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Journal of Molecular Biology

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https://www.readbyqxmd.com/read/28625850/structure-and-function-of-viral-deubiquitinating-enzymes
#1
REVIEW
Ben A Bailey-Elkin, Robert C M Knaap, Marjolein Kikkert, Brian L Mark
Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate and adaptive immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular deubiquitinating enzymes, which remove ubiquitin from cellular targets and depolymerize polyubiquitin chains. The importance of protein ubiquitination to host immunity has been underscored by the discovery of viruses that encode proteases with deubiquitinating activity, many of which have been demonstrated to actively corrupt cellular ubiquitin-dependent processes to suppress innate antiviral responses and promote viral replication...
June 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28625849/leveraging-reciprocity-to-identify-and-characterize-unknown-allosteric-sites-in-protein-tyrosine-phosphatases
#2
Danica S Cui, Victor Beaumont, Patrick S Ginther, James M Lipchock, J Patrick Loria
Drug-like molecules targeting allosteric sites in proteins are of great therapeutic interest, however identification of potential sites is not trivial. A straightforward approach to identify hidden allosteric sites is demonstrated in protein tyrosine phosphatases (PTP) by creation of single alanine mutations in the catalytic acid loop of PTP1B and VHR. This approach relies on the reciprocal interactions between an allosteric site and its coupled orthosteric site. The resulting NMR chemical shift perturbations of each mutant reveal clusters of distal residues affected by acid loop mutation...
June 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28625848/regulation-of-e2s-a-role-for-additional-ubiquitin-binding-sites
#3
REVIEW
Adam J Middleton, Joshua D Wright, Catherine L Day
Attachment of ubiquitin to proteins relies on a sophisticated enzyme cascade that is tightly regulated. The machinery of ubiquitylation responds to a range of signals, which remarkably includes ubiquitin itself. Thus ubiquitin is not only the central player in the ubiquitylation cascade, but also a key regulator. The ubiquitin E3 ligases provide specificity to the cascade and often bind the substrate, while the ubiquitin-conjugating enzymes (E2s) have a pivotal role in determining chain linkage and length. Interaction of ubiquitin with the E2 is important for activity, but the low affinity of these interactions has made them hard to identify and study...
June 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28625847/hnrnp-a1-alters-the-structure-of-a-conserved-enterovirus-ires-domain-to-stimulate-viral-translation
#4
Michele Tolbert, Christopher E Morgan, Marvin Pollum, Carlos E Crespo-Hernández, Mei-Ling Li, Gary Brewer, Blanton S Tolbert
Enteroviruses use a type I IRES structure to facilitate protein synthesis and promote genome replication. Type I IRES elements require auxiliary host proteins to organize RNA structure for 40S ribosomal subunit assembly. Heterogeneous nuclear ribonucleoprotein A1 stimulates Enterovirus 71 (EV71) translation in part through specific interactions with its stem loop II (SLII) IRES domain. Here, we determined a conjoined NMR-SAXS structure of the EV71 SLII domain and a mutant that significantly attenuates viral replication by abrogating hnRNP A1 interactions...
June 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28625846/biogenesis-of-the-flagellar-switch-complex-in-escherichia-coli-formation-of-sub-complexes-independently-of-the-basal-body-ms-ring
#5
Eun A Kim, Joseph Panushka, Trevor Meyer, Nicholas Ide, Ryan Carlisle, Samantha Baker, David F Blair
Direction switching in the flagellar motor of Escherichia coli is under the control of a complex on the rotor formed from the proteins FliG, FliM, and FliN. FliG lies at the top of the switch complex (i.e., nearest the membrane) and is arranged with its C-terminal domain (FliGC) resting on the middle domain (FliGM) of the neighboring subunit. This organization requires the protein to adopt an open conformation that exposes the surfaces engaging in inter-subunit FliGC/FliGM contacts. In a recent study, Baker and coworkers [Nat...
June 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28610839/fly-fishing-for-histones-catch-and-release-by-histone-chaperone-intrinsically-disordered-regions-and-acidic-stretches
#6
REVIEW
Christopher Warren, David Shechter
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly two-meter long human genome into a roughly ten-micron diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly, and thus the fluidity of the ever-changing chromatin landscape...
June 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28602818/cell-cycle-control-by-pten
#7
REVIEW
Andrew Brandmaier, Sheng-Qi Hou, Wen H Shen
Continuous and error-free chromosome inheritance through the cell cycle is essential for genomic stability and tumor suppression. However, accumulation of aberrant genetic materials often causes the cell cycle to go awry, leading to malignant transformation. In response to genotoxic stress, cells employ diverse adaptive mechanisms to halt or exit the cell cycle temporarily or permanently. The intrinsic machinery of cycling, resting, and exiting shapes the cellular response to extrinsic stimuli whereas prevalent disruption of the cell cycle machinery in tumor cells often confers resistance to anti-cancer therapy...
June 8, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28601495/structural-and-enzymatic-characterization-of-a-camp-dependent-diguanylate-cyclase-from-pathogenic-leptospira-species
#8
Fernanda Nogales da Costa Vasconcelos, Nikolas Koshiyama Maciel, Denize Cristina Favaro, Luciana Coutinho de Oliveira, Angela Silva Barbosa, Roberto Kopke Salinas, Robson Francisco de Souza, Chuck Shaker Farah, Cristiane Rodrigues Guzzo
Leptospira interrogans serovar Copenhageni is a human pathogen that causes leptospirosis, a worldwide zoonosis. The L. interrogans genome codes for a wide array of potential diguanylate cyclase enzymes with characteristic GGDEF domains capable of synthesizing the cyclic dinucleotide c-di-GMP, known to regulate transitions between different cellular behavioural states in bacteria. Among such enzymes, LIC13137 (Lcd1), which has an N-terminal GAF domain and a C-terminal GGDEF domain, is notable for having close orthologs present only in pathogenic Leptospira species...
June 7, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28601494/a-comparative-analysis-of-translesion-dna-synthesis-catalyzed-by-a-high-fidelity-dna-polymerase
#9
Anvesh Dasari, Tejal Deodhar, Anthony J Berdis
Translesion DNA synthesis (TLS) is the ability of DNA polymerases to incorporate nucleotides opposite and beyond damaged DNA. TLS activity is an important risk factor for the initiation and progression of genetic diseases such as cancer. In this study, we evaluate the ability of a high-fidelity DNA polymerase to perform TLS with 8-oxo-guanine, a highly pro-mutagenic DNA lesion formed by reactive oxygen species. Results of kinetic studies monitoring the incorporation of modified nucleotide analogs demonstrate that the binding affinity of the incoming dNTP is controlled by the overall hydrophobicity of the nucleobase...
June 7, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28591556/regulation-of-usp7-a-high-incidence-of-e3-complexes
#10
REVIEW
Robbert Q Kim, Titia K Sixma
Ubiquitin conjugation is a critical signalling process in eukaryotic cells. The precise regulation of deubiquitination is an important component of this signalling cascade. Here we discuss how USP7 (or HAUSP), one of the most abundant deubiquitinating enzymes (DUBs) is regulated by complex formation with regulatory proteins and targets. Full activity of USP7 requires that its C-terminal ubiquitin-like domains fold back onto the catalytic domain, to allow remodelling of the active site to a catalytically competent state by the very C-terminal peptide...
June 4, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28587925/siga-shigella-immune-complexes-interact-with-dectin-1-and-signr3-to-differentially-regulate-mouse-peyer-s-patch-and-mesenteric-lymph-node-dendritic-cell-s-responsiveness
#11
Josip Mikulic, Gilles Bioley, Blaise Corthésy
In addition to contributing to immune exclusion at mucosal surfaces, secretory IgA (SIgA) made of polymeric IgA and secretory component is able to selectively reenter via microfold cells into Peyer's patches (PPs) present along the intestine and to associate with dendritic cells (DCs) of the CD11c(+)CD11b(+)MHCII(+)F4/80(-)CD8(-)phenotype in the subepithelial dome region and the draining mesenteric lymph nodes (MLNs). However, the nature of the receptor(s) for SIgA on murine PP and MLN DCs is unknown. We find that glycosylated secretory component moiety and polymeric IgA are both involved in the specific interaction with these cells...
June 3, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28587924/prmt7-interacts-with-ass1-and-citrullinemia-mutations-disrupt-the-interaction
#12
Mamta Verma, Ramya Chandar M Charles, Baskar Chakrapani, Mohane Selvaraj Coumar, Gayathri Govindaraju, Arumugam Rajavelu, Sreenivas Chavali, Arunkumar Dhayalan
Protein Arginine Methyltransferase 7 (PRMT7) catalyzes the introduction of mono methylation marks at the arginine residues of substrate proteins. PRMT7 plays important roles in the regulation of gene expression, splicing, DNA damage, paternal imprinting, cancer and metastasis. However, little is known about the interaction partners of PRMT7. To address this, we performed yeast two hybrid screening of PRMT7 and identified argininosuccinate synthetase (ASS1) as a potential interaction partner of PRMT7. We confirmed that PRMT7 directly interacts with ASS1 using pull down studies...
June 3, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28587923/generation-and-validation-of-intracellular-ubiquitin-variant-inhibitors-for-usp7-and-usp10
#13
Wei Zhang, Maria A Sartori, Taras Makhnevych, Kelly E Federowicz, Xiaohui Dong, Li Liu, Satra Nim, Aiping Dong, Jingsong Yang, Yanjun Li, Dania Haddad, Andreas Ernst, Dirk Heerding, Yufeng Tong, Jason Moffat, Sachdev S Sidhu
Post-translational modification of the p53 signaling pathway plays an important role in cell cycle progression and stress-induced apoptosis. Indeed, a large body of work has shown that dysregulation of p53 and its E3 ligase MDM2 by the ubiquitin-proteasome system (UPS) promotes carcinogenesis and malignant transformation. Thus, drug discovery efforts have focused on restoration of wild-type p53 activity or inactivation of oncogenic mutant p53 by targeted inhibition of UPS components, particularly key deubiquitinases (DUBs) of the ubiquitin-specific protease (USP) class...
June 3, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28587922/molecular-basis-for-k63-linked-ubiquitination-processes-in-double-strand-dna-break-repair-a-focus-on-kinetics-and-dynamics
#14
REVIEW
Brian L Lee, Anamika, J N Mark Glover, Michael J Hendzel, Leo Spyracopoulos
Cells are exposed to thousands of DNA damage events on a daily basis. This damage must be repaired to preserve genetic information, and prevent development of disease. The most deleterious damage is a double strand break (DSB), which is detected and repaired by mechanisms known as non-homologous end joining (NHEJ), and homologous recombination (HR), components of the DNA damage response system. NHEJ is an error prone first line of defense, whereas HR invokes error free repair, and is the focus of this review...
June 3, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28583440/proteasome-structure-and-assembly
#15
REVIEW
Lauren Budenholzer, Chin Leng Cheng, Yanjie Li, Mark Hochstrasser
The eukaryotic 26S proteasome is a large multi-subunit complex that degrades the majority of proteins in the cell under normal conditions. The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle (RP) and the 20S core particle (CP). Most substrates are first covalently modified by ubiquitin, which then directs them to the proteasome. The function of the RP is to recognize, unfold, deubiquitylate and translocate substrates into the CP, which contains the proteolytic sites of the proteasome...
June 2, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28576472/redirecting-sr-protein-nuclear-trafficking-through-an-allosteric-platform
#16
Brandon E Aubol, Kendra L Hailey, Laurent Fattet, Patricia A Jennings, Joseph A Adams
Although phosphorylation directs serine-arginine (SR) proteins from nuclear storage speckles to the nucleoplasm for splicing function, dephosphorylation paradoxically induces similar movement, raising the question of how such chemical modifications are balanced in these essential splicing factors. In this new study, we investigated the interaction of protein phosphatase 1 (PP1) with the SR protein splicing factor (SRSF1) to understand the foundation of these opposing effects in the nucleus. We found that RNA recognition motif 1 (RRM1) in SRSF1 binds PP1 and represses its catalytic function through an allosteric mechanism...
May 31, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28576471/connection-of-protein-transport-and-organelle-contact-sites-in-mitochondria
#17
REVIEW
Lars Ellenrieder, Heike Rampelt, Thomas Becker
Mitochondrial biogenesis and function depend on the intensive exchange of molecules with other cellular compartments. The mitochondrial outer membrane plays a central role in this communication process. It is equipped with a number of specific protein machineries that enable the transport of proteins and metabolites. Furthermore, the outer membrane forms molecular contact sites with other cell organelles like the endoplasmic reticulum (ER), thus integrating mitochondrial function in cellular physiology. The best-studied mitochondrial organelle contact site, the ER-mitochondria encounter structure (ERMES) has been linked to many vital processes including mitochondrial division, inheritance, mitophagy, and phospholipid transport...
May 30, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28554731/rna-g-quadruplexes-in-biology-principles-and-molecular-mechanisms
#18
REVIEW
Marta M Fay, Shawn M Lyons, Pavel Ivanov
G-quadruplexes (G4s) are extremely stable DNA or RNA secondary structures formed by sequences rich in guanine. These structures are implicated in many essential cellular processes, and the number of biological functions attributed to them continues to grow. While DNA G4s are well understood on structural and, to some extent, functional levels, RNA G4s and their functions have received less attention. The presence of bona fide RNA G4s in cells has long been a matter of debate. The development of G4-specific antibodies and ligands hinted on their presence in vivo, but recent advances in RNA sequencing coupled with chemical footprinting suggested the opposite...
May 26, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28551336/structural-and-molecular-biology-of-a-protein-polymerising-nanomachine-for-pilus-biogenesis
#19
REVIEW
Gabriel Waksman
Bacteria produce protein polymers on their surface called pili or fimbriae that serve as either attachment devices or conduits for secreted substrates. This review will focus on the chaperone-usher pathway of pilus biogenesis, a widespread assembly line for pilus production at the surface of Gram-negative bacteria and the archetypical protein-polymerising nanomachine. Comparison with other nanomachines polymerising other types of biological units, such as nucleotides during DNA replication, provides some unifying principles as to how multi-domain proteins assemble biological polymers...
May 24, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28551335/transition-path-times-measured-by-single-molecule-spectroscopy
#20
REVIEW
Hoi Sung Chung
The transition path is a tiny fraction of a molecular trajectory during which the free-energy barrier is crossed. It is a single-molecule property and contains all mechanistic information of folding processes of biomolecules such as proteins and nucleic acids. However, the transition path has been difficult to probe because it is short and rarely visited when transitions actually occur. Recent technical advances in single-molecule spectroscopy have made it possible to directly probe transition paths, which has opened up new theoretical and experimental approaches to investigating folding mechanisms...
May 24, 2017: Journal of Molecular Biology
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