Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences including genetics, biochemistry, and cell biology. Progress in Nucleic Acid Research and Molecular Biology is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume.

Specialist Periodical Reports provide systematic and detailed review coverage of progress in the major areas of chemical research. Written by experts in their specialist fields the series creates a unique service for the active research chemist, supplying regular critical in-depth accounts of progress in particular areas of chemistry. For over 80 years the Royal Society of Chemistry and its predecessor, the Chemical Society, have been publishing reports charting developments in chemistry, which originally took the form of Annual Reports. However, by 1967 the whole spectrum of chemistry could no longer be contained within one volume and the series Specialist Periodical Reports was born. The Annual Reports themselves still existed but were divided into two, and subsequently three, volumes covering Inorganic, Organic and Physical Chemistry. For more general coverage of the highlights in chemistry they remain a 'must'. Since that time the SPR series has altered according to the fluctuating degree of activity in various fields of chemistry. Some titles have remained unchanged, while others have altered their emphasis along with their titles; some have been combined under a new name whereas others have had to be discontinued. The current list of Specialist Periodical Reports can be seen on the inside flap of this volume.

Driving further the research on mammalian alkaline phosphatase structure and function, Phosphatase Modulators collects expert contributions into one "how to" manual for basic scientists interested in initiating a drug discovery effort. While this book contains the traditional method chapters and some typical reviews on the structure and known functions of phosphatases, other contributions are meant to discuss approaches and alternatives useful in making "go/no-go" decisions in high throughput screening (HTS) and lead optimization campaigns. Many chapters focus on tissue-nonspecific alkaline phosphatase (TNAP) as well as protein phosphatases. Written for the highly successful Methods in Molecular Biology series, chapters in this volume include the kind of detail and key implementation advice that promotes reproducible results. Step-by-step and practical, Phosphatase Modulators offers a path to understanding many of the facets and complexities associated with undertaking a drug discovery effort and will serve as a roadmap to initiating those efforts.

Enzymes and whole cells are able to catalyze the most complex chemical processes under the most benign experimental and environmental conditions. In this way, enzymes and cells could be excellent catalysts for a much more sustainable chemical industry. However, enzymes and cells also have some limitations for nonbiological applications: fine chemistry, food chemistry, analysis, therapeutics, and so on. Enzymes and cells may be unstable, difficult to handle under nonconventional conditions, poorly selective toward synthetic substrates, and so forth. From this point of view, the transformation-from the laboratory to industry-of chemical processes catalyzed by enzymes and cells may be one of the most complex and exciting goals in biotechnology. For many industrial applications, enzymes and cells have to be immobilized, via very simple and cost-effective protocols, in order to be re-used over very long periods of time. From this point of view, immobilization, simplicity, and stabilization have to be strongly related concepts. Over the last 30 years, a number of protocols for the immobilization of cells and enzymes have been reported in scientific literature. However, only very few protocols are simple and useful enough to greatly improve the functional properties of enzymes and cells, activity, stability, selectivity, and related properties.

This book aims to bridge the gap in understanding how protein-tyrosine phosphatases (PTPs), which carry out the reverse reaction of tyrosine phosphorylation, feature in cancer cell biology. The expertly authored chapters will first review the general features of the PTP superfamily, including their overall structure and enzymological properties; use selected examples of individual PTP superfamily members, to illustrate emerging data on the role of PTPs in cancer; and will review the current status of PTP-based drug development efforts. Protein Tyrosine Phosphatases in Cancer,from renowned researchers Benjamin Neel and Nicholas Tonks, is invaluable reading for researchers in oncology, stem cell signaling,and biochemistry.

Poly (ADP-ribose) Polymerases (PARPs) are abundant and ubiquitous proteins that regulate crucial processes of the cell cycle, DNA repair, genomic stability, and transcriptional regulation. Being involved in basic cell functions, PARPs mediate rapid responses to such environmental factors as stress, infection, nutrition and hormonal signals. Whereas PARP inhibitors can suppress tumor growth and proliferation in certain breast, ovarian, and prostate cancers, understanding how PARP controls cellular functions is essential for the development of novel cancer treatments strategies. Divided into three convenient sections, Poly(ADP-Ribose) Polymerase: Methods and Protocols aims to explain how PARP proteins act within the normal development of an organism as well as in pathogenic conditions, seeks to advance the knowledge of developmental pathways regulation, and endeavors to facilitate the development of new therapeutic drugs and methods to target PARP-dependent processes. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Poly(ADP-Ribose) Polymerase: Methods and Protocols serves as an ideal guide to scientists who wish to continue exploring this exciting and progressive research field.

This volume arranged into three sections describes biochemical, in vitro, and in vivo protocols on Semaphorins. Chapters focus on approaches that would allow the novice to study Semaphorins and employ robust assays to characterize mechanisms of action. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Semaphorin Signaling: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Super secondary structure(SSS) helps to understand the relationship between primary and tertiary structure of proteins. In Protein Supersecondary Structure: Methods and Protocols expert researchers in the field detail the usefulness of the study of super secondary structure in different areas of protein research. This is done through four main studies SSS representation, SSS prediction, SSS and protein folding, and other application of SSS concept to protein biology. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Supersecondary Structure: Methods and Protocols highlight some of the major advances in the many fast-growing areas of supersecondary structure research.

Real-time PCR (RT-PCR) technology is highly flexible and many alternative instruments and fluorescent probe systems have been developed recently. The decreased hands-on time, increased reliability, and improved quantitative accuracy of RT-PCR methods have contributed to the adoption of RT-PCR for a wide range of new applications. This essential manual presents a comprehensive guide to the most up-to-date technologies and applications, as well as providing an overview of the theory of this increasingly important technique. Renowned experts in the field describe and discuss the latest PCR platforms, fluorescent chemistries, validation software, data analysis, and internal and external controls. This timely and authoritative volume also discusses a wide range of RT-PCR applications including clinical diagnostics, biodefense, RNA expression studies, validation of array data, mutation detection, food authenticity and legislation, NASBA, molecular halotyping, and much more. Real-Time PCR: Current Technology and Applications will be an essential book for all laboratories using PCR.

The critically acclaimed laboratory standard, Methods in Enzymology, is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. The series contains much material still relevant today - truly an essential publication for researchers in all fields of life sciences.
Molecular Evolution Producing the Biochemical Data part B is a continuation of methods published in Part A (1993, volume 224). The work is a very methodological look at markers, templates, genomes, datasets and analyses used in studies of biological diversity.
* One of the most highly respected publications in the field of biochemistry since 1955
* Frequently consulted, and praised by researchers and reviewers alike
* Truly an essential publication for anyone in any field of the life sciences

This is the first of three volumes in the "Ion Channels & Transporters in Tumor Biology" collection, which discusses the function of ion transport proteins in cellular and systemic homeostasis. The authors highlight the role of the so-called transportome, which is defined by the entirety of ion transporters and ion channels. Thereby, readers will get a better understanding of the impact dysregulated ion transport has on the whole spectrum of cancer types. Cancers display deficiencies in several, sometimes interdependent members of the transportome. Clinicians will be interested in the fact that controlled expression of ion transport proteins dramatically impacts the life span of cancer patients, as shown in recent studies. These observations offer a promising outlook for biomedical scientists, as members of the transportome could be the tumor markers of tomorrow - both for diagnostic and therapeutic purposes. As part of a three-volume collection, this book will fascinate members of the active research community, as well as clinicians from the cancer field.

Bioethanol has been recognized as a potential alternative to petroleum-derived transportation fuels. Even if cellulosic biomass is less expensive than corn and sugarcane, the higher costs for its conversion make the near-term price of cellulosic ethanol higher than that of corn ethanol and even more than that of sugarcane ethanol. Conventional process for bioethanol production from lignocellulose includes a chemical/physical pre-treatment of lignocellulose for lignin removal, mostly based on auto hydrolysis and acid hydrolysis, followed by saccharification of the free accessible cellulose portions of the biomass. The highest yields of fermentable sugars from cellulose portion are achieved by means of enzymatic hydrolysis, currently carried out using a mix of cellulases from the fungus Trichoderma reesei. Reduction of (hemi)cellulases production costs is strongly required to increase competitiveness of second generation bioethanol production. The final step is the fermentation of sugars obtained from saccharification, typically performed by the yeast Saccharomyces cerevisiae. The current process is optimized for 6-carbon sugars fermentation, since most of yeasts cannot ferment 5-carbon sugars. Thus, research is aimed at exploring new engineered yeasts abilities to co-ferment 5- and 6-carbon sugars. Among the main routes to advance cellulosic ethanol, consolidate bio-processing, namely direct conversion of biomass into ethanol by a genetically modified microbes, holds tremendous potential to reduce ethanol production costs. Finally, the use of all the components of lignocellulose to produce a large spectra of biobased products is another challenge for further improving competitiveness of second generation bioethanol production, developing a biorefinery.

The book provides an overview on various microorganisms and their industrialization in energy conversion, such as ethanol fermentation, butanol fermentation, biogas fermentation and fossil energy conversion. It also covers microbial oil production, hydrogen production and electricity generation. The content is up to date and suits well for both researchers and industrial audiences.

Studies in Natural Products Chemistry, Volume 10: Stereoselective Synthesis (Part F) is a collection of articles about studies on important organic molecules. The book covers studies such as that on the synthesis of cembranes as well as its natural occurrence and bioactivity; the stereoselective synthesis of Vitamin D; the synthesis of isoquinolinequinone antibiotics; and the nucleophilic addition chemistry of polyunsaturated carbonyl compounds. Also covered in the book are subjects such as developments in the synthesis of medium ring ethers; the biological properties, chemistry, and synthesis of didemnins; and natural products synthesis based on novel ring transformation. The text is recommended for organic chemists who would like to know more about the progresses in the study of important organic molecules and their implications in different fields.

This book highlights current approaches and future trends in the use of mass spectrometry to characterize protein therapies. As one of the most frequently utilized analytical techniques in pharmaceutical research and development, mass spectrometry has been widely used in the characterization of protein therapeutics due to its analytical sensitivity, selectivity, and specificity. This book begins with an overview of mass spectrometry techniques as related to the analysis of protein therapeutics, structural identification strategies, quantitative approaches, followed by studies involving characterization of process related protein drug impurities/degradants, metabolites, higher order structures of protein therapeutics. Both general practitioners in pharmaceutical research and specialists in analytical sciences will benefit from this book that details step-by-step approaches and new strategies to solve challenging problems related to protein therapeutics research and development.

This volume of Modern Aspects of Electrochemistry reviews the latest developments in electrochemical science and technology related to biomedical and pharmaceutical applications. In particular, this book discusses electrochemical applications to medical devices, implants, antimicrobially active materials, and drug delivery systems.

Fibrous Protein: Coiled-Coils, Collagen and Elastomers is the first of a three-part series on Fibrous Proteins. The books are based on a very successful workshop in Alpbach, Austria on the general topic of Fibrous Proteins that gave rise to the award winning issue of Journal of Structural Biology. Part II will contain an extensive discussion of Molecular Motors and Muscle, Part III on Amyloids, Prions and Beta Proteins.
Advances in Protein Chemistry is available online on ScienceDirect full-text online of volumes 53 onwards.
*Reveals new structural and functional aspects of fibrous proteins
*Based on Fibrous Protein workshop in Alpbach, Austria that gave rise to 2003 Nobel Prize winners in Chemistry

This book reflects the use of cyanobacteria for the bioremediation of wastewater through different mechanisms and pathways of transformation and transfer of hazardous substances from one medium to another. The application of microorganisms for bioremediation is determined by their ubiquity, small size, high rate of reproduction and large surface-to-volume cell ratio. Mechanisms of interaction of cyanobacteria with inorganic pollutants include biosorption, bioaccumulation with an opportunity to obtain metal nanoparticles both on the cell surface and inside the cells as well as chelation and inclusion of metals in the composition of certain organic structures. Data presented in the book provides specialists in the field with useful information for bioremediation technologies as well as for obtaining valuable preparations using cyanobacteria.

Michael D. Wendt
Protein-Protein Interactions as Drug Targets

Shaomeng Wang, Yujun Zhao, Denzil Bernard, Angelo Aguilar, Sanjeev Kumar
Targeting the MDM2-p53 Protein-Protein Interaction for New Cancer Therapeutics

Kurt Deshayes, Jeremy Murray, Domagoj Vucic
The Development of Small-Molecule IAP Antagonists for the Treatment of Cancer

John F. Kadow, David R. Langley, Nicholas A. Meanwell, Michael A. Walker, Kap-Sun Yeung, Richard Pracitto
Protein-Protein Interaction Targets to Inhibit HIV-1 Infection
Nicholas A. Meanwell, David R. Langley
Inhibitors of Protein-Protein Interactions in Paramyxovirus Fusion a Focus on Respiratory Syncytial Virus

Andrew B. Mahon, Stephen E. Miller, Stephen T. Joy, Paramjit S. Arora
Rational Design Strategies for Developing Synthetic Inhibitors of Helical Protein Interfaces

Michael D. Wendt
The Discovery of Navitoclax, a Bcl-2 Family Inhibitor

"

The volume focuses on the genomics, proteomics, metabolomics, and bioinformatics of a single cell, especially lymphocytes and on understanding the molecular mechanisms of systems immunology. Based on the author's personal experience, it provides revealing insights into the potential applications, significance, workflow, comparison, future perspectives and challenges of single-cell sequencing for identifying and developing disease-specific biomarkers in order to understand the biological function, activation and dysfunction of single cells and lymphocytes and to explore their functional roles and responses to therapies. It also provides detailed information on individual subgroups of lymphocytes, including cell characters, function, surface markers, receptor function, intracellular signals and pathways, production of inflammatory mediators, nuclear receptors and factors, omics, sequencing, disease-specific biomarkers, bioinformatics, networks and dynamic networks, their role in disease and future prospects. Dr. Xiangdong Wang is a Professor of Medicine, Director of Shanghai Institute of Clinical Bioinformatics, Director of Fudan University Center for Clinical Bioinformatics, Director of the Biomedical Research Center of Zhongshan Hospital, Deputy Director of Shanghai Respiratory Research Institute, Shanghai, China.

TheobservationthatabloodclotspontaneouslydissolveswasfirstdescribedbyDenys in1889. Subsequently,thebloodclottingsystemwasshowntobeinvolvedintumor growth. Forexample,asearlyas1925,Fisherreportedthataviantissueexplantstrans- formedtomalignancybyvirusesgeneratedhighlevelsoffibrinolyticactivityundercon- ditionsinwhichculturesofnormalcellsdidnot. In1958,theconceptthatan equilibriumexistedbetweenthetendencyofbloodtoclotandtoremainfluidwaspro- posedbyAstrup. Atthattime,itwasbelievedthatthishemostaticbalancewasexplained bytheabilityofpolymerizingfibrintoorchestrateitsownclearancebystimulatingfib- rinolyticactivity. Sincethesepioneeringstudies,considerableinformationhasaccumu- latedthathasdefinedthecomponentsofthecoagulationandfibrinolyticsystemsand howtheyareinvolvedinphysiologicalandpathophysiologicalprocesses. Plasminogen: Structure, activation, and regulationfocusesonthebasicprinciplesandrecentdevelop- mentsintheplasminogen/plasminresearchfieldandhowtheseresultsprovideacon- ceptualframeworkforanunderstandingofthephysiologicalroleofplasminogenin healthanddisease. Theenzymaticcascadetriggeredbyactivationofplasminogenhasbeenimplicated inavarietyofnormalandpathologicaleventssuchasfibrinolysis,woundhealing,tis- sueremodeling,embryogenesis,angiogenesis,andtheinvasionandmetastasisoftumor cells. Thisimpressivelistofphysiologicalfunctionsforplasminogenreinforcesthewide diversityofrolesthatplasminogenplaysinvariousphysiologicalprocesses. Productive plasmingenerationrequirestheassemblyofbothplasminogenactivatorsandplasmino- genonasolidsupportsuchasthefibrinpolymerorthecellsurface. Theregulationof plasminproductioninvolvesacomplexinterplaybetweentheseplasminogenactivators, plasminogenactivatorinhibitors,andplasmininhibitors. Clearly,theexplosivegrowth inthisresearchfieldandthemanyexcitingdiscoveriessuggeststhattheresearchefforts inthenextdecadewillrevealthemechanismsbywhichthecomponentsoftheplas- minogensysteminteractandregulatebothplasminactivationandfunctionatacellular level. Plasminogen: Structure, activation, and regulationisdividedintotwosections. Thefirstsectiondealswiththestructureandregulationofplasminogen. Thechapters inthissectionrangefromdiscussionsofthestructureofplasminogenandtheregulation oftheplasminogengenetodiscussionsofthestructureandregulationofplasminogen activatorsandplasminogenactivatorinhibitors. Alsoexaminedistherelativelynewdata concerningthegenerationofanti-angiogenicmoleculesfromplasminogen. Thesecond sectiondealswiththephysiologicalandpathophysiologicalrolesofplasminogenaswell astheconsequencesofplasminogengeneknockout. Discussionsinthissectioninclude examinationoftheroleofplasminogeninhematopoieticmalignancies,tumorcell progression,angiogenesis,mammaryglandinvolution,woundhealing,andbone readsorption. xi xii Preface Inclosing,Iwouldliketothankmyadministrativeassistant,Ms. ViSommerfeld,for herinvaluableassistanceandtimelesseffortswiththeorganizationandeditingofthebook. Lastly,Iwouldliketoacknowledgetheeffortsoftheauthorsoftheindividualchapters, whoareauthorities inthisfield,foragreeingtotaketimefrombusyschedulestoprovide thesechaptersinatimelyfashion. DavidMortonWaisman Contents Part I. Plasminogen: Structure and Regulation 1. Human Plasminogen: Structure, Activation, and Function FrancisJ. Castellino and Victoria A. Ploplis 1. Introduction 3 2. StructureofHumanPlasminogen...3 2. 1. PrimaryProteinStructure...3 2. 2. GeneOrganization 5 3. ActivationofHumanPlasminogen...6 3. 1. ActivationbyPhysiologicalActivators 7 3. 1. 1. Urokinase-typePlasminogenActivator...7 3. 1. 2. Tissue-typePlasminogenActivator...8 3. 2. ActivationbyBacterial-derivedPlasminogenActivators...9 3. 2. 1. Streptokinase 9 3. 2. 2. Staphylokinase...9 4. TargetsforPlasminActivity...9 5. DysplasminogenemiasandPhenotypicManifestations 10 6. Conclusions 11 References...11 2. Plasminogen Activators: Structure and Function Vincent Ellis 1. Introduction ...19 2. SerineProteases...20 3. UrokinasePlasminogenActivator,uPA...21 3. 1. SerineProteaseDomain 22 3. 2. N-terminalDomains...24 3. 2. 1. KRModule 24 3. 2. 2. EGModule 24 4. MechanismsRegulatinguPAFunction...25 4. 1. ZymogenActivation...25 4. 2. ZymogenActivity...26 4. 3. ReciprocalZymogenActivation 27 4. 4. uPARStimulationofPlasminogenActivation...27 4. 4. 1. uPAandtheTemplateMechanism 28 4. 4. 2. PlasminogenandtheTemplateMechanism 29 4. 5. AvianuPA,aSpecialCase? 30 xiii xiv Contents 5. TissuePlasminogenActivator,tPA...30 5. 1. SerineProteaseDomain 31 5. 2. N-terminalDomains ,...33 5. 2. 1. KRModules ,. . ,. . ,...33 5. 2. 2. F1-EGSupermodule 33 6.

-Encapsulation by Miniemulsion Polymerization By K. Landfester and C. K. Weiss -Enzyme-Encapsulated Layer-by-Layer Assemblies: Current Status and Challenges Toward Ultimate Nanodevices By K. Ariga, Q. Ji, and J. P. Hill -Non-LBL Assembly and Encapsulation Uses 1 of Nanoparticle-Shelled Hollow Spheres 2 By G.C. Kini, S. L. Biswal, and M. S. Wong -Polymersomes: A Synthetic Biological Approach to Encapsulation and Delivery By M. Massignani, H. Lomas, and G. Battaglia -Reaction Vessels Assembled by the Sequential Adsorption of Polymers By A.D. Price, A.P.R. Johnston, G.K. Such, and F. Caruso

Drug metabolism and transport are very important facets within the discipline of pharmaceutical sciences, with enzyme kinetic concepts utilized regularly in characterizing and modeling the disposition and elimination of drugs. Enzyme Kinetics in Drug Metabolism: Fundamentals and Applications focuses on very practical aspects of applying kinetic principles to drug metabolizing enzymes and transporters. Divided into five convenient sections, topics include the fundamental principles of enzyme kinetics, the kinetics of oxidative and conjugative drug metabolizing enzymes and drug transporters, modeling approaches for both drug metabolizing enzymes and transporters including novel systems biology approaches, understanding of variability both experimental and interindividual (pharmacogenomic), and case studies that provide real life examples of applying these principles. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics especially suitable for the novice, in some cases step-by-step, readily reproducible protocols, and insights to help with troubleshooting and avoiding known pitfalls with extensive cross referencing to assist in learning. Authoritative and easily accessible, Enzyme Kinetics in Drug Metabolism: Fundamentals and Applications serves as a very practical teaching tool for novice, non-mathematically trained scientists interested in these fundamental concepts and as an aid for their supervisors in teaching these principles.

The work reported in this book represents an excellent example of how creative experimentation and technology development, complemented by computational data analysis, can yield important insights that further our understanding of biological entities from a systems perspective. The book describes how the study of a single RNA-binding protein and its interaction sites led to the development of the novel 'protein occupancy profiling' technology that for the first time captured the mRNA sequence space contacted by the ensemble of expressed RNA binders. Application of protein occupancy profiling to eukaryotic cells revealed that extensive sequence stretches in 3' UTRs can be contacted by RBPs and that evolutionary conservation as well as negative selection act on protein-RNA contact sites, suggesting functional importance. Comparative analysis of the RBP-bound sequence space has the potential to unravel putative cis-acting RNA elements without a priori knowledge of the bound regulators. Here, Dr. Munschauer provides a comprehensive introduction to the field of post-transcriptional gene regulation, examines state-of-the-art technologies, and combines the conclusions from several journal articles into a coherent and logical story from the frontiers of systems-biology inspired life science. This thesis, submitted to the Department of Biology, Chemistry and Pharmacy at Freie Universitat Berlin, was selected as outstanding work by the Berlin Institute for Medical Systems Biology at the Max-Delbrueck Center for Molecular Medicine, Germany.