Wednesday, November 30, 2016

Highlighted Article: Enantioselective Phytotoxicity and the Relative Mechanism of Current Chiral Herbicides

Thursday, November 24, 2016

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Tuesday, November 8, 2016

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Wednesday, November 2, 2016

Highlighted Article: Plant PARPs, PARGs and PARP-like Proteins



Plant PARPs, PARGs and PARP-like Proteins



Author(s):

Julia P. Vainonen, Alexey Shapiguzov, Aleksia Vaattovaara and Jaakko Kangasjärvi   Pages 713 - 723 ( 11 )

Abstract:


Poly(ADP-ribos)ylation, originally described as a mechanism of DNA break repair, is now considered as part of a complex regulatory system involved in dynamic reorganization of chromatin structure, transcriptional control of gene expression and regulation of metabolism. In plants poly(ADPribos) ylation has received surprisingly little attention. It has been implicated in abiotic and biotic stress responses, cell cycle control and development; however, the molecular mechanisms and proteins involved are largely unknown. In this review we summarize current knowledge on plant PARP, PARG and PARP-like domain containing proteins and discuss their possible roles in plant development, immune responses, programmed cell death and stress responses in general. The genome of the model plant Arabidopsis contains three genes encoding PARP proteins, two of which have been shown to be active PARPs, and two genes encoding PARG proteins, one of which was shown to possess enzymatic activity. In addition, SROs (Similar to RCD One) represent a plant specific family of proteins containing a PARP-like domain. Although bioinformatics and biochemical data suggest that the PARP-like domain in SRO proteins does not have PARP activity, these proteins play a significant role in stress response as revealed by mutant analyses. SRO proteins interact with transcription factors involved in various stress and developmental responses and are suggested to serve as hubs in many signaling pathways. Altogether current data imply that poly(ADP-ribos)ylation plays significant regulatory role in many aspects of plant biology.

Keywords:

poly(ADP-ribos)ylation, PARP, PARG, SRO, RCD1, Arabidopsis thaliana, transcriptional regulation.

Affiliation:

Division of Plant Biology, Viikki Plant Science Centre, Department of Biosciences, University of Helsinki, POB 65 (Viikinkaari 1), FI-00014 Helsinki Finland.

Graphical Abstract:




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Monday, October 24, 2016

Most Cited Article: Amino Acid Network for the Discrimination of Native Protein Structures from Decoys


Amino Acid Network for the Discrimination of Native Protein Structures from Decoys


 Author(s):
Jianhong Zhou, Wenying Yan, Guang Hu and Bairong ShenPages 522-528 (7)
Abstract:

With the development of structural genomics projects, the discrimination of native proteins from decoys has become one of the major challenges in protein structure prediction. In comparison with the energy function based techniques, amino acid network provides a simple but efficient method for the native structure selection. Amino acid network (AAN) is a graph representation of protein structure where amino acids in the protein are the nodes and their interactions or contacts are the edges. In this review, we first briefly summarized the methods for the construction and characterization of AANs. Then the four network properties, i.e. average degree, complexity, clustering coefficient of the largest cluster (CCoe) and the size of the top large communities (CComS), applied to the native structure selection are discussed and summarized. We concluded with the discussion of the future perspective on the application of AAN for the native folding detecting among the decoy sets.
Keywords:
Amino acid network, network characterization, protein decoy discrimination.
Affiliation:
Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China.






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Tuesday, October 18, 2016

The Melanocortin Receptor System: A Target for Multiple Degenerative Diseases


Article Details

The Melanocortin Receptor System: A Target for Multiple Degenerative Diseases
[ Vol. 17 , Issue. 5 ]

 Author(s):
Minying Cai and Victor J. HrubyPages 488-496 (9)
Abstract:

The melanocortin receptor system consists of five closely related G-protein coupled receptors (MC1R, MC2R, MC3R, MC4R and MC5R). These receptors are involved in many of the key biological functions for multicellular animals, including human beings. The natural agonist ligands for these receptors are derived by processing of a primordial animal gene product, proopiomelanocortin (POMC). The ligand for the MC2R is ACTH (Adrenal Corticotropic Hormone), a larger processed peptide from POMC. The natural ligands for the other 4 melanocortin receptors are smaller peptides including α-melanocyte stimulating hormone (α-MSH) and related peptides from POMC (β-MSH and γ-MSH). They all contain the sequence His-Phe-Arg-Trp that is conserved throughout evolution. Thus, there has been considerable difficulty in developing highly selective ligands for the MC1R, MC3R, MC4R and MC5R. In this brief review, we discuss the various approaches that have been taken to design agonist and antagonist analogues and derivatives of the POMC peptides that are selective for the MC1R, MC3R, MC4R and MC5R receptors, via peptide, nonpeptide and peptidomimetic derivatives and analogues and their differential interactions with receptors that may help account for these selectivities.
Keywords:
Melanocortin Receptors (MCRs: MC1R, MC2R, MC3R, MC4R, MC5R); α-MSH: α -melanocyte stimulate hormone; POMC: Proopiomelanocortin; ACTH: adrenal corticotropic hormone; GPCRs: G-protein coupled receptors; ASIP: agouti signaling protein; AGRP: agouti related protein; MTI: Ac-Ser-Tyr-Ser-Met-Glu-His-DPhe-Arg-Trp-Gly-Lys-Pro-Val- NH2; MT-II: Ac-Nle4-c[Asp5, D-Phe7, Lys10]α-MSH(4-10)-NH2, (Ac-Nle-c[Asp-His-DPhe-Arg-Trp-Lys]-NH2). SHU9119: Ac- Nle4-c[Asp5, D-Nal(2’)7, Lys10]α-MSH(4-10)-NH2, (Ac-Nle-c[Asp-His- D-Nal(2’)-Arg-Trp-Lys]-NH2).
Affiliation:
Department of Chemistry & Biochemistry, University of Arizona, 1306 E. University Blvd, Tucson, AZ 85721, USA.
Graphical Abstract:



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Tuesday, October 4, 2016

Major Article Contributions by some of the Japanese Authors of Bentham Science Publishers Journal; Current Protein & Peptide Science



Journal Title: Current Protein & Peptide Science

Article Title: Exploring New CGRP Family Peptides and their Receptors in Vertebrates

Author(s): Yoshio Takei, Maho Ogoshi and Shigenori Nobata
Abstract:
Vertebrates have expanded their habitats from aquatic to terrestrial environments, which has accompanied the evolution of cardiovascular and osmoregulatory hormones. Specifically, mammals have developed mechanisms to maintain high blood pressure and blood volume, while extant fishes have developed hypotensive and Na-extruding mechanisms to adapt to the marine environment where they underwent a vast diversification. The CGRP family is one of the hormone systems that decrease blood pressure and blood volume. Within the CGRP family of teleost fishes, we found that adrenomedullins (AMs) have diversified and five paralogs (AM1-5) form an independent subfamily. Based on this discovery in fishes, we found AM2 and AM5 in mammals. In mammalian species that have AM2 and/or AM5, the peptides assume greater importance in the case of pathophysiological disturbances in pressure and fluid balance such as hypertension and cardiac and renal failure. In addition, novel functions of AM peptides have been suggested by the discovery of AM2 and AM5 in mammals. Current research on the CGRP family is focused on the identification of new receptors for AM2/AM5 and the establishment of AM2 knockout mice, which will enable new developments in the basic and clinical research on this intriguing hormone family. Importantly, comparative fish studies can contribute to new developments in our understanding of the function of the AM peptides.
Article Title: Functions of Third Extracellular Loop and Helix 8 of Family B GPCRs Complexed with RAMPs and Characteristics of their Receptor Trafficking
Author(s): Kenji Kuwasako, Debbie L Hay, Sayaka Nagata, Manabu Murakami, Kazuo Kitamura and Johji Kato

Abstract:

At least one of three receptor activity-modifying proteins (RAMP1, RAMP2 and RAMP3) can interact with 10 G protein-coupled receptors (GPCRs; nine Family B GPCRs and a Family C GPCR). All three RAMPs interact with the calcitonin (CT) receptor (CTR), the CTR-like receptor (CLR), the vasoactive intestinal peptide (VIP)/pituitary adenylate cyclase-activating polypeptide (PACAP) 1 (VPAC1) and the VPAC2 receptor, which are all Family B GPCRs. Three RAMPs enable CTR to function as three heterodimeric receptors for amylin, which is a feeding suppression peptide. These RAMPs also transport the CLR to the cell surface, where they function as a CT gene-related peptide (CGRP) receptor (CLR/RAMP1 heterodimer) and two adrenomedullin (AM) receptors (CLR/RAMP2 and CLR/RAMP3 heterodimers). CGRP and AM are potent hypotensive peptides that exert powerful protective effects against multi-organ damage. We recently reported that the third extracellular loop (ECL3) of CLR governs the activation of AM, but not CGRP, signaling in the three CLR/RAMP heterodimers. Furthermore, we showed that in the presence of RAMP2, the eighth helix (helix 8) in the proximal portion of the cytoplasmic C-terminal tail of the CLR, which is thought to be present in all family B GPCRs, participates in receptor signaling. In addition, we demonstrated that overexpression of GPCR kinase (GRK) 2, GRK3 and GRK4 enhances the AM-induced internalization of the CLR/RAMP2 heterodimer. In this review, we describe these studies and consider their implications for other Family B GPCRs that can interact with RAMPs.

Article Title: Adrenomedullin as a Potential Therapeutic Agent for Inflammatory Bowel Disease
Author(s): Shinya Ashizuka, Haruhiko Inatsu, Kyoko Inagaki-Ohara, Toshihiro Kita and Kazuo Kitamura
Abstract:
Adrenomedullin (AM) was originally isolated from human pheochromocytoma as a biologically active peptide with potent vasodilating action but is now known to exert a wide range of physiological effects, including cardiovascular protection, neovascularization, and apoptosis suppression. A variety of tissues, including the gastrointestinal tract, have been shown to constitutively produce AM. Pro-inflammatory cytokines, such as tumor necrosis factor-α and interleukin-1, and lipopolysaccharides, induce the production and secretion of AM. Conversely, AM induces the downregulation of inflammatory cytokines in cultured cells. Furthermore, AM downregulates inflammatory processes in a variety of different colitis models, including acetic acid-induced colitis and dextran sulfate sodium-induced colitis. AM exerts antiinflammatory and antibacterial effects and stimulates mucosal regeneration for the maintenance of the colonic epithelial barrier. Here, we describe the first use of AM to treat patients with refractory ulcerative colitis. The results strongly suggest that AM has potential as a new therapeutic agent for the treatment of refractory ulcerative colitis.
Article Title: Ectodomain Structures of the CGRP and AM Receptors
Author(s): Seisuke Kusano and Shigeyuki Yokoyama

Abstract:

Receptor activity-modifying proteins (RAMPs) 1–3, which are classified as type I transmembrane proteins, serve as the partner proteins of several family B GPCRs for physiologically active peptides, including the calcitonin receptor- like receptor (CLR). The properties of the GPCRs are defined by the RAMP and peptide ligand combination. The CLR•RAMP1 heterodimer functions mainly as the calcitonin gene-related peptide (CGRP) receptor, while the CLR•RAMP2 and CLR•RAMP3 heterodimers primarily function as the adrenomedullin 1 and adrenomedullin 2 (AM1 and AM2) receptors, respectively. The crystal structures of the RAMP1 and RAMP2 ectodomains exhibited three-helix bundles, and those of their complexes with the N-terminal extracellular domain of CLR revealed how the two ectodomains associate to form the CGRP and AM1 receptors, respectively. On this structural framework, the various intermolecular interactions of CLR with RAMP1 and RAMP2 result in the distinct shapes of the putative ligand-binding sites, where several residues are uniquely presented. Therefore, the differences in the shapes and the presented residues of the binding sites determine the specificities of the receptors to either CGRP or AM. These structural features of the ectodomains are consistent with mutagenesis results, and are useful to further examine the binding modes of the peptide ligands to the full-length CGRP and AM1 receptors.
Article Title: Insulin Resistance-Induced Hypertension and a Role of Perivascular CGRPergic Nerves
Author(s): Shingo Takatori, Yoshito Zamami, Narumi Hashikawa-Hobara and Hiromu Kawasaki

Abstract:

Insulin resistance is defined as a preliminary step of type 2 diabetes mellitus with decreased insulin action evoked by continuous postprandial hyperglycemia, which is provoked by high fat and calories dieting, a lack of physical activity and obesity. In the early phase of type 2 diabetes mellitus, patients have a hyperinsulinemia to compensate deficient insulin action by increased secretion from the pancreas to maintain euglycemia. Then, pancreatic β cells progressively decrease secretion function, resulting in the development of diabetes mellitus with decreased serum insulin levels. Accumulating evidences show that insulin resistance is associated with hypertension. However, the mechanisms underlying hypertension associated with type 2 diabetes mellitus have still unknown. Therefore, to elucidate the mechanisms of insulin resistance-induced hypertension, we investigated that the effects of hyperinsulinemia or hyperglycemia on vascular responses mediated by perivascular nerves including sympathetic adrenergic nerves and calcitonin gene-related peptide (CGRP)-containing nerves (CGRPergic nerves). In this article, we show evidence that insulin resistance-induced hypertension could be resulted from increased density and function of sympathetic nerve, and decreased density and function of CGRPergic nerves. Furthermore, our findings provide a new insight into the research of therapeutic drugs for insulin resistance- induced hypertension.
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