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1. Controlling proteolysis of Clp peptidase: a possible target for combating mitochondrial diseases

Author:
da Silva, Ronivaldo Rodrigues
Source:
The international journal of biochemistry & cell biology 2019 v.110 pp. 140-142
ISSN:
1357-2725
Subject:
proteolysis,   etc   ; apoptosis; mammals; mitochondria; peptidases;     Show all 5 Subjects
Abstract:
... Some mechanisms of cellular stress, aging, and apoptosis are related to proteolysis. With respect to ClpP, little is known about the mechanical manner in which the substrate is hydrolyzed in and released from the degradation chamber. Furthermore, what would be the real influence of ClpP in mammalian UPRmt? ...
DOI:
10.1016/j.biocel.2019.03.007

2. Engineered peptidic constructs metabolize amyloid β by self-assembly-driven reactions

Author:
Mondal, Tanmay; Mandal, Bhubaneswar
Source:
Chemical communications 2019 v.55 no.34 pp. 4933-4936
ISSN:
1364-548X
Subject:
proteolysis,   etc   ; amyloid; chemical compounds; enzymes;     Show all 4 Subjects
Abstract:
... Inspired by the unique mechanism of proteolytic maturation of host cell factor-1, we designed small peptide-based constructs that selectively recognized amyloid β (Aβ) and cleaved it in a non-catalytic manner initially around the α-secretase cleavage-site, thus termed as “artificial α-secretases”. “Artificial α-secretases” also cleaved Aβ on the cleavage-sites of other Aβ processing enzymes by pro ...
DOI:
10.1039/c9cc01582e

3. N-term 2017: Proteostasis via the N-terminus

Author:
Dissmeyer, Nico; Graciet, Emmanuelle; Holdsworth, Michael J.; Gibbs, Daniel J.
Source:
Trends in biochemical sciences 2019 v.44 no.4 pp. 293-295
ISSN:
0968-0004
Subject:
proteolysis,   etc   ; amino acid sequences; expert opinion; ubiquitin;     Show all 4 Subjects
Abstract:
... N-term 2017 was the first international meeting to bring together researchers from diverse disciplines with a shared interest in protein N-terminal modifications and the N-end rule pathway of ubiquitin-mediated proteolysis, providing a platform for interdisciplinary cross-kingdom discussions and collaborations, as well as strengthening the visibility of this growing scientific community. ...
DOI:
10.1016/j.tibs.2017.11.006

4. M17 aminopeptidases diversify function by moderating their macromolecular assemblies and active site environment

Author:
Drinkwater, Nyssa; Malcolm, Tess R.; McGowan, Sheena
Source:
Biochimie 2019
ISSN:
0300-9084
Subject:
proteolysis,   etc   ; active sites; amino acids; aminopeptidases; peptides;     Show all 5 Subjects
Abstract:
... The family of M17 aminopeptidases (alias ‘leucine aminopeptidases’, M17-LAPs) utilize a highly conserved hexameric structure and a binuclear metal center to selectively remove N-terminal amino acids from short peptides. However, M17-LAPs are responsible for a wide variety of functions that are seemingly unrelated to proteolysis. Herein, we aimed to investigate the myriad of functions attributed to ...
DOI:
10.1016/j.biochi.2019.01.007

5. Lys-C/Arg-C, a More Specific and Efficient Digestion Approach for Proteomics Studies

Author:
Wu, Zhen; Huang, Jichang; Huang, Jingnan; Li, Qingqing; Zhang, Xumin
Source:
Analytical chemistry 2018 v.90 no.16 pp. 9700-9707
ISSN:
1520-6882
Subject:
proteolysis,   etc   ; proteomics; trypsin;     Show all 3 Subjects
Abstract:
... Nowadays, bottom-up approaches are predominantly adopted in proteomics studies, which necessitate a proteolysis step prior to MS analysis. Trypsin is often the best protease in choice due to its high specificity and MS-favored proteolytic products. A lot of efforts have been made to develop a superior digestion approach but hardly succeed, especially in large-scale proteomics studies. Herein, we r ...
DOI:
10.1021/acs.analchem.8b02448

6. A novel and sensitive functional assay for complement Factor I based on the third proteolytic clip of C3b

Author:
Lachmann, Peter J.; Lay, Elizabeth; Seilly, David J.
Source:
Journal of immunological methods 2018
ISSN:
0022-1759
Subject:
proteolysis,   etc   ; complement; ionic strength;     Show all 3 Subjects
Abstract:
... A sensitive assay for the functional activity of complement Factor I is described. This is based on its third proteolytic clip whereby Factor I cleaves cell-bound iC3b to cell-bound C3dg and soluble C3c, thereby abolishing conglutination of the cells. Factor H is required as a co-factor for Factor I activity. Because of the low affinity of iC3b for Factor H, the assay needs to be performed at low ...
DOI:
10.1016/j.jim.2018.03.013

7. Discovery of AAA+ Protease Substrates through Trapping Approaches

Author:
Rei Liao, Jui-Yun; van Wijk, Klaas J.
Source:
Trends in biochemical sciences 2019 v.44 no.6 pp. 528-545
ISSN:
0968-0004
Subject:
proteolysis,   etc   ; genetic engineering; mass spectrometry; proteinases; proteome; trapping;     Show all 6 Subjects
Abstract:
... Proteases play essential roles in cellular proteostasis. Mechanisms through which proteases recognize their substrates are often hard to predict and therefore require experimentation. In vivo trapping allows systematic identification of potential substrates of proteases, their adaptors, and chaperones. This combines in vivo genetic modifications of proteolytic systems, stabilized protease–substrat ...
DOI:
10.1016/j.tibs.2018.12.006

8. RTX Adhesins are Key Bacterial Surface Megaproteins in the Formation of Biofilms

Author:
Guo, Shuaiqi; Vance, Tyler D.R.; Stevens, Corey A.; Voets, Ilja; Davies, Peter L.
Source:
Trends in microbiology 2019 v.27 no.5 pp. 453-467
ISSN:
0966-842X
Subject:
proteolysis,   etc   ; Gram-negative bacteria; adhesins; biofilm; cohesion; nutrients; secretion;     Show all 7 Subjects
Abstract:
... Gram-negative bacteria produce repeats-in-toxin adhesion proteins (RTX adhesins) to facilitate microbial adhesion. These large, multidomain proteins share a common architecture comprised of four regions. First to emerge from the bacterium, C terminal end leading, is the RTX export sequence that directs the protein through the type 1 secretion system (T1SS). This is followed by the ligand-binding r ...
DOI:
10.1016/j.tim.2018.12.003

9. Autophagy inducing cyclic peptides constructed by methionine alkylation

Author:
QinThese authors contributed equally to this work., Xuan; Shi, Xiaodong; Tu, Licheng; Ma, Yue; Zhou, Ziyuan; Zhao, Rongtong; Zhan, Meimiao; Yin, Feng; Li, Zigang
Source:
Chemical communications 2019 v.55 no.29 pp. 4198-4201
ISSN:
1364-548X
Subject:
proteolysis,   etc   ; alkylation; autophagy; cyclic peptides; macrocyclization reactions; methionine;     Show all 6 Subjects
Abstract:
... Peptides that induced autophagy at micromolar concentrations with improved proteolytic resistance properties were generated using the facile methionine bis-alkylation method. Notably, a short bicyclic peptide 7f was proven to be the most potent one among the designed peptides in regards to autophagy inducing activity. This study facilitated the development of a peptide-based autophagy inducer and ...
DOI:
10.1039/c9cc01027k

10. Effect of nitric oxide and calpastatin on the inhibition of µ-calpain activity, autolysis and proteolysis of myofibrillar proteins

Author:
Liu, Rui; Lonergan, Steven; Steadham, Edward; Zhou, Guanghong; Zhang, Wangang; Huff-Lonergan, Elisabeth
Source:
Food chemistry 2019 v.275 pp. 77-84
ISSN:
0308-8146
Subject:
proteolysis,   etc   ; autolysis; calcium; calpastatin; dose response; myofibrillar proteins; nitric oxide;     Show all 7 Subjects
Abstract:
... The aim of this study was to investigate the dual effect of the nitric oxide donor NOR-3 and calpastatin on µ-calpain activity, autolysis, and proteolytic ability. µ-Calpain and calpastatin were purified and allocated to the following five treatments: µ-calpain, µ-calpain + calpastatin, µ-calpain + NOR-3, µ-calpain + calpastatin + NOR-3, and µ-calpain + NOR-3 + calpastatin. µ-Calpain autolysis and ...
DOI:
10.1016/j.foodchem.2018.09.104

11. Investigations into PoyH, a promiscuous protease from polytheonamide biosynthesis

Author:
Helf, Maximilian J.; Freeman, Michael F.; Piel, Jörn
Source:
Journal of industrial microbiology & biotechnology 2019 v.46 no.3-4 pp. 551-563
ISSN:
1367-5435
Subject:
proteolysis,   etc   ; biosynthesis; cysteine proteinases; multigene family; peptides; proteinase inhibitors;     Show all 6 Subjects
Abstract:
... Polytheonamides are the most extensively modified ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) currently known. In RiPP biosynthesis, the processed peptide is usually released from a larger precursor by proteolytic cleavage to generate the bioactive terminal product of the pathway. For polytheonamides, which are members of a new RiPP family termed prot ...
DOI:
10.1007/s10295-018-02129-3

12. Peptide filtering differently affects the performances of XIC-based quantification methods

Author:
Belouah, Isma; Blein-Nicolas, Mélisande; Balliau, Thierry; Gibon, Yves; Zivy, Michel; Colombié, Sophie
Source:
Journal of proteomics 2019 v.193 pp. 131-141
ISSN:
1874-3919
Subject:
proteolysis,   etc   ; data collection; filters; models; peptides; proteins; proteomics;     Show all 7 Subjects
Abstract:
... In bottom-up proteomics, data are acquired on peptides resulting from proteolysis. In XIC-based quantification, the quality of the estimation of protein abundance depends on how peptide data are filtered and on which quantification method is used to express peptide intensity as protein abundance. So far, these two questions have been addressed independently. Here, we studied to what extent the rel ...
DOI:
10.1016/j.jprot.2018.10.003

13. Changing the Apoptosis Pathway through Evolutionary Protein Design

Author:
Shultis, David; Mitra, Pralay; Huang, Xiaoqiang; Johnson, Jarrett; Khattak, Naureen Aslam; Gray, Felicia; Piper, Clint; Czajka, Jeff; Hansen, Logan; Wan, Bingbing; Chinnaswamy, Krishnapriya; Liu, Liu; Wang, Mi; Pan, Jingxi; Stuckey, Jeanne; Cierpicki, Tomasz; Borchers, Christoph H.; Wang, Shaomeng; Lei, Ming; Zhang, Yang
Source:
Journal of molecular biology 2019 v.431 no.4 pp. 825-841
ISSN:
0022-2836
Subject:
proteolysis,   etc   ; apoptosis; calorimetry; caspase-9; luminescence; mutation; peptides; proteins;     Show all 8 Subjects
Abstract:
... One obstacle in de novo protein design is the vast sequence space that needs to be searched through to obtain functional proteins. We developed a new method using structural profiles created from evolutionarily related proteins to constrain the simulation search process, with functions specified by atomic-level ligand–protein binding interactions. The approach was applied to redesigning the BIR3 d ...
DOI:
10.1016/j.jmb.2018.12.016

14. PROTAC-mediated crosstalk between E3 ligases

Author:
SteinebachThese authors contributed equally., Christian; Kehm, Hannes; Lindner, Stefanie; Vu, Lan Phuong; Köpff, Simon; López Mármol, Álvaro; Weiler, Corinna; Wagner, Karl G.; Reichenzeller, Michaela; Krönke, Jan; Gütschow, Michael
Source:
Chemical communications 2019 v.55 no.12 pp. 1821-1824
ISSN:
1364-548X
Subject:
proteolysis,   etc   ; chemical communication; chimerism; dimerization; ligands; ligases; protein content;     Show all 7 Subjects
Abstract:
... Small-molecule heterobifunctional degraders can effectively control protein levels and are useful research tools. We assembled proteolysis targeting chimeras (PROTACs) from a cereblon (CRBN) and a von-Hippel-Lindau (VHL) ligase ligand and demonstrated a PROTAC-induced heterodimerization of the two E3 ligases leading to unidirectional and efficient degradation of CRBN. ...
DOI:
10.1039/c8cc09541h

15. DNA recovery from gelatin fingerprint lifters by direct proteolytic digestion

Author:
Zieger, Martin; Schneider, Christoph; Utz, Silvia
Source:
Forensic science international 2019 v.295 pp. 145-149
ISSN:
0379-0738
Subject:
proteolysis,   etc   ; DNA; DNA fingerprinting; forensic sciences; gelatin; magnetism; protocols; staining;     Show all 8 Subjects
Abstract:
... Fingerprints are a valuable source for DNA profiling in forensic investigations. In practice, the fingerprints are routinely visualized first by powder staining and then often transferred to tapes or gelatin lifters for storage or examination. If at all, fingerprints are usually sampled for DNA in a second step. To target the DNA sampling in an optimal way, it is essential to know how much of the ...
DOI:
10.1016/j.forsciint.2018.12.006

16. Proteolytic ceramic capillary membranes for the production of peptides under flow

Author:
Hoog Antink, Marieke M.; Sewczyk, Tim; Kroll, Stephen; Árki, Pál; Beutel, Sascha; Rezwan, Kurosch; Maas, Michael
Source:
Biochemical engineering journal 2019 v.147 pp. 89-99
ISSN:
1369-703X
Subject:
proteolysis,   etc   ; carboxylation; casein; ceramics; electrostatic interactions; hydrolysis; immobilized enzymes; leaching; models; peptides; proteinases;     Show all 11 Subjects
Abstract:
... In this study, we investigate the effect of membrane surface functionalization on the immobilization of the protease subtilisin A and its performance in the production of peptides from the model protein casein under flow. The surface of tubular ceramic membranes was silanized to yield carboxylated and aminated supports for enzyme immobilization via non-covalent and carbodiimide activated binding. ...
DOI:
10.1016/j.bej.2019.04.005

17. Understanding molecular features of aggregation-resistant tau conformer using oxidized monomer

Author:
Jebarupa, Benita; Mathew, Boby; Srinivasu, Bindu Y.; Sasikumaran, Aiswarya; Joseph, Smitha; Mandal, Amit K.; Thomas, Tinku; Mitra, Gopa
Source:
Biochimica et biophysica acta 2019 v.1863 no.6 pp. 993-1005
ISSN:
0304-4165
Subject:
proteolysis,   etc   ; Alzheimer disease; crosslinking; deuterium; disulfide bonds; fluorescence; hydrogen bonding; microtubules; models; oxidation; phase transition; therapeutics;     Show all 12 Subjects
Abstract:
... Aggregation of tau into paired helical filament (PHF) is a hallmark of Alzheimer's disease (AD), and Cys-mediated disulfide bond formation plays a vital role in tau fibrillation. While intermolecular disulfide bond between Cys residues in microtubule-binding repeat (MTBR) region facilitates tau aggregation, intramolecular disulfide bond attenuates the same, though the molecular basis for such phen ...
DOI:
10.1016/j.bbagen.2019.03.006

18. Eco-friendly anti-felting treatment of wool top based on biosurfactant and enzymes

Author:
Iglesias, Martín S.; Sequeiros, Cynthia; García, Sebastián; Olivera, Nelda L.
Source:
Journal of cleaner production 2019 v.220 pp. 846-852
ISSN:
0959-6526
Subject:
proteolysis,   etc   ; Bacillus subtilis; Merino; biosurfactants; environmental impact; markets; micelles; proteinases; surfactin; tensile strength; wool;     Show all 11 Subjects
Abstract:
... Anti-felting processes with low environmental impacts are important for improving wool fiber attributes, especially if fiber is intended for the organic market. The aim of this study was to assess the potential of proteolytic enzymes, alone or in combination with Bacillus subtilis O9 biosurfactant (surfactin), to reduce felting of Merino wool top. Different concentrations of extracellular proteoly ...
DOI:
10.1016/j.jclepro.2019.02.165

19. Proteomics turns functional

Author:
Monti, Chiara; Zilocchi, Mara; Colugnat, Ilaria; Alberio, Tiziana
Source:
Journal of proteomics 2019 v.198 pp. 36-44
ISSN:
1874-3919
Subject:
proteolysis,   etc   ; biochemical pathways; bioinformatics; diabetes; humans; neoplasms; neurodegenerative diseases; pathogenesis; protein-protein interactions; proteins; proteome; proteomics;     Show all 12 Subjects
Abstract:
... Proteomics is acquiring a pivotal role in the comprehensive understanding of human biology. Biochemical processes involved in complex diseases, such as neurodegenerative diseases, diabetes and cancer, can be identified by combining proteomics analysis and bioinformatics tools. In the last ten years, the main output of differential proteomics investigations evolved from long lists of proteins to th ...
DOI:
10.1016/j.jprot.2018.12.012

20. Generation of the heterogeneity of extracellular vesicles by membrane organization and sorting machineries

Author:
Harada, Yoichiro; Suzuki, Takehiro; Fukushige, Tomoko; Kizuka, Yasuhiko; Yagi, Hirokazu; Yamamoto, Mika; Kondo, Kiyotaka; Inoue, Hiromasa; Kato, Koichi; Taniguchi, Naoyuki; Kanekura, Takuro; Dohmae, Naoshi; Maruyama, Ikuro
Source:
Biochimica et biophysica acta 2019 v.1863 no.4 pp. 681-691
ISSN:
0304-4165
Subject:
proteolysis,   etc   ; RNA interference; biogenesis; detergents; hepatocyte growth factor receptor; metalloproteinases; precipitin tests; secretion; solubilization; sucrose; ultracentrifugation;     Show all 11 Subjects
Abstract:
... Cells secrete heterogeneous populations of extracellular vesicles (EVs) via unknown mechanisms. EV biogenesis has been postulated to involve lipid-protein clusters, also known as membrane microdomains.Membrane properties and heterogeneity of melanoma-derived EVs were analyzed by a detergent solubilization assay, sucrose density gradient ultracentrifugation and immunoprecipitation. EV secretion was ...
DOI:
10.1016/j.bbagen.2019.01.015