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https://www.readbyqxmd.com/read/28564553/structural-and-mechanistic-insights-into-protein-translocation
#1
Tom A Rapoport, Long Li, Eunyong Park
Many proteins are translocated across the endoplasmic reticulum (ER) membrane in eukaryotes or the plasma membrane in prokaryotes. These proteins use hydrophobic signal sequences or transmembrane (TM) segments to trigger their translocation through the protein-conducting Sec61/SecY channel. Substrates are first directed to the channel by cytosolic targeting factors, which use hydrophobic pockets to bind diverse signal and TM sequences. Subsequently, these hydrophobic sequences insert into the channel, docking into a groove on the outside of the lateral gate of the channel, where they also interact with lipids...
May 31, 2017: Annual Review of Cell and Developmental Biology
https://www.readbyqxmd.com/read/28516953/signal-recognition-particle-prevents-n-terminal-processing-of-bacterial-membrane-proteins
#2
Amitabh Ranjan, Evan Mercier, Arshiya Bhatt, Wolfgang Wintermeyer
Bacterial proteins are synthesized with an N-formylated amino-terminal methionine, and N-formylated peptides elicit innate-immunity responses against bacterial infections. However, the source of these formylated peptides is not clear, as most bacterial proteins are co-translationally deformylated by peptide deformylase. Here we develop a deformylation assay with translating ribosomes as substrates, to show that the binding of the signal recognition particle (SRP) to signal sequences in nascent proteins on the ribosome prevents deformylation, whereas deformylation of nascent proteins without signal sequence is not affected...
May 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28507157/translation-and-folding-of-single-proteins-in-real-time
#3
Florian Wruck, Alexandros Katranidis, Knud H Nierhaus, Georg Büldt, Martin Hegner
Protein biosynthesis is inherently coupled to cotranslational protein folding. Folding of the nascent chain already occurs during synthesis and is mediated by spatial constraints imposed by the ribosomal exit tunnel as well as self-interactions. The polypeptide's vectorial emergence from the ribosomal tunnel establishes the possible folding pathways leading to its native tertiary structure. How cotranslational protein folding and the rate of synthesis are linked to a protein's amino acid sequence is still not well defined...
May 30, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28494952/fast-protein-translation-can-promote-co-and%C3%A2-posttranslational-folding-of-misfolding-prone-proteins
#4
Fabio Trovato, Edward P O'Brien
Chemical kinetic modeling has previously been used to predict that fast-translating codons can enhance cotranslational protein folding by helping to avoid misfolded intermediates. Consistent with this prediction, protein aggregation in yeast and worms was observed to increase when translation was globally slowed down, possibly due to increased cotranslational misfolding. Observation of similar behavior in molecular simulations would confirm predictions from the simpler chemical kinetic model and provide a molecular perspective on cotranslational folding, misfolding, and the impact of translation speed on these processes...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28450130/from-gene-to-function-cell-free-electrophysiological-and-optical-analysis-of-ion-pumps-in-nanodiscs
#5
Erik Henrich, Janina Sörmann, Peter Eberhardt, Oliver Peetz, Julija Mezhyrova, Nina Morgner, Klaus Fendler, Volker Dötsch, Josef Wachtveitl, Frank Bernhard, Christian Bamann
Nanodiscs that hold a lipid bilayer surrounded by a boundary of scaffold proteins have emerged as a powerful tool for membrane protein solubilization and analysis. By combining nanodiscs and cell-free expression technologies, even completely detergent-free membrane protein characterization protocols can be designed. Nanodiscs are compatible with various techniques, and due to their bilayer environment and increased stability, they are often superior to detergent micelles or liposomes for membrane protein solubilization...
April 24, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28437479/conformational-dynamics-of-bacterial-trigger-factor-in-apo-and-ribosome-bound-states
#6
Mehmet Tarik Can, Zeynep Kurkcuoglu, Gokce Ezeroglu, Arzu Uyar, Ozge Kurkcuoglu, Pemra Doruker
The chaperone trigger factor (TF) binds to the ribosome exit tunnel and helps cotranslational folding of nascent chains (NC) in bacterial cells and chloroplasts. In this study, we aim to investigate the functional dynamics of fully-atomistic apo TF and its complex with 50S. As TF accomodates a high percentage of charged residues on its surface, the effect of ionic strength on TF dynamics is assessed here by performing five independent molecular dynamics (MD) simulations (total of 1.3 micro-second duration) at 29 mM and 150 mM ionic strengths...
2017: PloS One
https://www.readbyqxmd.com/read/28276018/reconstitution-of-mitochondrial-membrane-proteins-into-nanodiscs-by-cell-free-expression
#7
Ketan Malhotra, Nathan N Alder
The isolation and characterization of mitochondrial membrane proteins is technically challenging because they natively reside within the specialized environment of the lipid bilayer, an environment that must be recapitulated to some degree during reconstitution to ensure proper folding, stability, and function. Here we describe protocols for the assembly of a membrane protein into lipid bilayer nanodiscs in a series of cell-free reactions. Cell-free expression of membrane proteins circumvents problems attendant with in vivo expression such as cytotoxicity, low expression levels, and the formation of inclusion bodies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28210246/prospects-of-in-vivo-incorporation-of-non-canonical-amino-acids-for-the-chemical-diversification-of-antimicrobial-peptides
#8
Tobias Baumann, Jessica H Nickling, Maike Bartholomae, Andrius Buivydas, Oscar P Kuipers, Nediljko Budisa
The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-nature AMPs, and can contribute to tackle the ongoing emergence of antibiotic resistance in pathogens. Especially from a pharmacological point of view, desirable improvements span pH and protease resistance, solubility, oral availability and circulation half-life...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28138070/crystal-structure-of-eukaryotic-ribosome-and-its-complexes-with-inhibitors
#9
REVIEW
Gulnara Yusupova, Marat Yusupov
A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated...
March 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28134917/the-signal-recognition-particle-contacts-ul23-and-scans-substrate-translation-inside-the-ribosomal-tunnel
#10
Kärt Denks, Nadine Sliwinski, Veronika Erichsen, Bogdana Borodkina, Andrea Origi, Hans-Georg Koch
The signal recognition particle (SRP) delivers ∼25% of all bacterial proteins to the membrane for cotranslational insertion. However, a comprehensive model on how the low-abundant SRP scans the vast number of translating ribosomes to identify the correct substrates is lacking. Here, we show that the C-terminal helix of the signal-sequence-binding domain of SRP penetrates into the ribosomal tunnel and contacts the intra-tunnel loop of ribosomal protein uL23. This allows SRP to obtain information about the translational status of the ribosome and possibly the character of the approaching nascent chain...
January 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28122979/nucleic-and-amino-acid-sequences-support-structure-based-viral-classification
#11
Robert M Sinclair, Janne J Ravantti, Dennis H Bamford
Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification...
April 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28112730/cotranslational-folding-of-spectrin-domains-via-partially-structured-states
#12
Ola B Nilsson, Adrian A Nickson, Jeffrey J Hollins, Stephan Wickles, Annette Steward, Roland Beckmann, Gunnar von Heijne, Jane Clarke
How do the key features of protein folding, elucidated from studies on native, isolated proteins, manifest in cotranslational folding on the ribosome? Using a well-characterized family of homologous α-helical proteins with a range of biophysical properties, we show that spectrin domains can fold vectorially on the ribosome and may do so via a pathway different from that of the isolated domain. We use cryo-EM to reveal a folded or partially folded structure, formed in the vestibule of the ribosome. Our results reveal that it is not possible to predict which domains will fold within the ribosome on the basis of the folding behavior of isolated domains; instead, we propose that a complex balance of the rate of folding, the rate of translation and the lifetime of folded or partly folded states will determine whether folding occurs cotranslationally on actively translating ribosomes...
March 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28076289/from-bacteria-to-chloroplasts-evolution-of-the-chloroplast-srp-system
#13
REVIEW
Dominik Ziehe, Beatrix Dünschede, Danja Schünemann
Chloroplasts derive from a prokaryotic symbiont that lost most of its genes during evolution. As a result, the great majority of chloroplast proteins are encoded in the nucleus and are posttranslationally imported into the organelle. The chloroplast genome encodes only a few proteins. These include several multispan thylakoid membrane proteins which are synthesized on thylakoid-bound ribosomes and cotranslationally inserted into the membrane. During evolution, ancient prokaryotic targeting machineries were adapted and combined with novel targeting mechanisms to facilitate post- and cotranslational protein transport in chloroplasts...
May 1, 2017: Biological Chemistry
https://www.readbyqxmd.com/read/28067917/structural-insights-into-a-unique-hsp70-hsp40-interaction-in-the-eukaryotic-ribosome-associated-complex
#14
Felix Alexander Weyer, Andrea Gumiero, Genís Valentín Gesé, Karine Lapouge, Irmgard Sinning
Cotranslational chaperones assist de novo folding of nascent polypeptides, prevent them from aggregating and modulate translation. The ribosome-associated complex (RAC) is unique in that the Hsp40 protein Zuo1 and the atypical Hsp70 chaperone Ssz1 form a stable heterodimer, which acts as a cochaperone for the Hsp70 chaperone Ssb. Here we present the structure of the Chaetomium thermophilum RAC core comprising Ssz1 and the Zuo1 N terminus. We show how the conserved allostery of Hsp70 proteins is abolished and this Hsp70-Hsp40 pair is molded into a functional unit...
January 9, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27969102/regulation-evolution-and-consequences-of-cotranslational-protein-complex-assembly
#15
REVIEW
Eviatar Natan, Jonathan N Wells, Sarah A Teichmann, Joseph A Marsh
Most proteins assemble into complexes, which are involved in almost all cellular processes. Thus it is crucial for cell viability that mechanisms for correct assembly exist. The timing of assembly plays a key role in determining the fate of the protein: if the protein is allowed to diffuse into the crowded cellular milieu, it runs the risk of forming non-specific interactions, potentially leading to aggregation or other deleterious outcomes. It is therefore expected that strong regulatory mechanisms should exist to ensure efficient assembly...
February 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27941902/protective-role-for-lipid-modifications-of-src-family-kinases-against-chromosome-missegregation
#16
Takuya Honda, Shuhei Soeda, Kunihiko Tsuda, Chihiro Yamaguchi, Kazumasa Aoyama, Takao Morinaga, Ryuzaburo Yuki, Yuji Nakayama, Noritaka Yamaguchi, Naoto Yamaguchi
Src-family tyrosine kinases, which are expressed in various cell types, play critical roles in cell signalling at the cytoplasmic side of the plasma membrane through their lipid modifications. Src-family kinases are cotranslationally myristoylated and posttranslationally palmitoylated in the amino-terminal region. The Src-family member Lyn contains a myristoylation site at glycine-2 and a palmitoylation site at cysteine-3, whereas c-Src has a myristoylation site at glycine-2 but not any palmitoylation sites...
December 12, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27908229/localization-of-nuclear-encoded-mrnas-to-mitochondria-outer-surface
#17
REVIEW
A Golani-Armon, Y Arava
The diverse functions of mitochondria depend on hundreds of different proteins. The vast majority of these proteins is encoded in the nucleus, translated in the cytosol, and must be imported into the organelle. Import was shown to occur after complete synthesis of the protein, with the assistance of cytosolic chaperones that maintain it in an unfolded state and target it to the mitochondrial translocase of the outer membrane (TOM complex). Recent studies, however, identified many mRNAs encoding mitochondrial proteins near the outer membrane of mitochondria...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27895124/anionic-phospholipids-and-the-albino3-translocase-activate-signal-recognition-particle-receptor-interaction-during-light-harvesting-chlorophyll-a-b-binding-protein-targeting
#18
Sowmya Chandrasekar, Shu-Ou Shan
The universally conserved signal recognition particle (SRP) co-translationally delivers newly synthesized membrane and secretory proteins to the target cellular membrane. The only exception is found in the chloroplast of green plants, where the chloroplast SRP (cpSRP) post-translationally targets light-harvesting chlorophyll a/b-binding proteins (LHCP) to the thylakoid membrane. The mechanism and regulation of this post-translational mode of targeting by cpSRP remain unclear. Using biochemical and biophysical methods, here we show that anionic phospholipids activate the cpSRP receptor cpFtsY to promote rapid and stable cpSRP54·cpFtsY complex assembly...
January 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27882919/interaction-of-the-cotranslational-hsp70-ssb-with-ribosomal-proteins-and-rrna-depends-on-its-lid-domain
#19
Andrea Gumiero, Charlotte Conz, Genís Valentín Gesé, Ying Zhang, Felix Alexander Weyer, Karine Lapouge, Julia Kappes, Ulrike von Plehwe, Géza Schermann, Edith Fitzke, Tina Wölfle, Tamás Fischer, Sabine Rospert, Irmgard Sinning
Cotranslational chaperones assist in de novo folding of nascent polypeptides in all organisms. In yeast, the heterodimeric ribosome-associated complex (RAC) forms a unique chaperone triad with the Hsp70 homologue Ssb. We report the X-ray structure of full length Ssb in the ATP-bound open conformation at 2.6 Å resolution and identify a positively charged region in the α-helical lid domain (SBDα), which is present in all members of the Ssb-subfamily of Hsp70s. Mutational analysis demonstrates that this region is strictly required for ribosome binding...
November 24, 2016: Nature Communications
https://www.readbyqxmd.com/read/27881602/n-terminal-acetylation-promotes-synaptonemal-complex-assembly-in-c-elegans
#20
Jinmin Gao, Consuelo Barroso, Pan Zhang, Hyun-Min Kim, Shangtong Li, Leticia Labrador, James Lightfoot, Maxim V Gerashchenko, Vyacheslav M Labunskyy, Meng-Qiu Dong, Enrique Martinez-Perez, Monica P Colaiácovo
N-terminal acetylation of the first two amino acids on proteins is a prevalent cotranslational modification. Despite its abundance, the biological processes associated with this modification are not well understood. Here, we mapped the pattern of protein N-terminal acetylation in Caenorhabditis elegans, uncovering a conserved set of rules for this protein modification and identifying substrates for the N-terminal acetyltransferase B (NatB) complex. We observed an enrichment for global protein N-terminal acetylation and also specifically for NatB substrates in the nucleus, supporting the importance of this modification for regulating biological functions within this cellular compartment...
November 1, 2016: Genes & Development
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