Advances in Protein and Peptide Sciences

Volume 1

by

Ben M. Dunn

DOI: 10.2174/97816080548791130101
eISBN: 978-1-60805-487-9, 2013
ISBN: 978-1-60805-631-6
ISSN: 2213-9869

  
  




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Table of Contents

Foreword , Pp. i-ii (2)

Vladimir Uversky
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Preface , Pp. iii-v (3)

Ben M. Dunn
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List of Contributors , Pp. vi-xii (7)

Ben M. Dunn
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Linking New Paradigms in Protein Chemistry to Reversible Membrane-Protein Interactions , Pp. 3-57 (55)

Øyvind Halskau, Arturo Muga and Aurora Martínez
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β-Barrel Membrane Bacterial Proteins: Structure, Function, Assembly and Interaction with Lipids , Pp. 58-127 (70)

Stefania Galdiero, Marco Cantisani, Annarita Falanga, Maria T. Vitiello and Massimiliano Galdiero
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NMR of Membrane Proteins , Pp. 128-188 (61)

Guangshun Wang
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Activation, Exposure and Penetration of Virally Encoded, Membrane-Active Polypeptides During Non enveloped Virus Entry , Pp. 189-221 (33)

Manidipa Banerjee and John E. Johnson
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The Role of Pest Degron for Targeting Caspases Substrates to the Ubiquitin-Proteasome System , Pp. 222-255 (34)

José E. Belizario, Juliano Alves, Miguel Garay-Malpartida and João M. Occhiucci
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Cytokine-Regulated Protein Degradation by the Ubiquitination System , Pp. 256-271 (16)

Kwang-Hyun Baek
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Natural Proteasome Inhibitors for Battling Cancer , Pp. 272-308 (37)

Huanjie Yang, Kristin R. Landis-Piwowar, Di Chen, Vesna Milacic and Q. Ping Dou
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Proteins as Netwoks: Usefulness of Graph Theory in Protein Science , Pp. 309-317 (9)

Alessandro Giuliani, Luisa Di Paola, Paola Paci, Micol De Ruvo, Caterina Arcangeli, Daniele Santoni and Massimo Celino
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Computer Simulations of Biomolecules in Non-Aqueous and Semi-Aqueous Solvent Conditions , Pp. 318-381 (64)

Danilo Roccatano
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Methods for Calculating the Entropy and Free Energy of Biological Systems , Pp. 382-440 (59)

Hagai Meirovitch
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Predicting Protein Disorder and Induced Folding: A Practical Approach , Pp. 441-492 (52)

Philippe Lieutaud, François Ferron, Johnny Habchi, Bruno Canard and Sonia Longhi
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The Importance of Being Flexible: The Case of Basic Region Leucine Zipper Transcriptional Regulators , Pp. 493-558 (66)

Maria Miller
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The Acute Phase Protein α1-Acid Glycoprotein: A Model for Altered Glycosylation During Diseases. Updates and New Perspectives , Pp. 559-614 (56)

Fabrizio Ceciliani, Laura Restelli and Cristina Lecchi
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Immunology of MUC1 and Advancements in the Development of MUC1 Glycopeptide Tumor Vaccines: An Update , Pp. 615-636 (22)

Franz-Georg Hanisch
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Rooteomics: The Challenge of Discovering Defense-Related Proteins in Plants-An Update , Pp. 637-663 (27)

Angela Mehta, Beatriz S. Magalhães, Djair S.L. Souza, Erico A.R. Vasconcelos, Luciano P. Silva, Maria F. Grossi-de-Sa, Octávio L. Franco and Thales L. Rocha
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The Classic Basic Protein of Myelin–Conserved Structural Motifs and the Dynamic Molecular Barcode Involved in Membrane Adhesion, Protein-Protein Interactions, and Pathogenesis in Multiple Sclerosis , Pp. 664-716 (53)

George Harauz, David S. Libich, Eugenia Polverini and Kenrick A. Vassall
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The Allosteric Properties of Hemoglobin: Insights from Natural and Site Directed Mutants , Pp. 717-791 (75)

Andrea Bellelli, Maurizio Brunori, Adriana E. Miele, Gianna Panetta and Beatrice Vallone
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Extra-Cellular Proteins are Key Elements of a Global Molecular Network Enmeshing the Whole Central Nervous System: Physiological and Pathological Implications , Pp. 792-832 (41)

Guidolin Diego, Guescini Michele, Stocchi Vilberto, Genedani Susanna, Fuxe Kjell and Agnati L. Francesco
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Glycoprotein Targeting and Other Applications of Lectins in Biotechnology , Pp. 833-876 (44)

Aabgeena Naeem, M. Saleemuddin and Rizwan H. Khan
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Index , Pp. 868-891 (24)

Ben M. Dunn
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Foreword

Proteins are among the most critical building blocks of life. Virtually all processes taking place in a living cell are controlled, regulated, and executed by proteins. Biological roles and activities of proteins are extremely diverse, ranging from recognition, to binding, to catalysis, to various structural roles, to entropic functions, and to mechanical activities. In their functional endeavor, proteins can act alone or in complexes with other proteins, peptides, nucleic acids, membranes, various small molecules, and ions. Structurally too, proteins are very divergent and can be broadly classified as globular, membrane, fibrous, intrinsically disordered, and various hybrids of these four major groups. There is typically a great agreement between how protein looks like and what it can do. In other words, shapes, properties, and structures of proteins are tuned by evolution to be optimal for specific functions executed under specific conditions. On the other hand, mutations, dysfunction and mis regulation of proteins are commonly associated with the pathogenesis of various diseases.

For more than a century, proteins continue to be a fascinating subject of intensive scientific research. Numerous experimental and computational approaches are developed over the years for structural and functional characterization of these important biological molecules. Not surprisingly, protein-related literature is vast. In fact, in PubMed, there are more than 5,327,000 entries containing term “protein”. Research articles and reviews about various protein-related aspects are regularly published in general and specialized journals. Furthermore, hundreds of books and dozens of book series are dedicated to various aspects of protein research. With so many important topics to cover, there is a constant need for new books that traditionally represent a way of systematizing the existing knowledge.

The book edited by Prof. Ben Dunn features papers from a number of authors of manuscript originally published in Current Protein and Peptide Science. Papers for this volume were selected based on the number of citations that the original articles received. The papers were thoroughly updated with new information and references that have appeared since the date of original publication. This approach generated a unique slice through modern protein science, and the resulting volume covers a broad variety of topics ranging from focused look at membrane proteins, to systematic analysis of the roles of protein degradation in various diseases, to consideration of novel computational and theoretical approaches for protein analysis with some focus on intrinsically disordered proteins, to implication of proteins and pathogenesis of various diseases, to protein implementations in biotechnology. The volume would be particularly useful to basic investigators, applied scientists and clinicians interested in the latest advances in this exciting field.

Vladimir Uversky
College of Medicine Molecular Medicine
University of South Florida
USA


Preface

Progress in understanding the chemistry, biochemistry, and biological function of proteins and peptides continues to accelerate driven by many scientists utilizing new tools. This book collects together 19 contributions from authors around the world who are making seminal discoveries in this field.

The authors have all written for Current Protein and Peptide Science, a Bentham Science publication featuring only review papers. Based on citation data over several years, the authors whose papers received the highest number of citations (typically over 100) were asked to submit revised and updated versions of their work. The papers in this eBook are the result of that effort. All were extensively edited to ensure optimal quality. The book is divided into four sections to highlight current research in these areas: Membrane Proteins, Protein Lifetimes and Disease; Computational Methods; and Proteins in Disease and Biotechnology. Future editions of this eBook will highlight other emerging developments in the field of protein and peptide chemistry and biology.

Section I on Membrane Proteins contains four papers: the first, from Martinez and colleagues, considers different thermodynamic states of proteins to account for how a normally water-soluble protein can be membrane-associated. The second manuscript from Galdiero and associates describes in detail the ß-barrel proteins that interact with the outer membrane of gram-negative bacteria and their interactions with lipids. Guangshun Wang discusses the use of NMR to characterize membrane proteins that cannot be crystallized by normal methods, thus extending the scope of structural studies of membrane proteins. Banerjee and Johnson describe in the fourth paper of this section the complicated process by which non-enveloped viruses gain entry into host cells, again involving interactions with cellular membranes.

Section 2 of the book contains three papers dealing with degradation in the proteosome. In the first, Belizario and colleagues describe the process of protein degradation that targets the PEST sequences; i.e., amino acid sequences rich in Proline, Glutamic Acid, Aspartic Acid, Serine or Threonine. In the next paper, Baek considers the ubiquitin-mediated protein degradation process and focuses on the de-ubiquinating enzymes as important control elements in the overall process. Dou and associates describe a variety of inhibitors of proteosomal degradation in an effort to find compounds that will affect cancer cells more than normal human cells.

Section 3 of the book presents five papers that all deal with reviews of computational methods for the analysis of the properties of proteins. These useful contributions begin with a paper from Giuliani and colleagues describing the use of Graph Theory to deal with the growing appreciation of networks of protein interactions. The second contribution examines protein in non-aqueous and semi-aqueous environments and shows the utility of molecular dynamics analyses in these studies. Next, Meirovitch presents a discussion of the calculation of free energy and entropy of proteins with attention to the various sub-states of conformation that proteins experience. Sonia Longhi and colleagues describe the importance of intrinsic protein disorder and discuss methods to predict regions that will display this behavior. In the final paper of this section, Maria Miller continues the discussion of intrinsic flexibility of proteins and focuses on the important area of transcription factors that must bind to regions of DNA.

Section 4 of the book considers proteins in disease states and in biotechnology. This section begins with a paper from Ceciliani and associates on ?1-Acid Glycoprotein and its changes during altered health in humans, particularly with respect to glycosylation. The epithelial type 1 transmembrane mucin MUC1 and its glycosylation states are described by Hanisch in the next contribution. Franco and colleagues describe progress in solving problems associated with identification of proteins from plants that might play a role in host defense against invading organisms in the following paper. The important protein myelin and its association with membranes, other proteins, and its role in the pathogensis of multiple sclerosis are covered in the contribution from Harauz and colleagues. Hemoglobin has provided much insight into protein structure and function and Bellelli and associates describe the allosteric properties of this molecule based on natural and site-directed mutagenesis. Agnati and colleagues describe the important roles of a number of proteins for central nervous system function in both normal and pathological states. Finally, Khan and his colleagues discuss the use of lectins for many applications in biotechnology.

It was a pleasure to work with all the authors of these papers to bring this eBook together and I look forward to future opportunities to develop new editions/volumes of this work.

Ben M. Dunn
Department of Biochemistry and Molecular Biology
University of Florida
College of Medicine
USA

List of Contributors

Editor(s):
Ben M. Dunn
University of Florida
USA




Contributor(s):
Aabgeena Naeem
Interdisciplinary Biotechnology Unit
Aligarh Muslim University
India


Adriana E. Miele
Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”
Università degli Studi di Roma “La Sapienza”
Italy


Agnati L. Francesco
IRCCS San Camillo Lido
Italy


Alessandro Giuliani
Department of Environment and Health
Istituto Superiore di Sanità
00161 Rome
Italy


Andrea Bellelli
Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”
Università degli Studi di Roma “La Sapienza”
Italy


Angela Mehta
Embrapa Recursos Genéticos e Biotecnologia
Brazil


Annarita Falanga
Department of Pharmacy
University of Naples “Federico II”
Istituto di Biostrutture e Bioimmagini
CNR, Via Mezzocannone 16, 80134
Naples
Italy


Arturo Muga
Biophysics Unit (CSIC/UPV-EHU)
Department of Biochemistry and Molecular Biology
University of Basque Country (UPV-EHU)
48080 Bilbao
Spain


Aurora Martínez
Department of Biomedicine
Department of BiomedicineUniversity of Bergen
Jonas Lies vei 91
5009 Bergen
Norway


Beatrice Vallone
Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”
Università degli Studi di Roma “La Sapienza”
Italy


Beatriz S. Magalhães
Embrapa Recursos Genéticos e Biotecnologia
Brazil


Bruno Canard
Architecture et Fonction des Macromolécules Biologiques
UMR 7257 CNRS and Aix-Marseille Université
163 Avenue de Luminy
France


Caterina Arcangeli
Ente per le Nuove Tecnologie
l’Energia e l’Ambiente
Italy


Cristina Lecchi
Department of Veterinary Sciences and Public Health
University of Milan
Italy


Daniele Santoni
CNR-Institute of Systems Analysis
Computer Science (IASI)
Italy


Danilo Roccatano
Jacobs University Bremen
Campus Ring 1
Germany


David S. Libich
Department of Molecular and Cellular Biology
Biophysics Interdepartmental Group
and Collaborative Program in Neuroscience
University of Guelph
Canada


Di Chen
Barbara Ann Karmanos Cancer Institute
and Departments of Oncology
Pharmacology and Pathology
School of Medicine
Wayne State University
USA


Djair S. L. Souza
Departamento de Ciências Animais
Universidade Federal Rural do Semi-Árido
Brazil


Erico A. R. Vasconcelos
Embrapa Recursos Genéticos e Biotecnologia
Brazil


Eugenia Polverini
Department of Physics
University of Parma
Italy


Fabrizio Ceciliani
Department of Veterinary Sciences and Public Health
University of Milan
Italy


François Ferron
Architecture et Fonction des Macromolécules Biologiques
UMR 7257 CNRS and Aix-Marseille Université
163 Avenue de Luminy
France


Franz-Georg Hanisch
Institute of Biochemistry II
Medical Faculty, and Center of Molecular Medicine Cologne
University of Cologne
Germany


Fuxe Kjell
Department of Neuroscience
Karolinska Institutet
Stockholm
Sweden


Genedani Susanna
Department Biomedical Sciences
University of Modena and Reggio Emilia
Modena
Italy


George Harauz
Department of Molecular and Cellular Biology
Biophysics Interdepartmental Group
Collaborative Program in Neuroscience
University of Guelph
Canada


Gianna Panetta
Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”
Università degli Studi di Roma “La Sapienza”
Italy


Guangshun Wang
Department of Microbiology and Pathology
College of Medicine
University of Nebraska Medical Center
NE 68198-6495
USA


Guescini Michele
Department of Biomolecular Sciences
University of Urbino “Carlo Bo”
Italy


Guidolin Diego
Department of Human Anatomy and Physiology
University of Padova
Padova
Italy


Hagai Meirovitch
Department of Physics
Bar Ilan University
Israel


Huanjie Yang
Barbara Ann Karmanos Cancer Institute
and Departments of Oncology
Pharmacology and Pathology
School of Medicine
Wayne State University
USA


João M. Occhiucci
Department of Pharmacology
Biomedical Science Institute
University of Sao Paulo
Sao Paulo
Brazil


John E. Johnson
Department of Molecular Biology
The Scripps Research Institute
USA


Johnny Habchi
Architecture et Fonction des Macromolécules Biologiques
UMR 7257 CNRS and Aix-Marseille Université
163 Avenue de Luminy
France


José E. Belizario
Department of Pharmacology
Biomedical Science Institute
University of Sao Paulo
Sao Paulo
Brazil


Juliano Alves
Department of Pharmacology
Biomedical Science Institute
University of Sao Paulo
Sao Paulo
Brazil


Kenrick A. Vassall
Department of Molecular and Cellular Biology
Biophysics Interdepartmental Group
Collaborative Program in Neuroscience
University of Guelph
Canada


Kristin R. Landis-Piwowar
Barbara Ann Karmanos Cancer Institute
Departments of Oncology
Pharmacology and Pathology
School of Medicine
Wayne State University
USA


Kwang-Hyun Baek
Department of Biomedical Science
CHA University
CHA General Hospital
Republic of Korea


Laura Restelli
Department of Veterinary Sciences and Public Health
University of Milan
Italy


Luciano P. Silva
Embrapa Recursos Genéticos e Biotecnologia
Brazil


Luisa Di Paola
University Campus Biomedico
via Alvaro del Portillo 21
Italy


Manidipa Banerjee
Kusuma School of Biological Sciences
Indian Institute of Technology-Delhi
Hauz Khas
New Delhi -110016
India


Marco Cantisani
Department of Pharmacy
University of Naples “Federico II” and Istituto di Biostrutture e Bioimmagini
CNR, Via Mezzocannone 16, 80134
Naples
Italy


Maria Fátima Grossi-de-Sa
Embrapa Recursos Genéticos e Biotecnologia
Brazil


Maria Miller
Macromolecular Crystallography Laboratory
Center for Cancer Research
National Cancer Institute-Frederick
Frederick
USA


Maria T. Vitiello
Department of Experimental Medicine
Division of Microbiology - II
University of Naples
Italy


Massimiliano Galdiero
Department of Experimental Medicine
Division of Microbiology - II
University of Naples
Italy


Massimo Celino
Ente per le Nuove Tecnologie
l’Energia e l’Ambiente
Italy


Maurizio Brunori
Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”
Università degli Studi di Roma “La Sapienza”
Italy


Micol De Ruvo
University Campus Biomedico
via Alvaro del Portillo 21
Italy


Miguel Garay-Malpartida
Department of Pharmacology
Biomedical Science Institute
University of Sao Paulo
Sao Paulo
Brazil


Mohammad Saleemuddin
Interdisciplinary Biotechnology Unit
Aligarh Muslim University
India


Octávio L. Franco
Departamento de Biologia
Universidade Federal de Juiz de Fora
Brazil


Øyvind Halskau
Department of Biomedicine
University of Bergen
5009 Bergen
Norway


Paola Paci
CNR-Institute of Systems Analysis and Computer Science (IASI)
BioMathLab, viale Manzoni 30
Italy


Philippe Lieutaud
Architecture et Fonction des Macromolécules Biologiques
UMR 7257 CNRS and Aix-Marseille Université
163 Avenue de Luminy
France


Q. Ping Dou
Barbara Ann Karmanos Cancer Institute
and Departments of Oncology
Pharmacology and Pathology
School of Medicine
Wayne State University
USA


Rizwan H. Khan
Interdisciplinary Biotechnology Unit
Aligarh Muslim University
India


Sonia Longhi
Architecture et Fonction des Macromolécules Biologiques
UMR 7257 CNRS and Aix-Marseille Université
163 Avenue de Luminy
France


Stefania Galdiero
Department of Pharmacy
University of Naples “Federico II” and Istituto di Biostrutture e Bioimmagini
CNR, Via Mezzocannone 16, 80134
Naples
Italy


Stocchi Vilberto
Department of Biomolecular Sciences
University of Urbino “Carlo Bo”
Italy


Thales L. Rocha
Embrapa Recursos Genéticos e Biotecnologia
Brazil


Vesna Milacic
Barbara Ann Karmanos Cancer Institute
and Departments of Oncology
Pharmacology and Pathology
School of Medicine
Wayne State University
USA




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