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Chapter One Molecular Modeling and Chemoinformatics to Advance the Development of Modulators of Epigenetic Targets
Publication date: 2016 Source:Advances in Protein Chemistry and Structural Biology, Volume 105 Author(s): F.D. Prieto-Martínez, A. Peña-Castillo, O. Méndez-Lucio, E. Fernández-de Gortari, J.L. Medina-Franco In light of the emerging field of Epi-informatics, ie, computational methods applied to epigenetic research, molecular docking, and dynamics, pharmacophore and activity landscape modeling and QSAR play a key role in the development of modulators of DNA methyltransferases (DNMTs), one of the major epigenetic target families. The increased chemical information available for modulators of DNMTs has opened...
Source: Advances in Protein Chemistry and Structural Biology - August 25, 2016 Category: Biochemistry Source Type: research

Understanding the Multifaceted Role of Human Down Syndrome Kinase DYRK1A
Publication date: Available online 9 August 2016 Source:Advances in Protein Chemistry and Structural Biology Author(s): L.J. Kay, T.K. Smulders-Srinivasan, M. Soundararajan The dual-specificity tyrosine (Y) phosphorylation-regulated kinase DYRK1A, also known as Down syndrome (DS) kinase, is a dosage-dependent signaling kinase that was originally shown to be highly expressed in DS patients as a consequence of trisomy 21. Although this was evident some time ago, it is only in recent investigations that the molecular roles of DYRK1A in a wide range of cellular processes are becoming increasingly apparent. Since init...
Source: Advances in Protein Chemistry and Structural Biology - August 17, 2016 Category: Biochemistry Source Type: research

Cytochromes P450: History, Classes, Catalytic Mechanism, and Industrial Application
Publication date: Available online 9 August 2016 Source:Advances in Protein Chemistry and Structural Biology Author(s): D.J. Cook, J.D. Finnigan, K. Cook, G.W. Black, S.J. Charnock Cytochromes P450, a family of heme-containing monooxygenases that catalyze a diverse range of oxidative reactions, are so-called due to their maximum absorbance at 450nm, ie, “Pigment–450nm,” when bound to carbon monoxide. They have appeal both academically and commercially due to their high degree of regio- and stereoselectivity, for example, in the area of active pharmaceutical ingredient synthesis. Despite this potential, ...
Source: Advances in Protein Chemistry and Structural Biology - August 17, 2016 Category: Biochemistry Source Type: research

Recent Advances in Computational Models for the Study of Protein –Peptide Interactions
Publication date: Available online 3 August 2016 Source:Advances in Protein Chemistry and Structural Biology Author(s): D. Kilburg, E. Gallicchio We review computational models and software tools in current use for the study of protein–peptide interactions. Peptides and peptide derivatives are growing in interest as therapeutic agents to target protein–protein interactions. Protein–protein interactions are pervasive in biological systems and are responsible for the regulation of critical functions within the cell. Mutations or dysregulation of expression can alter the network of interactions among proteins an...
Source: Advances in Protein Chemistry and Structural Biology - August 3, 2016 Category: Biochemistry Source Type: research

Structural Plasticity in Globins: Role of Protein Dynamics in Defining Ligand Migration Pathways
Publication date: Available online 29 July 2016 Source:Advances in Protein Chemistry and Structural Biology Author(s): C. Estarellas, L. Capece, C. Seira, A. Bidon-Chanal, D.A. Estrin, F.J. Luque Globins are a family of proteins characterized by the presence of the heme prosthetic group and involved in variety of biological functions in the cell. Due to their biological relevance and widespread distribution in all kingdoms of life, intense research efforts have been devoted to disclosing the relationships between structural features, protein dynamics, and function. Particular attention has been paid to the ...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2016 Category: Biochemistry Source Type: research

Dynamic Reorganization and Enzymatic Remodeling of Type IV Collagen at Cell –Biomaterial Interface
Publication date: Available online 14 July 2016 Source:Advances in Protein Chemistry and Structural Biology Author(s): N.M. Coelho, V. Llopis-Hernández, M. Salmerón-Sánchez, G. Altankov Vascular basement membrane remodeling involves assembly and degradation of its main constituents, type IV collagen (Col IV) and laminin, which is critical during development, angiogenesis, and tissue repair. Remodeling can also occur at cell–biomaterials interface altering significantly the biocompatibility of implants. Here we describe the fate of adsorbed Col IV in contact with endothelial cells adhering on positively cha...
Source: Advances in Protein Chemistry and Structural Biology - July 24, 2016 Category: Biochemistry Source Type: research

Chapter Two Antitumor Lipids —Structure, Functions, and Medical Applications
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 101 Author(s): Aneliya Kostadinova, Tanya Topouzova-Hristova, Albena Momchilova, Rumiana Tzoneva, Martin R. Berger Cell proliferation and metastasis are considered hallmarks of tumor progression. Therefore, efforts have been made to develop novel anticancer drugs that inhibit both the proliferation and the motility of tumor cells. Synthetic antitumor lipids (ATLs), which are chemically divided into two main classes, comprise (i) alkylphospholipids (APLs) and (ii) alkylphosphocholines (APCs). They represent a new entity ...
Source: Advances in Protein Chemistry and Structural Biology - June 17, 2016 Category: Biochemistry Source Type: research

Chapter Ten Role of von Willebrand Factor —A1 Domain Variants P1266L, H1268D, C1272R, and C1272F in VWD
Publication date: 2016 Source:Advances in Protein Chemistry and Structural Biology, Volume 102 Author(s): C. George Priya Doss, Shabana Kouser Ali von Willebrand disease (VWD) is an autosomal inherited disorder related to trauma-related bleeding in affected people. VWD results from deficiency of von Willebrand factor (VWF)—a glycoprotein involved in hemostasis and carrier for factor VIII (FVIII). Mutations in A1 domain of von Willebrand factor (VWD) gene are exceptionally polymorphic and associated with adhesion movement, clearance, and binding properties that could be interfaced with thrombosis. To address this ...
Source: Advances in Protein Chemistry and Structural Biology - June 17, 2016 Category: Biochemistry Source Type: research

Molecular Modeling and Chemoinformatics to Advance the Development of Modulators of Epigenetic Targets: A Focus on DNA Methyltransferases
Publication date: Available online 14 June 2016 Source:Advances in Protein Chemistry and Structural Biology Author(s): F.D. Prieto-Martínez, A. Peña-Castillo, O. Méndez-Lucio, E. Fernández-de Gortari, J.L. Medina-Franco In light of the emerging field of Epi-informatics, ie, computational methods applied to epigenetic research, molecular docking, and dynamics, pharmacophore and activity landscape modeling and QSAR play a key role in the development of modulators of DNA methyltransferases (DNMTs), one of the major epigenetic target families. The increased chemical information available for modulators of DNM...
Source: Advances in Protein Chemistry and Structural Biology - June 14, 2016 Category: Biochemistry Source Type: research

Chapter Nine Contribution of Automated Technologies to Ion Channel Drug Discovery
Publication date: 2016 Source:Advances in Protein Chemistry and Structural Biology, Volume 104 Author(s): Arturo Picones, Arlet Loza-Huerta, Pedro Segura-Chama, Cesar O. Lara-Figueroa Automated technologies are now resolving the historical relegation that ion channels have endured as targets for the new drug discovery and development global efforts. The richness and adequacy of functional assay methodologies, remarkably fluorescence-based detection of ions fluxes and patch-clamp electrophysiology recording of ionic currents, are now automated and increasingly employed for the analysis of ion channel activity. W...
Source: Advances in Protein Chemistry and Structural Biology - March 31, 2016 Category: Biochemistry Source Type: research

Chapter Eight Targeting the Channel Activity of Viroporins
Publication date: 2016 Source:Advances in Protein Chemistry and Structural Biology, Volume 104 Author(s): Janet To, Wahyu Surya, Jaume Torres Since the discovery that certain small viral membrane proteins, collectively termed as viroporins, can permeabilize host cellular membranes and also behave as ion channels, attempts have been made to link this feature to specific biological roles. In parallel, most viroporins identified so far are virulence factors, and interest has focused toward the discovery of channel inhibitors that would have a therapeutic effect, or be used as research tools to understand the biologi...
Source: Advances in Protein Chemistry and Structural Biology - March 31, 2016 Category: Biochemistry Source Type: research

Chapter Seven The Modulation of Potassium Channels in the Smooth Muscle as a Therapeutic Strategy for Disorders of the Gastrointestinal Tract
Publication date: 2016 Source:Advances in Protein Chemistry and Structural Biology, Volume 104 Author(s): Diego Currò Alterations of smooth muscle contractility contribute to the pathophysiology of important functional gastrointestinal disorders (FGIDs) such as functional dyspepsia and irritable bowel syndrome. Consequently, drugs that decrease smooth muscle contractility are effective treatments for these diseases. Smooth muscle contraction is mainly triggered by Ca2+ influx through voltage-dependent channels located in the plasma membrane. Thus, the modulation of the membrane potential results in the regulation of...
Source: Advances in Protein Chemistry and Structural Biology - March 31, 2016 Category: Biochemistry Source Type: research

Chapter Six Calcium-Activated Potassium Channels
Publication date: 2016 Source:Advances in Protein Chemistry and Structural Biology, Volume 104 Author(s): De-Li Dong, Yun-Long Bai, Ben-Zhi Cai Ca2+-activated K+ channels (KCa) are classified into three subtypes: big conductance (BKCa), intermediate conductance (IKCa), and small conductance (SKCa) KCa channels. The three types of KCa channels have distinct physiological or pathological functions in cardiovascular system. BKCa channels are mainly expressed in vascular smooth muscle cells (VSMCs) and inner mitochondrial membrane of cardiomyocytes, activation of BKCa channels in these locations results in vasodilati...
Source: Advances in Protein Chemistry and Structural Biology - March 31, 2016 Category: Biochemistry Source Type: research

Chapter Five Ion Channels in the Eye
Publication date: 2016 Source:Advances in Protein Chemistry and Structural Biology, Volume 104 Author(s): Jonathan P. Giblin, Nuria Comes, Olaf Strauss, Xavier Gasull The eye is the sensory organ of vision. There, the retina transforms photons into electrical signals that are sent to higher brain areas to produce visual sensations. In the light path to the retina, different types of cells and tissues are involved in maintaining the transparency of avascular structures like the cornea or lens, while others, like the retinal pigment epithelium, have a critical role in the maintenance of photoreceptor function by ...
Source: Advances in Protein Chemistry and Structural Biology - March 31, 2016 Category: Biochemistry Source Type: research

Chapter Four TRPM8 Ion Channels as Potential Cancer Biomarker and Target in Pancreatic Cancer
This article provides a review and discussion of the transient receptor potential melastatin-subfamily member 8 (TRPM8) ion channel as a potential biomarker and target in cancer. TRPM8 is a Ca2+-permeable channel that plays a major physiological role in cellular sensation and transduction of cold temperature. TRPM8 is aberrantly expressed in a variety of solid tumors including pancreatic cancer. In pancreatic adenocarcinoma cell lines and tissues, TRPM8 is overexpressed as compared to normal pancreatic ductal epithelia. Analysis of anti-TRPM8 immunoreactivity in pancreatic adenocarcinoma indicates positive correlation of T...
Source: Advances in Protein Chemistry and Structural Biology - March 31, 2016 Category: Biochemistry Source Type: research