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1. Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations

Author:
Qing Li; Dimitra Apostolidou; Piotr E. Marszalek
Source:
Methods 2022 v.197 pp. 39-53
ISSN:
1046-2023
Subject:
polypeptides,   etc   ; computers; proteome; spectroscopy;     Show all 4 Subjects
Abstract:
... Most proteins in proteomes are large, typically consist of more than one domain and are structurally complex. This often makes studying their mechanical unfolding pathways challenging. Proteins composed of tandem repeat domains are a subgroup of multi-domain proteins that, when stretched, display a saw-tooth pattern in their mechanical unfolding force extension profiles due to their repetitive str ...
DOI:
10.1016/j.ymeth.2021.05.012

2. Sequencing the origins of life

Author:
Tony Z. Jia; Shota Nishikawa; Kosuke Fujishima
Source:
BBA advances 2022 v.2 pp. 100049
ISSN:
2667-1603
Subject:
polypeptides,   etc   ; biopolymers; evolution; polymerization;     Show all 4 Subjects
Abstract:
... One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing technique ...
DOI:
10.1016/j.bbadva.2022.100049

3. Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase

Author:
Zhejian Ji; Hao Li; Daniele Peterle; Joao A. Paulo; Scott B. Ficarro; Thomas E. Wales; Jarrod A. Marto; Steven P. Gygi; John R. Engen; Tom A. Rapoport
Source:
Molecular cell 2022 v.82 no.3 pp. 570-584.e8
ISSN:
1097-2765
Subject:
polypeptides,   etc   ; adenosinetriphosphatase; proteasome endopeptidase complex; ubiquitin;     Show all 4 Subjects
Abstract:
... The hexameric Cdc48 ATPase (p97 or VCP in mammals) cooperates with its cofactor Ufd1/Npl4 to extract polyubiquitinated proteins from membranes or macromolecular complexes for degradation by the proteasome. Here, we clarify how the Cdc48 complex unfolds its substrates and translocates polypeptides with branchpoints. The Cdc48 complex recognizes primarily polyubiquitin chains rather than the attache ...
DOI:
10.1016/j.molcel.2021.11.033

4. Effects of Nanometer Confinement on the Self-Assembly and Dynamics of Poly(γ-benzyl-l-glutamate) and Its Copolymer with Poly(isobutylene)

Author:
Marianna Spyridakou; Kostas Tsimenidis; Manos Gkikas; Martin Steinhart; Robert Graf; George Floudas
Source:
Macromolecules 2022 v.55 no.7 pp. 2615-2626
ISSN:
1520-5835
Subject:
polypeptides,   etc   ; X-ray diffraction; composite polymers; dielectric spectroscopy;     Show all 4 Subjects
Abstract:
... Poly(γ-benzyl-l-glutamate) (PBLG) and its copolymer with poly(isobutylene) (PIB) are studied in the bulk and under nanometer confinement in pores with emphasis on the self-assembly and dynamics, respectively, with X-ray diffraction, ¹³C NMR, dielectric spectroscopy, and differential scanning calorimetry. PBLG segments located within the α-helical and amorphous regions have distinct dielectric fing ...
DOI:
10.1021/acs.macromol.2c00077

5. Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo

Author:
Taekjip Ha; Christian Kaiser; Sua Myong; Bin Wu; Jie Xiao
Source:
Molecular cell 2022 v.82 no.2 pp. 304-314
ISSN:
1097-2765
Subject:
polypeptides,   etc   ; energy transfer; fluorescence; gene expression regulation; genomics;     Show all 5 Subjects
Abstract:
... Owing to their unique abilities to manipulate, label, and image individual molecules in vitro and in cellulo, single-molecule techniques provide previously unattainable access to elementary biological processes. In imaging, single-molecule fluorescence resonance energy transfer (smFRET) and protein-induced fluorescence enhancement in vitro can report on conformational changes and molecular interac ...
DOI:
10.1016/j.molcel.2021.12.019

6. Short-Range Backbone Dihedral Rotations Modulate Internal Friction in Intrinsically Disordered Proteins

Author:
Debapriya Das; Lisha Arora; Samrat Mukhopadhyay
Source:
Journal of the American Chemical Society 2022 v.144 no.4 pp. 1739-1747
ISSN:
1520-5126
Subject:
polypeptides,   etc   ; anisotropy; fluorescence; friction; models; proline; solvents; viscosity;     Show all 8 Subjects
Abstract:
... Protein folding and dynamics are governed by an intricate interplay of thermal and viscosity-mediated effects. The solvent viscosity contributes to the frictional drag in protein dynamics. In addition to this viscosity-dependent effect, there is also an intriguing viscosity-independent component that represents the intrinsic resistance of the polypeptide chain to changing its conformation. This so ...
DOI:
10.1021/jacs.1c11236

7. Biflavones inhibit the fibrillation and cytotoxicity of the human islet amyloid polypeptide

Author:
Jufei Xu; Yanan Wang; Ting Zheng; Yan Huo; Weihong Du
Source:
Journal of materials chemistry B 2022 v.10 no.24 pp. 4650-4661
ISSN:
2050-7518
Subject:
polypeptides,   etc   ; amyloid; amyloidosis; cytotoxicity; flavones; humans; hydrogen; hydrophobicity; oligomerization;     Show all 9 Subjects
Abstract:
... Biflavones are a kind of natural compound with a variety of biological activities, which have the capability of reversing diabetes and neurodegenerative diseases. The human islet amyloid polypeptide (hIAPP) is closely related to the pathological process of type II diabetes mellitus (T2DM). The development of new inhibitors is crucial to prevent hIAPP aggregation against T2DM. However, the influenc ...
DOI:
10.1039/d2tb00230b

8. Engineering multifunctional enzymes for agro-biomass utilization

Author:
Aarjoo Sharma; Sanjeev Balda; Neena Capalash; Prince Sharma
Source:
Bioresource technology 2022 v.347 pp. 126706
ISSN:
0960-8524
Subject:
polypeptides,   etc   ; biomass; cost effectiveness; lignocellulose; renewable resources; secretion; technology;     Show all 7 Subjects
Abstract:
... Lignocellulosic biomass is a plentiful renewable resource that can be converted into a wide range of high-value-added industrial products. However, the complexity of its structural integrity is one of the major constraints and requires combinations of different fibrolytic enzymes for the cost-effective, industrially and environmentally feasible transformation. An interesting approach is constructi ...
DOI:
10.1016/j.biortech.2022.126706

9. Resource efficient collagen extraction from common starfish with the aid of high shear mechanical homogenization and ultrasound

Author:
Naveen Kumar Vate; Ingrid Undeland; Mehdi Abdollahi
Source:
Food chemistry 2022 v.393 pp. 133426
ISSN:
0308-8146
Subject:
polypeptides,   etc   ; Asteroidea; collagen; food chemistry; homogenization; thermal stability; ultrasonics;     Show all 7 Subjects
Abstract:
... Processes currently used for collagen extraction are complicated requiring a great deal of time and chemicals. Here, high shear mechanical homogenization (HSMH) and ultrasound (US) were integrated in the pretreatment step of collagen extraction from common starfish to reduce chemical use and time consumption. Effects of the assistant technologies on yield, structural integrity and functionality of ...
DOI:
10.1016/j.foodchem.2022.133426

10. Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons

Author:
Howard Gamper; Isao Masuda; Ya-Ming Hou
Source:
Journal of molecular biology 2022 v.434 no.8 pp. 167440
ISSN:
0022-2836
Subject:
polypeptides,   etc   ; biotechnology; codons; genome expansion; molecular biology; protein synthesis; ribosomes;     Show all 7 Subjects
Abstract:
... Inducing tRNA +1 frameshifting to read a quadruplet codon has the potential to incorporate a non-canonical amino acid (ncAA) into the polypeptide chain. While this strategy is attractive for genome expansion in biotechnology and bioengineering endeavors, improving the yield is hampered by a lack of understanding of where the shift can occur in an elongation cycle of protein synthesis. Lacking a cl ...
DOI:
10.1016/j.jmb.2021.167440

11. Sequestration of the ionizing proton in singly charged metastable protein ions generated by MALDI

Author:
Fagerquist Clifton K.; Dodd Claire E.
Source:
International Journal of Mass Spectrometry pp. -
ISSN:
1387-3806
Subject:
polypeptides,   etc   ; Shiga-like toxin 2; arginine; lysine; proteolysis; protonation; thioredoxins;     Show all 7 Subjects
Abstract:
... A hypothesis is proposed for the preferential ionization/protonation of arginine residues in metastable protein ions. This phenomenon has significant consequences for detection of protein fragments resulting from polypeptide backbone cleavage. Preferential ionization at arginine (when present) is based upon MS/MS analysis of singly charged/protonated metastable protein ions: YahO, CspC, CspE, B-su ...
DOI:
10.1016/j.ijms.2021.116736
CHORUS:
10.1016/j.ijms.2021.116736

12. hIAPP-Amyloid-Core Derived d-Peptide Prevents hIAPP Aggregation and Destabilizes Its Protofibrils

Author:
Rituparna Roy; Sandip Paul
Source:
Journal of physical chemistry 2022 v.126 no.4 pp. 822-839
ISSN:
1520-5207
Subject:
polypeptides,   etc   ; amino acids; amyloid; cytotoxicity; humans; hydrogen; hydrophobicity; molecular dynamics;     Show all 8 Subjects
Abstract:
... The aberrant misfolding of human islet amyloid polypeptide into cytotoxic amyloid aggregates is the hallmark of type II diabetes. In order to avert the formation of amyloid aggregation, a variety of peptides has been used as inhibitors. Recently, a peptide derived from the amyloidogenic core of hIAPP (hIAPP₂₂–₂₇) and consisting of all d-amino acid residues (D-nl), was found to efficiently prevent ...
DOI:
10.1021/acs.jpcb.1c10395

13. Activity-Dependent Neuroprotective Protein (ADNP)-Derived Peptide (NAP) Counteracts UV-B Radiation-Induced ROS Formation in Corneal Epithelium

Author:
Grazia Maugeri; Agata Grazia D’Amico; Salvatore Giunta; Cesarina Giallongo; Daniele Tibullo; Claudio Bucolo; Salvatore Saccone; Concetta Federico; Davide Scollo; Antonio Longo; Teresio Avitabile; Giuseppe Musumeci; Velia D’Agata
Source:
Antioxidants 2022 v.11 no.1 pp. -
ISSN:
2076-3921
Subject:
polypeptides,   etc   ; apoptosis; cornea; endothelium; humans; irradiation; protective effect; therapeutics; ultraviolet radiation;     Show all 9 Subjects
Abstract:
... The corneal epithelium, the outermost layer of the cornea, acts as a dynamic barrier preventing access to harmful agents into the intraocular space. It is subjected daily to different insults, and ultraviolet B (UV-B) irradiation represents one of the main causes of injury. In our previous study, we demonstrated the beneficial effects of pituitary adenylate cyclase-activating polypeptide (PACAP) a ...
DOI:
10.3390/antiox11010128

14. Bioactive Anti-Inflammatory Thermocatalytic Nanometal-Polyphenol Polypeptide Scaffolds for MRSA-Infection/Tumor Postsurgical Tissue Repair

Author:
Yidan Wang; Wen Niu; Xiaoyan Qu; Bo Lei
Source:
ACS applied materials & interfaces 2022 v.14 no.4 pp. 4946-4958
ISSN:
1944-8252
Subject:
polypeptides,   etc   ; biocompatible materials; catalytic activity; medicine; nanocomposites; neoplasms; resection; tissue repair;     Show all 8 Subjects
Abstract:
... Postsurgical tumor recurrence, infection, and tissue defect are still the challenges in clinical medicine. The development of multifunctional biomaterial scaffolds with a microenvironment-responsive tumor-infection therapy-tissue repair is highly desirable. Herein, we report a bioactive, injectable, adhesive, self-healing, antibacterial, and anti-inflammatory metal-polyphenol polypeptide nanocompo ...
DOI:
10.1021/acsami.1c21082

15. Correlating the Local and Global Dynamics of an Enzyme in the Crowded Milieu

Author:
Harshita Rastogi; Pramit K. Chowdhury
Source:
Journal of physical chemistry 2022 v.126 no.17 pp. 3208-3223
ISSN:
1520-5207
Subject:
polypeptides,   etc   ; activation energy; adenylate kinase; dextran; energy; ficoll; solvation; temperature; tryptophan;     Show all 9 Subjects
Abstract:
... Enzymes are dynamic biological macromolecules, with their catalytic function(s) being largely influenced by the changes in local fluctuations of amino acid side chains as well as global structural modulations that the enzyme undergoes. Such local and global motions can be highly affected inside the crowded physiological interior of the cell. Here, we have addressed the role of dynamic structural f ...
DOI:
10.1021/acs.jpcb.1c09759

16. Effects and signaling pathways of Elabela in the cardiovascular system

Author:
Meiling Zhou; Yinan Wu
Source:
Peptides 2022 v.147 pp. 170674
ISSN:
0196-9781
Subject:
polypeptides,   etc   ; G-protein coupled receptors; cardiovascular system; cell proliferation; embryogenesis; ligands;     Show all 6 Subjects
Abstract:
... For a long time, Apelin has been considered as the only endogenous ligand of G protein-coupled receptor APJ. Until recently, the discovery of Elabela (Apela/Toddler) as a new polypeptide that can act through APJ and has a similar function to Apelin broke this situation. Elabela promotes a variety of cell proliferation processes, including embryonic development, and has especially beneficial effect ...
DOI:
10.1016/j.peptides.2021.170674

17. Oral delivery of marine shellfish supramolecule peptides for skin wound healing

Author:
Faming Yang; Di Zhao; Kun Zhang; Zhouchi Wang; Yuxin Wang; Changcheng Wu; Shenghao Cui; Tingting Guo; Liqi Chen; Jingdi Chen
Source:
Colloids and surfaces 2022 v.216 pp. 112592
ISSN:
0927-7765
Subject:
polypeptides,   etc   ; collagen; fibroblasts; hair follicles; hydrolysis; inflammation; oral administration; proteinases; shellfish; shellfish meat;     Show all 10 Subjects
Abstract:
... Oral administration of peptides/proteins with superior efficacy and fewer side effects is the most advantageous route of administration. In this study, we utilized controllable enzymatic (animal protease) hydrolysis technology to prepare active polypeptide self-assembling supramolecular (APs) from marine shellfish meat to explore the functional mechanism of APs in in vitro and in vivo (oral admini ...
DOI:
10.1016/j.colsurfb.2022.112592

18. Synthesis, characterization of tuna polypeptide selenium nanoparticle, and its immunomodulatory and antioxidant effects in vivo

Author:
Wenyi Jiang; Shan He; Dongxiao Su; Meijun Ye; Qingzhu Zeng; Yang Yuan
Source:
Food chemistry 2022 v.383 pp. 132405
ISSN:
0308-8146
Subject:
polypeptides,   etc   ; animal experimentation; antioxidant activity; antioxidants; food chemistry; hydrophobicity; liver; phagocytosis; selenium; tuna;     Show all 10 Subjects
Abstract:
... The tuna polypeptide (TP) was used as the reducing agent and the stabilizing agent to synthesize a tuna polypeptide selenium nanoparticle (TP-SeNP) via a green method. An animal experiment was conducted to investigate its immunomodulatory and antioxidant effects in vivo. The results indicated that the TP regulated the accumulation and stabilization of the TP-SeNP. And the conversion of selenium wa ...
DOI:
10.1016/j.foodchem.2022.132405

19. Type C mutation of nucleophosmin 1 acute myeloid leukemia: Consequences of intrinsic disorder

Author:
Sara La Manna; Daniele Florio; Concetta Di Natale; Elena Lagreca; Teresa Sibillano; Cinzia Giannini; Daniela Marasco
Source:
Biochimica et biophysica acta 2022 v.1866 no.8 pp. 130173
ISSN:
0304-4165
Subject:
polypeptides,   etc   ; amino acid sequences; amyloid; cytosol; genes; mutation; myeloid leukemia; structural biology; therapeutics;     Show all 9 Subjects
Abstract:
... Nucleophosmin 1 (NPM1) protein is a multifunctional nucleolar chaperone and its gene is the most frequently mutated in Acute Myeloid Leukemia (AML). AML mutations cause the unfolding of the C-terminal domain (CTD) and the protein delocalizing in the cytosol (NPM1c+). Marked aggregation endowed with an amyloid character was assessed as consequences of mutations. Herein we analyzed the effects of ty ...
DOI:
10.1016/j.bbagen.2022.130173

20. Biomimetic Glycosylated Polythreonines by N-Carboxyanhydride Polymerization

Author:
Anna C. Deleray; Jessica R. Kramer
Source:
Biomacromolecules 2022 v.23 no.3 pp. 1453-1461
ISSN:
1526-4602
Subject:
polypeptides,   etc   ; biomimetics; catalytic activity; collagen; glycosylation; medicine; mucins; polymerization; protein structure; threonine; water solubility;     Show all 11 Subjects
Abstract:
... Glycosylated threonine (Thr) is a structural motif found in seemingly disparate natural proteins from deep-sea collagen to mucins. Synthetic mimics of these important proteins are of great interest in biomedicine. Such materials also provide ready access to probe the contributions of individual amino acids to protein structure in a controlled and tunable manner. N-Carboxyanhydride (NCA) polymeriza ...
DOI:
10.1021/acs.biomac.2c00020