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https://www.readbyqxmd.com/read/29732143/understanding-gpcr-recognition-and-folding-from-nmr-studies-of-fragments
#1
Jacopo Marino, Reto Walser, Martin Poms, Oliver Zerbe
Cotranslational protein folding is a vectorial process, and for membrane proteins, N-terminal helical segments are the first that become available for membrane insertion. While structures of many G-protein coupled receptors (GPCRs) in various states have been determined, the details of their folding pathways are largely unknown. The seven transmembrane (TM) helices of GPCRs often contain polar residues within the hydrophobic core, and some of the helices in isolation are predicted to be only marginally stable in a membrane environment...
2018: RSC Advances
https://www.readbyqxmd.com/read/29725062/hsp90-shapes-protein-and-rna-evolution-to-balance-trade-offs-between-protein-stability-and-aggregation
#2
Ron Geller, Sebastian Pechmann, Ashley Acevedo, Raul Andino, Judith Frydman
Acquisition of mutations is central to evolution; however, the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, may alleviate the effects of destabilizing mutations thus promoting sequence diversification. To illuminate how chaperones can influence protein evolution, we examined the effect of reduced activity of the chaperone Hsp90 on poliovirus evolution. We find that Hsp90 offsets evolutionary trade-offs between protein stability and aggregation...
May 3, 2018: Nature Communications
https://www.readbyqxmd.com/read/29671261/using-the-2a-protein-coexpression-system-multicistronic-2a-vectors-expressing-gene-s-of-interest-and-reporter-proteins
#3
Garry A Luke, Martin D Ryan
To date, a huge range of different proteins-many with cotranslational and posttranslational subcellular localization signals-have been coexpressed together with various reporter proteins in vitro and in vivo using 2A peptides. The pros and cons of 2A co-expression technology are considered below, followed by a simple example of a "how to" protocol to concatenate multiple genes of interest, together with a reporter gene, into a single gene linked via 2As for easy identification or selection of transduced cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29668275/structural-basis-for-the-specific-cotranslational-incorporation-of-p-boronophenylalanine-into-biosynthetic-proteins
#4
André Schiefner, Lea Nästle, Marietta Landgraf, Andreas J Reichert, Arne Skerra
The site-specific incorporation of the non-natural amino acid p-boronophenylalanine (Bpa) into recombinant proteins enables the development of novel carbohydrate-binding functions as well as bioorthogonal chemical modification. To this end, Bpa is genetically encoded by an amber stop codon and cotranslationally inserted into the recombinant polypeptide chain at the ribosome by means of an artificial aminoacyl-tRNA synthetase (aaRS) in combination with a compatible suppressor tRNA. We describe the crystal structure of an aaRS specific for Bpa, which had been engineered on the basis of the TyrRS from M...
April 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29661790/translation-in-prokaryotes
#5
Marina V Rodnina
This review summarizes our current understanding of translation in prokaryotes, focusing on the mechanistic and structural aspects of each phase of translation: initiation, elongation, termination, and ribosome recycling. The assembly of the initiation complex provides multiple checkpoints for messenger RNA (mRNA) and start-site selection. Correct codon-anticodon interaction during the decoding phase of elongation results in major conformational changes of the small ribosomal subunit and shapes the reaction pathway of guanosine triphosphate (GTP) hydrolysis...
April 16, 2018: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/29581307/structural-determinants-and-cellular-environment-define-processed-actin-as-the-sole-substrate-of-the-n-terminal-acetyltransferase-naa80
#6
Marianne Goris, Robert S Magin, Håvard Foyn, Line M Myklebust, Sylvia Varland, Rasmus Ree, Adrian Drazic, Parminder Bhambra, Svein I Støve, Markus Baumann, Bengt Erik Haug, Ronen Marmorstein, Thomas Arnesen
N-terminal (Nt) acetylation is a major protein modification catalyzed by N-terminal acetyltransferases (NATs). Methionine acidic N termini, including actin, are cotranslationally Nt acetylated by NatB in all eukaryotes, but animal actins containing acidic N termini, are additionally posttranslationally Nt acetylated by NAA80. Actin Nt acetylation was found to regulate cytoskeletal dynamics and motility, thus making NAA80 a potential target for cell migration regulation. In this work, we developed potent and selective bisubstrate inhibitors for NAA80 and determined the crystal structure of NAA80 in complex with such an inhibitor, revealing that NAA80 adopts a fold similar to other NAT enzymes but with a more open substrate binding region...
March 26, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29567675/promoter-architecture-determines-cotranslational-regulation-of-mrna
#7
Lorena Espinar, Miquel Àngel Schikora Tamarit, Júlia Domingo, Lucas B Carey
Information that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of cotranslational regulation on mRNA levels is determined by promoter architecture. By using a novel computational genetic screen of 6402 RNA-seq experiments, we identify the RNA helicase Dbp2 as the mechanism by which cotranslational regulation is reduced specifically for inducible promoters...
March 22, 2018: Genome Research
https://www.readbyqxmd.com/read/29523692/membrane-protein-serendipity
#8
Gunnar von Heijne
My scientific career has taken me from chemistry, via theoretical physics and bioinformatics, to molecular biology and even structural biology. Along the way, serendipity led me to work on problems such as the identification of signal peptides that direct protein trafficking, membrane protein biogenesis, and cotranslational protein folding. I've had some great collaborations that came about because of a stray conversation or from following up on an interesting paper. And I've had the good fortune to be asked to sit on the Nobel Committee for Chemistry, where I am constantly reminded of the amazing pace and often intricate history of scientific discovery...
March 9, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29507394/ribothrypsis-a-novel-process-of-canonical-mrna-decay-mediates-ribosome-phased-mrna-endonucleolysis
#9
Fadia Ibrahim, Manolis Maragkakis, Panagiotis Alexiou, Zissimos Mourelatos
mRNAs transmit the genetic information that dictates protein production and are a nexus for numerous pathways that regulate gene expression. The prevailing view of canonical mRNA decay is that it is mediated by deadenylation and decapping followed by exonucleolysis from the 3' and 5' ends. By developing Akron-seq, a novel approach that captures the native 3' and 5' ends of capped and polyadenylated RNAs, respectively, we show that canonical human mRNAs are subject to repeated cotranslational and ribosome-phased endonucleolytic cuts at the exit site of the mRNA ribosome channel, in a process that we term ribothrypsis...
April 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29462795/positive-zip-coding-in-small-protein-translocation
#10
Yukari Okamoto, Sojin Shikano
Most newly synthesized proteins destined for the secretory pathway contain a signal peptide (SP) that triggers cotranslational translocation into the endoplasmic reticulum (ER). However, how small polypeptides undergo ER translocation is not fully understood. In this issue of JBC , Guo et al. describe a mechanism for posttranslational translocation of small secretory proteins featuring a positive charge within the SP N-terminal region. Defects in this element disrupt proper secretion and explain the effects of genetic mutations associated with one type of diabetes...
February 9, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29434345/cotranslational-protein-assembly-imposes-evolutionary-constraints-on-homomeric-proteins
#11
Eviatar Natan, Tamaki Endoh, Liora Haim-Vilmovsky, Tilman Flock, Guilhem Chalancon, Jonathan T S Hopper, Bálint Kintses, Peter Horvath, Lejla Daruka, Gergely Fekete, Csaba Pál, Balázs Papp, Erika Oszi, Zoltán Magyar, Joseph A Marsh, Adrian H Elcock, M Madan Babu, Carol V Robinson, Naoki Sugimoto, Sarah A Teichmann
Cotranslational protein folding can facilitate rapid formation of functional structures. However, it can also cause premature assembly of protein complexes, if two interacting nascent chains are in close proximity. By analyzing known protein structures, we show that homomeric protein contacts are enriched toward the C termini of polypeptide chains across diverse proteomes. We hypothesize that this is the result of evolutionary constraints for folding to occur before assembly. Using high-throughput imaging of protein homomers in Escherichia coli and engineered protein constructs with N- and C-terminal oligomerization domains, we show that, indeed, proteins with C-terminal homomeric interface residues consistently assemble more efficiently than those with N-terminal interface residues...
March 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29408362/biosynthesis-of-human-myeloperoxidase
#12
REVIEW
William M Nauseef
Members of Chordata peroxidase subfamily [1] expressed in mammals, including myeloperoxidase (MPO), eosinophil peroxidase (EPO), lactoperoxidase (LPO), and thyroid peroxidase (TPO), express conserved motifs around the heme prosthetic group essential for their activity, a calcium-binding site, and at least two covalent bonds linking the heme group to the protein backbone. Although most studies of the biosynthesis of these peroxidases have focused on MPO, many of the features described occur during biosynthesis of other members of the protein subfamily...
March 15, 2018: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29396426/the-peroxisome-biogenesis-factors-posttranslationally-target-reticulon-homology-domain-containing-proteins-to-the-endoplasmic-reticulum-membrane
#13
Yasunori Yamamoto, Toshiaki Sakisaka
The endoplasmic reticulum (ER) is shaped by a class of membrane proteins containing reticulon homology domain (RHD), the conserved hydrophobic domain encompassing two short hairpin transmembrane domains. RHD resides in the outer leaflet of the ER membrane, generating high-curvature ER membrane. While most of the membrane proteins destined to enter the secretory pathway are cotranslationally targeted and inserted into ER membrane, the molecular mechanism how the RHD-containing proteins are targeted and inserted into the ER membrane remains to be clarified...
February 2, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348368/defining-the-physiological-role-of-srp-in-protein-targeting-efficiency-and-specificity
#14
Elizabeth A Costa, Kelly Subramanian, Jodi Nunnari, Jonathan S Weissman
The signal recognition particle (SRP) enables cotranslational delivery of proteins for translocation into the endoplasmic reticulum (ER), but its full in vivo role remains incompletely explored. We combined rapid auxin-induced SRP degradation with proximity-specific ribosome profiling to define SRP's in vivo function in yeast. Despite the classic view that SRP recognizes amino-terminal signal sequences, we show that SRP was generally essential for targeting transmembrane domains regardless of their position relative to the amino terminus...
February 9, 2018: Science
https://www.readbyqxmd.com/read/29286490/a-facile-protocol-to-generate-site-specifically-acetylated-proteins-in-escherichia-coli
#15
Sumana Venkat, Caroline Gregory, Kexin Meng, Qinglei Gan, Chenguang Fan
Post-translational modifications that occur at specific positions of proteins have been shown to play important roles in a variety of cellular processes. Among them, reversible lysine acetylation is one of the most widely distributed in all domains of life. Although numerous mass spectrometry-based acetylome studies have been performed, further characterization of these putative acetylation targets has been limited. One possible reason is that it is difficult to generate purely acetylated proteins at desired positions by most classic biochemical approaches...
December 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29282902/construction-of-green-fluorescence-protein-mutant-to-monitor-stt3b-dependent-n-glycosylation
#16
Toshihiko Kitajima, Wei Xue, Yi-Shi Liu, Chun-Di Wang, Si-Si Liu, Morihisa Fujita, Xiao-Dong Gao
Oligosaccharyltransferases (OSTs) mediate the en bloc transfer of N-glycan intermediates onto the asparagine residue in glycosylation sequons (N-X-S/T, X≠P). These enzymes are typically heteromeric complexes composed of several membrane-associated subunits, in which STT3 is highly conserved as a catalytic core. Metazoan organisms encode two STT3 genes (STT3A and STT3B) in their genome, resulting in the formation of at least two distinct OST isoforms consisting of shared subunits and complex specific subunits...
March 2018: FEBS Journal
https://www.readbyqxmd.com/read/29226470/photo-crosslinkable-unnatural-amino-acids-enable-facile-synthesis-of-thermoresponsive-nano-to-microgels-of-intrinsically-disordered-polypeptides
#17
Simone A Costa, Joseph R Simon, Miriam Amiram, Lei Tang, Stefan Zauscher, Eric M Brustad, Farren J Isaacs, Ashutosh Chilkoti
Hydrogel particles are versatile materials that provide exquisite, tunable control over the sequestration and delivery of materials in pharmaceutics, tissue engineering, and photonics. The favorable properties of hydrogel particles depend largely on their size, and particles ranging from nanometers to micrometers are used in different applications. Previous studies have only successfully fabricated these particles in one specific size regime and required a variety of materials and fabrication methods. A simple yet powerful system is developed to easily tune the size of polypeptide-based, thermoresponsive hydrogel particles, from the nano- to microscale, using a single starting material...
February 2018: Advanced Materials
https://www.readbyqxmd.com/read/29203677/dynamics-of-translation-can-determine-the-spatial-organization-of-membrane-bound-proteins-and-their-mrna
#18
Elgin Korkmazhan, Hamid Teimouri, Neil Peterman, Erel Levine
Unlike most macromolecules that are homogeneously distributed in the bacterial cell, mRNAs that encode inner-membrane proteins can be concentrated near the inner membrane. Cotranslational insertion of the nascent peptide into the membrane brings the translating ribosome and the mRNA close to the membrane. This suggests that kinetic properties of translation can determine the spatial organization of these mRNAs and proteins, which can be modulated through posttranscriptional regulation. Here we use a simple stochastic model of translation to characterize the effect of mRNA properties on the dynamics and statistics of its spatial distribution...
December 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29183994/translation-efficiency-is-maintained-at-elevated-temperature-in-escherichia-coli
#19
Gareth J Morgan, David H Burkhardt, Jeffery W Kelly, Evan T Powers
Cellular protein levels are dictated by the balance between gene transcription, mRNA translation, and protein degradation, among other factors. Translation requires the interplay of several RNA hybridization processes, which are expected to be temperature-sensitive. We used ribosome profiling to monitor translation in Escherichia coli at 30 °C and to investigate how this changes after 10-20 min of heat shock at 42 °C. Translation efficiencies are robustly maintained after thermal heat shock and after mimicking the heat-shock response transcriptional program at 30 °C by overexpressing the heat shock σ factor encoded by the rpoH gene...
January 19, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29136098/sequential-search-leads-to-faster-more-efficient-fragment-based-de-novo-protein-structure-prediction
#20
Saulo H P de Oliveira, Eleanor C Law, Jiye Shi, Charlotte M Deane
Motivation: Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally. Results: We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction...
April 1, 2018: Bioinformatics
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