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1. Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein

Author:
Bhatia, Sandhya; Krishnamoorthy, Guruswamy; Udgaonkar, Jayant B.
Source:
Journal of the American Chemical Society 2021 v.143 no.3 pp. 1447-1457
ISSN:
1520-5126
Subject:
polypeptides,   etc   ; evolution; kinetics; models;     Show all 4 Subjects
Abstract:
... To determine experimentally how the multiple folding pathways of a protein differ, in the order in which the structural parts are assembled, has been a long-standing challenge. To resolve whether structure formation during folding can progress in multiple ways, the complex folding landscape of monellin has been characterized, structurally and temporally, using the multisite time-resolved FRET meth ...
DOI:
10.1021/jacs.0c11097

2. Directed Evolution of CRISPR/Cas Systems for Precise Gene Editing

Author:
Liu, Rongming; Liang, Liya; Freed, Emily F.; Gill, Ryan T.
Source:
Trends in biotechnology 2021 v.39 no.3 pp. 262-273
ISSN:
0167-7799
Subject:
polypeptides,   etc   ; biotechnology; directed evolution; genes;     Show all 4 Subjects
Abstract:
... CRISPR technology is a universal tool for genome engineering that has revolutionized biotechnology. Recently identified unique CRISPR/Cas systems, as well as re-engineered Cas proteins, have rapidly expanded the functions and applications of CRISPR/Cas systems. The structures of Cas proteins are complex, containing multiple functional domains. These protein domains are evolutionarily conserved pol ...
DOI:
10.1016/j.tibtech.2020.07.005

3. Metal effect on intein splicing: A review

Author:
Panda, Sunita; Nanda, Ananya; Nasker, Sourya Subhra; Sen, Debjani; Mehra, Ashwaria; Nayak, Sasmita
Source:
Biochimie 2021 v.185 pp. 53-67
ISSN:
0300-9084
Subject:
polypeptides,   etc   ; divalent metals; drug design; inteins;     Show all 4 Subjects
Abstract:
... Inteins are intervening polypeptides that interrupt the functional domains of several important proteins across the three domains of life. Inteins excise themselves from the precursor protein, ligating concomitant extein residues in a process called protein splicing. Post-translational auto-removal of inteins remain critical for the generation of active proteins. The perspective of inteins in scie ...
DOI:
10.1016/j.biochi.2021.03.006

4. Functional recombinant human complement C1q with different affinity tags

Author:
Bally, Isabelle; Ancelet, Sarah; Reiser, Jean-Baptiste; Rossi, Véronique; Gaboriaud, Christine; Thielens, Nicole M.
Source:
Journal of immunological methods 2021 v.492 pp. 113001
ISSN:
0022-1759
Subject:
polypeptides,   etc   ; blood serum; complement; humans; ligands; proteinases;     Show all 6 Subjects
Abstract:
... Complement C1q is a multifunctional protein able to sense pathogens and immune molecules such as immunoglobulins and pentraxins, and to trigger the classical complement pathway through activation of its two associated proteases, C1r and C1s. C1q is a multimeric protein composed of three homologous yet distinct polypeptide chains A, B, and C, each composed of an N-terminal collagen-like sequence an ...
DOI:
10.1016/j.jim.2021.113001

5. Live-cell imaging reveals kinetic determinants of quality control triggered by ribosome stalling

Author:
Goldman, Daniel H.; Livingston, Nathan M.; Movsik, Jonathan; Wu, Bin; Green, Rachel
Source:
Molecular cell 2021 v.81 no.8 pp. 1830-1840.e8
ISSN:
1097-2765
Subject:
polypeptides,   etc   ; degradation; dynamics; frequency; quality control; ribosomes;     Show all 6 Subjects
Abstract:
... Translation of problematic mRNA sequences induces ribosome stalling, triggering quality-control events, including ribosome rescue and nascent polypeptide degradation. To define the timing and regulation of these processes, we developed a SunTag-based reporter to monitor translation of a problematic sequence (poly[A]) in real time on single mRNAs. Although poly(A)-containing mRNAs undergo continuou ...
DOI:
10.1016/j.molcel.2021.01.029

6. Glycan structure-based perspectives on the entry and release of glycoproteins in the calnexin/calreticulin cycle

Author:
Kuribara, Taiki; Usui, Ruchio; Totani, Kiichiro
Source:
Carbohydrate research 2021 v.502 pp. 108273
ISSN:
0008-6215
Subject:
polypeptides,   etc   ; calnexin; calreticulin; glycoproteins; research; secretion;     Show all 6 Subjects
Abstract:
... N-glycans are attached to newly synthesised polypeptides and are involved in the folding, secretion, and degradation of N-linked glycoproteins. In particular, the calnexin/calreticulin cycle, which is the central mechanism of the entry and release of N-linked glycoproteins depending on the folding sates, has been well studied. In addition to biological studies on the calnexin/calreticulin cycle, s ...
DOI:
10.1016/j.carres.2021.108273

7. sORF-Encoded Polypeptide SEP1 Is a Novel Virulence Factor of Phytophthora Pathogens

Author:
Wang, Nan; Yin, Zhiyuan; Duan, Weiwei; Zhang, Xiong; Pi, Lei; Zhang, Yifan; Dou, Daolong
Source:
Molecular plant-microbe interactions 2021 v.34 no.2 pp. 157-167
ISSN:
1943-7706
Subject:
polypeptides,   etc   ; Nicotiana benthamiana; apoplast; cell death; virulence;     Show all 5 Subjects
Abstract:
... Diseases caused by the notorious Phytophthora spp. result in enormous economic losses to crops and forests. Increasing evidence suggests that small open reading frame-encoded polypeptides (SEPs) participate in environmental responses of animals, plants, and fungi. However, it remains largely unknown whether Phytophthora pathogens produce SEPs. Here, we systematically predicted and identified 96 SE ...
DOI:
10.1094/MPMI-06-20-0160-R

8. GIP-GIPR promotes neurite outgrowth of cortical neurons in Akt dependent manner

Author:
Teng, Long; Guan, Tuchen; Guo, Beibei; Ma, Chao; Lin, Ge; Wu, Ronghua; Xu, Man; Liu, Mei; Liu, Yan
Source:
Biochemical and biophysical research communications 2021 v.534 pp. 121-127
ISSN:
0006-291X
Subject:
gastric inhibitory polypeptide; gastric inhibitory polypeptide receptors,   etc   ; genes; ligands; models; neurites; phosphorylation; rats; research; transcriptome;     Show all 10 Subjects
Abstract:
... The intrinsic capacity of axonal growth is varied among the neurons form different tissues or different developmental stages. In this study, we established an in vitro model to compare the axonal growth of neurons from embryonic 18 days, post-natal 1 day and post-natal 3 days rat. The E18 neurons showed powerful ability of neuritogenensis and axon outgrowth and the ability decreased rapidly along ...
DOI:
10.1016/j.bbrc.2020.11.120

9. Cotranslational Translocation and Folding of a Periplasmic Protein Domain in Escherichia coli

Author:
Sandhu, Hena; Hedman, Rickard; Cymer, Florian; Kudva, Renuka; Ismail, Nurzian; von Heijne, Gunnar
Source:
Journal of molecular biology 2021 v.433 no.15 pp. 167047
ISSN:
0022-2836
Subject:
polypeptides,   etc   ; Escherichia coli; molecular biology; protein domains; proteinases; ribosomes;     Show all 6 Subjects
Abstract:
... In Gram-negative bacteria, periplasmic domains in inner membrane proteins are cotranslationally translocated across the inner membrane through the SecYEG translocon. To what degree such domains also start to fold cotranslationally is generally difficult to determine using currently available methods. Here, we apply Force Profile Analysis (FPA) – a method where a translational arrest peptide is use ...
DOI:
10.1016/j.jmb.2021.167047

10. Development of a RPLC-UV method for monitoring uncleaved HIV-1 envelope glycoprotein

Author:
Schneck, Nicole A.; Vinitsky, Alison L.; Ivleva, Vera B.; Wang, Xiangchun; Gowetski, Daniel B.; Lei, Q. Paula
Source:
Analytical methods 2021 v.13 no.19 pp. 2183-2188
ISSN:
1759-9679
Subject:
polypeptides,   etc   ; antigens; disulfide bonds; glycoproteins; immune response; vaccine development; vaccines;     Show all 7 Subjects
Abstract:
... One of the HIV-1 vaccine design efforts has focused on developing a recombinant HIV-1 trimeric envelope glycoprotein (Env) as an immunogen to induce broadly neutralizing antibodies. A native-like immunogen, the BG505.DS.SOSIP.664 gp140 (Env) construct has been well-characterized as a vaccine candidate. This vaccine candidate comprises of three identical gp120 and truncated gp41 subunits that form ...
DOI:
10.1039/d1ay00072a

11. Bacterial RF3 senses chaperone function in co-translational folding

Author:
Zhao, Liang; Castanié-Cornet, Marie-Pierre; Kumar, Sneha; Genevaux, Pierre; Hayer-Hartl, Manajit; Hartl, F. Ulrich
Source:
Molecular cell 2021
ISSN:
1097-2765
Subject:
polypeptides,   etc   ; Escherichia coli; amino acids; cell viability; peptidyltransferase; proteomics; ribosomes;     Show all 7 Subjects
Abstract:
... Molecular chaperones assist with protein folding by interacting with nascent polypeptide chains (NCs) during translation. Whether the ribosome can sense chaperone defects and, in response, abort translation of misfolding NCs has not yet been explored. Here we used quantitative proteomics to investigate the ribosome-associated chaperone network in E. coli and the consequences of its dysfunction. Tr ...
DOI:
10.1016/j.molcel.2021.05.016

12. Redox-Mediated Reversible Supramolecular Assemblies Driven by Switch and Interplay of Peptide Secondary Structures

Author:
Yao, Qingxin; Wu, Guangqi; Hao, Hao; Lu, Hua; Gao, Yuan
Source:
Biomacromolecules 2021 v.22 no.6 pp. 2563-2572
ISSN:
1526-4602
Subject:
polypeptides,   etc   ; biocompatibility; biocompatible materials; cancer therapy; hydrophilicity; nanofibers; oxidation;     Show all 7 Subjects
Abstract:
... The construction of reversible supramolecular self-assembly in vivo remains a significant challenge. Here, we demonstrate the redox-triggered reversible supramolecular self-assembly governed by the “check and balance” of two secondary conformations within a brushlike peptide–selenopolypeptide conjugate. The conjugate constitutes a polypeptide backbone whose side chain contains selenoether function ...
DOI:
10.1021/acs.biomac.1c00300

13. BamA forms a translocation channel for polypeptide export across the bacterial outer membrane

Author:
Doyle, Matthew Thomas; Bernstein, Harris David
Source:
Molecular cell 2021 v.81 no.9 pp. 2000-2012.e3
ISSN:
1097-2765
Subject:
polypeptides,   etc   ; bacterial outer membranes; crosslinking; disulfides; exports; virulence;     Show all 6 Subjects
Abstract:
... The β-barrel assembly machine (BAM) integrates β-barrel proteins into the outer membrane (OM) of Gram-negative bacteria. An essential BAM subunit (BamA) catalyzes integration by promoting the formation of a hybrid-barrel intermediate state between its own β-barrel domain and that of its client proteins. Here we show that in addition to catalyzing the integration of β-barrel proteins, BamA function ...
DOI:
10.1016/j.molcel.2021.02.023

14. Amyloids: The History of Toxicity and Functionality

Author:
Yakupova, Elmira I.; Bobyleva, Liya G.; Shumeyko, Sergey A.; Vikhlyantsev, Ivan M.; Bobylev, Alexander G.
Source:
Biology 2021 v.10 no.5
ISSN:
2079-7737
Subject:
polypeptides,   etc   ; amyloid; amyloidosis; chemical structure; proteinases; proteolysis; therapeutics; toxicity;     Show all 8 Subjects
Abstract:
... Proteins can perform their specific function due to their molecular structure. Partial or complete unfolding of the polypeptide chain may lead to the misfolding and aggregation of proteins in turn, resulting in the formation of different structures such as amyloid aggregates. Amyloids are rigid protein aggregates with the cross-β structure, resistant to most solvents and proteases. Because of thei ...
DOI:
10.3390/biology10050394

15. Inosine in Biology and Disease

Author:
Srinivasan, Sundaramoorthy; Torres, Adrian Gabriel; Ribas de Pouplana, Lluís
Source:
Genes 2021 v.12 no.4
ISSN:
2073-4425
Subject:
polypeptides,   etc   ; adenosine; anticodons; biosynthesis; genes; human health; inosine; secondary metabolites;     Show all 8 Subjects
Abstract:
... The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequenc ...
DOI:
10.3390/genes12040600

16. The role of micropeptides in biology

Author:
Vitorino, Rui; Guedes, Sofia; Amado, Francisco; Santos, Manuel; Akimitsu, Nobuyoshi
Source:
Cellular and molecular life sciences 2021 v.78 no.7 pp. 3285-3298
ISSN:
1420-682X
Subject:
polypeptides,   etc   ; bioinformatics; genome; homeostasis; mammals; mass spectrometry; proteome; ribosomes; transcriptome;     Show all 9 Subjects
Abstract:
... Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance ha ...
DOI:
10.1007/s00018-020-03740-3

17. In Vivo Models of HDV Infection: Is Humanizing NTCP Enough?

Author:
Giersch, Katja; Dandri, Maura
Source:
Viruses 2021 v.13 no.4
ISSN:
1999-4915
Subject:
polypeptides,   etc   ; ; hepatitis B; hepatocytes; humans; mice; taurocholic acid; therapeutics; viruses;     Show all 9 Subjects
Abstract:
... The discovery of sodium taurocholate co-transporting polypeptide (NTCP) as a hepatitis B (HBV) and delta virus (HDV) entry receptor has encouraged the development of new animal models of infection. This review provides an overview of the different in vivo models that are currently available to study HDV either in the absence or presence of HBV. By presenting new advances and remaining drawbacks, w ...
DOI:
10.3390/v13040588

18. Freshwater Fungi as a Source of Chemical Diversity: A Review

Author:
El-Elimat, Tamam; Raja, Huzefa A.; Figueroa, Mario; Al Sharie, Ahmed H.; Bunch, Rick L.; Oberlies, Nicholas H.
Source:
Journal of natural products 2021 v.84 no.3 pp. 898-916
ISSN:
1520-6025
Subject:
polypeptides,   etc   ; Ascomycota; bioactive properties; freshwater; fungi; meroterpenoids; metabolites; phenylpropanoids; polyketides;     Show all 9 Subjects
Abstract:
... As their name indicates, freshwater fungi occur on submerged substrates in fresh water habitats. This review brings together the chemical diversity and biological activity of 199 of the 280 known freshwater fungal metabolites published from 1992 to 2020, representing at least seven structural classes, including polyketides, phenylpropanoids, terpenoids, meroterpenoids, alkaloids, polypeptides, and ...
DOI:
10.1021/acs.jnatprod.0c01340

19. Quantification of 13C, 15N labelled compounds with 13C, 15N edited 1H Nuclear Magnetic Resonance spectroscopy

Author:
Qu, Runlian; Shan, Lu; Sun, Qun; Wei, Yao; Deng, Pengchi; Hou, Xiandeng
Source:
Talanta 2021 v.224 pp. 121839
ISSN:
0039-9140
Subject:
polypeptides,   etc   ; isotope labeling; melamine; nuclear magnetic resonance spectroscopy; protocols;     Show all 5 Subjects
Abstract:
... It was significant to detect isotope labelled compounds in biology and pharmacy. Based on a novel ¹H Nuclear Magnetic Resonance (¹H-NMR) technique, a simple, fast and green method has been successfully established to quantitatively detect ¹³C, ¹⁵N isotope labelled compounds. In this protocol, the couples between ¹H and ¹³C, ¹⁵N nearby were removed, which greatly simplified the spectrum. At mean ti ...
DOI:
10.1016/j.talanta.2020.121839

20. An Integrated Sequencing Approach for Updating the Pseudorabies Virus Transcriptome

Author:
Torma, Gábor; Tombácz, Dóra; Csabai, Zsolt; Göbhardter, Dániel; Deim, Zoltán; Snyder, Michael; Boldogkői, Zsolt
Source:
Pathogens 2021 v.10 no.2
ISSN:
2076-0817
Subject:
polypeptides,   etc   ; Suid alphaherpesvirus 1; gene expression; nanopores; transcriptome;     Show all 5 Subjects
Abstract:
... In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression. In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencing w ...
DOI:
10.3390/pathogens10020242