abstract：:In the crowded cell, a strong selective pressure operates on the proteome to limit the competition between functional and non-functional protein-protein interactions. We developed an original theoretical framework in order to interrogate how this competition constrains the behavior of proteins with respect to their pa...

journal_title：Journal of molecular biology

authors： Schweke H,Mucchielli MH,Sacquin-Mora S,Bei W,Lopes A

更新日期：2020-02-14 00:00:00

abstract：:Transmembrane proteins (TMPs) play important roles in many biological processes, such as cell recognition and communication. Their structures are crucial for revealing complex functions but are hard to obtain. A variety of computational algorithms have been proposed to fill the gap by predicting structures from primar...

journal_title：Journal of molecular biology

authors： Feng SH,Zhang WX,Yang J,Yang Y,Shen HB

更新日期：2020-02-14 00:00:00

abstract：:The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divale...

journal_title：Journal of molecular biology

authors： Welty R,Rau M,Pabit S,Dunstan MS,Conn GL,Pollack L,Hall KB

更新日期：2020-02-14 00:00:00

abstract：:Precise regulation of dNTPs within the cellular nucleotide pool is essential for high accuracy of DNA replication and is critical for retaining the genomic integrity. Recently, human dCTPase (deoxycytidine triphosphatase), also known as DCTPP1 (human all-alpha dCTP pyrophosphatase 1), has been revealed to be a key pla...

journal_title：Journal of molecular biology

authors： Scaletti E,Claesson M,Helleday T,Jemth AS,Stenmark P

更新日期：2020-02-14 00:00:00

abstract：:Transcription activator-like effectors (TALEs) recognize DNA through repeat-variable diresidues (RVDs), and TALE-DNA interactions are sensitive to DNA modifications. Our previous study deciphered the recognition of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) by TALEs. Here, we report seven crystal struct...

journal_title：Journal of molecular biology

authors： Liu L,Zhang Y,Liu M,Wei W,Yi C,Peng J

更新日期：2020-02-14 00:00:00

abstract：:The ability of homologous chromosomes (or selected chromosomal loci) to pair specifically in the apparent absence of DNA breakage and recombination represents a prominent feature of eukaryotic biology. The mechanism of homology recognition at the basis of such recombination-independent pairing has remained elusive. A ...

journal_title：Journal of molecular biology

authors： Mazur AK,Nguyen TS,Gladyshev E

更新日期：2020-02-07 00:00:00

abstract：:Although chemical signaling during embryogenesis is readily addressed by a plethora of available techniques, the developmental functions of ionic signaling are still poorly understood. It is increasingly realized that bioelectric events in nonneural cells are critical for pattern regulation, but their study has been h...

journal_title：Journal of molecular biology

authors： McMillen P,Novak R,Levin M

更新日期：2020-01-17 00:00:00

abstract：:Rho-dependent transcription termination is a well-conserved process in bacteria. The Psu and YaeO proteins are the two established inhibitors of the ATP-dependent RNA helicase Rho protein of Escherichia coli. Here, we show a detailed sequence and phylogenetic analysis demonstrating that Vibrio cholerae YaeO (VcYaeO) i...

journal_title：Journal of molecular biology

authors： Pal K,Yadav M,Jain S,Ghosh B,Sen R,Sen U

更新日期：2019-12-06 00:00:00

abstract：:Staphyloferrin B is a hydroxycarboxylate siderophore that is crucial for the invasion and virulence of Staphylococcus aureus in mammalian hosts where free iron ions are scarce. The assembly of staphyloferrin B involves four enzymatic steps, in which SbnH, a pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, catalyz...

journal_title：Journal of molecular biology

authors： Tang J,Ju Y,Gu Q,Xu J,Zhou H

更新日期：2019-12-06 00:00:00

abstract：:The effects of RNA methylation on HIV-1 replication remain largely unknown. Recent studies have discovered new insights into the effect of 2'-O-methylation and 5-methylcytidine marks on the HIV-1 RNA genome. As so far, HIV-1 benefits from diverse RNA methylations through distinct mechanisms. In this review, we summari...

journal_title：Journal of molecular biology

authors： Kong W,Rivera-Serrano EE,Neidleman JA,Zhu J

更新日期：2019-12-06 00:00:00

abstract：:The human pathogen Staphylococcus aureus is a gram-positive bacterium that causes difficult-to-treat infections. One of the reasons why S. aureus is such as successful pathogen is due to the cell-to-cell physiological variability that exists within microbial communities. Many laboratories around the world study the ge...

journal_title：Journal of molecular biology

authors： García-Betancur JC,Lopez D

更新日期：2019-11-22 00:00:00

abstract：:Salmonellais a foodborne pathogen that causes annually millions of cases of salmonellosis globally, yet Salmonella-specific antibacterials are not available. During inflammation, Salmonella utilizes the Amadori compound fructose-asparagine (F-Asn) as a nutrient through the successive action of three enzymes, including...

journal_title：Journal of molecular biology

authors： Sengupta A,Wu J,Seffernick JT,Sabag-Daigle A,Thomsen N,Chen TH,Capua AD,Bell CE,Ahmer BMM,Lindert S,Wysocki VH,Gopalan V

更新日期：2019-11-08 00:00:00

abstract：:Many viruses employ ATP-powered motors for genome packaging. We combined genetic, biochemical, and single-molecule techniques to confirm the predicted Walker-B ATP-binding motif in the phage λ motor and to investigate the roles of the conserved residues. Most changes of the conserved hydrophobic residues resulted in >...

journal_title：Journal of molecular biology

authors： delToro D,Ortiz D,Ordyan M,Pajak J,Sippy J,Catala A,Oh CS,Vu A,Arya G,Smith DE,Catalano CE,Feiss M

更新日期：2019-11-08 00:00:00

abstract：:MeCP2 is a reader of the DNA methylome that occupies a large proportion of the genome due to its high abundance and the frequency of its target sites. It has been the subject of extensive study because of its link with 'MECP2-related disorders', of which Rett syndrome is the most prevalent. This review integrates evid...

journal_title：Journal of molecular biology

authors： Tillotson R,Bird A

更新日期：2019-10-17 00:00:00

abstract：:Research on filoviruses has historically focused on the highly pathogenic ebola- and marburgviruses. Indeed, until recently, these were the only two genera in the filovirus family. Recent advances in sequencing technologies have facilitated the discovery of not only a new ebolavirus, but also three new filovirus gener...

journal_title：Journal of molecular biology

authors： Hume AJ,Mühlberger E

更新日期：2019-10-04 00:00:00

abstract：:Enzymes exhibit a strong long-range evolutionary constraint that extends from their catalytic site and affects even distant sites, where site-specific evolutionary rate increases monotonically with distance. While protein-protein sites in enzymes were previously shown to induce only a weak conservation gradient, a com...

journal_title：Journal of molecular biology

authors： Sharir-Ivry A,Xia Y

更新日期：2019-09-06 00:00:00

abstract：:Neurofibromatosis type I (NF1) and Legius syndrome are rare inherited disorders that share diagnostic symptoms including dermal abnormalities like axillary and inguinal freckling and café au lait spots. In addition, patients suffering from NF1 have a demanding risk for the development of severe tumors of the periphera...

journal_title：Journal of molecular biology

authors： Führer S,Tollinger M,Dunzendorfer-Matt T

更新日期：2019-09-06 00:00:00

abstract：:Many medically relevant Gram-negative bacteria use the type III secretion system (T3SS) to translocate effector proteins into the host for their invasion and intracellular survival. A multi-protein complex located at the cytosolic interface of the T3SS is proposed to act as a sorting platform by selecting and targetin...

journal_title：Journal of molecular biology

authors： Bernal I,Börnicke J,Heidemann J,Svergun D,Horstmann JA,Erhardt M,Tuukkanen A,Uetrecht C,Kolbe M

更新日期：2019-09-06 00:00:00

abstract：:The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens su...

journal_title：Journal of molecular biology

authors： Tooke CL,Hinchliffe P,Bragginton EC,Colenso CK,Hirvonen VHA,Takebayashi Y,Spencer J

更新日期：2019-08-23 00:00:00

abstract：:The increased incidence of bacterial resistance to available antibiotics represents a major global health problem and highlights the need for novel anti-infective therapies. Antimicrobial peptides (AMPs) represent promising alternatives to conventional antibiotics. AMPs are versatile, have almost unlimited sequence sp...

journal_title：Journal of molecular biology

authors： Torres MDT,Sothiselvam S,Lu TK,de la Fuente-Nunez C

更新日期：2019-08-23 00:00:00

abstract：:Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterized VgaA, LsaA and MsrE confer resistance to antibiotics that target the pe...

journal_title：Journal of molecular biology

authors： Murina V,Kasari M,Takada H,Hinnu M,Saha CK,Grimshaw JW,Seki T,Reith M,Putrinš M,Tenson T,Strahl H,Hauryliuk V,Atkinson GC

更新日期：2019-08-23 00:00:00

abstract：:Isoniazid (INH) was the first synthesized drug that mediated bactericidal killing of the bacterium Mycobacterium tuberculosis, a major clinical breakthrough. To this day, INH remains a cornerstone of modern tuberculosis (TB) chemotherapy. This review describes the serendipitous discovery of INH, its effectiveness on T...

journal_title：Journal of molecular biology

authors： Vilchèze C,Jacobs WR Jr

更新日期：2019-08-23 00:00:00

abstract：:A long-standing goal in biology is the complete annotation of function and structure on all protein-protein interactions, a large fraction of which is mediated by intrinsically disordered protein regions (IDRs). However, knowledge derived from experimental structures of such protein complexes is disproportionately sma...

journal_title：Journal of molecular biology

authors： Wong ETC,Gsponer J

更新日期：2019-08-09 00:00:00

abstract：:α-Synuclein (αSyn) is an intrinsically disordered protein that can form amyloid fibrils. Fibrils of αSyn are implicated with the pathogenesis of Parkinson's disease and other synucleinopathies. Elucidating the mechanism of fibril formation of αSyn is therefore important for understanding the mechanism of the pathogene...

journal_title：Journal of molecular biology

authors： Fujiwara S,Kono F,Matsuo T,Sugimoto Y,Matsumoto T,Narita A,Shibata K

更新日期：2019-08-09 00:00:00

abstract：:Enterococcus faecalis, a ubiquitous member of the healthy human gut microbiota, is also a common opportunistic pathogen and leading cause of nosocomial infections. This tenacious microbe is well adapted to infect and persist in multiple niches within the mammalian host and can rapidly tune its metabolism to respond to...

journal_title：Journal of molecular biology

authors： Kao PHN,Kline KA

更新日期：2019-07-26 00:00:00

abstract：:Allosteric communication between different subunits in metabolic enzyme complexes is of utmost physiological importance but only understood for few systems. We analyzed the structural basis of allostery in aminodeoxychorismate synthase (ADCS), which is a member of the family of glutamine amidotransferases and catalyze...

journal_title：Journal of molecular biology

authors： Semmelmann F,Straub K,Nazet J,Rajendran C,Merkl R,Sterner R

更新日期：2019-07-12 00:00:00

abstract：:Prion diseases are neurodegenerative disorders caused by the misfolding of the cellular prion protein (PrPC). Gerstmann-Sträussler-Scheinker syndrome is an inherited prion disease with one early-onset allele (HRdup) containing an eight-amino-acid insertion; this LGGLGGYV insert is positioned after valine 129 (human Pr...

journal_title：Journal of molecular biology

authors： Fu ZL,Holmes PC,Westaway D,Sykes BD

更新日期：2019-06-28 00:00:00

abstract：:Proton transfer through membrane-bound ion channels is mediated by both water and polar residues of proteins, but the detailed molecular mechanism is challenging to determine. The tetrameric influenza A and B virus M2 proteins form canonical proton channels that use an HxxxW motif for proton selectivity and gating. Th...

journal_title：Journal of molecular biology

authors： Kwon B,Roos M,Mandala VS,Shcherbakov AA,Hong M

更新日期：2019-06-28 00:00:00

abstract：:Small, fast-growing bacteria make ideal subjects for genetic and quantitative analysis alike. Long the darling of theoreticians, efforts to understand the relationship between cell growth and cell cycle progression in bacterial systems have been propelled by modelers and empiricist in equal measure. Taking a historica...

journal_title：Journal of molecular biology

authors： Levin PA,Taheri-Araghi S

更新日期：2019-05-17 00:00:00

abstract：:Specificity engineering is challenging and particularly difficult for enzymes that have the catalytic machinery and specificity determinants in close proximity. Restriction endonucleases have been used as a paradigm for protein engineering, but successful cases are rare. Here, we present the results of a directed evol...

journal_title：Journal of molecular biology

authors： Czapinska H,Siwek W,Szczepanowski RH,Bujnicki JM,Bochtler M,Skowronek KJ

更新日期：2019-05-17 00:00:00

abstract：:Microglia, the resident macrophages of the central nervous system, critically influence neural function during development and in adulthood. Microglia are also profoundly sensitive to insults to the brain to which they respond with process of activation that includes spectrum of changes in morphology, function, and ge...

journal_title：Journal of molecular biology

authors： Ferro A,Sheeler C,Rosa JG,Cvetanovic M

更新日期：2019-04-19 00:00:00

abstract：:RNA splicing brings diversity to the eukaryotic proteome. Different spliced variants of a gene may differ in their structure, function, localization, and stability influencing protein stoichiometry and physiological outcomes. Alternate spliced variants of different genes are known to associate with various chronic pat...

journal_title：Journal of molecular biology

authors： Chauhan K,Kalam H,Dutt R,Kumar D

更新日期：2019-04-05 00:00:00

abstract：:Membrane-embedded pyrophosphatase (M-PPase) hydrolyzes pyrophosphate to drive ion (H+ and/or Na+) translocation. We determined crystal structures and functions of Vigna radiata M-PPase (VrH+-PPase), the VrH+-PPase-2Pi complex and mutants at hydrophobic gate (residue L555) and exit channel (residues T228 and E225). Ion...

journal_title：Journal of molecular biology

authors： Tsai JY,Tang KZ,Li KM,Hsu BL,Chiang YW,Goldman A,Sun YJ

更新日期：2019-04-05 00:00:00

abstract：:During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic pathways: deformylation of the N-terminal methionine by the enzyme peptide deformylase (PDF), followed by methionine excision ...

journal_title：Journal of molecular biology

authors： Bhakta S,Akbar S,Sengupta J

更新日期：2019-03-29 00:00:00

abstract：:Building on the substantial progress that has been made in using free energy perturbation (FEP) methods to predict the relative binding affinities of small molecule ligands to proteins, we have previously shown that results of similar quality can be obtained in predicting the effect of mutations on the binding affinit...

journal_title：Journal of molecular biology

authors： Clark AJ,Negron C,Hauser K,Sun M,Wang L,Abel R,Friesner RA

更新日期：2019-03-29 00:00:00

abstract：:We show here that the specific use of fast or slowly translated codons in the early coding region of a gene may influence both the mRNA stability and premature transcription termination. We first inserted a pair of nearly identical 42-base-pair (bp)-long sequences into codon 3 of the Escherichia coli lacZ gene. The on...

journal_title：Journal of molecular biology

authors： Pedersen S,Terkelsen TB,Eriksen M,Hauge MK,Lund CC,Sneppen K,Mitarai N

更新日期：2019-03-15 00:00:00

abstract：:Chromatin remodeling is fundamental for the dynamical changes in transcriptional programs that occur during development and stem cell differentiation. The histone acetyltransferase Kat6b is relevant for neurogenesis in mouse embryos, and mutations of this gene cause intellectual disability in humans. However, the mole...

journal_title：Journal of molecular biology

authors： Cosentino MS,Oses C,Vázquez Echegaray C,Solari C,Waisman A,Álvarez Y,Petrone MV,Francia M,Schultz M,Sevlever G,Miriuka S,Levi V,Guberman A

更新日期：2019-03-15 00:00:00

abstract：:Phosphorylation of short linear peptide motifs is a widespread process for the dynamic regulation of protein-protein interactions. However, the global impact of phosphorylation events on the protein-protein interactome is rarely addressed. The disordered C-terminal tail of ribosomal S6 kinase 1 (RSK1) binds to PDZ dom...

journal_title：Journal of molecular biology

authors： Gógl G,Biri-Kovács B,Durbesson F,Jane P,Nomine Y,Kostmann C,Bilics V,Simon M,Reményi A,Vincentelli R,Trave G,Nyitray L

更新日期：2019-03-15 00:00:00

abstract：:Bovine leukemia virus (BLV) is a deltaretrovirus that infects domestic cattle. The structural protein Gag, found in all retroviruses, is a polyprotein comprising three major functional domains: matrix (MA), capsid (CA), and nucleocapsid (NC). Previous studies have shown that both mature BLV MA and NC are able to bind ...

journal_title：Journal of molecular biology

authors： Qualley DF,Cooper SE,Ross JL,Olson ED,Cantara WA,Musier-Forsyth K

更新日期：2019-03-15 00:00:00

abstract：:To address the mechanism of thermosensing and its implications for molecular engineering, we previously deconstructed the functional components of the bacterial thermosensor DesK, a histidine kinase with a five-span transmembrane domain that detects temperature changes. The system was first simplified by building a se...

journal_title：Journal of molecular biology

authors： Inda ME,Vazquez DB,Fernández A,Cybulski LE

更新日期：2019-03-01 00:00:00