bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Phytochromes
Authors: Tu Shih‐Long , Lagarias Clark 
Published: March 2008

AbstractOriginally 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: 3‐527‐31019‐7The sections in this article areIntroductionPhotomorphogenesis and PhytochromesThe Central Dogma of Phytochrome ActionMolecular Properties of Eukaryotic and Prokaryotic PhytochromesMolecular Properties of Plant PhytochromesMolecular Properties of Cyanobacterial PhytochromesPhotochemical and Nonphotochemical Conversions of PhytochromeThe Phytochrome ChromophorePhytochrome PhotointerconversionsDark ReversionPhytochrome Biosynthesis and TurnoverPhytobilin Biosynthesis in Plants and CyanobacteriaFerredoxin‐dependent Heme OxygenasesFerredoxin‐dependent Phytobilin Synthases (Bilin Reductases)Apophytochrome Biosynthesis and Holophytochrome AssemblyApophytochrome BiosynthesisHolophytochrome AssemblyPhytochrome TurnoverMolecular Mechanism of Phytochrome Signaling: Future PerspectiveRegulation of Protein‐Protein Interactions by PhosphorylationRegulation of Tetrapyrrole MetabolismAcknowledgements
Microbial Rhodopsins
Authors: Spudich John L. , Jung Kwang‐Hwan 
Published: March 2008

Abstract
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

AbstractOriginally 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: 3‐527‐30783‐8The sections in this article areIntroductionThe Properties of Caged ProteinsExtents of Caging and PhotoactivationThe Rate of Uncaging: Continuous IrradiationThe Rate of Uncaging: Breakdown of IntermediatesThe Effects ofpHon PhotolysisProblems with the Released Caging GroupPhotochemistry Peculiar to ProteinsPolypeptide Chain CleavageDominant Negative EffectSites of Modification in Caged ProteinsRandom ModificationActive‐site Directed ModificationThe Use of CrosslinkersCaging atCysResiduesSites other thanCysfor Site‐specific ModificationReagents for Caging by Protein ModificationDetermining the Extent of Protein ModificationTrue Residual ActivityIncomplete UncagingMeans of Caging other than Chemical ModificationApplications of Caged ProteinsFuture ProspectsTurning Proteins OnandOffGenetically Encoded Caged Proteins and Caging within CellsImproved Spatial ControlTemporal ControlMedical ApplicationsAcknowledgmentsNote added in proof
Ubiquitin and Ubiquitin‐like Protein Conjugation
Authors: Hochstrasser Mark 
Published: March 2008

Abstract
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

Abstract
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

Abstract
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

Summary
Hydrogen Bonds in Protein‐Ligand Complexes
Authors: Williams M. A. , Ladbury J. E. 
Published: March 2008

AbstractOriginally published in: Protein‐Ligand Interactions.Edited by Hans‐Joachim Böhm, Gisbert Schneider. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30521‐6The sections in this article areIntroductionThe Importance of Hydrogen BondsDefining the Hydrogen BondPhysical Character of Hydrogen BondsCrystallographic Studies of Hydrogen BondsThe Geometry of Hydrogen BondsInfrared Spectroscopy of Hydrogen BondsNMR Studies of Hydrogen BondsThermodynamics of Hydrogen BondingExperimental Thermodynamics of Biomolecular Hydrogen BondsInteractions with WaterBulk and Surface Water MoleculesBuried Water MoleculesHydrogen Bonds in Drug DesignDiverse Effects of Hydrogen Bonding on Drug PropertiesOptimizing Inhibitor AffinityComputational Tools for Hydrogen Bond Analysis and DesignConclusion
Enzyme Inhibitor Design
Authors: Banner D. W. 
Published: March 2008

AbstractOriginally published in: Protein‐Ligand Interactions.Edited by Hans‐Joachim Böhm, Gisbert Schneider. Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30521‐6The sections in this article areIntroductionThe Active SiteThe Heuristic ApproachMechanism‐based Covalent InhibitorsParallelde novoDesign of InhibitorsEvolution of InhibitorsInhibitors from Progressive DesignLessons from Classical InhibitorsEstimating the Energies of InteractionsWater and SolventDisplacing a Tightly Bound WaterBinding of Solvent MoleculesScreeningStructure‐Activity Relationships (SAR)Present Clinical Status of Thrombin InhibitorsConclusionsAcknowledgments
Protein Kinase Inhibitors
Authors: Adams Jerry L. , Veal James , Shewchuk Lisa 
Published: March 2008

AbstractOriginally 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: 3‐527‐30678‐7The sections in this article areIntroductionStructure and FunctionTertiary StructureCatalysis and Substrate BindingRegulation and Conformational FlexibilityActivation Loop ConformationGlycine Rich LoopC‐Helix OrientationLobe OrientationSolvent ChannelCrystallizationDefining the ConstructMutagenesisPhosphorylationInhibitor DesignBinding in ATP CleftATP Binding SitesGatekeeper‐Dependent Binding PocketLipophilic PlugPolar Surface SiteConformational ConsiderationsInhibitor‐Induced BindingWhat is the Most Appropriate Enzyme Form for Crystallography?Homology Models and Surrogate KinasesParadigms for Kinase Drug DiscoveryHigh Throughput ScreeningStructure‐Based DesignMechanism‐Based and Ligand Mimetic DesignComputational Chemistry and Virtual ScreeningSelectivityConclusion
Molecular Recognition of Nuclear Hormone Receptor‐Ligand Complexes
Authors: Babine Robert E. 
Published: March 2008

Abstract
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

Abstract
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

AbstractOriginally published in: Protein‐Lipid Interactions. Edited by Lukas K. Tamm. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31151‐4The sections in this article areIntroductionFusion of Pure Lipid BilayersViral Protein Sequences that Mediate Lipid Bilayer FusionFusion PeptidesTransmembrane DomainsOther Regions of the Fusion ProteinInteractions of Fusion Peptides with Lipid BilayersHIV Fusion Peptide‐Bilayer InteractionsInfluenza Fusion Peptide StructureInfluenza Fusion Peptide MutantsBinding of Fusion Peptides to Lipid BilayersSendai, Measles and Ebola Fusion Peptide–Bilayer InteractionsPerturbation of Bilayer Structure by Fusion PeptidesInteractions of Transmembrane Domains with Lipid BilayersStructure–Function (Fusion) Relationships of Membrane‐interactive Viral Fusion Protein DomainsFusion Peptide MutantsTransmembrane Domain MutantsPossible Mechanisms for Initiating the Formation of Viral Fusion PoresAcknowledgments
The Calponin Homology (CH) Domain
Authors: Gimona Mario , Winder Steven J. 
Published: March 2008

AbstractOriginally 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: 3‐527‐30813‐2The sections in this article areIntroduction and Brief HistoryStructure of the Domain – The CH Domain FoldStructures of Single CH DomainsStructures of Tandem CH DomainsMolecular and Signaling FunctionActin‐binding DomainsSingle EB‐type CH Domains Function as Microtubule AnchorsKinases, Phospholipids, and Other Cytoskeletal ComponentsCH Domain‐containing Proteins and Human DiseasesThe Dystrophin ABD and Muscular DystrophyThe Filamin ABD and Otopalatodigital SyndromesThe α‐Actinin ABD and GlomerulosclerosisThe β‐Spectrin ABD and SpherocytosisEmerging Research Directions and Recent DevelopmentsConclusionsAcknowledgements
PDZ Domains: Intracellular Mediators of Carboxy‐Terminal Protein Recognition and Scaffolding
Authors: Lasky Laurence A. , Skelton Nicholas J. , Sidhu Sachdev S. 
Published: March 2008

Abstract
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

AbstractOriginally 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: 3‐527‐30813‐2The sections in this article areIntroductionFunction of PTB Domain ProteinsRole of PTB Domain Proteins in Tyrosine Kinase SignalingShcProteins with PTBI DomainsAdditional PTB Domain Proteins Involved in Tyrosine Kinase SignalingPTB Domain Proteins That Function Independent of PhosphotyrosinePTB Domain Proteins That Bind APPPTB Domain Proteins That Bind IntegrinsPTB Domain Proteins That Control EndocytosisPTB Domain StructureBroad Binding SpecificityDiverse Modes of EngagementPhospholipid BindingConclusions
Phosphoserine/Threonine Binding Domains
Authors: Elia Andrew E. H. , Yaffe Michael B. 
Published: March 2008

Abstract
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

AbstractOriginally 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: 3‐527‐30813‐2The sections in this article areIntroductionOccurrence and Distribution of EVH1 DomainsProteins Containing EVH1 DomainsModular Architecture of EVH1‐containing Proteins: Domain Location, Domain Combinations, and Copy NumberClassification of EVH1 DomainsStructures of EVH1 Domains and Their ComplexesHigh‐resolution Structures of EVH1 and Related DomainsStructures of EVH1 Complexes and Determinants of Ligand SpecificityComparisons with RanBDs, PTB Domains, and PH DomainsBiological Function and Signaling Pathways Involving EVH1 DomainsEna/VASP InteractionsHomer/Vesl InteractionsWASP/N‐WASP InteractionsSpred InteractionsEmerging Research Directions and Recent DevelopmentsUse of Sequence and Structural Data in Prediction of Binding PartnersUse of Structural Data from Complexes to Guide the Rational Design of New LigandsConclusions
SH3 Domains
Authors: Mayer Bruce J. , Saksela Kalle 
Published: March 2008

AbstractOriginally 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: 3‐527‐30813‐2The sections in this article areIntroductionHistorical PerspectiveGenetics to the RescueStructure and SpecificityPredicting Binding PartnersCore Peptide Docking vs. Extended InteractionsAtypical SH3 Docking MotifsExperimental Exploitation of SH3 SpecificityConclusionAcknowledgements
The SH2 Domain: A Prototype for Protein Interaction Modules
Authors: Pawson Tony , Gish Gerald D. , Nash Piers 
Published: March 2008

AbstractOriginally 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: 3‐527‐30813‐2The sections in this article areThe Multidomain Nature of Signaling Proteins and Identification of the SH2 DomainSH2 Domains as a Prototype for Interaction DomainsStructure and Binding Properties of SH2 DomainsDifferent Modes of SH2 Domain‐Phosphopeptide RecognitionSignaling Pathways and NetworksPlasticity of SH2 DomainsSH2 Domain DimerizationTandem SH2 DomainsComposite and Complex Interaction DomainsAllosteric RegulationSH2 Domains and DiseaseConclusions
The WW Domain
Authors: Sudol Marius 
Published: March 2008

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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