisher..The gene silencing suppressor activity of CMV2b protein was reduced by the RPS11 knockdown. This study demonstrated that the function of viral LS2b protein was remarkably affected by the interaction with host RPS11 protein. ..
- Wylie T, Garg R, Ridley A, Conte M. Analysis of the interaction of Plexin-B1 and Plexin-B2 with Rnd family proteins. PLoS ONE. 2017;12:e0185899 pubmed publisher..These results suggest that Rnd proteins do not have a clear-cut specificity for different Plexin-B-RBDs, possibly implying the contribution of additional regions of Plexin-B proteins in conferring functional substrate selection. ..
- Karg E, Smets M, Ryan J, Forne I, Qin W, Mulholland C, et al. Ubiquitome Analysis Reveals PCNA-Associated Factor 15 (PAF15) as a Specific Ubiquitination Target of UHRF1 in Embryonic Stem Cells. J Mol Biol. 2017;: pubmed publisher..In summary, we identified novel ubiquitination targets that link UHRF1 to transcriptional regulation and DNA damage response...
- Peralta Castro A, Baruch Torres N, Brieba L. Plant organellar DNA primase-helicase synthesizes RNA primers for organellar DNA polymerases using a unique recognition sequence. Nucleic Acids Res. 2017;45:10764-10774 pubmed publisher..This mechanism contrasts to lagging-strand DNA replication in metazoan mitochondria, in which transcripts synthesized by mitochondrial RNA polymerase prime mitochondrial DNA polymerase ?. ..
- Murphy K, Cutter A, Fang H, Postnikov Y, Bustin M, Hayes J. HMGN1 and 2 remodel core and linker histone tail domains within chromatin. Nucleic Acids Res. 2017;45:9917-9930 pubmed publisher..Our studies provide new insights into the molecular mechanisms whereby HMGNs affect chromatin structure...
- Gonzalez Carranza Z, Zhang X, Peters J, Boltz V, Szecsi J, Bendahmane M, et al. HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression. PLoS ONE. 2017;12:e0185106 pubmed publisher..Loss of function of HWS is associated with larger petal size due to alterations in cell proliferation and mitotic growth, a role shared with the CUC1 gene. ..
- Krishnamoorthy V, Kannanganat S, Maienschein Cline M, Cook S, Chen J, Bahroos N, et al. The IRF4 Gene Regulatory Module Functions as a Read-Write Integrator to Dynamically Coordinate T Helper Cell Fate. Immunity. 2017;47:481-497.e7 pubmed publisher..We propose that the Irf4 locus functions as the "reader" of TCR signal strength, and in turn, concentration-dependent activity of Irf4 "writes" T helper fate choice. ..
- Varrault A, Dantec C, Le Digarcher A, Chotard L, Bilanges B, Parrinello H, et al. Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network. Nucleic Acids Res. 2017;45:10466-10480 pubmed publisher..Altogether, this work identified Plagl1 as a transcription factor that coordinated the regulation of a subset of IGN genes and controlled extracellular matrix composition. ..
- Thomas G, Renjith M, Manna T. Kinetochore-microtubule interactions in chromosome segregation: lessons from yeast and mammalian cells. Biochem J. 2017;474:3559-3577 pubmed publisher..The present review focuses on the most recent advances in understanding of the molecular and structural aspects of kinetochore-microtubule interaction based on the studies in yeast and vertebrate cells...
- Moncada R, Blackshear K, Garrett T. The Arabidopsis thaliana lysophospholipid acyltransferase At1g78690p acylates lysocardiolipins. Biochem Biophys Res Commun. 2017;493:340-345 pubmed publisher..No transfer of the linoleoyl chains was detected in an At1g78690 dependent manner suggesting that, despite the strong homology, these enzymes catalyze unique reactions. ..
- Xu Z, Gakhar L, Bain F, Spies M, Fuentes E. The Tiam1 guanine nucleotide exchange factor is auto-inhibited by its pleckstrin homology coiled-coil extension domain. J Biol Chem. 2017;292:17777-17793 pubmed publisher..Our results highlight the role of the PHn-CC-Ex domain in Tiam1 GEF regulation and suggest a combinatorial model for GEF inhibition and activation of the Rac1 signaling pathway. ..
- Bahrami A, Lin M, Ren X, Hurley J, Hummer G. Scaffolding the cup-shaped double membrane in autophagy. PLoS Comput Biol. 2017;13:e1005817 pubmed publisher..Fusion of a small number of vesicles followed by Atg17-guided membrane shape-remodeling thus emerges as a viable route to phagophore formation. ..
- Nidetz N, Gallagher T, Wiethoff C. Inhibition of type I interferon responses by adenovirus serotype-dependent Gas6 binding. Virology. 2018;515:150-157 pubmed publisher..We hypothesize that rare AdV serotypes might be engineered to include Gas6 binding motifs, thereby generating novel vectors that are more effective. ..
- HernÃ¡ndez G, RamÃrez M, MinguillÃ³n J, Quiles P, Ruiz de Garibay G, Aza Carmona M, et al. Decapping protein EDC4 regulates DNA repair and phenocopies BRCA1. Nat Commun. 2018;9:967 pubmed publisher..Collectively, this study recognizes EDC4 with a dual role in decapping and DNA repair whose inactivation phenocopies BRCA1 deficiency. ..
- Goto G, Ogi H, Biswas H, Ghosh A, Tanaka S, Sugimoto K. Two separate pathways regulate protein stability of ATM/ATR-related protein kinases Mec1 and Tel1 in budding yeast. PLoS Genet. 2017;13:e1006873 pubmed publisher..Asa1 and Pih1 are required for proper DNA damage checkpoint signaling. Our findings provide a model in which two different Tel2 pathways promote protein stabilization of Mec1 and Tel1 in budding yeast. ..
- Wang W, Perens E, Oikonomou G, Wallace S, Lu Y, Shaham S. IGDB-2, an Ig/FNIII protein, binds the ion channel LGC-34 and controls sensory compartment morphogenesis in C. elegans. Dev Biol. 2017;430:105-112 pubmed publisher..Our findings reveal a novel membrane protein complex and suggest possible mechanisms for how sensory compartment size is controlled. ..
- Gehne N, Lamik A, Lehmann M, Haseloff R, Andjelkovic A, Blasig I. Cross-over endocytosis of claudins is mediated by interactions via their extracellular loops. PLoS ONE. 2017;12:e0182106 pubmed publisher..TJ-remodeling via cross-over endocytosis represents a general mechanism for the degradation of transmembrane proteins in cell-cell contacts and directly links junctional membrane turnover to autophagy. ..
- Ferry L, Fournier A, Tsusaka T, Adelmant G, Shimazu T, Matano S, et al. Methylation of DNA Ligase 1 by G9a/GLP Recruits UHRF1 to Replicating DNA and Regulates DNA Methylation. Mol Cell. 2017;67:550-565.e5 pubmed publisher..These results further elucidate the function of UHRF1, identify a non-histone target of G9a and GLP, and provide an example of a histone mimic that coordinates DNA replication and DNA methylation maintenance. ..
- Kihara T, Sugimoto Y, Shinohara S, Takaoka S, Miyake J. Cysteine-rich protein 2 accelerates actin filament cluster formation. PLoS ONE. 2017;12:e0183085 pubmed publisher..This F-actin clustering activity of CRP2 was cooperative with ?-actinin. Thus, binding of CRP2 to F-actin accelerates actin polymerization and F-actin cluster formation. ..
- Sangwung P, Zhou G, Lu Y, Liao X, Wang B, Mutchler S, et al. Regulation of endothelial hemoglobin alpha expression by Kruppel-like factors. Vasc Med. 2017;22:363-369 pubmed publisher..Chromatin immunoprecipitation studies showed that KLF4 bound to the HBA promoter in ECs. Thus, KLF2 and KLF4 serve as important regulators that promote HBA expression in the endothelium. ..
- Mbanwi A, Lin G, Wang K, Watts T. Constitutive interaction between 4-1BB and 4-1BBL on murine LPS-activated bone marrow dendritic cells masks detection of 4-1BBL by TKS-1 but not 19H3 antibody. J Immunol Methods. 2017;450:81-89 pubmed publisher..These data suggest that 19H3 is the preferable antibody to use to detect 4-1BBL in the presence of its receptor. ..
- Walter N, Wentsch H, Bührmann M, Bauer S, Döring E, Mayer Wrangowski S, et al. Design, Synthesis, and Biological Evaluation of Novel Type I1/2 p38? MAP Kinase Inhibitors with Excellent Selectivity, High Potency, and Prolonged Target Residence Time by Interfering with the R-Spine. J Med Chem. 2017;60:8027-8054 pubmed publisher..Moreover, microsomal studies showed convenient metabolic stability of the most potent, herein reported representatives. ..
- Tam L, Jiang J, Wang P, Li L, Miao W, Dong X, et al. Arsenite Binds to the Zinc Finger Motif of TIP60 Histone Acetyltransferase and Induces Its Degradation via the 26S Proteasome. Chem Res Toxicol. 2017;30:1685-1693 pubmed publisher..Our results also shed some new light on the mechanisms underlying the arsenic-induced epigenotoxicity and carcinogenesis in humans. ..
- Mutisya D, Hardcastle T, Cheruiyot S, Pallan P, Kennedy S, Egli M, et al. Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs. Nucleic Acids Res. 2017;45:8142-8155 pubmed publisher..Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs. ..
- Dai Y, Chen T, Ijaz H, Cho E, Steinberg M. SIRT1 activates the expression of fetal hemoglobin genes. Am J Hematol. 2017;92:1177-1186 pubmed publisher..SIRT1 is a potential therapeutic target for ?-globin gene induction, and small molecule SIRT1 activators might serve as a lead compound for the development of new HbF inducers. ..
- Vorobyeva N, Kurilova S, Anashkin V, Rodina E. Inhibition of Escherichia coli Inorganic Pyrophosphatase by Fructose-1-phosphate. Biochemistry (Mosc). 2017;82:953-956 pubmed publisher..Substitutions of Lys112, Lys115, Lys148, and Arg43 in the regulatory site completely or partially abolished the inhibition. Thus, Fru-1-P is a physiological inhibitor of pyrophosphatase that acts via a regulatory site in this enzyme. ..
- Mukherjee P, Bentzien J, Bosanac T, Mao W, Burke M, Muegge I. Kinase Crystal Miner: A Powerful Approach to Repurposing 3D Hinge Binding Fragments and Its Application to Finding Novel Bruton Tyrosine Kinase Inhibitors. J Chem Inf Model. 2017;57:2152-2160 pubmed publisher..Prospective scaffold hopping using the KCM identified two potent and selective Bruton tyrosine kinase (BTK) inhibitors with hinge binding fragments novel to BTK. ..
- Acevedo L, Greenwood A, Nicholson L. A Noncanonical Binding Site in the EVH1 Domain of Vasodilator-Stimulated Phosphoprotein Regulates Its Interactions with the Proline Rich Region of Zyxin. Biochemistry. 2017;56:4626-4636 pubmed publisher..These results have broader implications for other multivalent VASP EVH1 domain binding partners and for furthering our understanding of the role of Y39 phosphorylation in regulating VASP localization and cellular function. ..
- Gautam G, Rehman S, Pandey P, Gourinath S. Crystal structure of the PEG-bound SH3 domain of myosin IB from Entamoeba histolytica reveals its mode of ligand recognition. Acta Crystallogr D Struct Biol. 2017;73:672-682 pubmed publisher..histolytica infections. ..
- Cunden L, Brophy M, Rodriguez G, Flaxman H, Nolan E. Biochemical and Functional Evaluation of the Intramolecular Disulfide Bonds in the Zinc-Chelating Antimicrobial Protein Human S100A7 (Psoriasin). Biochemistry. 2017;56:5726-5738 pubmed publisher..Metal substitution experiments suggest that the disulfide bonds in S100A7 may enhance metal sequestration by the His3Asp sites and thereby confer growth inhibitory properties to S100A7ox. ..
- Hayoz S, Tiwari P, Piszczek G, Uren A, Brelidze T. Investigating cyclic nucleotide and cyclic dinucleotide binding to HCN channels by surface plasmon resonance. PLoS ONE. 2017;12:e0185359 pubmed publisher..Taken together, our results suggest that interaction of the C-linker/CNBD with other parts of the channel is necessary for cyclic-dinucleotide binding in HCN4 channels. ..
- Wang G, Wang J, Ansari G, Khan M. Autoimmune potential of perchloroethylene: Role of lipid-derived aldehydes. Toxicol Appl Pharmacol. 2017;333:76-83 pubmed publisher..Our studies thus provide an experimental evidence that PCE induces/exacerbates an autoimmune response and lipid-derived aldehydes (such as MDA) contribute to this response. ..
- Oliva C, Sánchez Murcia P, Rico E, Bravo A, Menendez M, Gago F, et al. Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences. Nucleic Acids Res. 2017;45:9030-9045 pubmed publisher
- Yu P, Song L, Qin J, Wang J. Capturing the photo-signaling state of a photoreceptor in a steady-state fashion by binding a transition metal complex. Protein Sci. 2017;26:2249-2256 pubmed publisher..The organometallic reagents hold promise as protein engineering tools. This work highlights a novel approach to structurally accessing short lived intermediates of proteins in a steady-state fashion. ..
- Zuidscherwoude M, Worah K, van der Schaaf A, Buschow S, van Spriel A. Differential expression of tetraspanin superfamily members in dendritic cell subsets. PLoS ONE. 2017;12:e0184317 pubmed publisher..This study demonstrates that tetraspanins are differentially expressed by human and murine DC subsets which provides a valuable resource that will aid the understanding of tetraspanin function in DC biology. ..
- Eichwald C, Kim J, Nibert M. Dissection of mammalian orthoreovirus µ2 reveals a self-associative domain required for binding to microtubules but not to factory matrix protein µNS. PLoS ONE. 2017;12:e0184356 pubmed publisher..These findings suggest that ?2 monomers or oligomers can bind to MTs and ?NS, but that self-association involving ?2 residues 283-325 is specifically relevant for MT-association during viral factories formation. ..