abstract：:Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringin...

journal_title：Journal of molecular biology

authors： Gumińska N,Zakryś B,Milanowski R

更新日期：2021-02-05 00:00:00

abstract：:Lysine methylation is a key regulator of protein-protein binding. The amine group of lysine can accept up to three methyl groups, and experiments show that protein-protein binding free energies are sensitive to the extent of methylation. These sensitivities have been rationalized in terms of chemical and structural fe...

journal_title：Journal of molecular biology

authors： Rahman S,Wineman-Fisher V,Al-Hamdani Y,Tkatchenko A,Varma S

更新日期：2021-02-05 00:00:00

abstract：:Intrinsically disordered proteins (IDPs) lack stable tertiary structure under physiological conditions. The unique composition and complex dynamical behaviour of IDPs make them a challenge for structural biology and molecular evolution studies. Using NMR ensembles, we found that IDPs evolve under a strong site-specifi...

journal_title：Journal of molecular biology

authors： Palopoli N,Marchetti J,Monzon AM,Zea DJ,Tosatto SCE,Fornasari MS,Parisi G

更新日期：2021-02-05 00:00:00

abstract：:Na+/H+antiportersare a category of ubiquitous transmembrane proteins with various important physiological roles in almost all living organisms ranging from bacteria to humans. However, the knowledge of novel Na+/H+antiporters remains to be broadened, and the functional roles ofoligomerization in theseantiportershave n...

journal_title：Journal of molecular biology

authors： Shao L,Xu T,Zheng X,Shao D,Zhang H,Chen H,Zhang Z,Yan M,Abdel-Motaal H,Jiang J

更新日期：2021-01-22 00:00:00

abstract：:Protein self-assembly is a common and essential biological phenomenon, and bacterial microcompartments present a promising model system to study this process. Bacterial microcompartments are large, protein-based organelles which natively carry out processes important for carbon fixation in cyanobacteria and the surviv...

journal_title：Journal of molecular biology

authors： Kennedy NW,Ikonomova SP,Slininger Lee M,Raeder HW,Tullman-Ercek D

更新日期：2021-01-22 00:00:00

abstract：:Forkhead box O4 (FOXO4) is a human transcription factor (TF) that participates in cell homeostasis. While the structure and DNA binding properties of the conserved forkhead domain (FHD) have been thoroughly investigated, how the transactivation domain (TAD) regulates the DNA binding properties of the protein remains e...

journal_title：Journal of molecular biology

authors： Kim J,Ahn D,Park CJ

更新日期：2021-01-13 00:00:00

abstract：:Apical sodium-dependent bile acid transporter (ASBT) catalyses uphill transport of bile acids using the electrochemical gradient of Na+ as the driving force. The crystal structures of two bacterial homologues ASBTNM and ASBTYf have previously been determined, with the former showing an inward-facing conformation, and ...

journal_title：Journal of molecular biology

authors： Lu PH,Li CC,Chiang YW,Liu JH,Chiang WT,Chao YH,Li GS,Weng SE,Lin SY,Hu NJ

更新日期：2021-01-13 00:00:00

abstract：:B lymphocytes play a central role in host immunity. They orchestrate humoral immune responses that modulate activities of other immune cells and produce neutralizing antibodies that confer lasting immunity to infectious diseases including smallpox, measles and poliomyelitis. In addition to these traditional functions ...

journal_title：Journal of molecular biology

authors： Choi JK,Egwuagu CE

更新日期：2021-01-08 00:00:00

abstract：:BCR signaling triggers a cascade of intracellular mediators that eventuates in transcription factor activation. Signaling is proximally mediated by Src family tyrosine kinases, the most abundant being Lyn. Key mediators are grouped together as the signalosome, and failure of any single member of this group leads to fa...

journal_title：Journal of molecular biology

authors： Khan N,Rothstein TL

更新日期：2021-01-08 00:00:00

abstract：:It is now appreciated that in addition to their role in humoral immunity, B cells also exert regulatory mechanisms that lead to attenuation of inflammatory responses. The concept of B-cell regulation became well recognized when mice deficient in B cells due to genetic disruption were shown to be refractory to recovery...

journal_title：Journal of molecular biology

authors： Khalil MI,Gurski CJ,Dittel LJ,Neu SD,Dittel BN

更新日期：2021-01-08 00:00:00

abstract：:Many proteins are composed of independently-folded domains connected by flexible linkers. The primary sequence and length of such linkers can set the effective concentration for the tethered domains, which impacts rates of association and enzyme activity. The length of such linkers can be sensitive to environmental co...

journal_title：Journal of molecular biology

authors： Basak S,Sakia N,Dougherty L,Guo Z,Wu F,Mindlin F,Lary JW,Cole JL,Ding F,Bowen ME

更新日期：2021-01-01 00:00:00

abstract：:Many unanswered questions remain in understanding the biosynthesis of the peptide hormone insulin. Here we elucidate new aspects in the mechanism of co-translational translocation initiation of pre-proinsulin in the endoplasmic reticulum. We utilize a translational arrest peptide derived from the x-box-binding protein...

journal_title：Journal of molecular biology

authors： Kriegler T,Kiburg G,Hessa T

更新日期：2020-12-04 00:00:00

abstract：:In antibody light chain amyloidosis (AL), mutant light chains (LCs) or their variable domains (VLs) form fibrils, which accumulate in organs and lead to their failure. The molecular mechanism of this disease is still poorly understood. One of the key open issues is whether the mutant VLs and LCs differ in fibril forma...

journal_title：Journal of molecular biology

authors： Weber B,Hora M,Kazman P,Pradhan T,Rührnößl F,Reif B,Buchner J

更新日期：2020-11-20 00:00:00

abstract：:Cytokines orchestrate responses to pathogens and in inflammatory processes, but they also play an important role in cancer by shaping the expression levels of cytokine response genes. Here, we conducted a large profiling study comparing miRNome and mRNA transcriptome data generated following different cytokine stimula...

journal_title：Journal of molecular biology

authors： Kirchmeyer M,Servais F,Ginolhac A,Nazarov PV,Margue C,Philippidou D,Nicot N,Behrmann I,Haan C,Kreis S

更新日期：2020-11-06 00:00:00

abstract：:Chromatin compacts genomic DNA in eukaryotes. The primary chromatin unit is the nucleosome core particle, composed of four pairs of the core histones, H2A, H2B, H3, and H4, and 145-147 base pairs of DNA. Since replication, recombination, repair, and transcription take place in chromatin, the structure and dynamics of ...

journal_title：Journal of molecular biology

authors： Kurumizaka H,Kujirai T,Takizawa Y

更新日期：2020-10-14 00:00:00

abstract：:Selective autophagy is the capture of specific cytosolic contents in double-membrane vesicles that subsequently fuse with the vacuole or lysosome, thereby delivering cargo for degradation. Selective autophagy receptors (SARs) mark the cargo for degradation and, in yeast, recruit Atg11, the scaffolding protein for sele...

journal_title：Journal of molecular biology

authors： Margolis HK,Katzenell S,Leary KA,Ragusa MJ

更新日期：2020-10-02 00:00:00

abstract：:Protein interactions play a crucial role among the different functions of a cell and are central to our understanding of cellular processes both in health and disease. Here we present Galaxy InteractoMIX (http://galaxy.interactomix.com), a platform composed of 13 different computational tools each addressing specific ...

journal_title：Journal of molecular biology

authors： Mirela-Bota P,Aguirre-Plans J,Meseguer A,Galletti C,Segura J,Planas-Iglesias J,Garcia-Garcia J,Guney E,Oliva B,Fernandez-Fuentes N

更新日期：2020-09-23 00:00:00

abstract：:A hallmark of the catalytically essential Walker B motif of P-loop NTPases is the presence of an acidic residue (aspartate/glutamate) for efficient Mg2+ coordination. Although the Walker B motif has been identified in well-studied examples of P-loop NTPases, its identity is ambiguous in many families, for example, in ...

journal_title：Journal of molecular biology

authors： Kanade M,Chakraborty S,Shelke SS,Gayathri P

更新日期：2020-09-18 00:00:00

abstract：:The stability of membrane proteins differs from globular proteins due to the presence of nonpolar membrane-spanning regions. Using a dataset of 929 membrane protein mutations whose effects on thermal stability (ΔTm) were experimentally determined, we found that the average ΔTm due to 190 stabilizing and 232 destabiliz...

journal_title：Journal of molecular biology

authors： Kulandaisamy A,Zaucha J,Frishman D,Gromiha MM

更新日期：2020-09-10 00:00:00

abstract：:MEF2 and NKX2-5 transcription factors interact with each other in cardiogenesis and are necessary for normal heart formation. Despite evidence suggesting that these two transcription factors function synergistically and possibly through direct physical interactions, molecular mechanisms by which they interact are not ...

journal_title：Journal of molecular biology

authors： Lei X,Zhao J,Sagendorf JM,Rajashekar N,Xu J,Dantas Machado AC,Sen C,Rohs R,Feng P,Chen L

更新日期：2020-09-04 00:00:00

abstract：:Eicosanoids are potent lipid mediators involved in central physiological processes such as hemostasis, renal function and parturition. When formed in excess, eicosanoids become critical players in a range of pathological conditions, in particular pain, fever, arthritis, asthma, cardiovascular disease and cancer. Eicos...

journal_title：Journal of molecular biology

authors： Thulasingam M,Haeggström JZ

更新日期：2020-08-21 00:00:00

abstract：:Intramembrane enzymes are often difficult for biochemical characterization. Human vitamin K epoxide reductase (VKOR) is the target of warfarin. However, this intramembrane enzyme becomes insensitive to warfarin inhibition in vitro, preventing the characterization of inhibition kinetics for decades. Here we employ stru...

journal_title：Journal of molecular biology

authors： Li S,Liu S,Yang Y,Li W

更新日期：2020-08-21 00:00:00

abstract：:Tafazzin is a mitochondrial enzyme that exchanges fatty acids between phospholipids by phospholipid-lysophospholipid transacylation. The reaction alters the molecular species composition and, as a result, the physical properties of lipids. In vivo, the most important substrate of tafazzin is the mitochondria-specific ...

journal_title：Journal of molecular biology

authors： Schlame M,Xu Y

更新日期：2020-08-21 00:00:00

abstract：:Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important intracellular signaling molecule that affects diverse physiological processes in bacteria. The intracellular levels of c-di-GMP are controlled by proteins acting as diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes that synthesiz...

journal_title：Journal of molecular biology

authors： Pallegar P,Canuti M,Langille E,Peña-Castillo L,Lang AS

更新日期：2020-08-07 00:00:00

abstract：:The cellular prion protein (PrPC) comprises two domains: a globular C-terminal domain and an unstructured N-terminal domain. Recently, copper has been observed to drive tertiary contact in PrPC, inducing a neuroprotective cis interaction that structurally links the protein's two domains. The location of this interacti...

journal_title：Journal of molecular biology

authors： Schilling KM,Tao L,Wu B,Kiblen JTM,Ubilla-Rodriguez NC,Pushie MJ,Britt RD,Roseman GP,Harris DA,Millhauser GL

更新日期：2020-07-24 00:00:00

abstract：:Despite the condensed nature of terminal sequences, the telomeres are transcribed into a group of noncoding RNAs, including the TElomeric Repeat-containing RNA (TERRA). Since the discovery of TERRA, its evolutionary conserved function has been confirmed, and its involvement in telomere length regulation, heterochromat...

journal_title：Journal of molecular biology

authors： Coulon S,Vaurs M

更新日期：2020-07-10 00:00:00

abstract：:RNA polymerase II (Pol II) and its general transcription factors assemble on the promoters of mRNA genes to form large macromolecular complexes that initiate transcription in a regulated manner. During early transcription, these complexes undergo dynamic rearrangement and disassembly as Pol II moves away from the star...

journal_title：Journal of molecular biology

authors： Ly E,Powell AE,Goodrich JA,Kugel JF

更新日期：2020-06-26 00:00:00

abstract：:The impenetrability of the blood-brain barrier (BBB) to most conventional drugs impedes the treatment of central nervous system (CNS) disorders. Interventions for diseases like brain cancer, neurodegeneration, or age-associated inflammatory processes require varied approaches to CNS drug delivery. Cystine-dense peptid...

journal_title：Journal of molecular biology

authors： Crook ZR,Girard E,Sevilla GP,Merrill M,Friend D,Rupert PB,Pakiam F,Nguyen E,Yin C,Ruff RO,Hopping G,Strand AD,Finton KAK,Coxon M,Mhyre AJ,Strong RK,Olson JM

更新日期：2020-06-26 00:00:00

abstract：:Auxin is a plant hormone that is central to plant growth and development from embryogenesis to senescence. Auxin signaling is mediated by auxin response transcription factors (ARFs) and Aux/IAA repressors that regulate the expression of a multitude of auxin response genes. ARF and Aux/IAA proteins assemble into homome...

journal_title：Journal of molecular biology

authors： Kim Y,Park C,Cha S,Han M,Ryu KS,Suh JY

更新日期：2020-06-26 00:00:00

abstract：:Non-coding RNAs play pivotal roles in bacterial signaling. However, RNAs from certain phyla (specially high-GC actinobacteria) still remain elusive. Here, by re-engineering the existing genome-wide search approach, we discover a family of structurally conserved RNAs that are present ubiquitously across actinobacteria,...

journal_title：Journal of molecular biology

authors： Mehta D,Koottathazhath A,Ramesh A

更新日期：2020-06-26 00:00:00

abstract：:RNA polymerase transcribes certain genomic loci with higher errors rates. These transcription error-enriched genomic loci (TEELs) have implications in disease. Current deep-sequencing methods cannot distinguish TEELs from post-transcriptional modifications, stochastic transcription errors, and technical noise, impedin...

journal_title：Journal of molecular biology

authors： Cheung PP,Jiang B,Booth GT,Chong TH,Unarta IC,Wang Y,Suarez GD,Wang J,Lis JT,Huang X

更新日期：2020-06-12 00:00:00

abstract：:A family of Structural Maintenance of Chromosome (SMC) complexes is essential for key cellular processes ensuring proper cohesion, condensation and replication. They share a common SMC-kleisin architecture allowing them to embrace DNA. In SMC5/6, the NSE1 and NSE3 KITE and NSE4 kleisin subunits form a stable subcomple...

journal_title：Journal of molecular biology

authors： Adamus M,Lelkes E,Potesil D,Ganji SR,Kolesar P,Zabrady K,Zdrahal Z,Palecek JJ

更新日期：2020-06-12 00:00:00

abstract：:Pseudomonas aeruginosa is a priority pathogen for the development of new antibiotics, particularly because multi-drug-resistant strains of this bacterium cause serious nosocomial infections and are the leading cause of death in cystic fibrosis patients. Pyocins, bacteriocins of P. aeruginosa, are potent and diverse pr...

journal_title：Journal of molecular biology

authors： Atanaskovic I,Mosbahi K,Sharp C,Housden NG,Kaminska R,Walker D,Kleanthous C

更新日期：2020-06-12 00:00:00

abstract：:Protein expression in multicellular organisms varies widely across tissues. Codon usage in the transcriptome of each tissue is derived from genomic codon usage and the relative expression level of each gene. We created a comprehensive computational resource that houses tissue-specific codon, codon-pair, and dinucleoti...

journal_title：Journal of molecular biology

authors： Kames J,Alexaki A,Holcomb DD,Santana-Quintero LV,Athey JC,Hamasaki-Katagiri N,Katneni U,Golikov A,Ibla JC,Bar H,Kimchi-Sarfaty C

更新日期：2020-05-15 00:00:00

abstract：:Noncoding RNAs (ncRNAs), such as lncRNAs, circRNAs and pri-miRNAs, play important roles in physiological and pathological processes. Recently, it was demonstrated that they could encode proteins or peptides. However, relevant information is scattered across numerous published articles, which is inconvenient for the ex...

journal_title：Journal of molecular biology

authors： Liu H,Zhou X,Yuan M,Zhou S,Huang YE,Hou F,Song X,Wang L,Jiang W

更新日期：2020-05-15 00:00:00

abstract：:To expand the repertoire of chemogenetic tools tailored for molecular and cellular engineering, we describe herein the design of cpRAPID as a circularly permuted rapamycin-inducible dimerization system composed of the canonical FK506-binding protein (FKBP) and circular permutants of FKBP12-rapamycin binding domain (cp...

journal_title：Journal of molecular biology

authors： Lee YT,He L,Zhou Y

更新日期：2020-05-01 00:00:00

abstract：:Neurons are electrically excitable, postmitotic cells that perform sensory, relaying, and motor functions. Because of their unique morphological and functional specialization, cells of this type are sensitive to the stress caused by accumulation of misfolded proteins or damaged organelles. Autophagy is the fundamental...

journal_title：Journal of molecular biology

authors： Conway O,Akpinar HA,Rogov VV,Kirkin V

更新日期：2020-04-03 00:00:00

abstract：:One of the last uncharted territories in evolutionary biology concerns the link with cell biology. Because all phenotypes ultimately derive from events at the cellular level, this connection is essential to building a mechanism-based theory of evolution. Given the impressive developments in cell biological methodologi...

journal_title：Journal of molecular biology

authors： Lynch M,Trickovic B

更新日期：2020-03-27 00:00:00

abstract：:The cylindrical chaperonin GroEL and its cofactor GroES mediate ATP-dependent protein folding in Escherichia coli by transiently encapsulating non-native substrate in a nano-cage formed by the GroEL ring cavity and the lid-shaped GroES. Mechanistic studies of GroEL/ES with heterologous protein substrates suggested tha...

journal_title：Journal of molecular biology

authors： Singh AK,Balchin D,Imamoglu R,Hayer-Hartl M,Hartl FU

更新日期：2020-03-27 00:00:00

abstract：:The portal proteins of tailed bacteriophage and Herpesvirus capsids form dodecameric rings that occupy one capsid vertex and are incorporated during the assembly of capsid precursors called procapsids or proheads. Portals are essential and serve as the pore for DNA transit and the site of tail attachment; however, bac...

journal_title：Journal of molecular biology

authors： Maurer JB,Oh B,Moyer CL,Duda RL

更新日期：2020-03-27 00:00:00