Open Access Medical Books



Edited by Eshel Faraggi .

408 pages .
Open Access .
ISBN 978-953-51-0555-8 .

Protein structure is as wide a scientific field of research as any. The word protein comes from the Greek word for primary and indeed proteins serve as the primary machinery of all known living systems. Some of the earliest experiments on proteins, in the 1850's, were of growing protein crystals by solvating red blood cells and slowly evaporating the solution. These crystals were signalling that well-defined structure is an inherent aspect of the protein universe. However, it took more than a hundred years until the central role of the ordered structure in proteins gained a firm scientific position.
Not only are structured proteins essential for life, and are being heavily studied using analytical tools because of that, the study of proteins is leading to answers for nonorganic matter. Indeed the lessons we have learned from structured proteins are showing up in various fields. As science and engineering explore the ever smaller, the borderline to the size of proteins is nearing. In that nano-scale the lessons learned from proteomics will be invaluable to the design and fabrication of nano-machines.
What is the relationship between the amino-acid sequence of a protein and its three dimensional structure? Unfortunately, although the basic ideas behind proteins have been known for over fifty years, in many respects very little theoretical progress has been made on this fundamental question. The complexity of this problem is such that most of our analytical tools still seem either unsatisfactory or intangible. Fortunately, we are increasing our knowledge base, and in both the experimental and the phenomenological fronts significant advances have been made.
In this collection of studies a sample of current protein research is given. It is organized in such a way that a non-expert can gain some appreciation for the intricacies involved and the current state of affairs. The expert, we hope, can gain a deep understanding of the topics discussed herein.
The first section provides an introduction to the topic. The first chapter answers the basic question of relevance, describing the fundamental connection between medicine and proteins as exemplified by neurological disorders. Chapters two and three deal with the experimental techniques that are used to determine protein structure.
In section two, questions in protein structure prediction are discussed. Chapter four discusses some of the numerical and predictive questions associated with experimental techniques. Chapters five and six discuss question associated with numerically defining the sequence and the structure. Specifically for alignment, indexing and retrieval.
Section three of this collection is dedicated to question associated with the energetics of proteins in their dynamic environment. The first chapter in this section introduces the reader to the use of light in the study of proteins. The next chapter is an example on how light is used to study the hydrogen bond, the most significant interaction after the peptide bond in determining both the structure and the dynamics of a protein. The remaining chapters in the section discuss the relationship between solvent accessibility and thermal fluctuations, and other aspects in the stability of proteins.
Section four discusses the interactions and functions that proteins are involved in living systems. Chapter twelve introduces the reader to the interaction of proteins with small molecules. Chapter thirteen summarizes the function difference between proteins in water and in heavy water. Chapter fourteen discusses particular protein functions associated with inflammation.
The last three chapters comprise the fifth and last section of this book. This section presents some of the applications where protein structure comes into play. Chapter fifteen gives an example of a protein activity responsible for the removal of blood clots. In this case the source of these promising proteins is naturally occurring medicinal mushrooms. Chapter sixteen discusses another particular example of a protein pathway and ways of modifying it for pharmacological purposes. Finally, the last chapter is devoted to the medically pressing issue of designing new antibiotics. It shows that by combining new knowledge with new problems, new solutions may arise. That is, after all, the aim of most scientists.

Dr Eshel Faraggi
Department of Biochemistry and Molecular Biology,
Indiana University School of Medicine,
Indianapolis, Indiana,


Section 1 Introduction .

 1 An Evolutionary Biology Approach to Understanding Neurological Disorders 3 Azhari Aziz, Jasmina Ilievska, Paul R. Fisher and Naomi E. Bishop

 2 Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy 43 Homayoun Valafar and Stephanie J. Irausquin

 3 Anhydrous and Hydrated Protein Models Derived from High-Resolution and Low-Resolution Techniques 69 Helmut Durchschlag and Peter Zipper

Section 2 Structure Prediction .

 4 Refinement of Protein Tertiary Structure by Using Spin-Spin Coupling Constants from Nuclear Magnetic Resonance Measurements 95 Jürgen M. Schmidt and Frank Löhr

 5 An Exhaustive Shape-Based Approach for Proteins' Secondary, Tertiary and Quaternary Structures Indexing, Retrieval and Docking 121 Eric Paquet and Herna L. Viktor

 6 Protein Structure Alphabetic Alignment 133 Jiaan Yang and Wei-Hua Lee

Section 3 Energy and Thermodynamics .

 7 Theoretical Analyses of Photoinduced Electron Transfer from Aromatic Amino Acids to the Excited Flavins in Some Flavoproteins 159 Kiattisak Lugsanangarm, Nadtanet Nunthaboot, Somsak Pianwanit, Sirirat Kokpol and Fumio Tanaka

 8 Estimating Hydrogen Bond Energy in Integral Membrane Chromoproteins by High Hydrostatic Pressure Optical Spectroscopy 191 Liina Kangur, John D. Olsen, C. Neil Hunter and Arvi Freiberg

 9 On the Relationship Between Residue Solvent Exposure and Thermal Fluctuations in Proteins 213 Yu-Tung Chien, Jenn-Kang Hwang and Shao-Wei Huang

 10 Preserving Proteins Under High Pressure and Low Temperature 229 Takahiro Takekiyo, Minoru Kato and Yukihiro Yoshimura

 11 A Stable Protein – CutA1 249 Azumi Hirata, Aya Sato, Takashi Tadokoro, Yuichi Koga, Shigenori Kanaya and Kazufumi Takano

Section 4 Function and Interaction .

 12 Ligand-Binding Proteins: Structure, Stability and Practical Application 265 Olga Stepanenko, Alexander Fonin, Olesya Stepanenko, Irina Kuznetsova and Konstantin Turoverov

 13 Functional Difference Between Deuterated and Protonated Macromolecules 291 Takashi Sugiyama and Tohru Yoshioka

 14 Slit/Robo Signaling: Inhibition of Directional Leukocyte Migration 309 Ilya M. Mukovozov and Lisa A. Robinson

Section 5 Applications .

 15 Fibrinolytic Enzymes from Medicinal Mushrooms 337 Chung-Lun Lu and Shiu-Nan Chen

 16 Phospholipases A2 Protein Structure and Natural Products Interactions in Development of New Pharmaceuticals 363 Marcos Toyama, Selma D. Rodrigues, Daneila O. Toyama, Veronica C.G. Soares, Camila Ap Cotrim, Rafael Ximenes and Marcelo L. Santos

 17 Prediction and Rational Design of Antimicrobial Peptides 377 William F. Porto, Osmar N. Silva and Octávio L. Franco  .

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Published by: younes younes - Saturday, June 22, 2013


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