Monday, October 24, 2016


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


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



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.


Current Protein & Peptide Science publishes review articles on specific aspects involving proteins, peptides, and interactions between the enzymes, the binding interactions of hormones and their receptors; the properties of transcription factors and other molecules that regulate gene expression; the reactions leading to the immune response; the process of signal transduction; the structure and function of proteins involved in the cytoskeleton and molecular motors; the properties of membrane channels and transporters; and the generation and storage of metabolic energy. In addition, reviews of experimental studies of protein folding and design are given special emphasis. Manuscripts submitted to Current Protein and Peptide Science should cover a field by discussing research from the leading laboratories in a field and should pose questions for future studies. Original papers, research articles and letter articles/short communications are not considered for publication in Current Protein & Peptide Science.
NEW ISSUE 3

Articles from the journal in Current Protein & Peptide Science, Volume 17 Issue 2:

  • Editorial (Thematic Issue: Chemistry Towards Biology: Proceedings of the Katowice Conference)
  • Reactions of Dinuclear Platinum(II) Complexes with Peptides
  • On Spontaneously Pulsating Proline-Phenylalanine Peptide Microfibers
  • Cellulose Template Assembled Synthetic Peptides as Molecular Receptors
  • Advances in Peptide-based DNA/RNA-Intercalators
  • Advances in peptidic and peptidomimetic-based approaches to inhibit STAT signaling in human diseases
  • Bacterial expression and/or solid phase peptide synthesis of 20-40 amino acid long polypeptides and miniproteins, the case study of Class B GPCR ligands
  • Pentameric models as alternative molecular targets for the design of new antiaggregant agents
  • Protein Folding and Misfolding, Endoplasmic Reticulum Stress in Neurodegenerative Diseases: in Trace of Novel Drug Targets
  • Characterization of a Bacteriophage-Derived Murein Peptidase for Elimination of Antibiotic-Resistant Staphylococcus aureus
  • Rescue of the activity of HNH nuclease mutants – towards controlled enzymes for gene therapy
  • Analysis of Aged Human Serum Albumin Affinity for Doxazosin

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Current Protein & Peptide Science publishes review articles on specific aspects involving proteins, peptides, and interactions between the enzymes, the binding interactions of hormones and their receptors; the properties of transcription factors and other molecules that regulate gene expression; the reactions leading to the immune response; the process of signal transduction; the structure and function of proteins involved in the cytoskeleton and molecular motors; the properties of membrane channels and transporters; and the generation and storage of metabolic energy. In addition, reviews of experimental studies of protein folding and design are given special emphasis. Manuscripts submitted to Current Protein and Peptide Science should cover a field by discussing research from the leading laboratories in a field and should pose questions for future studies. Original papers, research articles and letter articles/short communications are not considered for publication in Current Protein & Peptide Science.
Current Impact Facter : 3.154
Ranking and Category:
  • 113th of 289 in Biochemistry & Molecular Biology
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Current Protein & Peptide Science publishes review articles on specific aspects involving proteins, peptides, and interactions between the enzymes, the binding interactions of hormones and their receptors; the properties of transcription factors and other molecules that regulate gene expression; the reactions leading to the immune response; the process of signal transduction; the structure and function of proteins involved in the cytoskeleton and molecular motors; the properties of membrane channels and transporters; and the generation and storage of metabolic energy. In addition, reviews of experimental studies of protein folding and design are given special emphasis. Manuscripts submitted to Current Protein and Peptide Science should cover a field by discussing research from the leading laboratories in a field and should pose questions for future studies. Original papers, research articles and letter articles/short communications are not considered for publication in Current Protein & Peptide Science.
Following are the articles from the journal Current Protein & Peptide Science, 16 Issue 6:
Article: Commentary: Drugs From Bugs
Author(s): Laszlo Otvos

Article: Integrase Interactor 1 in Health and Disease
Author(s): Supratik Das

Article: ADP-Ribosyltransferases and Poly ADP-Ribosylation
Author(s): Chao Liu and Xiaochun Yu

Article: The Aromatic Stacking Interactions Between Proteins and their Macromolecular Ligands
Author(s): Mohammad Mizanur Rahman, Ziyad Tariq Muhseen, Muhammad Junaid and Houjin Zhang

Article: Reshaping the Protein Folding Pathway by Osmolyte via its Effects on the Folding Intermediates
Author(s): Gurumayum Suraj Sharma, Tanveer Ali Dar and Laishram Rajendrakumar Singh

Article: The Role of Structural Flexibility and Stability in the Interaction of Serine Proteases with their Inhibitors
Author(s): Laszlo Graf, Tamas Molnar, Jozsef Kardos, Zoltan Gaspari and Gergely Katona

Article: Disintegrins from Snake Venoms and their Applications in Cancer Research and Therapy
Author(s): Jessica Kele Arruda Macedo, Jay W. Fox and Mariana de Souza Castro

Article: The Sactibiotic Subclass of Bacteriocins: An Update
Author(s): Harsh Mathur, Mary C. Rea, Paul D. Cotter, Colin Hill and R. Paul Ross

Article: Targeting EZH2 for Cancer Therapy: Progress and Perspective
Author(s): Chi Han Li and Yangchao Chen

Article: Erratum: The Polymorphic Nature of Membrane-Active Peptides from Biophysical and Structural Investigations
Author(s): Burkhard Bechinger and Christopher Aisenbrey

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