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BIOCHEMISTRY Edited by Deniz Ekinci Biochemistry Edited by Deniz Ekinci Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Masa Vidovic Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published March, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Biochemistry, Edited by Deniz Ekinci p. cm. ISBN 978-953-51-0076-8 Contents Preface IX Part 1 Proteins and hormones 1 Chapter 1 Protein Flexibility and Coiled-Coil Propensity: New Insights Into Type III and Other Bacterial Secretion Systems 3 Spyridoula N. Charova, Anastasia D. Gazi, Marianna Kotzabasaki, Panagiotis F. Sarris, Vassiliki E. Fadouloglou, Nickolas J. Panopoulos and Michael Kokkinidis Chapter 2 Peptides and Peptidomimetics as Tools to Probe Protein-Protein Interactions – Disruption of HIV-1 gp41 Fusion Core and Fusion Inhibitor Design 39 Lifeng Cai, Weiguo Shi and Keliang Liu Chapter 3 Profilin, and Vascular Diseases 65 Mohammad T. Elnakish and Hamdy H. Hassanain Chapter 4 E. coli Alpha Hemolysin and Properties 107 Bakás Laura, Maté Sabina, Vazquez Romina and Herlax Vanesa Chapter 5 Human ERα and ERβ Splice Variants: Understanding Their Domain Structure in Relation to Their Biological Roles in Breast Cancer Cell Proliferation 141 Ana M. Sotoca, Jacques Vervoort, Ivonne M.C.M. Rietjens and Jan-Åke Gustafsson Chapter 6 GPCRs and G Protein Activation 161 Waelbroeck Magali Chapter 7 Application of Quantitative Immunogold Electron Microscopy to Determine the Distribution and Relative Expression of Homo- and Heteromeric Purinergic Adenosine A1 and P2Y Receptors 189 Kazunori Namba VI Contents Part 2 Enzymes 203 Chapter 8 Carbonic Anhydrase and Heavy Metals 205 Maria Giulia Lionetto, Roberto Caricato, Maria Elena Giordano, Elisa Erroi and Trifone Schettino Chapter 9 Enzymology of Bacterial Lysine Biosynthesis 225 Con Dogovski, Sarah. C. Atkinson, Sudhir R. Dommaraju, Matthew Downton, Lilian Hor, Stephen Moore, Jason J. Paxman, Martin G. Peverelli, Theresa W. Qiu, Matthias Reumann, Tanzeela Siddiqui, Nicole L. Taylor, John Wagner, Jacinta M. Wubben and Matthew A. Perugini Chapter 10 Enzyme-Mediated Preparation of Flavonoid Esters and Their Applications 263 Jana Viskupicova, Miroslav Ondrejovic and Tibor Maliar Part 3 Metabolism and Mechanism 287 Chapter 11 Glucose Metabolism and Cancer 289 Lei Zheng, Jiangtao Li and Yan Luo Chapter 12 HIV-1 Selectively Integrates Into Host DNA In Vitro 305 Tatsuaki Tsuruyama Chapter 13 Distinct Role for ARNT/HIF-1β in Pancreatic Beta-Cell Function, Insulin Secretion and Type 2 Diabetes 321 Renjitha Pillai and Jamie W. Joseph Chapter 14 Modulation of EAAC1-Mediated Glutamate Uptake by Addicsin 341 Mitsushi J. Ikemoto and Taku Arano Chapter 15 Functional Genomics of Anoxygenic Green Bacteria Chloroflexi Species and Evolution of Photosynthesis 365 Kuo-Hsiang Tang Chapter 16 Mechanism of Cargo Recognition During Selective Autophagy 381 Yasunori Watanabe and Nobuo N. Noda Part 4 Regulatory Molecules 397 Chapter 17 Role of Ceramide 1-Phosphate in the Regulation of Cell Survival and Inflammation 399 Alberto Ouro, Lide Arana, Patricia Gangoiti and Antonio Gomez-Muñoz Contents VII Chapter 18 Cholesterol: Biosynthesis, Functional Diversity, Homeostasis and Regulation by Natural Products 419 J. Thomas, T.P. Shentu and Dev K. Singh Chapter 19 Stobadine – An Indole Type Alternative to the Phenolic Antioxidant Reference Trolox 443 Ivo Juranek, Lucia Rackova and Milan Stefek Preface Biochemistry includes the chemical processes in living systems which govern all living organisms and living processes. It deals with the structures and functions of biomolecules. Over the recent years, biochemistry has become responsible for explaining living processes such that many scientists in the life sciences from agronomy to medicine are engaged in biochemical research. The main focus of biochemistry is in understanding how biomolecules give rise to the chemical processes that occur within living cells. Although extensive research has been performed on biochemistry for many years, there is still deep need of understanding the biochemical reactions as well as the structures of biomolecules. This book titled “Biochemistry” contains a selection of chapters focused on the research area of proteins, enzymes, cellular mechanisms and chemical compounds used in relevant approaches. The book provides an overview on basic issues and some of the recent developments in biochemical science and technology. Particular emphasis is devoted to both theoretical and experimental aspect of modern biochemistry. The primary target audience for the book includes students, researchers, biologists, chemists, chemical engineers and professionals who are interested in biochemistry, molecular biology and associated areas. The textbook is written by international scientists with expertise in protein biochemistry, enzymology, molecular biology and genetics many of which are active in biochemical and biomedical research. I would like to acknowledge the authors for their contribution to the book. We hope that the textbook will enhance the knowledge of scientists in the complexities of some biochemical approaches; it will stimulate both professionals and students to dedicate part of their future research in understanding relevant mechanisms and applications. Dr. Deniz Ekinci Assistant Professor of Biochemistry Ondokuz Mayıs University Turkey