bluuebunny/crossref_metadata_2025 huggingface dataset:
The 26S Proteasome
Authors: Rechsteiner Martin
Published: March 2008

The 26S proteasome is a large ATP‐dependent protease composed of more than 30 different polypeptide chains. Like the ribosome, the 26S proteasome is assembled from two “subunits”, the 19S regulatory complex and the 20S proteasome. The 19S regulatory complex confers the ability to recognize and unfold protein substrates, and the 20S proteasome provides the proteolytic activities needed to degrade the substrates. The 26S proteasome is the only enzyme known to degrade ubiquitylated proteins, and it also degrades intracellular proteins that have not been marked by ubiquitin. The 26S proteasome is located in the nucleus and cytosol of eukaryotic cells, where the enzyme is responsible for the selective degradation of a vast number of important cellular proteins. Because rapid proteolysis is a pervasive regulatory mechanism, the 26S proteasome is essential for the proper functioning of many physiological processes.

Originally published in: Protein Degradation, Volume 1. Edited by R. John Mayer, Aaron Ciechanover and Martin Rechsteiner. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30837‐8

The sections in this article are

Introduction

The 20S Proteasome

Structure

Enzyme Mechanism and Proteasome Inhibitors

Immunoproteasomes

The 26S Proteasome

The Ubiquitin–Proteasome System

Ultrastructure of the 26S Proteasome and Regulatory Complex

The 19S Regulatory Complex

ATPases of the RC

The non‐ATPase Subunits

Biochemical Properties of the Regulatory Complex

Nucleotide Hydrolysis

Chaperone‐like Activity

Proteasome Activation

Ubiquitin Isopeptide Hydrolysis

Substrate Recognition

Substrate Recognition by Proteasomes

Degradation Signals (Degrons)

Ubiquitin‐dependent Recognition of Substrates

Substrate Selection Independent of Ubiquitin

Proteolysis by the 26S Proteasome

Presumed Mechanism

Contribution of Chaperones to Proteasome‐mediated Degradation

Substrate Binding to the 26S Proteasome

Translocation of the Polypeptide Substrate to the Central Proteolytic Chamber

Processing by the 26S Proteasome

Proteasome Biogenesis

Subunit Synthesis

Biogenesis of the 20S Proteasome

Biogenesis of the RC

Post‐translational Modification of Proteasome Subunits

Assembly of the 26S Proteasome

Proteasome Activators

REGs or PA28s

REGs

PA200

Hybrid Proteasomes

ECM29

Protein Inhibitors of the Proteasome

Physiological Aspects

Tissue and Subcellular Distribution of Proteasomes

Physiological Importance

Conclusions
Molecular Machines for Protein Degradation
Authors: Bochtler Matthias , Groll Michael , Brandstetter Hans , Clausen Tim , Huber Robert
Published: March 2008

Originally published in: Protein Degradation, Volume 1. Edited by R. John Mayer, Aaron Ciechanover and Martin Rechsteiner. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30837‐8

The sections in this article are

Introduction

The ATP‐dependent Protease HslVU

HslVU Physiology and Biochemistry

HslV Peptidase

HslU ATPase

The HslVU–Protease Complex

Allosteric Activation

A Comparison of HslVU with ClpXP and ClpAP

HslVU Peptidase as a Model for the Eukaryotic 26S Proteasome?

The Yeast 20S Proteasome

The Proteasome, a Threonine Protease

Inhibiting the Proteasome

Access to the Proteolytic Chamber

The Tricorn Protease and its Structural and Functional Relationship with Dipeptidyl Peptidase IV

Architecture of the Tricorn Protease

Catalytic Residues and Mechanism

Substrate Access and Product Egress Through β‐propellers

Structural and Functional Relationship of Tricorn and DPIV

The DegP Protease Chaperone: A Molecular Cage with Bouncers

The DegP Protomer, a PDZ Protease

The Two Forms of the DegP Hexamer

DegP, a Chaperone

The Protease Form

Working Model for an ATP‐independent Heat‐shock Protein

Acknowledgment
Protein Sorting to the Lysosome
Authors: McCullough John , Clague Michale J. , Urbé Sylvie
Published: March 2008

Originally published in: Protein Degradation, Volume 3. Edited by R. John Mayer, Aaron Ciechanover and Martin Rechsteiner. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31435‐0

The sections in this article are

Introduction

Identification of Ubiquitin as an Endosomal Sorting Signal

Ubiquitin‐mediated Sorting at the Endosome: The MVB Sorting Machinery

Endosome‐associated Ubiquitin Interacting Domains: Structure and Function

The Hrs‐STAM Complex and the Endosomal Clathrin Coat

GGA and Tom1: Alternative Sorting Adapters?

The ESCRT Machinery

Vps4‐SKD1

Ubiquitin Ligases and Endosomal Sorting

Nedd4 Family

c‐Cbl

Endosomal DUBs

Ubp1 and Ubp2

Doa4

UBPY

AMSH

Polyubiquitin Linkages and Endocytosis

Proteasome Involvement in Endocytic Sorting

K63‐linked Ubiquitin

Conclusions

Acknowledgements
Regulation of Proteolysis at the Proteasome Portal
Authors: Bajorek Monika , Glickman Michael H.
Published: March 2008

The proteolytic active sites of the 26S proteasome are sequestered within the central chamber of its 20S catalytic core particle. Access to this chamber is through a narrow channel defined by the outer alpha subunits. An intricate lattice of interactions anchors the N‐termini of these alpha subunits, blocking access to the channel in free 20S core particles of eukaryotes. Entry of substrates can be enhanced by attachment of activators or regulatory particles to the proteolytic 20S core. Regulatory particles rearrange the blocking residues to form an open pore and promote substrate entry into the proteolytic chamber. Channel gating is apparently partially rate limiting for proteasome activity, as facilitating substrate entry in the open channel state leads to enhanced overall proteolysis rates. Interestingly, some substrates, particularly hydrophobic ones, can activate gate opening themselves, thus facilitating their own destruction. Properties of channel gating and the interactions required to maintain stable closed and open conformations and their consequences for proteasome function are discussed.

Originally published in: Protein Degradation, Volume 2. Edited by R. John Mayer, Aaron Ciechanover and Martin Rechsteiner. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31130‐0

The sections in this article are

Background

The Importance of Channel Gating

A Porthole into the Proteasome

The Closed State

The Open State

Facilitating Traffic Through the Gated Channel

Regulatory Complexes

Substrate‐facilitated Traffic

Conclusions
Tailoring Protein Scaffolds for Ligand Recognition
Authors: Skerra A.
Published: March 2008

Originally published in: Protein‐Ligand Interactions.Edited by Hans‐Joachim Böhm, Gisbert Schneider. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30521‐6

The sections in this article are

Introduction

Lipocalins: A Class of Natural Compound Carriers

Anticalins: Lipocalins Reshaped via Combinatorial Biotechnology

Structural Aspects of Ligand Recognition by Engineered Lipocalins

Prospects and Future Applications of Anticalins
Evolutionary Generation of Enzymes with Novel Substrate Specificities
Authors: Bornscheuer Uwe T.
Published: March 2008

Originally published in: Directed Molecular Evolution of Proteins. Edited by Susanne Brakmann, Kai Johnsson. Copyright © 2002 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30423‐1

The sections in this article are

Introduction

General Considerations

Examples

Group 1

Group 2

Group 3

Conclusions

Acknowledgements
Design of Restriction Endonucleases with Novel Specificity
Authors: Lanio Thomas , Jeltsch Albert , Pingoud Alfred
Published: March 2008

Originally published in: Directed Molecular Evolution of Proteins. Edited by Susanne Brakmann, Kai Johnsson. Copyright © 2002 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30423‐1

The sections in this article are

Introduction

Biology of restriction/modification systems

Biochemical properties of type II restriction endonucleases

Applications for type II restriction endonucleases

Setting the stage for protein engineering of type II restriction endonucleases

Design of Restriction Endonucleases with New Specificities

Rational design

Attempts to employ rational design to change the specificity of restriction enzymes

Changing the substrate specificity of type IIs restriction enzymes by domain fusion

Rational design to extend specificities of type II restriction enzymes

Evolutionary design of extended specificities

Conclusions

Acknowledgements
Protein Engineering by Evolutionary Methods
Authors: Lutz Stefan , Benkovk* Stephen J.
Published: March 2008

Originally published in: Directed Molecular Evolution of Proteins. Edited by Susanne Brakmann, Kai Johnsson. Copyright © 2002 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30423‐1

The sections in this article are

Introduction

Mechanisms of Protein Evolution in Nature

Gene duplication

Tandem duplication

Proteases

βα‐barrels

Circular permutation

Oligomerization

Gene fusion

Domain recruitment

Substrate specificity

Regulation

Chemistry

Exon shuffling

Engineering Genes and Gene Fragments

Protein fragmentation

Rational swapping of secondary structure elements and domains

Combinatorial gene fragment shuffling

DNA shuffling

Homology‐independent fragment swapping

Homology‐independent fragment shuffling

Modular recombination and protein folding

Rational domain assembly – engineering zinc fingers

Combinatorial domain recombination – exon shuffling

Gene Fusion – From Bi‐ to Multifunctional Enzymes

End‐to‐end gene fusions

Gene insertions

Modular design in multifunctional enzymes

Conclusions

Acknowledgements
Engineered Nanopores
Authors: Bayley Hagan , Braha Orit , Cheley Stephen , Gu Li‐Qun
Published: March 2008

Originally published in: Nanobiotechnology. Edited by Christof M. Niemeyer and Chad A. Mirkin. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30658‐9

The sections in this article are

Overview

What is a Nanopore?

Engineering Nanopores

What Can a Nanopore Do?

What are the Potential Applications of Nanopores?

Keeping Nanopores Happy

Methods

Protein Production

Protein Engineering

Electrical Recording

Other Systems

Outlook

Rugged Pores

Supported Bilayers

Membrane Arrays

Alternative Protein Pores

Pores with New Attributes and Applications

Theory

Acknowledgments
Design and Stability of α‐Helices
Authors: Doig Andrew J. , Errington Neil , Iqbalsyah Teuku M.
Published: March 2008

Originally published in: Protein Folding Handbook. Part I. Edited by Johannes Buchner and Thomas Kiefhaber. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30784‐2

The sections in this article are

Introduction

Structure of the α‐Helix

Capping Motifs

Metal Binding

The 3
10
‐Helix

The π‐Helix

Design of Peptide Helices

Host–Guest Studies

Helix Lengths

The Helix Dipole

Acetylation and Amidation

Side Chain Spacings

Solubility

Concentration Determination

Design of Peptides to Measure Helix Parameters

Helix Templates

Design of 3
10
‐Helices

Design of π‐helices

Helix Coil Theory

Zimm‐Bragg Model

Lifson‐Roig Model

The Unfolded State and Polyproline II Helix

Single Sequence Approximation

N‐ and C‐Caps

Capping Boxes

Side‐chain Interactions

N1, N2, and N3 Preferences

Helix Dipole

3
10
‐ and π‐Helices

AGADIR

Lomize‐Mosberg Model

Extension of the Zimm‐Bragg Model

Availability of Helix/Coil Programs

Forces Affecting α‐helix Stability

Helix Interior

Caps

Phosphorylation

Noncovalent Side‐chain Interactions

Covalent Side‐chain interactions

Capping Motifs

Ionic Strength

Temperature

Trifluoroethanol

p
K
a
Values

Relevance to Proteins

Acknowledgments
Design and Stability of Peptide β‐sheets
Authors: Searle Mark S.
Published: March 2008

Originally published in: Protein Folding Handbook. Part I. Edited by Johannes Buchner and Thomas Kiefhaber. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30784‐2

The sections in this article are

Introduction

β‐Hairpins Derived from Native Protein Sequences

Role of β‐turns in Nucleating β‐hairpin Folding

Intrinsic ϕ, Ψ Propensities of Amino Acids

Side‐chain Interactions and β‐hairpin Stability

Aromatic Clusters Stabilize β‐hairpins

Salt Bridges Enhance Hairpin Stability

Cooperative Interactions in β‐sheet Peptides: Kinetic Barriers to Folding

Quantitative Analysis of Peptide Folding

Thermodynamics of β‐hairpin Folding

Multistranded Antiparallel β‐sheet Peptides

Conclusions
Engineering Proteins for Stability and Efficient Folding
Authors: Schimmele Bernhard , Plückthun Andreas
Published: March 2008

Originally published in: Protein Folding Handbook. Part II. Edited by Johannes Buchner and Thomas Kiefhaber. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30784‐2

The sections in this article are

Introduction

Kinetic and Thermodynamic Aspects of Natural Proteins

The Stability of Natural Proteins

Different Kinds of “Stability”

Thermodynamic Stability

Kinetic Stability

Folding Efficiency

The Engineering Approach

Consensus Strategies

Principles

Examples

Structure‐based Engineering

Entropic Stabilization

Hydrophobic Core Packing

Charge Interactions

Hydrogen Bonding

Disallowed Phi‐Psi Angles

Local Secondary Structure Propensities

Exposed Hydrophobic Side Chains

Inter‐domain Interactions

Case Study: Combining Consensus Design and Rational Engineering to Yield Antibodies with Favorable Biophysical Properties

The Selection and Evolution Approach

Principles

Screening and Selection Technologies Available for Improving Biophysical Properties

In Vitro Display Technologies

Partial in Vitro Display Technologies

In Vivo Selection Technologies

Selection for Enhanced Biophysical Properties

Selection for Solubility

Selection for Protein Display Rates

Selection on the Basis of Cellular Quality Control

Selection for Increased Stability

General Strategies

Protein Destabilization

Selections Based on Elevated Temperature

Selections Based on Destabilizing Agents

Selection for Proteolytic Stability

Conclusions

Acknowledgements
Protein‐based Artificial Enzymes
Authors: Duckworth Ben , Distefano Mark D.
Published: March 2008

Originally published in: Artificial Enzymes. Edited by Ronald Breslow. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31165‐1

The sections in this article are

Introduction

Artificial Nucleases Based on DNA and RNA Binding Proteins

Introduction

Artificial Nucleases from Native Protein Scaffolds

OP Nuclease Design by Mutagenesis and Chemical Modification

Additional Applications for OP Conjugates

A Fe‐EDTA Artificial Nuclease

Concluding Remarks

Catalysts Based on Hollow Lipid‐binding Proteins

Lipid‐binding Proteins

Initial Work

Exploiting the Advantage of a Protein‐based Scaffold

Catalytic Turnover with Rate Acceleration

Modulation of Cofactor Reactivity with Metal Ions

Chemogenetic Approach

Adding Functional Groups within the Cavity

Scaffold Redesign

Hydrolytic Reactions

A Flavin‐containing Conjugate

Some Limitations

Myoglobin as a Starting Point for Oxidase Design

Artificial Metalloproteins and Myoglobin

Non‐covalent Attachment of a Redox Center

Dual Anchoring Strategy

Antibodies as Scaffolds for Catalyst Design

Antibodies as Specificity Elements

Incorporation of an Imidazole Functional Group into an Antibody for Catalysis

Comparison of Imidazole‐containing Antibodies Produced by Chemical Modification and Site‐directed Mutagenesis

Conclusions
Force Generation in Molecular Motors
Authors: Oster George , Wang Hongyun
Published: March 2008

Originally published in: Molecular Motors. Edited by Manfred Schliwa. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30594‐0

The sections in this article are

Introduction

A Brief Description of ATP Synthase Structure

The F
1
Motor: A Power Stroke

The F
0
Motor: A Brownian Ratchet

A Pure Brownian Ratchet

A Pure Power Stroke

Coupling and Coordination of Motors

Measures of Efficiency

Discussion

Appendix: Example Models to Illustrate the Difference between Ratchets and Power Strokes

Example 1: A power stroke without Brownian fluctuations

Example 2: A power stroke with Brownian fluctuations

Example 3: A Brownian ratchet that biases fluctuations

Example 4: A Brownian ratchet that rectifies fluctuations

A Closer Look at Binding Free Energy
Catalytic Antibodies as Mechanistic and Structural Models of Hydrolytic Enzymes
Authors: Lindner Ariel B. , Eshhar Zelig , Tawfik Dan S.
Published: March 2008

Originally published in: Catalytic Antibodies. Edited by Ehud Keinan. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30688‐6

The sections in this article are

Abbreviations

Introduction

Chapter Overview

Catalysis by Oxyanion Stabilization (OAS)

Fidelity of TSA design

Esterolytic Antibodies Based Solely on Oxyanion Stabilization

Antibody Oxyanion Holes

Oxyanion holes–Antibodies vs. Enzymes

Antibody Affinity and Rate Acceleration Limitation

Nucleophilic Catalysis

Endogenous Nucleophiles in Hydrolytic Antibodies

Reactive immunization (RI)

Serendipity and 43C9 Antibody

Exogenous Nucleophiles and Chemical Rescue in Hydrolytic Antibodies

General Acid/Base Mechanisms in Hydrolytic Antibodies

Metal‐Activated Catalytic Antibodies

Substrate Destabilization

The Role of Conformational Changes in Catalytic Antibodies

Conformational changes in catalytic antibodies

The contribution of structural isomerization to catalysis

Conclusions
Chemical Microarrays for Small Molecule Ligand Screening
Authors: Metz G. , Ottleben H. , Vetter D.
Published: March 2008

Originally published in: Protein‐Ligand Interactions. Edited by Hans‐Joachim Böhm, Gisbert Schneider. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30521‐6

The sections in this article are

Introduction

Fragment Approaches

Conceptual Ideas

Choice of Screening Fragments

Experimental Approaches

Chemical Microarrays

Background

On‐array Synthesis

Off‐array Synthesis and Spotting

Screening on Microarrays

Detection Technology

Protein Affinity Fingerprints

Conclusion

Acknowledgement
Single Molecule Measurements of Molecular Motors
Authors: Ishii Yoshiharu , Yanagida Toshio
Published: March 2008

Single molecule detection was developed to measure the unique operation of molecular motors. The function of molecular motors has been ascribed to the movement of a single motor molecule along a partner protein track. Manipulating single protein tracks and single motors and imaging single molecules has allowed the behaviour of such unitary machines to be measured. The mechanical responses to the energy input from the hydrolysis of ATP molecules have been determined and the underlying mechanism explored. The results indicate that the movement of molecular motors is driven by thermal motion rather than structural changes occurring in the motor molecules. Thermal Brownian motion must be biased in one direction. In this article, we summarize the methods and results of single molecule measurements of molecular motors.

Originally published in: Molecular Motors. Edited by Manfred Schliwa. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30594‐0

The sections in this article are

Introduction

Manipulation of Actin Filaments

Nanometry of Actin Filaments

Movement of Actin Filaments Caused by Single Myosin Molecules

Visualization of Single Molecules

Visualization of ATP Turnover and Mechano‐chemical Coupling

Visualization of the Movement of Single Kinesin Motors

Visualization of the Processive Movement of Single Myosin Motors

Manipulation of Single Myosin Molecules with a Scanning Probe and Nanometry

Biased Brownian Movement

Conclusions
Analysis of Receptor‐Ligand Interaction
Authors: Höfliger M. M. , Beck‐Sickinger A. G.
Published: March 2008

Originally published in: Protein‐Ligand Interactions. Edited by Hans‐Joachim Böhm, Gisbert Schneider. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30521‐6

The sections in this article are

Receptors

The G‐Protein‐Coupled Receptors

Ligand‐binding Theory

Characterization of the Receptor‐Ligand Interaction

Receptor Material

Binding Studies

Binding Kinetics

Binding Assays

Separation Assays

Radioligand‐binding Assay

Fluorometric Assays

Fluorescence Labels

Fluorescence Correlation Spectroscopy (FCS)

Fluorescence Microscopy

Fluorescence Resonance Energy Transfer (FRET)

Surface Plasmon Resonance

Molecular Characterization of the Receptor‐Ligand Interaction

Antibodies

Applications of Antibodies

Receptor and Ligand Detection

Receptor Characterization

Functional Characterization of the Receptor‐Ligand Interaction

Aptamers

Receptor Mutation and Ligand Modification

Receptor Mutagenesis

Ligand Modification

Combination of Receptor Mutation and Ligand Modification

Cross‐linking

Conclusion
Protein Microarrays: Surface Chemistry and Coupling Schemes
Authors: Schäferling Michael , Kambhampati Dev
Published: March 2008

Originally published in: Protein Microarray Technology. Edited by Dev Kambhampati. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30597‐1

Efficient immobilization of biomolecules is a key factor in determining the overall success of a microarray or, for that matter, any high‐throughput (HTP) screening tool. If the immobilized probes are not correctly oriented on the microarray surface or are denatured, it can dramatically affect the downstream biomolecular interaction events. Here, various schemes for immobilizing biomolecules on glass, gold, polymer and semiconductor surfaces are described. In addition to tailoring the surface chemistry on the above substrates, various schemes for manipulating the probes with tags will also be addressed to achieve efficient and biocompatible screening platforms.

The sections in this article are

Introduction

Background and Current State of Biomolecule Libraries

Microarrays Based on Glass Substrates

Surface Modification

Current State of Glass‐Based Protein Microarrays

Microarrays based on Gold Substrates

Surface Modifications

Current State of Gold‐based Protein Microarrays

Microarrays based on Polymer Substrates

Surface Modifications

Current State of Polymer‐based Microarrays

Special Formats: Microfluidic Devices and Integrated Semiconductor Chips

Chemical Immobilization Techniques for Proteins

Covalent Chemical Coupling

Photochemical Cross‐Coupling

Tagged Proteins

Site‐Specific Immobilization of Antibodies

Conclusions
Surface Plasmon Resonance Imaging Measurements of Biomolecular Arrays
Authors: Wegner Greta J. , Lee Hye Jin , Corn Robert M.
Published: March 2008

Originally published in: Protein Microarray Technology. Edited by Dev Kambhampati. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30597‐1

The sections in this article are

Introduction

Surface Plasmon Resonance Imaging

Surface Attachment Chemistries

SSMCC
Attachment Chemistry

SATP
Attachment Chemistry

SPR
Imaging Experiments Using Photopatterned Arrays

DNA
–
DNA
Hybridization

Mismatch Binding Protein,
Mut
S

Bacterial Response Regulators,
Omp
R
and
Van
R

SPR
Imaging Experiments of Arrays Created by Microfluidic Stencils

1‐D Peptide Array for Antibody Binding Measurements

2‐D
DNA
Array for
RNA
Hybridization

2‐D Peptide Array for Antibody Binding Measurements

2‐D Protein Array

Conclusions

Acknowledgments
Real‐time Characterization of
B
iomolecular Interactions using Biacore's Optical Biosensors
Authors: Franklin Gary , McWhirter Alan
Published: March 2008

Originally published in: Protein Microarray Technology. Edited by Dev Kambhampati. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30597‐1

The sections in this article are

Introduction

The Proteomics Revolution

Biacore Technology

Surface Plasmon Resonance

The Sensor Surface and Immobilization Chemistry

Sensor chips

Immobilization Chemistry

General Capture Methods

Specialized Capture Methods

Lipids and Membrane Proteins

The Microfluidics System

Biacore Assay Basics

Correlation of
SPR
Response with Surface Binding

Assay Design: Assay Formats

Assay Design: Surface Preparation

Regeneration

Theoretical and Practical Implications of Technology Design for Biacore Assays

Label‐free Detection

The Optical Detection System and Bulk Effects

Surface‐based Versus Solution‐based Analysis

The Microfluidic Design and Mass Transport Effects

Biacore Applications in Basic and Clinical Research

Introduction

Applications of
B
iacore in Cancer Research

Applications of
B
iacore in Clinical Research

Applications of
B
iacore in Neuroscience

Drug: Plasma Protein Interactions

Drug:
DNA
Interactions

Nucleic Acid Structure and Analysis

Protein:
RNA
Interactions

Current Developments and Future Perspectives

SPR
‐
MS

The Challenges of High‐throughput Protein Analysis and Array Technologies
Cellular Assays and Their Application in Drug Discovery
Authors: Albrecht Hugo , Brodbeck‐Hummel Daniela , Hoever Michael , Nickel Beatrice , Regenass Urs
Published: March 2008

Originally published in: Molecular Biology in Medicinal Chemistry. Edited by Theodor Dingermann, Dieter Steinhilber and Gerd Folkers. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30431‐8

The sections in this article are

Introduction

Positioning Cellular Assays

Impact on Drug Discovery

Classification of Cellular Assays

Progress in Tools and Technologies for Cellular Compound Profiling

Membrane Proteins and Fast Cellular Responses

Receptors

FLIPR Technology for Detection of Intracellular Calcium Release

Competitive Immunoassay for Detection of Intracellular cAMP

Enzyme Fragment Complementation (EFC) Technology

Membrane Transport Proteins

Ion Channels

MDR Proteins

Gene and Protein Expression Profiling in High‐throughput Formats

Reporter Gene Assays in Lead Finding

Reporter Gene Assays in Lead Optimization

Spatio‐temporal Assays and Subpopulation Analysis

Phosphorylation Stage‐specific Antibodies

Target‐protein‐specific Antibodies

Protein–GFP Fusions

Fluorescence Resonance Energy Transfer (FRET)

GPCR Activation using Bioluminescence Resonance Energy Transfer (BRET)

Protein Fragment Complementation Assays (PCA)

Phenotypic Assays

Proliferation/Respiration/Toxicity

Apoptosis

Differentiation

Monitoring Cell Metabolism

Other Phenotypic Assays

Acknowledgments
Mass Spectrometry of Peptides and Proteins
Authors: Warscheid Bettina
Published: March 2008

Originally published in: Proteomics in Drug Research. Edited by Michael Hamacher, Katrin Marcus, Kai Stühler, André van Hall, Bettina Warscheid and Helmut E. Meyer. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31226‐9

Rapid advances in biological mass spectrometry have promoted proteomics to being a key technology in molecular cell biology and biomedical research. Current mass spectrometry‐based proteomics provides the capability for the identification of cellular and subcellular proteomes, the study of changes in protein concentrations via stable isotope labeling methods and the mapping of functional protein modules isolated by means of affinity purification. The large potential of proteomics techniques to identify and accurately quantify proteins from complex biological samples has been well recognized in the larger scientific community and it will in all probability have a great impact on future drug research.

The sections in this article are

Introduction

Ionization Principles

Matrix‐Assisted Laser Desorption/Ionization (
MALDI
)

Electrospray Ionization

Mass Spectrometric Instrumentation

Protein Identification Strategies

Quantitative Mass Spectrometry for Comparative and Functional Proteomics

Metabolic Labeling Approaches

15
N
Labeling

Stable Isotope Labeling by Amino Acids in Cell Culture (
SILAC
)

Chemical Labeling Approaches

Chemical Isotope Labeling at the Protein Level

Stable Isotope Labeling at the Peptide Level

Quantitative
MS
for Deciphering Protein‐Protein Interactions

Conclusions

Acknowledgements
Electrophysiological Analysis of Ion Channels
Authors: Pusch Michael
Published: March 2008

Originally published in: Expression and Analysis of Recombinant Ions Channels. Edited by Jeffrey J. Clare and Derek J. Trezise. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31209‐2

This article outlines electrophysiological methods for extracting biophysical parameters that describe two fundamental properties of ion channels: gating and permeation. The Introduction provides a broad overview of the general concepts of ion channel biophysics and the text a review of the kind of information that can be extracted from electrophysiological recordings. The later sections introduce several methods for the analysis of electrophysiological experiments on heterologously expressed ion channels. Many parts are explicit and can be directly applied “at the bench”. Other, more advanced topics (gating current measurements, single‐channel kinetic analysis) are touched upon only superficially since their application requires further background that can be found in the references.

The sections in this article are

Introduction

Expression Systems and Related Recording Techniques

Expression in

Xenopus

Oocytes

Expression in Mammalian Cells

Leak and Capacitance Subtraction

Macroscopic Recordings

Analysis of Pore Properties–Permeation

Analysis of Fast Voltage‐dependent Block – the Woodhull Model

Information on Gating Properties from Macroscopic Measurements

Equilibrium Properties–Voltage‐gated Channels

Equilibrium Properties–Ligand Gated Channels

Macroscopic Kinetics

Channel Block

Nonstationary Noise Analysis

Gating Current Measurements in Voltage Gated Channels

Single Channel Analysis

Amplitude Histogram Analysis

Kinetic Single Channel Analysis

Conclusion

Acknowledgements
Ion Channel Assays Using Fluorescent Probes
Authors: González Jesús E. , Worley Jennings , Van Goor Fredrick
Published: March 2008

Originally published in: Expression and Analysis of Recombinant Ions Channels. Edited by Jeffrey J. Clare and Derek J. Trezise. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31209‐2

The sections in this article are

Introduction

Membrane Potential Probes

Redistribution Probes

FRETProbes

Advantages and Limitations of Membrane Potential Probes

Ion‐sensitive Fluorescent Probes

Calcium Dyes

Indicators of Other Ions

Fluorescence Assays for Ion Channels

Calcium Channels

Non‐voltage‐gated Cation Permeable Channels

Sodium Channels

Potassium Channels

Chloride Channels

Assays for Monitoring Channel Trafficking

Conclusion
Enzyme Activity Fingerprinting Methods for Hydrolases
Authors: Grognux Johann , Reymond Jean‐Louis
Published: March 2008

Originally published in: Enzyme Assays. Edited by Jean‐Louis Reymond. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31095‐1

The sections in this article are

Introduction

One Enzyme – One Substrate

Enzyme Activity Profiles

TheAPIZYMSystem for Microbial Strain Identification

Hydrolase Fingerprinting

Fingerprinting with Fluorogenic and Chromogenic Substrates

Procedure 1 Esterase/lipase Fingerprinting on Impregnated Silicagel Plates

Fingerprinting with Indirect Chromogenic Assays

Procedure 2: Lipase/esterase Fingerprinting Using the Adrenaline Test for Enzymes

Cocktail Fingerprinting

Classification from Fingerprinting Data

Fingerprint Representation

Procedure 3: Data Treatment for Representation of Colored Selectivity Arrays

Data Normalization

Hierarchical Clustering of Enzyme Fingerprints

Analysis of Substrate Similarities

Conclusions

Acknowledgment
Chemical Complementation Assays
Authors: Lefurgy Scott , Cornish Virginia
Published: March 2008

Originally published in: Enzyme Assays. Edited by Jean‐Louis Reymond. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31095‐1

The sections in this article are

Introduction

Complementation Assays

Introduction

Early Complementation Assays

Enzymology by Complementation

Directed Evolution by Complementation

Development of Chemical Complementation

Introduction

Three‐hybrid Assay

Original Yeast Three‐hybrid System

Dexamethasone–Methotrexate Yeast Three‐hybrid System

Technical Considerations

Other Three‐hybrid Systems

Chemical Complementation

Selection Scheme and Model Reaction

Results

General Considerations

Related Methods

Applications of Chemical Complementation

Introduction

Enzyme‐Inhibitor Interactions

Rationale

Screen Strategy

Enzyme Library Screen

General Considerations

Glycosynthase Evolution

Rationale

Selection Scheme

Glycosynthase Assay

Directed Evolution

General Considerations

Conclusion
High‐throughput Screening Methods for Oxidoreductases
Authors: Johannes Tyler W. , Woodyer Ryan D. , Zhao Huimin
Published: March 2008

Originally published in: Enzyme Assays. Edited by Jean‐Louis Reymond. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31095‐1

The sections in this article are

Introduction

High‐throughput Methods for Various Oxidoreductases

Dehydrogenases

Colorimetric Screen Based on
NAD
(
P
)
H
Generation

Screens Based on
NAD
(
P
)
H
Depletion

Oxidases

Galactose Oxidase

d
‐Amino Acid Oxidase

Peroxidases

Oxygenases

Assays Based on Optical Properties of Substrates and Products

Assays Based on
G
ibbs' Reagent and 4‐Aminoantipyrine

para
‐Nitrophenoxy Analog (
p
NA
) Assay

Horseradish Peroxidase‐coupled Assay

Indole Assay

Laccases

ABTS
Assay

Poly
R
‐478 Assay

Other Assays

Conclusions

Acknowledgements
Quantitative Assay of Hydrolases for Activity and Selectivity Using Color Changes
Authors: Kazlauskas Romas J.
Published: March 2008

Originally published in: Enzyme Assays. Edited by Jean‐Louis Reymond. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31095‐1

The sections in this article are

Introduction

Direct Assays Using Chromogenic Substrates

Indirect Assays Using Coupled Reactions –
p
H
Indicators

Overview of Quantitative Use of pH Indicator Assay

Applications

Searching for an Active Hydrolase (Testing Many Hydrolases Toward One Substrate)

Substrate Mapping of New Hydrolases (Testing Many Substrates Toward Hydrolase)

Comparison with Other Methods

Estimating and Measuring Selectivity

Estimating Selectivity without a Reference Compound

Quantitative Measure of Selectivity Using a Reference Compound (Quick

E

and Related Methods)

Chromogenic Substrate

p
H
Indicators

Application

Substrate Mapping of Hydrolases

Screening of Mutants in Directed Evolution

Advantages and Disadvantages

Acknowledgments
Protease Substrate Profiling
Authors: Harris Jennifer L.
Published: March 2008

Originally published in: Enzyme Assays. Edited by Jean‐Louis Reymond. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31095‐1

The sections in this article are

Introduction

Functional Protease Profiling – Peptide Substrate Libraries

Solution‐based Peptide Substrate Libraries

Solid Support‐based Synthesis and Screening of Peptide Libraries

Genetic Approaches to Identifying Protease Substrate Specificity

Identification of Macromolecular Substrates

Genetic Approach to the Identification of Macromolecular Substrates

Proteomic Approaches to Identifying Protease Substrates

Conclusions
Photochemical Enzyme Regulation
Authors: Peng Ling , Goeldner Maurice
Published: March 2008

Originally published in: Dynamic Studies in Biology. Edited by Maurice Goeldner and Richard S. Givens. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30783‐8

The sections in this article are

Introduction

Photoregulation ofATPases

ATPases using CagedATPMolecules

Na,K‐ATPase

TransportATPasesand Carriers

Molecular Motors

Ca2+‐ATPase

Ca2+‐ATPaseusing CagedATP

Ca2+‐ATPaseusing Caged Inhibitor

Ca2+‐ATPaseusing CagedCa2+

Photoregulation ofGTPases: Ras Protein

Time‐resolved Crystallographic Studies with CagedGTP

Time‐resolvedFTIRStudies with CagedGTP

Photoregulation of Kinases

cAMP‐dependent Protein Kinase

PKAusing CagedcAMP

PKAusing Caged Inhibitor

PKC

PKCusing Caged Activators

PKCusing Caged Fluorescent Substrates

Calmodulin‐dependent Protein Kinases

Myosin Light Chain Kinase (MLCK) using Caged Peptide Inhibitors

Calmodulin‐dependent Protein KinaseII(CaMKII) using Caged Peptide Inhibitors

Photoregulation of Alcohol Dehydrogenases

Isocitrate Dehydrogenase (IDH): CagedNADandNADP

Glucose‐6‐Phosphate Dehydrogenase (G6PDH): Caged Glucose 6‐Phosphate and CagedNADP

7α‐Hydroxy Steroid Dehydrogenase (7α‐HSDH): Caged Cholic Acid

Caged Benzyl Alcohol

Photoregulation of Cholinesterases

Caged Choline Derivatives

Caged Cholinesterase Substrate

Miscellaneous Examples of Caged Enzyme Modulators

Caged Nitric Oxide Synthase (NOS) Inhibitor

Caged Substrate of Quinol‐oxidizing Enzymes

Caged Urease Substrate

Caged Ribonuclease Reductase Substrate

Conclusions
Kinetic Protein Crystallography using Caged Compounds
Authors: Bourgeois Dominique , Weik Martin
Published: March 2008

Originally published in: Dynamic Studies in Biology. Edited by Maurice Goeldner and Richard S. Givens. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30783‐8

The sections in this article are

Introduction

Protein Activity and Conformational Changes in Crystals

Timescales and Activation States

Accumulating Unstable Species in the Crystal

Real‐time Crystallography and the Laue Technique

A Favorable Case: Isocitrate Dehydrogenase

The Case of
Ha
‐
ras
p
21: From Laue to Monochromatic Diffraction and Further Difficulties with Caged Compounds in Kinetic Crystallography

Trapping of Intermediate States

Cryo‐photolysis of
NPE
‐caged Compounds

Temperature‐dependent Enzymatic Activity and Dynamical Transitions

Potential Applications of Cryo‐photolysis Combined with Temperature‐controlled Protein Crystallography

Cryo‐photolysis Wavelength and Cryo‐radiolysis of
NPE
‐caged Compounds

X
‐ray Data Collection Strategy

Conclusion

Acknowledgments
Luminescent Proteins in Binding Assays
Authors: Roda Aldo , Guardigli Massimo , Michelini Elisa , Mirasoli Mara , Pasini Patrizia
Published: March 2008

Originally published in: Photoproteins in Bioanalysis. Edited by Sylvia Daunert and Sapna K. Deo. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31016‐6

The sections in this article are

Introduction

Protein–Protein and Protein–Ligand Interaction Assays

FRETandBRETMTechniques

FRET and BRET Applications

Other Detection Principles

Antibody‐based Binding Assays

Chemical Conjugation

Gene Fusion

Dual‐analyte Assays

Expression Immunoassays

BRET‐based Immunoassays

Biotin–Avidin Binding Assays

Nucleic Acid Hybridization Assays

Other Binding Assays

Conclusions
Sensory Defects Caused by Mutant Motor Proteins
Authors: Avraham Karen B.
Published: March 2008

Originally published in: Molecular Motors. Edited by Manfred Schliwa. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30594‐0

The sections in this article are

Introduction

Development of the Visual and Auditory Sensory Systems

Visual Impairment

Hearing Impairment

Myosins Involved In Sensory Defects

MyosinVIIA

Structure, function, and expression of myosinVIIA

Shaker 1 Mice and Other Models

Usher Syndrome Type 1B

DFNB2 andDFNA11

MyosinVI

Structure, function, and expression of myosinVI

Snell's waltzer mice and other models

DFNA22

MyosinXVA

Structure, function, and expression of myosinXVA

Shaker 2

DFNB3

MYH9

Structure, function, and expression ofMYH9

DFNA17

MyosinIIIA

Structure, function, and expression of myosinIIIA

MyosinIIIAmutants

DFNB30

Conclusions

Acknowledgements
Myosin Myopathies
Authors: Konhilas John P. , Leinwand Leslie A.
Published: March 2008

Originally published in: Molecular Motors. Edited by Manfred Schliwa. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30594‐0

The sections in this article are

Introduction

Cardiac Myosin Heavy Chains

My
HC
Structure and Function

Cardiac Muscle Regulation and Disease

Cardiac
My
HC
Myopathy

Functional Characterization of
My
HC
Motor Domain Mutations

Transgenic Models of Myosin‐based
FHC

My
HC
Interacting Proteins and
FHC

The Essential and Regulatory Light chains

Myosin Light Chain‐based
FHC

Myosin Binding Protein
C
‐Based
FHC

Titin‐based Familial Hypertrophic Cardiomyopathy

Myosin‐based Myopathies in Skeletal Muscle

Conclusions
Protein Sequence Variants: Resources and Tools
Authors: Yip Yum Lina , Famiglietti Maria Livia , Gasteiger Elisabeth , Bairoch Amos
Published: March 2008

Originally published in: Biomedical Applications of Proteomics. Edited by Jean‐Charles Sanchez, Garry L. Corthals and Denis F. Hochstrasser. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30807‐1

The sections in this article are

Introduction

Medical Protein Annotation

Databases

Central Databases

Online Mendelian Inheritance in Man (OMIM)

The Human Gene Mutation Database (HGMD)

The SNP Databases

Advantages and Drawbacks of Central Databases

Specialized Databases

An Example of a Locus‐specific Database: the IARC TP53 Database

An Example of a Disease‐oriented Specialized Database: Retina International's Scientific Newsletter – Mutation Database

Other Locus‐specific Databases

Advantages and Drawbacks of Specialized Databases

The Swiss‐Prot Protein Knowledgebase and Information on Disease and Sequence Variations

Gene Names

Description of Diseases

Proteins as Therapeutic Drugs

Data on Variants

Cross‐references

Medical‐oriented Keywords

Techniques of Search

Challenges for Databases

Analysis Tools in the Context of Protein Variants

Proteomic Tools for Protein Identification and the Characterization of Variants

Protein Identification Tools

Peptide Characterization Tools

Tools for Analyzing and/or Predicting the Effects of Protein Variants

Sequence‐based Analysis or Prediction Tools

Structure‐based Analysis or Prediction Tools

The Swiss‐Prot Variant Page and Comparative Modeling

Remarks

Conclusions
PPARs and Cancer
Authors: Gill J. H. , Roberts Ruth A.
Published: March 2008

Originally published in: Cellular Proteins and Their Fatty Acids in Health and Disease. Edited by Asim K. Duttaroy and Friedrich Spener. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30437‐0

The sections in this article are

Introduction

The PPAR Family

PPARα

Expression and Activation

PPARα and Cancer

Species Differences

PPARα as a Therapeutic Target?

PPARγ

Expression and Activation

PPARγ and Cancer

PPARγ as a Therapeutic Target?

PPARβ

Expression and Activation

PPARβ and Cancer

PPARβ as a Therapeutic Target?

Conclusions
PPARs in Atherosclerosis
Authors: Plutzky Jorge
Published: March 2008

Originally published in: Cellular Proteins and Their Fatty Acids in Health and Disease. Edited by Asim K. Duttaroy and Friedrich Spener. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30437‐0

The sections in this article are

Atherosclerosis

Introduction

Atherosclerosis as a Clinical Syndrome

Cellular Constituents of Atherosclerosis

Atherosclerosis as an Inflammatory Disorder

Atherosclerosis as a Metabolic Disorder

PPAR in the Vasculature

PPARs in Vascular Biology and Atherosclerosis

Examining Evidence for PPAR in Vascular Responses

PPARγ in Vascular Biology and Atherosclerosis

In vitroEvidence

In vivoEvidence

PPARα in Vascular Biology and Atherosclerosis

In vitroEvidence

In vivoEvidence

PPARδ in Vascular Biology and Atherosclerosis

Conclusion
Biochemistry and Structural Biology of Mammalian Prion Disease
Authors: Glockshuber Rudi
Published: March 2008

Originally published in: Protein Folding Handbook. Part II. Edited by Johannes Buchner and Thomas Kiefhaber. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30784‐2

The sections in this article are

Introduction

Prions and the “Protein‐Only” Hypothesis

Models ofPrPScPropagation

Properties ofPrPCandPrPSc

Three‐dimensional Structure and Folding of RecombinantPrP

Expression of the Recombinant Prion Protein for Structural and Biophysical Studies

Three‐dimensional Structures of Recombinant Prion Proteins from Different Species and Their Implications for the Species Barrier of Prion Transmission

Solution Structure of MurinePrP

Comparison of Mammalian Prion Protein Structures and the Species Barrier of Prion Transmission

Biophysical Characterization of the Recombinant Prion Protein

Folding and Stability of RecombinantPrP

Role of the Disulfide Bond inPrP

Influence of Point Mutations Linked With InheritedTSEs on the Stability of RecombinantPrP

Generation of Infectious Prionsin vitro: Principal Difficulties in Proving the Protein‐Only Hypothesis

Understanding the Strain Phenomenon in the Context of the Protein‐Only Hypothesis: Are Prions Crystals?

Conclusions
Prion Protein
Authors: Derreumaux Philippe
Published: March 2008

Originally published in: Amyloid Proteins. Edited by Jean D. Sipe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31072‐X

The sections in this article are

Introduction

Conformations of PrPCand PrPSc

Stability and Unfolding/Folding of PrPCIn Vitro

Mechanisms of Prion ReplicationIn Vivo

Conclusions
Protein Aggregates in Neurodegenerative Disorders
Authors: Giaccone Giorgio , Salmona Mario , Tagliavini Fabrizio , Forloni Gianluigi
Published: March 2008

Originally published in: Amyloid Proteins. Edited by Jean D. Sipe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31072‐X

The sections in this article are

Introduction

Neuropathology

Alzheimer's Disease

Tauopathies

Prion Diseases

Synucleinopathies

The Neurotoxic Proteins

Alzheimer's Disease

Prion Diseases

Synucleinopathies

Conclusions

Acknowledgments
Cellular Toxicity of Protein Aggregates
Authors: Kagan Bruce
Published: March 2008

Originally published in: Amyloid Proteins. Edited by Jean D. Sipe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31072‐X

The sections in this article are

Introduction

Aggregation

Cellular Mechanisms of Oligomeric Toxicity

Loss of Function Hypothesis

Receptors for Advanced End‐products of Glycation (RAGE) Receptors

Oxidative Stress

The Channel Hypothesis

Aβ

PrP106‐126

IAPP

ANP

SAA

AS

β
2
M

AL Amyloidosis

PG

HypF

Calcitonin (CT)

Lysozyme
Protein Folding and Aggregation in the Expanded Polyglutamine Repeat Diseases
Authors: Wetzel Ronald
Published: March 2008

Originally published in: Protein Folding Handbook. Part II. Edited by Johannes Buchner and Thomas Kiefhaber. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30784‐2

The sections in this article are

Introduction

Key Features of the Polyglutamine Diseases

The Variety of Expanded Poly
Gln
Diseases

Clinical Features

Repeat Expansions and Repeat Length

The Role of Poly
Gln
and Poly
Gln
Aggregates

PolyGln Peptides in Studies of the Molecular Basis of Expanded Polyglutamine Diseases

Conformational Studies

Preliminary
in vitro
Aggregation Studies

In Vivo Aggregation Studies

Analyzing Polyglutamine Behavior With Synthetic Peptides: Practical Aspects

Disaggregation of Synthetic Polyglutamine Peptides

Growing and Manipulating Aggregates

Polyglutamine Aggregation by Freeze Concentration

Preparing Small Aggregates

In vitro Studies of Poly
Gln
Aggregation

The Universe of Protein Aggregation Mechanisms

Basic Studies on Spontaneous Aggregation

Nucleation Kinetics of Poly
Gln

Elongation Kinetics

Microtiter Plate Assay for Elongation Kinetics

Repeat‐length and Aggregate‐size Dependence of Elongation Rates

The Structure of PolyGln Aggregates

Electron Microscopy Analysis

Analysis with Amyloid Dyes Thioflavin T and Congo Red

Circular Dichroism Analysis

Presence of a Generic Amyloid Epitope in Poly
Gln
Aggregates

Proline Mutagenesis to Dissect the Polyglutamine Fold Within the Aggregate

Polyglutamine Aggregates and Cytotoxicity

Direct Cytotoxicity of Poly
Gln
Aggregates

Delivery of Aggregates into Cells and Cellular Compartments

Cell Killing by Nuclear‐targeted Poly
Gln
Aggregates

Visualization of Functional, Recruitment‐positive Aggregation Foci

Inhibitors of Poly
Gln
Aggregation

Designed Peptide Inhibitors

Screening for Inhibitors of Poly
Gln
Elongation

Conclusions

Acknowledgements