bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermodynamics of Amyloid Formation
Authors: Baskakov Ilia V.
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

Thermodynamic versus Kinetic Control of Protein Folding

What Thermodynamic Forces are Responsible for the Exceptional Stability of Amyloid Aggregates?

Single Polypeptide Chain‐Multiple β‐Sheet‐rich Abnormal Isoforms

Does the Process of Prion Propagation Differ from Formation of Ordered Amyloid Aggregates?

Prion Propagation is an Autocatalytic Process

Conformational Diversity of Self‐propagating Prion Aggregates

High Species Specificity of Prion Propagation

Conclusions
Post‐translational Chemical Modifications in Amyloid Fibril Formation
Authors: Nilsson Melanie R.
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

Common Modifications that May Play a Significant Role
In Vivo

Cleavage by Proteases or Non‐enzymatic Hydrolysis

Deamidation, Isomerization, Racemization and Protein
l
‐Isoaspartyl Methyltransferase (
PIMT
)

Oxidative Damage

AGE
s

Phosphorylation

Proposed Mechanisms by which Chemical Modifications may Affect Amyloid Deposition

Conclusions

Acknowledgments
Serum amyloid P Component
Authors: Wood Steve P. , Coker Alun R.
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

Amyloid Fibrils and their Formation

The Structure of SAP

The Calcium‐binding Site

Comparative studies ofCRP

SAP Structure in the Absence of Calcium

Binding of Small Molecule Ligands to SAP

The Role of Glycosaminoglycans (GAGs)

SAP, Protein Folding and Amyloid Fibril Formation

Conclusion
Amyloid Fibril Formation of Natively Unfolded Proteins
Authors: Uversky Vladimir N. , Fink Anthony L.
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

Molecular Mechanisms of Amyloid Fibril Formation by a Natively Unfolded Protein: α‐Synuclein

α‐Synuclein in Parkinson's Disease and other Neurodegenerative Disorders

Key Structural Properties of α‐Synuclein: A Natively Unfolded Protein

Major Structural Characteristics of Partially Folded α‐Synuclein

Fibril Formation by α‐Synuclein and the Partially Folded Amyloidogenic Conformation

Fibrillogenesis of Natively Unfolded Proteins Requires Partial Folding

Fibril Formation by Proteins Involved in Conformational Disorders

Amyloid β protein (Aβ)

Tau protein

Islet Amyloid Polypeptide (IAPP) or Amylin

Prion Protein

Polyglutamine Repeat Diseases

Fibrillation of Proteins Unrelated to Conformational Disease

Yeast Prions

Prothymosin α

Apolipoprotein CII (ApoCII)

Histones

Conclusions

Acknowledgments
Kinesin Superfamily Proteins
Authors: Hirokawa Nobutaka , Takemura Reiko
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

The Kinesin Superfamily Proteins

N‐Kinesins

N
‐1 Kinesins

N
‐2 Kinesins

N
‐3 Kinesins

The
Unc
104/
KIF
1 family

The
KIF
13 family

The
KIF
16 family

N‐4 Kinesins

The
KIF
3 family

The
Osm
3/
KIF
17 family

N‐5 Kinesins

N‐6 Kinesins

The
CHO
1/
KIF
23 family

The
KIF
20/
Rab
6 kinesin family

N‐7 Kinesins

N‐8 Kinesins

The
K
id/
KIF
22 family

The
KIF
18 family

N
‐9 Kinesins

N
‐10 Kinesins

N
‐11 Kinesins

M‐Kinesins

C
‐Kinesins

C
‐1 Kinesins

C
‐2 Kinesins

Orphans

Cargoes of KIFs; Specificity and Redundancy

Recognition and Binding to Cargoes

How to Determine the Direction of Transport
Myosin Superfamily Proteins
Authors: Kieke Michele C. , Titus Margaret 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

Functional Properties of Myosins

Directionality and Processivity

Protein Motifs Found in Myosins

Myosin Regulation

Diverse Functions for Myosins

Non‐muscle Contractile Structures

Cell Motility and Adhesion

Organelle/Cellular Component Transport

Maintenance of Actin‐rich Extensions

Membrane Trafficking

Signal Transduction

Myosins in Disease

Griscelli Syndrome

Roles for Myosins in Hearing

New Myosins and Myosin Functions on the Horizon

Conclusions

Acknowledgements
Plasma‐MembraneH+‐ATPaseFrom Yeast
Authors: Lecchi Silvia , Slayman Carolyn W.
Published: March 2008

Originally published in: Handbook of ATPase. Edited by Masamitsu Futai, Yoh Wada and Jack H. Kaplan. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30689‐3

The sections in this article are

Introduction

Structure

Ca2+‐ATPaseas a Model

Applicability of theCa2+‐ATPaseStructure to OtherP2‐ATPase, Including the Pma1H+‐ATPase

H+‐ATPaseOligomers

Associated Proteolipids

Reaction Mechanism

Overview of the Reaction Cycle

ATPBinding and Phosphorylation

E1–E2 Conformational Change

H+Pumping

Biogenesis

Pma1 Mutants with Defects in Folding and Biogenesis

Use of Pma1 Mutants to Screen for Other Genes that Play a Role in Biogenesis and Quality Control

Role of Lipid Rafts

Regulation

Emerging Knowledge of Other Yeast P‐typeATPase

Acknowledgments
GastricH+,K+‐ATPase
Authors: Shin Jaim Moo , Vagin Olga , Munson Keith , Sachs George
Published: March 2008

Originally published in: Handbook of ATPase. Edited by Masamitsu Futai, Yoh Wada and Jack H. Kaplan. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30689‐3

The sections in this article are

GastricH+,K+‐ATPase

α Subunit of GastricH+,K+‐ATPase

β Subunit of GastricH+,K+‐ATPase

Regions of Association Between the α and β Subunits

Regions of Association of the α Subunits

Kinetics of theH+,K+‐ATPase

Conformations of theH+,K+‐ATPase

Functional Residues of theH+,K+‐ATPase

Structural Model of theH+,K+‐ATPase

Crystal Structure of theH+,K+‐ATPase

Molecular Modeling of the GastricH+,K+‐ATPase

Acid Secretion and theH+,K+‐ATPase

Inhibitors of theH+,K+‐ATPase

Substituted Benzimidazoles

Substituted Imidazo[1,2α]pyridines and other K+‐competitive Antagonists

Trafficking of theH+,K+‐ATPase
Proton TranslocatingATPases
Authors: Futai Masamitsu , Sun‐Wada Ge‐Hong , Wada Yoh
Published: March 2008

Originally published in: Handbook of ATPase. Edited by Masamitsu Futai, Yoh Wada and Jack H. Kaplan. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30689‐3

The sections in this article are

Introduction

Catalytic Mechanism ofF‐ATPase

Roles of the γ subunit: energy coupling by mechanical rotation

Roles of the γ Subunit in Energy Coupling

γ Subunit Rotation

Mutational Analysis of the γ Subunit Rotation

Rotational Catalysis of theF‐ATPaseHoloenzyme

Structure ofFoSector and Proton Transport Pathway

Rotational Catalysis of theF‐ATPaseHoloenzyme

Rotational Catalysis ofF‐ATPasein Membranes

Rotational catalysis ofV‐ATPase

Catalytic Site and Proton Pathway

Subunit Rotation ofV‐ATPaseDuring Catalysis

Conclusion

Acknowledgments
VacuolarH+‐ATPases: Structure, Mechanism and Regulation
Authors: Shao Elim , Forgac Michael
Published: March 2008

Originally published in: Handbook of ATPases. Edited by Masamitsu Futai, Yoh Wada and Jack H. Kaplan. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30689‐3

The sections in this article are

Introduction

Function ofV‐ATPases

Overall Structure ofV‐ATPases and Relationship toF‐ATPases

Structure and Function of the Nucleotide‐binding Subunits

Structure and Function of otherV1Subunits and Arrangement of Subunits in theV‐ATPase Complex

Structure and Function ofV0Subunits

Mechanism ofATP‐dependent Proton Transport

Regulation ofV‐ATPase ActivityIn Vivo

Conclusions

Acknowledgments
Anchoring Proteins of the Erythrocyte Membrane
Authors: Yawata Yoshihito
Published: March 2008

Originally published in: Cell Membrane. Yoshihito Yawata. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30463‐9

The sections in this article are

Ankyrin

Introduction

Structure of Red Cell Ankyrin

Membrane (Band 3)‐Binding Domain of Ankyrin

Spectrin‐Binding Domain of Ankyrin

Regulatory Domain of Ankyrin

Functions of Ankyrin

Erythroid and Nonerythroid Ankyrins

Protein 4.2

Protein Chemistry of Protein 4.2

Functions of Protein 4.2

Binding Properties of Protein 4.2

Transglutaminase Activity of Protein 4.2

Phosphorylation of Protein 4.2

Protein 4.2 in Red Cell Membrane Ultrastructure

Protein 4.2 Gene

Characteristics of GenomicDNA

cDNAof the Protein 4.2 Gene

Protein 4.2 Gene in Mouse Red Cells

Tissue‐Specific Expression of the Mouse Protein 4.2 Gene and the Pallid Mutation
Skeletal Proteins of the Erythrocyte Membrane
Authors: Yawata Yoshihito
Published: March 2008

Originally published in: Cell Membrane. Yoshihito Yawata. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30463‐9

The sections in this article are

α‐ and β‐Spectrins

Introduction

Structure of Red Cell Spectrins

Functions of Red Cell Spectrins

Erythroid and Nonerythroid Spectrins

Protein 4.1

Structure of Protein 4.1

Binding to Other Membrane Proteins

Extensive Alternative Splicings

Nonerythroid Protein 4.1 Isoforms

Actin

Other Minor Skeletal Proteins

Thep55 Protein

Adducin

Dematin (Protein 4.9)

Tropomyosin

Tropomodulin

Other Membrane Proteins
Integral Proteins of the Erythrocyte Membrane
Authors: Yawata Yoshihito
Published: March 2008

Originally published in: Cell Membrane. Yoshihito Yawata. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30463‐9

The sections in this article are

Band 3

Structure of Band 3

Functions of Band 3

Membrane Protein Binding by the Cytoplasmic Domain of Band 3

Binding to Glycolytic Enzymes by the Cytoplasmic Domain of Band 3

Binding to Hemoglobin by the Cytoplasmic Domain of Band 3

Anion Exchange Channel by the Transmembrane Domain of Band 3

Lateral and Rotational Mobility of Band 3

Blood Type Antigens and Band 3

Band 3 in Nonerythyroid Cells

Glycophorins

GlycophorinsA,B, andE

GlycophorinA(GPA)

GlycophorinB(GPB)

GlycophorinE(GPE)

GylcophorinsCandD

GlycophorinC(GPC)

GlycophorinD(GPD)

Blood Group Antigens

ABOBlood Group

Rh Blood Group

PBlood Group

Lutheran Blood Group

Kell Blood Group

Lewis Blood Group

Duffy Blood Group

Kidd Blood Group

LWBlood Group

IiBlood Group

TheDiego andWright Blood Group Antigens on Band 3

Other Minor Blood Group Antigens

Glycosyl Phoshatidylinositol (GPI) Anchor Proteins
Retinoid Receptors RAR and RXR: Structure and Function
Authors: Mata de Urquiza Alexander , Perlmann Thomas
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

Retinoids in Development

Retinoid Receptors Transduce Retinoic Acid Signals

Retinoid Receptors Belong to the Nuclear Hormone Receptor Family

Nuclear Receptors Share a Common Structure

The LBD and Ligand‐dependent Transactivation

Cross‐talk

Co‐activators

Co‐repressors

Nuclear Receptors from an Evolutionary Perspective

Fatty acids as Endogenous Ligands for RXR

Conclusions

Acknowledgements
HumanABCTransporters: Function, Expression, and Regulation
Authors: Schmitz Gerd , Langmann Thomas
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

Structural Features ofATPBinding Cassette (ABC) Transporters

Overview of HumanABCGene Subfamilies

The ABCA (ABC1) Subfamily

The ABCB (MDR/TAP) Subfamily

The ABCC (CFTR/MRP) Subfamily

The ABCD (ALD) Subfamily

The ABCE (OABP) and ABCF (GCN20) Subfamilies

The ABCG (White) Subfamily

Diseases and Phenotypes Caused byABCMTransporters

Familial HDL‐deficiency andABCA1

Retinal Degeneration andABCA4 (ABCR)

Cystic Fibrosis (ABCC7/CFTR)

Multidrug Resistance (ABCB1/MDR1,ABCC1/MRP1,ABCG2)

Adrenoleukodystrophy (ABCD1/ALD)

Sulfonylurea Receptor (ABCC8/SUR)

Function and Regulation ofABCTransporters in Lipid Transport

ABCA1 in Macrophage Lipid Transport

ABCG1 and OtherABCGMembers in Sterol Homeostasis

ABCTransporters involved in Hepatobiliary Transport

Conclusions
The Photoproteins
Authors: Shimomura Osamu
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

Various Types of Photoproteins Presently Known

Radiolarian (Protozoa) Photoproteins

Coelenterate Photoproteins

Ctenophore Photoproteins

Pholasin (PholasLuciferin)

ChaetopterusPhotoprotein

Polynoidin

Symplectin

LuminodesmusPhotoprotein

OphiopsilaPhotoprotein

Basic Strategy of Extracting and Purifying Photoproteins

The Photoprotein Aequorin

Extraction and Purification of Aequorin

Hydrophobic Interaction Chromatography

Properties of Aequorin

Stability

Freeze‐drying

Specificity toCa2+

Luminescence of Aequorin by Substances Other Than Divalent Cations

Mechanism of Aequorin Luminescence and Regeneration of Aequorin

Structure of Aequorin

Luminescence Reaction

Regeneration

Inhibitors of Aequorin Luminescence

Recombinant Aequorin

Semi‐synthetic Aequorins

e‐Aequorins
The Outer Mitochondrial Membrane Pore (Voltage‐Dependent Anion Channel)
Authors: Vyssokikh Mikhail , Brdiczka Dieter
Published: March 2008

Originally published in: Bacterial and Eukaryotic Porins. Edited by Roland Benz. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30775‐3

The sections in this article are

Introduction

Structure and Isotypes of VDAC

The Influence of Phospholipids on VDAC Structure

VDAC Conductance and Ion Selectivity

Physiological Significance of the Voltage Dependence

Porins as Specific Binding Sites

VDAC senses Inner Membrane Functions in the Contact Site

Cytochromecis a Component of the Contact Sites

Isolation and Characterization of VDAC‐ANT Complexes

Reconstitution of VDAC‐ANT Complexes

Importance of Metabolic Channeling in Regulation of Energy Metabolism

The VDAC‐ANT Complex as Permeability Transition Pore

The VDAC‐ANT Complex as a Target for Bax‐dependent CytochromecRelease

The VDAC–ANT Complexes contain Cytochromec

The Importance of the Kinases in Regulation of Apoptosis

Suppression of Bax‐dependent CytochromecRelease and Permeability Transition by Hexokinase

Suppression of Permeability Transition by Mitochondrial Creatine Kinase

Conclusion
The Phytochromes
Authors: Tu Shih‐Long , Lagarias Clark
Published: March 2008

Originally published in: Handbook of Photosensory Receptors. Edited by Winslow R. Briggs and John L. Spudich. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31019‐7

The sections in this article are

Introduction

Photomorphogenesis and Phytochromes

The Central Dogma of Phytochrome Action

Molecular Properties of Eukaryotic and Prokaryotic Phytochromes

Molecular Properties of Plant Phytochromes

Molecular Properties of Cyanobacterial Phytochromes

Photochemical and Nonphotochemical Conversions of Phytochrome

The Phytochrome Chromophore

Phytochrome Photointerconversions

Dark Reversion

Phytochrome Biosynthesis and Turnover

Phytobilin Biosynthesis in Plants and Cyanobacteria

Ferredoxin‐dependent Heme Oxygenases

Ferredoxin‐dependent Phytobilin Synthases (Bilin Reductases)

Apophytochrome Biosynthesis and Holophytochrome Assembly

Apophytochrome Biosynthesis

Holophytochrome Assembly

Phytochrome Turnover

Molecular Mechanism of Phytochrome Signaling: Future Perspective

Regulation of Protein‐Protein Interactions by Phosphorylation

Regulation of Tetrapyrrole Metabolism

Acknowledgements
Microbial Rhodopsins
Authors: Spudich John L. , Jung Kwang‐Hwan
Published: March 2008

Originally published in: Handbook of Photosensory Receptors. Edited by Winslow R. Briggs and John L. Spudich. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31019‐7

The sections in this article are

Introduction

Archaeal Rhodopsins

Clues to Newfound Microbial Rhodopsin Function from Primary Sequence Comparison to Archaeal Rhodopsins

Bacterial Rhodopsins

Green‐absorbing Proteorhodopsin (“
GPR
”) from Monterey Bay Surface Plankton

Blue‐absorbing Proteorhodopsin (“
BPR
”) from Hawaiian Deep Sea Plankton

Anabaena
Sensory Rhodopsin

Other Bacterial Rhodopsins

Magnetospirillum

Gloeobacter violaceus
PCC
7421

Eukaryotic Microbial Rhodopsins

Fungal Rhodopsins

Algal Rhodopsins

Spectral Tuning

A Unified Mechanism for Molecular Function?

Opsin‐related Proteins without the Retinal‐binding Site

Conclusions

Acknowledgements
Light‐activated Proteins
Authors: Loudwig Sandra , Bayley Hagan
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

The Properties of Caged Proteins

Extents of Caging and Photoactivation

The Rate of Uncaging: Continuous Irradiation

The Rate of Uncaging: Breakdown of Intermediates

The Effects ofpHon Photolysis

Problems with the Released Caging Group

Photochemistry Peculiar to Proteins

Polypeptide Chain Cleavage

Dominant Negative Effect

Sites of Modification in Caged Proteins

Random Modification

Active‐site Directed Modification

The Use of Crosslinkers

Caging atCysResidues

Sites other thanCysfor Site‐specific Modification

Reagents for Caging by Protein Modification

Determining the Extent of Protein Modification

True Residual Activity

Incomplete Uncaging

Means of Caging other than Chemical Modification

Applications of Caged Proteins

Future Prospects

Turning Proteins OnandOff

Genetically Encoded Caged Proteins and Caging within Cells

Improved Spatial Control

Temporal Control

Medical Applications

Acknowledgments

Note added in proof
Ubiquitin and Ubiquitin‐like Protein Conjugation
Authors: Hochstrasser Mark
Published: March 2008

Protein modification by ubiquitin and ubiquitin‐like proteins (Ubls) plays a pervasive role in eukaryotic cell regulation. One aim of this article is to survey the ubiquitin and Ubl conjugation systems in order to highlight key mechanistic and functional features. Another is to discuss some of the gaps in our understanding of both the evolutionary origins of these conjugation systems and the changes Ubl attachment can impart on a conjugated protein. The ubiquitin and Ubl systems use related enzymes to activate and attach ubiquitin and Ubls to proteins (and, in at least one case, to phospholipids). Most ubiquitin and Ubl attachments are dynamic, with efficient reversal of the modifications by a battery of deconjugating enzymes. The versatility of these systems is reflected in the enormous array of biological processes they control. It is likely that ubiquitin and Ubl attachments function fundamentally as a means of regulating macromolecular interactions. Best known is the ability of polyubiquitinated protein to bind with high affinity to polyubiquitin receptor sites on the proteasome, causing the rapid degradation of the tagged protein. Specific examples of physiological deployment of ubiquitin and Ubl attachment will be used to illustrate distinct mechanisms of regulation by these highly conserved protein modifiers.

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

Introduction

The Ubiquitin Conjugation Pathway

Ubiquitin Polymers

Ubiquitin Attachment Dynamics

Ubls: A Typical Modification Cycle by an Atypical Set of Modifiers

Some Unusual Ubl Conjugation Features

Origins of the Ubiquitin System

Sulfurtransferases and Ubl Activation Enzymes

The E1‐E2 Couple

Ubiquitin‐binding Domains and Ubiquitin Receptors in the Proteasome Pathway

A Proteasome “Ubiquitin Receptor”

A Plethora of Ubiquitin‐binding Domains

Ubiquitin‐Conjugate Adaptor Proteins

Ubiquitin‐binding Domains and Membrane Protein Trafficking

The MVB Pathway and RNA Virus Budding

Sumoylation and SUMO‐binding Motifs

A SUMO‐binding Motif

A SUMO‐induced Conformational Change

Interactions Between Different Sumoylated Proteins

General Biochemical Functions of Protein‐Protein Conjugation

Negative Regulation by Ubl Conjugation

Positive Regulation by Ubl Conjugation

Cross‐regulation by Ubls

Conclusions

Acknowledgments
Allosteric Regulation by Membrane‐binding Domains
Authors: Canagarajah Bertram , Smith William J. , Hurley James H.
Published: March 2008

Originally published in: Protein‐Lipid Interactions. Edited by Lukas K. Tamm. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31151‐4

The sections in this article are

Introduction

How Membranes and
PH
Domains Regulate Rho Family‐specific Guanine Nucleotide Exchange Factors (
GEF
s)

DH
and
PH
Domain Rho
GEF
s

Regulation of
GEF
Activity by
PH
Domains

Regulation of
G
‐protein Receptor Kinase (
GRK
) 2 Activity by Lipids and the
G
βγ Subunit at the Membrane

Lipid Activation of
R
ac‐
GAP
Activity: β2‐Chimaerin

The
C
1 Domain of β2‐Chimaerin is Buried

Mechanism of Allosteric
R
ac‐
GTP
ase Activation by the
C
1 Domain

Acknowledgment
Thermodynamics of Protein‐Ligand Interactions
Authors: Raffa R. B.
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

Basic Thermodynamics of Protein‐Ligand Interactions

Measurement of Thermodynamic Parameters

Calorimetric Determination of Thermodynamic Parameters

van't Hoff Determination of Thermodynamic Parameters

Relationship to Equilibrium Constant

Obtaining the Equilibrium Constant

Applications

Calorimetric Determination of Thermodynamic Parameters

van't Hoff Determination of Thermodynamic Parameters

Caveats
Hydrogen Bonds in Protein‐Ligand Complexes
Authors: Williams M. A. , Ladbury J. E.
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

The Importance of Hydrogen Bonds

Defining the Hydrogen Bond

Physical Character of Hydrogen Bonds

Crystallographic Studies of Hydrogen Bonds

The Geometry of Hydrogen Bonds

Infrared Spectroscopy of Hydrogen Bonds

NMR Studies of Hydrogen Bonds

Thermodynamics of Hydrogen Bonding

Experimental Thermodynamics of Biomolecular Hydrogen Bonds

Interactions with Water

Bulk and Surface Water Molecules

Buried Water Molecules

Hydrogen Bonds in Drug Design

Diverse Effects of Hydrogen Bonding on Drug Properties

Optimizing Inhibitor Affinity

Computational Tools for Hydrogen Bond Analysis and Design

Conclusion
Enzyme Inhibitor Design
Authors: Banner D. W.
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

The Active Site

The Heuristic Approach

Mechanism‐based Covalent Inhibitors

Parallelde novoDesign of Inhibitors

Evolution of Inhibitors

Inhibitors from Progressive Design

Lessons from Classical Inhibitors

Estimating the Energies of Interactions

Water and Solvent

Displacing a Tightly Bound Water

Binding of Solvent Molecules

Screening

Structure‐Activity Relationships (SAR)

Present Clinical Status of Thrombin Inhibitors

Conclusions

Acknowledgments
Protein Kinase Inhibitors
Authors: Adams Jerry L. , Veal James , Shewchuk Lisa
Published: March 2008

Originally published in: Protein Crystallography in Drug Discovery. Edited by Robert E. Babine and Sherin S. Abdel‐Meguid. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30678‐7

The sections in this article are

Introduction

Structure and Function

Tertiary Structure

Catalysis and Substrate Binding

Regulation and Conformational Flexibility

Activation Loop Conformation

Glycine Rich Loop

C‐Helix Orientation

Lobe Orientation

Solvent Channel

Crystallization

Defining the Construct

Mutagenesis

Phosphorylation

Inhibitor Design

Binding in ATP Cleft

ATP Binding Sites

Gatekeeper‐Dependent Binding Pocket

Lipophilic Plug

Polar Surface Site

Conformational Considerations

Inhibitor‐Induced Binding

What is the Most Appropriate Enzyme Form for Crystallography?

Homology Models and Surrogate Kinases

Paradigms for Kinase Drug Discovery

High Throughput Screening

Structure‐Based Design

Mechanism‐Based and Ligand Mimetic Design

Computational Chemistry and Virtual Screening

Selectivity

Conclusion
Molecular Recognition of Nuclear Hormone Receptor‐Ligand Complexes
Authors: Babine Robert E.
Published: March 2008

Originally published in: Protein Crystallography in Drug Discovery. Edited by Robert E. Babine and Sherin S. Abdel‐Meguid. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30678‐7

The sections in this article are

Introduction

Nuclear Hormone Receptors: Ligand Binding Domains

Dimerization and Interactions with Co‐activators and Co‐repressors

Steroid Receptors

The Role of the Ligand

Estradiol Estrogen Receptor Complex

Other Estrogen Receptor Agonists Complexes

Estrogen Receptor Antagonists Complexes

Genistein — An
ER
‐β Partial Agonist

R,R‐5,11‐
cis
‐Diethyl‐5,6,11,12‐tetrahydrochrysene‐2,8‐diol: An
ER
‐α Agonist and
ER
‐β Antagonist

Structural Basis for Agonism and Antagonism and Partial Agonism: The Role of the Ligand

Progesterone/Progesterone Receptor Complex

Androgen Receptor Complexes

Glucocorticoid Receptor

Steroid Ligand Selectivity

The Vitamin D Receptor‐Ligand Complexes

The Retinoic Acid Receptors
RAR
and
RXR

Introduction

RAR
‐γ and
RXR
‐α Retinoid Complexes

Selectivity of
RAR
Ligands and
RAR
Isotypes

RXR
Complexes with Unnatural Ligands

PPAR
: Isotype‐Selective Ligands

Conclusions

Acknowledgements
The Determination of Equilibrium Dissociation Constants of Protein‐Ligand Complexes by NMR
Authors: Roberts Gordon C.K.
Published: March 2008

Originally published in: BioNMR in Drug Research. Edited by Oliver Zerbe. Copyright © 2002 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30465‐7

The sections in this article are

Introduction

Chemical Exchange and NMR

The Basic Equations

Slow Exchange

Intermediate Exchange

Fast Exchange

Very Fast Exchange

The General Case of Fast Exchange

Paramagnetic Relaxation

Conclusions
Protein‐Lipid Interactions during Virus Entry by Membrane Fusion
Authors: Lai Alex L. , Li Yinling , Tamm Lukas K.
Published: March 2008

Originally published in: Protein‐Lipid Interactions. Edited by Lukas K. Tamm. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31151‐4

The sections in this article are

Introduction

Fusion of Pure Lipid Bilayers

Viral Protein Sequences that Mediate Lipid Bilayer Fusion

Fusion Peptides

Transmembrane Domains

Other Regions of the Fusion Protein

Interactions of Fusion Peptides with Lipid Bilayers

HIV Fusion Peptide‐Bilayer Interactions

Influenza Fusion Peptide Structure

Influenza Fusion Peptide Mutants

Binding of Fusion Peptides to Lipid Bilayers

Sendai, Measles and Ebola Fusion Peptide–Bilayer Interactions

Perturbation of Bilayer Structure by Fusion Peptides

Interactions of Transmembrane Domains with Lipid Bilayers

Structure–Function (Fusion) Relationships of Membrane‐interactive Viral Fusion Protein Domains

Fusion Peptide Mutants

Transmembrane Domain Mutants

Possible Mechanisms for Initiating the Formation of Viral Fusion Pores

Acknowledgments
The Calponin Homology (CH) Domain
Authors: Gimona Mario , Winder Steven J.
Published: March 2008

Originally published in: Modular Protein Domains. Edited by Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30813‐2

The sections in this article are

Introduction and Brief History

Structure of the Domain – The CH Domain Fold

Structures of Single CH Domains

Structures of Tandem CH Domains

Molecular and Signaling Function

Actin‐binding Domains

Single EB‐type CH Domains Function as Microtubule Anchors

Kinases, Phospholipids, and Other Cytoskeletal Components

CH Domain‐containing Proteins and Human Diseases

The Dystrophin ABD and Muscular Dystrophy

The Filamin ABD and Otopalatodigital Syndromes

The α‐Actinin ABD and Glomerulosclerosis

The β‐Spectrin ABD and Spherocytosis

Emerging Research Directions and Recent Developments

Conclusions

Acknowledgements
PDZ Domains: Intracellular Mediators of Carboxy‐Terminal Protein Recognition and Scaffolding
Authors: Lasky Laurence A. , Skelton Nicholas J. , Sidhu Sachdev S.
Published: March 2008

Originally published in: Modular Protein Domains. Edited by Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30813‐2

The sections in this article are

Introdution

Structural Analysis of PDZ Domains

Analysis of PDZ Domain–Ligand Interactions with Mutagenesis and Synthetic Peptides

Molecular and Signaling Functions of PDZ Domains

INAD as a Molecular Scaffold

LIN‐7‐Receptor Tyrosine Kinase Interactions and Subcellular Localization

PDZ Domain Proteins and Epithelial Polarity Induction and Maintenance

A Few Miscellaneous Examples: The Synapse, Disheveled, CARD MAGUKs, and Beta Adrenergic Receptors

Conclusions

Acknowledgements
PTB Domains
Authors: Margolis Ben , Traub Linton M.
Published: March 2008

Originally published in: Modular Protein Domains. Edited by Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30813‐2

The sections in this article are

Introduction

Function of PTB Domain Proteins

Role of PTB Domain Proteins in Tyrosine Kinase Signaling

Shc

Proteins with PTBI Domains

Additional PTB Domain Proteins Involved in Tyrosine Kinase Signaling

PTB Domain Proteins That Function Independent of Phosphotyrosine

PTB Domain Proteins That Bind APP

PTB Domain Proteins That Bind Integrins

PTB Domain Proteins That Control Endocytosis

PTB Domain Structure

Broad Binding Specificity

Diverse Modes of Engagement

Phospholipid Binding

Conclusions
Phosphoserine/Threonine Binding Domains
Authors: Elia Andrew E. H. , Yaffe Michael B.
Published: March 2008

Originally published in: Modular Protein Domains. Edited by Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30813‐2

The sections in this article are

Introduction

The 14‐3‐3 Proteins

History and Functions

Structure and Binding

WW Domains

FHA Domains

WD40 Repeats of F‐box Proteins

Polo‐box Domains

Conclusions

Acknowledgements
EVH1/WH1 Domains
Authors: Ball Linda J. , Wiedemann Urs , Zimmermann Jürgen , Jarchau Thomas
Published: March 2008

Originally published in: Modular Protein Domains. Edited by Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30813‐2

The sections in this article are

Introduction

Occurrence and Distribution of EVH1 Domains

Proteins Containing EVH1 Domains

Modular Architecture of EVH1‐containing Proteins: Domain Location, Domain Combinations, and Copy Number

Classification of EVH1 Domains

Structures of EVH1 Domains and Their Complexes

High‐resolution Structures of EVH1 and Related Domains

Structures of EVH1 Complexes and Determinants of Ligand Specificity

Comparisons with RanBDs, PTB Domains, and PH Domains

Biological Function and Signaling Pathways Involving EVH1 Domains

Ena/VASP Interactions

Homer/Vesl Interactions

WASP/N‐WASP Interactions

Spred Interactions

Emerging Research Directions and Recent Developments

Use of Sequence and Structural Data in Prediction of Binding Partners

Use of Structural Data from Complexes to Guide the Rational Design of New Ligands

Conclusions
SH3 Domains
Authors: Mayer Bruce J. , Saksela Kalle
Published: March 2008

Originally published in: Modular Protein Domains. Edited by Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30813‐2

The sections in this article are

Introduction

Historical Perspective

Genetics to the Rescue

Structure and Specificity

Predicting Binding Partners

Core Peptide Docking vs. Extended Interactions

Atypical SH3 Docking Motifs

Experimental Exploitation of SH3 Specificity

Conclusion

Acknowledgements
The SH2 Domain: A Prototype for Protein Interaction Modules
Authors: Pawson Tony , Gish Gerald D. , Nash Piers
Published: March 2008

Originally published in: Modular Protein Domains. Edited by Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30813‐2

The sections in this article are

The Multidomain Nature of Signaling Proteins and Identification of the SH2 Domain

SH2 Domains as a Prototype for Interaction Domains

Structure and Binding Properties of SH2 Domains

Different Modes of SH2 Domain‐Phosphopeptide Recognition

Signaling Pathways and Networks

Plasticity of SH2 Domains

SH2 Domain Dimerization

Tandem SH2 Domains

Composite and Complex Interaction Domains

Allosteric Regulation

SH2 Domains and Disease

Conclusions
The WW Domain
Authors: Sudol Marius
Published: March 2008

Originally published in: Modular Protein Domains. Edited by Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30813‐2

The sections in this article are

Introduction and Brief History of Module Discovery

Structure of the WW Domain‐Ligand Complex

WW domains and Human Diseases

From Liddle's Syndrome to Liddle's Disease

Amyloid Precursor Protein: APP and FE65

Dystrophin WW Domain and Muscular Dystrophy

Emerging Directions and Recent Developments

AxCell's Map

ErbB4 Receptor Protein‐Tyrosine Kinase and its WW Domain‐containing Adaptor, YAP

Membrane Proteins with PPxYs Implicated in Cancer

Conclusions

Acknowledgements
High‐Throughput Crystallography
Authors: Jhoti Harren
Published: March 2008

Originally published in: Protein Crystallography in Drug Discovery. Edited by Robert E. Babine and Sherin S. Abdel‐Meguid. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30678‐7

The sections in this article are

Introduction

Technological Advances

Clone to Crystal

Protein Production

Crystallization

Crystal to Structure

Progress in Structural Genomics

High‐throughput Crystallography in Lead Discovery

Protein‐Ligand Crystal Structures

Fragment‐Based Lead Discovery

Fragment‐Based Lead Discovery Using X‐ray Crystallography

Structure‐Based Optimization of Fragment Hits

Conclusions

Acknowledgements
Micro‐Crystallization of Proteins
Authors: Hansen Carl L. , Sommer Morten , Self Kyle , Berger James M. , Quake Stephen R.
Published: March 2008

Originally published in: Protein Crystallography in Drug Discovery. Edited by Robert E. Babine and Sherin S. Abdel‐Meguid. Copyright © 2004 Wiley‐VCH GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30678‐7

The sections in this article are

Introduction

Microfluidics ‐ Method and Design

Utility of Microfluidics for Crystallization
NMR
of Membrane‐Associated Peptides and Proteins
Authors: Bader Reto , Lerch Mirjam , Zerbe Oliver
Published: March 2008

Originally published in: BioNMR in Drug Research. Edited by Oliver Zerbe. Copyright © 2002 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30465‐7

The sections in this article are

The Biochemistry of Membrane Interactions

Introduction

Biological Membranes

Protein‐Membrane Interactions

Aggregate Structures of Lipids and their Biophysics

Micelles

Bicelles

Vesicles or Liposomes

The NMR Sample

Synthesis of Peptides and Proteins

Choice of Detergent

Choice of pH

Choice of Temperature

Salt Concentrations

Practical Tips for Sample Preparation

The Structure and Dynamics of Membrane‐Associated Peptides – A Case Study of Neuropeptide
Y
(
NPY
)

Introduction

Structure Determination of Micelle‐Bound
NPY

The Determination of the Topology of the Membrane‐
NPY
Interface

Spin Labels

Amide
H
,
D
Exchange

Measurement of Internal Dynamics of
NPY
/
DPC
Determination of Protein Dynamics Using
15
N
Relaxation Measurements
Authors: Fushman David
Published: March 2008

Originally published in: BioNMR in Drug Research. Edited by Oliver Zerbe. Copyright © 2002 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30465‐7

The sections in this article are

Introduction

Spectroscopic Techniques

Accuracy and Precision of the Method

Sampling Schemes

Peak Integration

Estimation of Experimental Errors

Noise Reduction

Temperature Control

Basic Equations

The Model‐Free Approach

Reduced Spectral Densities Mapping

Multi‐Field Approach

Strategies for the Analysis of Protein Dynamics from
15
N
Relaxation Data

Overall Tumbling

How Can We Derive the Rotational Diffusion Tensor of a Molecule from Spin‐Relaxation Data?

Theoretical Background

Derivation of the Diffusion Tensor when Protein Structure is Known

What Can We Do when Protein Structure is not Known? Preliminary Characterization of the Diffusion Tensor

Isotropic Overall Model

Model Selection for
NH
Bond Dynamics

Accuracy and Precision of the Model‐Free Parameters

Motional Models

Conformational Exchange

Effects of Self‐Association

Using
13
C
Relaxation to Study Protein Dynamics

Conclusions

Acknowledgements
Membrane Protein Crystallization Mediated by Antibody Fragments
Authors: Hunte Carola , Münke Cornelia
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

Crystallization of Membrane Proteins Mediated by Antibody Fragments

Overview

Generation of Antibodies Suitable for Co‐crystallization

Immunization

Selection of Antibodies

Antibody Fragments

Protein Purification and Crystallization

Indirect Immunoaffinity Purification

Crystallization

Alternative Approaches for Expansion of the Polar Surface

Conclusions

Acknowledgments
13C‐ and15N‐Isotopic Labeling of Proteins
Authors: Klammt Christian , Bernhard Frank , Rüterjans Heinz
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

Expression Systems for theIn VivoIncorporation of13C and15N Labels into Proteins

Protein Production and13C and15N‐labeling inE. coliExpression Systems

13C‐ and15N‐labeling of Proteins inP. pastoris

13C‐ and15N‐labeling of Proteins by Expression in Chinese Hamster Ovary (CHO) Cells

13C‐ and15N‐labeling of Proteins in Other Organisms

Strategies for the Production of Selectively13C‐ and15N‐labeled Proteins

Selective Labeling of Amino Acids

Specific Isotope Labeling with13C

Segmental Isotope Labeling

Cell‐free Isotope Labeling

Components of Cell‐free Expression Systems

Cell‐free Expression Techniques

Specific Applications of the Cell‐free Labeling Technique
Studying Protein Folding and Aggregation by Laser Light Scattering
Authors: Gast Klaus , Modler Andreas J.
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

Basic Principles of Laser Light Scattering

Light Scattering by Macromolecular Solutions

Molecular Parameters Obtained from Static Light Scattering (SLS)

Molecular Parameters Obtained from Dynamic Light Scattering (DLS)

Advantages of Combined SLS and DLS Experiments

Laser Light Scattering of Proteins in Different Conformational States – Equilibrium Folding/Unfolding Transitions

General Considerations, Hydrodynamic Dimensions in the Natively Folded State

Changes in the Hydrodynamic Dimensions during Heat‐induced Unfolding

Changes in the Hydrodynamic Dimensions upon Cold Denaturation

Denaturant‐induced Changes of the Hydrodynamic Dimensions

Acid‐induced Changes of the Hydrodynamic Dimensions

Dimensions in Partially Folded States – Molten Globules and States

Comparison of the Dimensions of Proteins in Different Conformational States

Scaling Laws for the Native and Highly Unfolded States, Hydrodynamic Modeling

Studying Folding Kinetics by Laser Light Scattering

General Considerations, Attainable Time Regions

Hydrodynamic Dimensions of the Kinetic Molten Globule of Bovine α‐Lactalbumin

RNase A is Only Weakly Collapsed During the Burst Phase of Folding

Misfolding and Aggregation Studied by Laser Light Scattering

Overview: Some Typical Light Scattering Studies of Protein Aggregation

Studying Misfolding and Amyloid Formation by Laser Light Scattering

Overview: Initial States, Critical Oligomers, Protofibrils, Fibrils

Aggregation Kinetics of Aβ Peptides

Kinetics of Oligomer and Fibril Formation of PGK and Recombinant Hamster Prion Protein

Mechanisms of Misfolding and Misassembly, Some General Remarks

Protocols and Instrumentation

Laser Light Scattering Instrumentation

Basic Experimental Set‐up, General Requirements

Supplementary Measurements and Useful Options

Commercially Available Light Scattering Instrumentation

Experimental Protocols for the Determination of Molecular Mass and Stokes Radius of a Protein in a Particular Conformational State

Acknowledgments
Spectroscopic Techniques to Study Protein Conformation
Authors: Schmid Franz
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

Introduction

Absorbance

Absorbance of Proteins

Practical Considerations for the Measurement of Protein Absorbance

Data Interpretation

Fluorescence

The Fluorescence of Proteins

Energy Transfer and Fluorescence Quenching in a Protein: Barnase

Protein Unfolding Monitored by Fluorescence

Environmental Effects on Tyrosine and Tryptophan Emission

Practical Considerations

Circular Dichroism

CD Spectra of Native and Unfolded Proteins

Measurement of Circular Dichroism

Evaluation of CD Data
Ion Channel Structural Studies
Authors: Bass Randal B. , Spencer Robert H.
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

Expression of Membrane Proteins for Structural Studies

Mammalian Expression

Insect Expression

Yeast Expression

Bacterial Expression

The Detergent Factor

Purification

Crystallization

Use of Antibody Fragments

Generation of First Diffraction Datasets

Selenomethionine Phasing of Membrane Proteins

MAD
Phasing and Edge Scanning

Negative
B
‐factor Application (Structure Factor Sharpening)

Conclusions
Computational Analysis of Modular Protein Architectures
Authors: Linding Rune , Letunic Ivica , Gibson Toby J. , Bork Peer
Published: March 2008

Originally published in: Modular Protein Domains. Edited by Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30813‐2

The sections in this article are

Introduction

Protein Architecture: Sequence, Structure, and Function

The Modular Model of Protein Function

Partitioning of Protein Space

Analyzing Globular Domains

Globularity of Domains

Resources for Analysis of Globular Domains

SMART: Simple Modular Architecture Research Tool

The SMART Alignment Set

SMART Relational Database System

Web Interface

Application of SMART

Other Features and Resources

Globular Repeats

Domain Interaction Prediction

No Domains?

Analyzing Nonglobular Protein Segments

Unstructured Regions: Protein Disorder

What Role Does Protein Disorder Play in Biology?

What is Protein Disorder?

Methods for Finding Protein Disorder

GlobPlotting

Prediction of Multiple Types of Disorder with DisEMBL

Design of Protein Expression Vectors

Function Prediction for Nonglobular Protein Segments

Available Resources

The Eukaryotic Linear Motif Resource: ELM

ELM
Annotation – ‘Site seeing’

ELM Resource Architecture

Knowledge‐based Decision Support (KBDS): ELM Filtering

Using ELM

URLs

Conclusions

Acknowledgements
Mass Spectrometry for the Detection and Identification of Proteins
Authors: König Simone , Haberland Jörg , Grote Jens , Zeller Martin , Gedig Erk , Fobker Manfred , Erren Michael , Pursley Stephen W. , Pearl John E. , Cullen Paul , Lorkowski Stefan
Published: March 2008

Originally published in: Analysing Gene Expression. Edited by Stefan Lorkowski, Paul Cullen. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30488‐2

The sections in this article are

Introduction

How does mass spectrometry work?

Ionisation of molecules

Detection of ions

Appearance of spectra

Modes of operation

Proteomic mass spectrometry

Data analysis tools for mass spectroscopic experiments

Proteomics servers and databases

An example: Identification of an isolated and unknown protein

Is quantification possible with mass spectrometry?

Analysis of protein modifications

Phosphorylation

Glycosylation

Access to protein tertiary structure

Analysis of intact proteins and non‐covalent protein complexes

Affinity mass spectrometry

Conclusion
Protein Microarrays
Authors: König Simone , Haberland Jörg , Grote Jens , Zeller Martin , Gedig Erk , Fobker Manfred , Erren Michael , Pursley Stephen W. , Pearl John E. , Cullen Paul , Lorkowski Stefan
Published: March 2008

Originally published in: Analysing Gene Expression. Edited by Stefan Lorkowski, Paul Cullen. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30488‐2

The sections in this article are

Introduction

Principles and basics, typical results and applications

Conclusion
Separation Strategies for Proteomics
Authors: König Simone , Haberland Jörg , Grote Jens , Zeller Martin , Gedig Erk , Fobker Manfred , Erren Michael , Pursley Stephen W. , Pearl John E. , Cullen Paul , Lorkowski Stefan
Published: March 2008

Originally published in: Analysing Gene Expression. Edited by Stefan Lorkowski, Paul Cullen. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30488‐2

The sections in this article are

Introduction

Conventional slab gel electrophoresis

Isoelectric focusing (IEF)

Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS‐PAGE) and Western blotting

Two‐dimensional polyacrylamide gel electrophoresis (2D‐PAGE)

Two‐dimensional difference gel electrophoresis (2D‐DIGE)

High‐performance liquid chromatography (HPLC)

Ion exchange chromatography (IEC)

Size exclusion chromatography (SEC)

Affinity chromatography

Reverse phase chromatography (RPC)

Normal phase chromatography

Capillary electrophoresis (CE) and capillary electrochromatography (CEC)

Multi‐dimensional separations

New approaches

Isotope‐coded affinity tag method (ICAT™)

Multi‐epitope ligand‐Kartographie (MELK)

Conclusion