Table Of ContentPROTEIN STRUCTURE
Edited by Eshel Faraggi
Protein Structure
Edited by Eshel Faraggi
Published by InTech
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Copyright © 2012 InTech
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First published April, 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]
Protein Structure, Edited by Eshel Faraggi
p. cm.
ISBN 978-953-51-0555-8
Contents
Preface IX
Section 1 Introduction 1
Chapter 1 An Evolutionary Biology Approach
to Understanding Neurological Disorders 3
Azhari Aziz, Jasmina Ilievska, Paul R. Fisher and Naomi E. Bishop
Chapter 2 Structure and Dynamics of Proteins
from Nuclear Magnetic Resonance Spectroscopy 43
Homayoun Valafar and Stephanie J. Irausquin
Chapter 3 Anhydrous and Hydrated Protein Models Derived
from High-Resolution and Low-Resolution Techniques 69
Helmut Durchschlag and Peter Zipper
Section 2 Structure Prediction 93
Chapter 4 Refinement of Protein Tertiary Structure
by Using Spin-Spin Coupling Constants
from Nuclear Magnetic Resonance Measurements 95
Jürgen M. Schmidt and Frank Löhr
Chapter 5 An Exhaustive Shape-Based Approach
for Proteins' Secondary, Tertiary and Quaternary
Structures Indexing, Retrieval and Docking 121
Eric Paquet and Herna L. Viktor
Chapter 6 Protein Structure Alphabetic Alignment 133
Jiaan Yang and Wei-Hua Lee
Section 3 Energy and Thermodynamics 157
Chapter 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
VI Contents
Chapter 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
Chapter 9 On the Relationship Between Residue Solvent
Exposure and Thermal Fluctuations in Proteins 213
Yu-Tung Chien, Jenn-Kang Hwang and Shao-Wei Huang
Chapter 10 Preserving Proteins Under
High Pressure and Low Temperature 229
Takahiro Takekiyo, Minoru Kato and Yukihiro Yoshimura
Chapter 11 A Stable Protein – CutA1 249
Azumi Hirata, Aya Sato, Takashi Tadokoro, Yuichi Koga,
Shigenori Kanaya and Kazufumi Takano
Section 4 Function and Interaction 263
Chapter 12 Ligand-Binding Proteins: Structure,
Stability and Practical Application 265
Olga Stepanenko, Alexander Fonin, Olesya Stepanenko,
Irina Kuznetsova and Konstantin Turoverov
Chapter 13 Functional Difference Between Deuterated
and Protonated Macromolecules 291
Takashi Sugiyama and Tohru Yoshioka
Chapter 14 Slit/Robo Signaling: Inhibition
of Directional Leukocyte Migration 309
Ilya M. Mukovozov and Lisa A. Robinson
Section 5 Applications 335
Chapter 15 Fibrinolytic Enzymes from Medicinal Mushrooms 337
Chung-Lun Lu and Shiu-Nan Chen
Chapter 16 Phospholipases A Protein Structure and Natural Products
2
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
Chapter 17 Prediction and Rational Design
of Antimicrobial Peptides 377
William F. Porto, Osmar N. Silva and Octávio L. Franco
Preface
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 non-
organic 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.
X Preface
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,
USA
