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State-of-the-Art Biochemistry in USA
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State-of-the-Art Biochemistry in USA

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 9537

Special Issue Editor

Prof. Dr. Vsevolod V. Gurevich

E-Mail Website
Collection Editor
Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
Interests: arrestin proteins; structure-function; protein engineering; GPCR signaling; GPCR trafficking; receptor regulation; cell proliferation; apoptosis; MAP kinases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This regional project aims to collect high-quality research articles, review articles, and communications on all aspects of biochemistry from the USA. We encourage the submission of manuscripts that provide novel and mechanistic insights and papers that report significant advances in the field.

The areas of interest for this regional collection include but are not limited to:

  • Cellular function and structure;
  • Cell signaling;
  • Protein biosynthesis;
  • Gene and protein structure and expression;
  • Cancer pathology and biology;
  • Drugs and pharmaceutics;
  • Membrane function and post-translational modifications;
  • New approaches in the management of hypoxic tumors;
  • Cancer molecular genetics;
  • Enzymology and structural biology;
  • Metalloenzymes;
  • Enzyme activation and inhibition;
  • Targeting human enzymes involved in tumorigenesis;
  • Function and structure of protein membrane and drug distribution in the body;
  • Protein interactions and functional nucleic acids;
  • Epigenetic and genetic regulatory mechanisms;
  • Lipid metabolism;
  • Drug resistance;
  • Role of intestinal microbes in diseases and human health;
  • Characterization and development of small molecules for targeting metabolic pathways essential for the life cycle of human pathogens.

Prof. Dr. Vsevolod V. Gurevich
Collection Editor

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 submissions that pass pre-check are 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

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21 pages, 3950 KiB  
Article
Delineation of G Protein-Coupled Receptor Kinase Phosphorylation Sites within the D1 Dopamine Receptor and Their Roles in Modulating β-Arrestin Binding and Activation
by Amy E. Moritz, Nora S. Madaras, Michele L. Rankin, Laura R. Inbody and David R. Sibley
Int. J. Mol. Sci. 2023, 24(7), 6599; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24076599 - 01 Apr 2023
Cited by 2 | Viewed by 1507
Abstract
The D1 dopamine receptor (D1R) is a G protein-coupled receptor that signals through activating adenylyl cyclase and raising intracellular cAMP levels. When activated, the D1R also recruits the scaffolding protein β-arrestin, which promotes receptor desensitization and internalization, as well as additional downstream [...] Read more.
The D1 dopamine receptor (D1R) is a G protein-coupled receptor that signals through activating adenylyl cyclase and raising intracellular cAMP levels. When activated, the D1R also recruits the scaffolding protein β-arrestin, which promotes receptor desensitization and internalization, as well as additional downstream signaling pathways. These processes are triggered through receptor phosphorylation by G protein-coupled receptor kinases (GRKs), although the precise phosphorylation sites and their role in recruiting β-arrestin to the D1R remains incompletely described. In this study, we have used detailed mutational and in situ phosphorylation analyses to completely identify the GRK-mediated phosphorylation sites on the D1R. Our results indicate that GRKs can phosphorylate 14 serine and threonine residues within the C-terminus and the third intracellular loop (ICL3) of the receptor, and that this occurs in a hierarchical fashion, where phosphorylation of the C-terminus precedes that of the ICL3. Using β-arrestin recruitment assays, we identified a cluster of phosphorylation sites in the proximal region of the C-terminus that drive β-arrestin binding to the D1R. We further provide evidence that phosphorylation sites in the ICL3 are responsible for β-arrestin activation, leading to receptor internalization. Our results suggest that distinct D1R GRK phosphorylation sites are involved in β-arrestin binding and activation. Full article
(This article belongs to the Special Issue State-of-the-Art Biochemistry in USA)
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16 pages, 7707 KiB  
Article
Role of Histone Tails and Single Strand DNA Breaks in Nucleosomal Arrest of RNA Polymerase
by Nadezhda S. Gerasimova, Nikolay A. Pestov and Vasily M. Studitsky
Int. J. Mol. Sci. 2023, 24(3), 2295; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24032295 - 24 Jan 2023
Cited by 3 | Viewed by 1944
Abstract
Transcription through nucleosomes by RNA polymerases (RNAP) is accompanied by formation of small intranucleosomal DNA loops (i-loops). The i-loops form more efficiently in the presence of single-strand breaks or gaps in a non-template DNA strand (NT-SSBs) and induce arrest of transcribing RNAP, thus [...] Read more.
Transcription through nucleosomes by RNA polymerases (RNAP) is accompanied by formation of small intranucleosomal DNA loops (i-loops). The i-loops form more efficiently in the presence of single-strand breaks or gaps in a non-template DNA strand (NT-SSBs) and induce arrest of transcribing RNAP, thus allowing detection of NT-SSBs by the enzyme. Here we examined the role of histone tails and extranucleosomal NT-SSBs in i-loop formation and arrest of RNAP during transcription of promoter-proximal region of nucleosomal DNA. NT-SSBs present in linker DNA induce arrest of RNAP +1 to +15 bp in the nucleosome, suggesting formation of the i-loops; the arrest is more efficient in the presence of the histone tails. Consistently, DNA footprinting reveals formation of an i-loop after stalling RNAP at the position +2 and backtracking to position +1. The data suggest that histone tails and NT-SSBs present in linker DNA strongly facilitate formation of the i-loops during transcription through the promoter-proximal region of nucleosomal DNA. Full article
(This article belongs to the Special Issue State-of-the-Art Biochemistry in USA)
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12 pages, 2230 KiB  
Article
Short Arrestin-3-Derived Peptides Activate JNK3 in Cells
by Nicole A. Perry-Hauser, Tamer S. Kaoud, Henriette Stoy, Xuanzhi Zhan, Qiuyan Chen, Kevin N. Dalby, Tina M. Iverson, Vsevolod V. Gurevich and Eugenia V. Gurevich
Int. J. Mol. Sci. 2022, 23(15), 8679; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23158679 - 04 Aug 2022
Cited by 6 | Viewed by 1567
Abstract
Arrestins were first discovered as suppressors of G protein-mediated signaling by G protein-coupled receptors. It was later demonstrated that arrestins also initiate several signaling branches, including mitogen-activated protein kinase cascades. Arrestin-3-dependent activation of the JNK family can be recapitulated with peptide fragments, which [...] Read more.
Arrestins were first discovered as suppressors of G protein-mediated signaling by G protein-coupled receptors. It was later demonstrated that arrestins also initiate several signaling branches, including mitogen-activated protein kinase cascades. Arrestin-3-dependent activation of the JNK family can be recapitulated with peptide fragments, which are monofunctional elements distilled from this multi-functional arrestin protein. Here, we use maltose-binding protein fusions of arrestin-3-derived peptides to identify arrestin elements that bind kinases of the ASK1-MKK4/7-JNK3 cascade and the shortest peptide facilitating JNK signaling. We identified a 16-residue arrestin-3-derived peptide expressed as a Venus fusion that leads to activation of JNK3α2 in cells. The strength of the binding to the kinases does not correlate with peptide activity. The ASK1-MKK4/7-JNK3 cascade has been implicated in neuronal apoptosis. While inhibitors of MAP kinases exist, short peptides are the first small molecule tools that can activate MAP kinases. Full article
(This article belongs to the Special Issue State-of-the-Art Biochemistry in USA)
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15 pages, 2549 KiB  
Article
Human PARP1 Facilitates Transcription through a Nucleosome and Histone Displacement by Pol II In Vitro
by Elena Y. Kotova, Fu-Kai Hsieh, Han-Wen Chang, Natalia V. Maluchenko, Marie-France Langelier, John M. Pascal, Donal S. Luse, Alexey V. Feofanov and Vasily M. Studitsky
Int. J. Mol. Sci. 2022, 23(13), 7107; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23137107 - 26 Jun 2022
Cited by 9 | Viewed by 2118
Abstract
Human poly(ADP)-ribose polymerase-1 (PARP1) is a global regulator of various cellular processes, from DNA repair to gene expression. The underlying mechanism of PARP1 action during transcription remains unclear. Herein, we have studied the role of human PARP1 during transcription through nucleosomes by RNA [...] Read more.
Human poly(ADP)-ribose polymerase-1 (PARP1) is a global regulator of various cellular processes, from DNA repair to gene expression. The underlying mechanism of PARP1 action during transcription remains unclear. Herein, we have studied the role of human PARP1 during transcription through nucleosomes by RNA polymerase II (Pol II) in vitro. PARP1 strongly facilitates transcription through mononucleosomes by Pol II and displacement of core histones in the presence of NAD+ during transcription, and its NAD+-dependent catalytic activity is essential for this process. Kinetic analysis suggests that PARP1 facilitates formation of “open” complexes containing nucleosomal DNA partially uncoiled from the octamer and allowing Pol II progression along nucleosomal DNA. Anti-cancer drug and PARP1 catalytic inhibitor olaparib strongly represses PARP1-dependent transcription. The data suggest that the negative charge on protein(s) poly(ADP)-ribosylated by PARP1 interact with positively charged DNA-binding surfaces of histones transiently exposed during transcription, facilitating transcription through chromatin and transcription-dependent histone displacement/exchange. Full article
(This article belongs to the Special Issue State-of-the-Art Biochemistry in USA)
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Review

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13 pages, 1522 KiB  
Review
Solo vs. Chorus: Monomers and Oligomers of Arrestin Proteins
by Vsevolod V. Gurevich and Eugenia V. Gurevich
Int. J. Mol. Sci. 2022, 23(13), 7253; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23137253 - 29 Jun 2022
Cited by 7 | Viewed by 1636
Abstract
Three out of four subtypes of arrestin proteins expressed in mammals self-associate, each forming oligomers of a distinct kind. Monomers and oligomers have different subcellular localization and distinct biological functions. Here we summarize existing evidence regarding arrestin oligomerization and discuss specific functions of [...] Read more.
Three out of four subtypes of arrestin proteins expressed in mammals self-associate, each forming oligomers of a distinct kind. Monomers and oligomers have different subcellular localization and distinct biological functions. Here we summarize existing evidence regarding arrestin oligomerization and discuss specific functions of monomeric and oligomeric forms, although too few of the latter are known. The data on arrestins highlight biological importance of oligomerization of signaling proteins. Distinct modes of oligomerization might be an important contributing factor to the functional differences among highly homologous members of the arrestin protein family. Full article
(This article belongs to the Special Issue State-of-the-Art Biochemistry in USA)
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