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Special Issue "Protein Modifications and Bioconjugation"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: closed (15 December 2017)

Special Issue Editors

Guest Editor
Prof. Zhaohui Sunny Zhou

Department of Chemistry and Chemical Biology, Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA 02115-5000, USA
Website | E-Mail
Interests: protein chemistry, protein modifications, bioconjugation, protein pharmaceuticals, biotechnology, mass spectrometry, bioanalysis, bioorganic chemistry and enzymology
Guest Editor
Professor Litai Jin

School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325000, China
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Special Issue Information

Dear Colleagues,

You are cordially invited to contribute to a Special Issue of “Protein Modifications and Bioconjugation”. Since structures determine functions, modifications of proteins modulate their functions, and, thus, play diverse and crucial roles in chemistry, biology, medicine and engineering. For example, various post-translational modifications (PTM’s) are essential key players in gene regulation and disease development, and many of the enzymes involved (e.g., methyltransferases, kinases and deacetylases) have been actively pursued as drug targets. Pertinent to PTMs, a battery of selective derivatization methods has been developed to label or tag modified amino acids, thereby permitting facile detection and affinity enrichment. From an engineering point of view, bioconjugation introduces new functions to proteins. For therapeutic applications, PEGylation has widely employed to enhance circulation half-lives, to reduce immunogenicity and to shield from proteolysis. Recently, antibody-drug conjugates (ADCs) have introduced new opportunities for battling diseases that were not possible with either antibodies or drugs alone. With the advent of many site-specific bioconjugation techniques, hybrid modality engineering of peptides and proteins represents a promising fertile frontier in the next-generation of materials and medicine.

All aspects of the topics are welcome, including both method developments and novel discoveries. Topics include but limited to bioconjugation of peptides and proteins, protein synthesis, post-translational modifications (PTMs), unnatural amino acids, peptide and protein pharmaceuticals (e.g., antibody-drug conjugates and hybrid modality engineering), functional probes and proteomics (e.g., activity-based protein profiling), specific chemo-enzymatic tagging and affinity labeling, and protein analysis (e.g., mass spectrometry) that involve chemical derivatization. Both original report and review are accepted.

Prof. Dr. Zhaohui Sunny Zhou
Prof. Dr. Litai Jin
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (5 papers)

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Research

Open AccessCommunication Analysis of Protein-Phenolic Compound Modifications Using Electrochemistry Coupled to Mass Spectrometry
Molecules 2018, 23(2), 264; doi:10.3390/molecules23020264
Received: 13 December 2017 / Revised: 18 January 2018 / Accepted: 24 January 2018 / Published: 29 January 2018
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Abstract
In the last decade, electrochemical oxidation coupled with mass spectrometry has been successfully used for the analysis of metabolic studies. The application focused in this study was to investigate the redox potential of different phenolic compounds such as the very prominent chlorogenic acid.
[...] Read more.
In the last decade, electrochemical oxidation coupled with mass spectrometry has been successfully used for the analysis of metabolic studies. The application focused in this study was to investigate the redox potential of different phenolic compounds such as the very prominent chlorogenic acid. Further, EC/ESI-MS was used as preparation technique for analyzing adduct formation between electrochemically oxidized phenolic compounds and food proteins, e.g., alpha-lactalbumin or peptides derived from a tryptic digestion. In the first step of this approach, two reactant solutions are combined and mixed: one contains the solution of the digested protein, and the other contains the phenolic compound of interest, which was, prior to the mixing process, electrochemically transformed to several oxidation products using a boron-doped diamond working electrode. As a result, a Michael-type addition led to covalent binding of the activated phenolic compounds to reactive protein/peptide side chains. In a follow-up approach, the reaction mix was further separated chromatographically and finally detected using ESI-HRMS. Compound-specific, electrochemical oxidation of phenolic acids was performed successfully, and various oxidation and reaction products with proteins/peptides were observed. Further optimization of the reaction (conditions) is required, as well as structural elucidation concerning the final adducts, which can be phenolic compound oligomers, but even more interestingly, quite complex mixtures of proteins and oxidation products. Full article
(This article belongs to the Special Issue Protein Modifications and Bioconjugation)
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Open AccessArticle Biochemical Analysis of the Role of Leucine-Rich Repeat Receptor-Like Kinases and the Carboxy-Terminus of Receptor Kinases in Regulating Kinase Activity in Arabidopsis thaliana and Brassica oleracea
Molecules 2018, 23(1), 236; doi:10.3390/molecules23010236
Received: 11 December 2017 / Revised: 8 January 2018 / Accepted: 15 January 2018 / Published: 22 January 2018
PDF Full-text (3461 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Protein post-translational modification by phosphorylation is essential for the activity and stability of proteins in higher plants and underlies their responses to diverse stimuli. There are more than 300 leucine-rich repeat receptor-like kinases (LRR-RLKs), a major group of receptor-like kinases (RLKs) that plays
[...] Read more.
Protein post-translational modification by phosphorylation is essential for the activity and stability of proteins in higher plants and underlies their responses to diverse stimuli. There are more than 300 leucine-rich repeat receptor-like kinases (LRR-RLKs), a major group of receptor-like kinases (RLKs) that plays an important role in growth, development, and biotic stress responses in higher plants. To analyze auto- and transphosphorylation patterns and kinase activities in vitro, 43 full-length complementary DNA (cDNA) sequences were cloned from genes encoding LRR-RLKs. Autophosphorylation activity was found in the cytoplasmic domains (CDs) of 18 LRR-RLKs; 13 of these LRR-RLKs with autophosphorylation activity showed transphosphorylation in Escherichia coli. BRI1-Associated Receptor Kinase (BAK1), which is critically involved in the brassinosteroid and plant innate immunity signal transduction pathways, showed strong auto- and transphosphorylation with multi-specific kinase activity within 2 h of induction of Brassica oleraceae BAK1-CD (BoBAK1-CD) in E. coli; moreover, the carboxy-terminus of LRR-RLKs regulated phosphorylation and kinase activity in Arabidopsis thaliana and vegetative crops. Full article
(This article belongs to the Special Issue Protein Modifications and Bioconjugation)
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Open AccessArticle The Major Chromophore Arising from Glucose Degradation and Oxidative Stress Occurrence during Lens Proteins Glycation Induced by Glucose
Molecules 2018, 23(1), 6; doi:10.3390/molecules23010006
Received: 13 November 2017 / Revised: 13 December 2017 / Accepted: 14 December 2017 / Published: 22 December 2017
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Abstract
Glucose autoxidation has been proposed as a key reaction associated with deleterious effects induced by hyperglycemia in the eye lens. Little is known about chromophores generated during glucose autoxidation. In this study, we analyzed the effect of oxidative and dicarbonyl stress in the
[...] Read more.
Glucose autoxidation has been proposed as a key reaction associated with deleterious effects induced by hyperglycemia in the eye lens. Little is known about chromophores generated during glucose autoxidation. In this study, we analyzed the effect of oxidative and dicarbonyl stress in the generation of a major chromophore arising from glucose degradation (GDC) and its association with oxidative damage in lens proteins. Glucose (5 mM) was incubated with H2O2 (0.5–5 mM), Cu2+ (5–50 μM), glyoxal (0.5–5 mM) or methylglyoxal (0.5–5 mM) at pH 7.4, 5% O2, 37 °C, from 0 to 30 days. GDC concentration increased with incubation time, as well as when incubated in the presence of H2O2 and/or Cu2+, which were effective even at the lowest concentrations. Dicarbonylic compounds did not increase the levels of GDC during incubations. 1H, 13C and FT-IR spectra from the purified fraction containing the chromophore (detected by UV/vis spectroscopy) showed oxidation products of glucose, including gluconic acid. Lens proteins solutions (10 mg/mL) incubated with glucose (30 mM) presented increased levels of carboxymethyl-lysine and hydrogen peroxide that were associated with GDC increase. Our results suggest a possible use of GDC as a marker of autoxidative reactions occurring during lens proteins glycation induced by glucose. Full article
(This article belongs to the Special Issue Protein Modifications and Bioconjugation)
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Open AccessArticle Pathogenic Acanthamoeba castellanii Secretes the Extracellular Aminopeptidase M20/M25/M40 Family Protein to Target Cells for Phagocytosis by Disruption
Molecules 2017, 22(12), 2263; doi:10.3390/molecules22122263
Received: 23 November 2017 / Revised: 14 December 2017 / Accepted: 15 December 2017 / Published: 18 December 2017
PDF Full-text (3813 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Acanthamoeba is free-living protist pathogen capable of causing a blinding keratitis and granulomatous encephalitis. However, the mechanisms of Acanthamoeba pathogenesis are still not clear. Here, our results show that cells co-cultured with pathogenic Acanthamoeba would be spherical and floated, even without contacting the
[...] Read more.
Acanthamoeba is free-living protist pathogen capable of causing a blinding keratitis and granulomatous encephalitis. However, the mechanisms of Acanthamoeba pathogenesis are still not clear. Here, our results show that cells co-cultured with pathogenic Acanthamoeba would be spherical and floated, even without contacting the protists. Then, the Acanthamoeba protists would contact and engulf these cells. In order to clarify the contact-independent pathogenesis mechanism in Acanthamoeba, we collected the Acanthamoeba-secreted proteins (Asp) to incubate with cells for identifying the extracellular virulent factors and investigating the cytotoxicity process. The Asps of pathogenic Acanthamoeba express protease activity to reactive Leu amino acid in ECM and induce cell-losing adhesion ability. The M20/M25/M40 superfamily aminopeptidase protein (ACA1_264610), an aminopeptidase be found in Asp, is upregulated after Acanthamoeba and C6 cell co-culturing for 6 h. Pre-treating the Asp with leucine aminopeptidase inhibitor and the specific antibodies of Acanthamoeba M20/M25/M40 superfamily aminopeptidase could reduce the cell damage during Asp and cell co-incubation. These results suggest an important functional role of the Acanthamoeba secreted extracellular aminopeptidases in the Acanthamoeba pathogenesis process. This study provides information regarding clinically pathogenic isolates to target specific molecules and design combined drugs. Full article
(This article belongs to the Special Issue Protein Modifications and Bioconjugation)
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Open AccessArticle The Eukaryotic Elongation Factor 1 Alpha (eEF1α) from the Parasite Leishmania infantum Is Modified with the Immunomodulatory Substituent Phosphorylcholine (PC)
Molecules 2017, 22(12), 2094; doi:10.3390/molecules22122094
Received: 27 October 2017 / Accepted: 24 November 2017 / Published: 29 November 2017
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Abstract
Proteins and glycolipids have been found to be decorated with phosphorylcholine (PC) both in protozoa and nematodes that parasitize humans and animals. PC epitopes can provoke various effects on immune cells leading to an immunomodulation of the host’s immune system that allows long-term
[...] Read more.
Proteins and glycolipids have been found to be decorated with phosphorylcholine (PC) both in protozoa and nematodes that parasitize humans and animals. PC epitopes can provoke various effects on immune cells leading to an immunomodulation of the host’s immune system that allows long-term persistence of the parasites. So far, only a limited number of PC-modified proteins, mainly from nematodes, have been identified. Infections caused by Leishmania spp. (e.g., L. infantum in southern Europe) affect about 12 million people worldwide and are characterized by a wide spectrum of clinical forms in humans, ranging from cutaneous to fatal visceral leishmaniasis. To establish and maintain the infection, these protozoa are dependent on the secretion of effector molecules into the host for modulating their immune system. In this project, we analyzed the PC modification of L. infantum promastigotes by 2D-gel based proteomics. Western blot analysis with the PC-specific antibody TEPC-15 revealed one PC-substituted protein in this organism, identified as eEF1α. We could demonstrate that the binding of eEF1α to one of its downstream effectors is dependent on its PC-modification. In this study we provide evidence that in this parasite the modification of eEF1α with PC may be essential for its function as an important virulence factor. Full article
(This article belongs to the Special Issue Protein Modifications and Bioconjugation)
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