bluuebunny/crossref_metadata_2025 huggingface dataset:
Denaturation of Proteins by Urea and Guanidine Hydrochloride
Authors: Pace C. Nick , Grimsley Gerald R. , Scholtz J. Martin
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

How Urea Denatures Proteins

Linear Extrapolation Method

Δ
G
(H
2
O)

m
‐Values

Conclusions

Practical Considerations

How to Choose the Best Denaturant for your Study

How to Prepare Denaturant Solutions

Preparation of a urea stock solution

How to Determine Solvent Denaturation Curves

Determining a Urea or GdmCl Denaturation Curve

How to Analyze Urea or GdmCl Denaturant Curves

Determining Differences in Stability

Acknowledgments
Thermal Unfolding of Proteins
Authors: Makhatadze George I.
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

Two‐state Unfolding

Cold Denaturation

Mechanisms of Thermostabilization

Thermodynamic Dissection of Forces Contributing to Protein Stability

Heat Capacity Changes, ΔCp

Enthalpy of Unfolding, ΔH

Entropy of Unfolding, ΔS

Multistate Transitions

Two‐state Dimeric Model

Two‐state Multimeric Model

Three‐state Dimeric Model

Two‐state Model with Ligand Binding

Four‐state (Two‐domain Protein) Model

Differential Scanning Calorimetry (DSC)

How to Prepare forDSCExperiments

How to Choose Appropriate Conditions

Critical Factors in RunningDSCExperiments
Pressure‐Temperature Phase Diagrams of Proteins
Authors: Doster Wolfgang , Friedrich Josef
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 Aspects of Phase Diagrams of Proteins and Early Experiments

Thermodynamics of Pressure–Temperature Phase Diagrams

Measuring Phase Stability Boundaries with Optical Techniques

Fluorescence Experiments with Cytochromec

Results

What Do We Learn from the Stability Diagram?

Thermodynamics

Determination of the Equilibrium Constant of Denaturation

Microscopic Aspects

Structural Features of the Pressure‐denatured State

Conclusions and Outlook

Acknowledgment
Conformational Properties of Unfolded Proteins
Authors: Fleming Patrick J. , Rose George D.
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

Unfolded vs. Denatured Proteins

Early History

The Random Coil

The Random Coil–Theory

The Random Coil Model Prompts Three Questions

The Folding Funnel

Transition State Theory

Other Examples

Implicit Assumptions from the Random Coil Model

The Random Coil–Experiment

Intrinsic Viscosity

SAXSandSANS

Questions about the Random Coil Model

Questions from Theory

TheFlory Isolated‐pair Hypothesis

Structure vs. Energy Duality

The “Rediscovery” of Polyproline II Conformation

PIIin Unfolded Peptides and Proteins

Questions from Experiment

Residual Structure in Denatured Proteins and Peptides

The Reconciliation Problem

Organization in the Unfolded State – the Entropic Conjecture

Steric Restrictions beyond the Dipeptide

Future Directions

Acknowledgments
Kinetic Mechanisms in Protein Folding
Authors: Bachmann Annett , Kiefhaber Thomas
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

Analysis of Protein Folding Reactions using Simple Kinetic Models

General Treatment of Kinetic Data

Two‐state Protein Folding

Complex Folding Kinetics

Heterogeneity in the Unfolded State

Folding through Intermediates

Rapid Pre‐equilibria

Folding through an On‐pathway High‐energy Intermediate

A Case Study: the Mechanism of Lysozyme Folding

Lysozyme Folding atpH5.2 and Low Salt Concentrations

Lysozyme Folding at pH 9.2 or at High Salt Concentrations

Non‐exponential Kinetics

Conclusions and Outlook

Protocols–Analytical Solutions of Three‐state Protein Folding Models

Triangular Mechanism

On‐pathway Intermediate

Off‐pathway Mechanism

Folding Through an On‐pathway High‐Energy Intermediate

Acknowledgments
Association and Folding of Small Oligomeric Proteins
Authors: Bosshard Hans‐Rudolf
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

Experimental Methods Used to Follow the Folding of Oligomeric Proteins

Equilibrium Methods

Kinetic Methods

Dimeric Proteins

Two‐state Folding of Dimeric Proteins

Examples of Dimeric Proteins Obeying Two‐state Folding

Folding of Dimeric Proteins through Intermediate States

Trimeric and Tetrameric Proteins

Conclusions

Appendix–Concurrent Association and Folding of Small Oligomeric Proteins

Equilibrium Constants for Two‐state Folding

Homooligomeric Protein

Heterooligomeric Protein

Calculation of Thermodynamic Parameters from Equilibrium Constants

Basic Thermodynamic Relationships

Linear Extrapolation of Denaturant Unfolding Curves of Two‐state Reaction

Calculation of the van't Hoff Enthalpy Change from Thermal Unfolding Data

Calculation of the van't Hoff Enthalpy Change from the Concentration‐dependence ofTm

Extrapolation of Thermodynamic Parameters to Different Temperatures:Gibbs‐Helmholtz Equation

Kinetics of Reversible Two‐state Folding and Unfolding: Integrated Rate Equations

Two‐state Folding of Dimeric Protein

Two‐state Unfolding of Dimeric Protein

Reversible Two‐state Folding and Unfolding

Homodimeric protein

Heterodimeric protein

Kinetics of Reversible Two‐state Folding: Relaxation after Disturbance of a Preexisting Equilibrium (Method ofBernasconi)

Acknowledgments
Disulfide Bond Formation in Prokaryotes
Authors: Collet Jean‐Francois , Bardwell James C.
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

Disulfide Bond Formation in the

E
.
coli

Periplasm

A Small Bond, a Big Effect

Disulfide Bond Formation Is a Catalyzed Process

Dsb
A
, a Protein‐folding Catalyst

How is
Dsb
A
Re‐oxidized?

From Where Does the Oxidative Power of
Dsb
B
Originate?

How Are Disulfide Bonds Transferred From
Dsb
B
to
Dsb
A
?

How Can
Dsb
B
Generate Disulfide by Quinone Reduction?

Disulfide Bond Isomerization

The Protein Disulfide Isomerases
Dsb
C
and
Dsb
G

Dimerization of
Dsb
C
and
Dsb
G
Is Important for Isomerase and Chaperone Activity

Dimerization Protects from
Dsb
B
Oxidation

Import of Electrons from the Cytoplasm:
Dsb
D

Conclusions
Folding of Membrane Proteins
Authors: Tamm Lukas K. , Hong Heedeok
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

Thermodyamics of Residue Partitioning into Lipid Bilayers

Stability of β‐Barrel Proteins

Stability of Helical Membrane Proteins

Helix and Other Lateral Interactions in Membrane Proteins

The Membrane Interface as an Important Contributor to Membrane Protein Folding

Membrane Toxins as Models for Helical Membrane Protein Insertion

Mechanisms of β‐Barrel Membrane Protein Folding

Experimental Protocols

SDS Gel Shift Assay for Heat‐modifiable Membrane Proteins

Reversible Folding and Unfolding Protocol Using OmpA as an Example

Tryptophan Fluorescence and Time‐resolved Distance Determination by Tryptophan Fluorescence Quenching

TDFQ Protocol for Monitoring the Translocation of Tryptophans across Membranes

Circular Dichroism Spectroscopy

Fourier Transform Infrared Spectroscopy

Protocol for Obtaining Conformation and Orientation of Membrane Proteins and Peptides by Polarized ATR‐FTIR Spectroscopy

Acknowledgments
Molecular Dynamics Simulations to Study Protein Folding and Unfolding
Authors: Caflisch Amedeo , Paci Emanuele
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

Molecular Dynamics Simulations of Peptides and Proteins

Folding of Structured Peptides

Reversible Folding and Free Energy Surfaces

Non‐Arrhenius Temperature Dependence of the Folding Rate

Denatured State and Levinthal Paradox

Folding Events of Trp‐cage

Unfolding Simulations of Proteins

High‐temperature Simulations

Biased Unfolding

Forced Unfolding

Determination of the Transition State Ensemble

MD Techniques and Protocols

Techniques to Improve Sampling

Replica Exchange Molecular Dynamics

Methods Based on Path Sampling

MD with Restraints

Distributed Computing Approach

Implicit Solvent Models versus Explicit Water

Conclusion
Molecular Dynamics Simulations of Proteins and Peptides
Authors: Tavan Paul , Carstens Heiko , Mathias Gerald
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 Physics of Protein Structure and Dynamics

Protein Electrostatics

Relaxation Times and Spatial Scales

Solvent Environment

Water

Polarizability of the Peptide Groups and of Other Protein Components

State of the Art

Control of Thermodynamic Conditions

Long‐range Electrostatics

Polarizability

Higher Multipole Moments of the Molecular Components

MM Models of Water

Complexity of Protein–Solvent Systems and Consequences for MM‐MD

What about Successes of MD Methods?

Accessible Time Scales and Accuracy Issues

Continuum Solvent Models

Are there Further Problems beyond Electrostatics and Structure Prediction?

Conformational Dynamics of a Light‐switchable Model Peptide

Computational Methods

Results and Discussion

Acknowledgments
Electrostatics of Proteins: Principles, Models and Applications
Authors: Braun‐Sand Sonja , Warshel Arieh
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

Historical Perspectives

Electrostatic Models: From Microscopic to Macroscopic Models

All‐Atom Models

Dipolar Lattice Models and the PDLD Approach

The PDLD/S‐LRA Model

Continuum (Poisson‐Boltzmann) and Related Approaches

Effective Dielectric Constant for Charge–charge Interactions and the GB Model

The Meaning and Use of the Protein Dielectric Constant

Validation Studies

Systems Studied

Solvation Energies of Small Molecules

Calculation of p
K
a
Values of Ionizable Residues

Redox and Electron Transport Processes

Ligand Binding

Enzyme Catalysis

Ion Pairs

Protein‐Protein Interactions

Ion Channels

Helix Macrodipoles versus Localized Molecular Dipoles

Folding and Stability

Conclusions

Acknowledgments
Folding and Association of Multi‐domain and Oligomeric
Authors: Lilie Hauke , Seckler Robert
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

Folding of Multi‐domain Proteins

Domain Architecture

γ‐Crystallin as a Model for a Two‐domain Protein

The Giant Protein Titin

Folding and Association of Oligomeric Proteins

Why Oligomers?

Inter‐subunit Interfaces

Domain Swapping

Stability of Oligomeric Proteins

Methods Probing Folding/Association

Chemical Cross‐linking

Analytical Gel Filtration Chromatography

Scattering Methods

Fluorescence Resonance Energy Transfer

Hybrid Formation

Kinetics of Folding and Association

General Considerations

Reconstitution Intermediates

Rates of Association

Homo‐ versus Heterodimerization

Renaturation versus Aggregation

Case Studies on Protein Folding and Association

Antibody Fragments

Trimeric Tail Spike Protein of BacteriophageP22
Chaperone Function in Vitro
Authors: Buchner Johannes , Walter Stefan
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

Basic Functional Principles of Molecular Chaperones

Recognition of Nonnative Proteins

Induction of Conformational Changes in the Substrate

Energy Consumption and Regulation of Chaperone Function

Limits and Extensions of the Chaperone Concept

Co‐chaperones

Specific Chaperones

Working with Molecular Chaperones

Natural versus Artificial Substrate Proteins

Stability of Chaperones

Acknowledgments
Peptidyl‐prolylcis/transIsomerases
Authors: Fischer Gunter
Published: March 2008

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

The sections in this article are

Introduction

Peptidyl‐prolylcis/transIsomerization

Monitoring Peptidyl‐prolylcis/transIsomerase Activity

Prototypical Peptidyl‐prolylcis/transIsomerases

General Considerations

Prototypic Cyclophilins

PrototypicFK506‐binding Proteins

Prototypic Parvulins

Conclusions
Proteins Import into Mitochondria
Authors: Neupert Walter , Brunner Michael , Hell Kai
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

Translocation Machineries and Pathways of the Mitochondrial Protein Import System

Import of Proteins Destined for the Mitochondrial Matrix

Import into Mitochondria Requires Protein Unfolding

Mechanisms of Unfolding by the Mitochondrial Import Motor

Targeted Brownian Ratchet

Power‐stroke Model

Studies to Discriminate between the Models

Studies on the Unfolding of Preproteins

Comparison of the Import of Folded and Unfolded Proteins

Import of Preproteins With Different Presequence Lengths

Import of Titin Domains

Unfolding by the Mitochondrial Membrane Potential ΔΨ

Mechanistic Studies of the Import Motor

Brownian Movement of the Polypeptide Within the Import Channel

Recruitment of mtHsp70 by Tim44

Import Without Recruitment of mtHsp70 by Tim44

MtHsp70 Function in the Import Motor

Conclusions
Hsp70 Chaperones
Authors: Craig Elizabeth A. , Huang Peggy
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

“Soluble”Hsp70s/J‐proteins Function in General Protein Folding

The SolubleHsp70 ofE.coli,DnaK

SolubleHsp70sof Major Eukaryotic Cellular Compartments

Eukaryotic Cytosol

Matrix of Mitochondria

Lumen of the Endoplasmic Reticulum

“Tethered”Hsp70s/J‐proteins: Roles in Protein Folding on the Ribosome and in Protein Translocation

Membrane‐tetheredHsp70/J‐protein

Ribosome‐associatedHsp70/J‐proteins

Modulating of Protein Conformation byHsp70s/J‐proteins

Assembly ofFe/SCenters

Uncoating of Clathrin‐coated Vesicles

Regulation of the Heat Shock Response

Regulation of Activity ofDNAReplication‐initiator Proteins

Cases of a SingleHsp70 Functioning With MultipleJ‐Proteins

Hsp70s/J‐proteins – When anHsp70 Maybe Isn't Really a Chaperone

The Ribosome‐associated “Hsp70”Ssz1

MitochondrialHsp70 as the Regulatory Subunit of an Endonuclease

Conclusions
Protein Folding in the Endoplasmic Reticulum
Authors: Shen Ying , Chung Kyung Tae , Hendershot Linda M.
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

BiPInteractions with Unfolded Proteins

ER‐localizedDnaJHomologues

ER‐localized Nucleotide‐exchange/releasing Factors

Organization and Relative Levels of Chaperones in theER

Regulation ofERChaperone Levels

Disposal of BiP‐associated Proteins That Fail to Fold or Assemble

Other Roles ofBiPin theER

Conclusions

Acknowledgements
Procollagen Biosynthesis in Mammalian Cells
Authors: Tasab Mohammed , Bulleid Neil J.
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

Variety and Complexity of Collagen Proteins

Fibrillar Procollagen

Expression of Fibrillar Collagens

The Procollagen Biosynthetic Process: An Overview

Disulfide Bonding in Procollagen Assembly

The Influence of Primary Amino Acid Sequence on Intracellular Procollagen Folding

Chain Recognition and Type‐specific Assembly

Assembly of Multi‐subunit Proteins

Coordination of Type‐specific Procollagen Assembly and Chain Selection

Hypervariable Motifs: Components of a Recognition Mechanism That Distinguishes Between Procollagen Chains?

Modeling the
C
‐propeptide

Chain Association

Posttranslational Modifications That Affect Procollagen Folding

Hydroxylation and Triple‐helix Stability

Procollagen Chaperones

Prolyl 4‐Hydroxylase

Protein Disulfide Isomerase

Hsp
47

PPI
and
Bi
P

Analysis of Procollagen Folding
The

E
.
coli

Gro
E
Chaperone
Authors: Burston Steven G. , Walter Stefan
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

The Structure of
Gro
EL

The Structure of
Gro
EL
‐
ATP

The Structure of
Gro
ES
and its Interaction with
Gro
EL

The Interaction Between
Gro
EL
and Substrate Polypeptides

Gro
EL
is a Complex Allosteric Macromolecule

The Reaction Cycle of the
Gro
E
Chaperone

The Effect of
Gro
E
on Protein‐folding Pathways

Conclusions

Acknowledgements
TheHsp90 Family of Molecular Chaperones
Authors: Richter Klaus , Meinlschmidt Birgit , Buchner Johannes
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

TheHsp90 Familyin vivo

Evolutionary Relationships within theHsp90 Gene Family

In Vivo Functions ofHsp90

Regulation ofHsp90 Expression and Posttranscriptional Activation

Chemical Inhibition ofHsp90

Identification of NaturalHsp90 Substrates

In Vitro Investigation of the ChaperoneHsp90

Hsp90: A Special Kind of ATPase

TheATPaseCycle ofHsp90

Interaction ofHsp90 with Model Substrate Proteins

InvestigatingHsp90 Substrate Interactions Using Native Substrates

Partner Proteins: Does Complexity Lead to Specificity?

Hop,p23, and PPIases: The Chaperone Cycle ofHsp90

Hop/Sti1: Interactions Mediated by TPR Domains

p23/Sba1: Nucleotide‐specific Interaction withHsp90

Large PPIases: Conferring Specificity to Substrate Localization?

Pp5: Facilitating Dephosphorylation

Cdc37: Building Complexes with Kinases

Tom70: Chaperoning Mitochondrial Import

CHIPandSgt1: Multiple Connections to Protein Degradation

Aha1 andHch1: Just Stimulating the ATPase?

Cns1,Sgt2, andXap2: Is aTPREnough to Become anHsp90 Partner?

Conclusion

Acknowledgements
Small Heat Shock Proteins
Authors: Narberhaus Franz , Haslbeck Martin
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

α‐Crystallins and the Small Heat Shock Protein Family: Diverse Yet Similar

Cellular Functions of α‐Hsps

Chaperone Activityin vitro

Chaperone Functionin vivo

Other Functions

The Oligomeric Structure of α‐Hsps

Dynamic Structures as Key to Chaperone Activity

Acknowledgements
Transmemebrane Domains in Proteins
Authors: Ridder Anja , Langosch Dieter
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

Structure of Transmembrane Domains

The Biosynthetic Route towards Folded and Oligomeric Integral Membrane Proteins

Structure and Stability ofTMSs

Amino Acid Composition ofTMSs and Flanking Regions

Stability of Transmembrane Helices

The Nature of Transmembrane Helix‐Helix Interactions

General Considerations

Attractive Forces within Lipid Bilayers

Forces between Transmembrane Helices

Entropic Factors Influencing Transmembrane Helix‐Helix Interactions

Lessons from Sequence Analyses and High‐resolution Structures

Lessons from Bitopic Membrane Proteins

Transmembrane Segments Forming Right‐handed Pairs

Transmembrane Segments Forming Left‐handed Assemblies

Selection of Self‐interactingTMSs from Combinatorial Libraries

Role of Lipids in Packing/Assembly of Membrane Proteins

Conformational Flexibility of Transmembrane Segments

Experimental Techniques

Biochemical and Biophysical Techniques

Visualization of Oligomeric States by Electrophoretic Techniques

Hydrodynamic Methods

Fluorescence Resonance Transfer

Genetic Assays

TheToxRSystem

Other Genetic Assays

Identification ofTMS‐TMSInterfaces by Mutational Analysis
The Structures of General Porins
Authors: Schulz Georg E.
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

Bacterial Outer Membrane Proteins

Construction of General Porins

Trimer Association and Folding

Pore Geometry

Permeation

Conclusion

Acknowledgments
Lipid Bilayers, Translocons and the Shaping of Polypeptide Structure
Authors: White Stephen H. , Hessa Tara , von Heijne Gunnar
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

Membrane Proteins: Intrinsic Interactions

Physical Determinants of Membrane Protein Stability: The Bilayer Milieu

Physical Determinants of Membrane Protein Stability: Energetics of Peptides in Bilayers

Physical Determinants of Membrane Protein Stability: Helix‐Helix Interactions in Bilayers

Membrane Proteins: Formative Interactions

Connecting Translocon‐assisted Folding to Physical Hydrophobicity Scales: The Interfacial Connection

Connecting Translocon‐assisted Folding to Physical Hydrophobicity Scales: Transmembrane Insertion of Helices

Conclusions

Acknowledgments
Expression of Proteins in Isotopically Enriched Form
Authors: Patzelt Heiko , Goto Natalie , Iwai Hideo , Lundstrom Kenneth , Fernholz Erhard
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

Isotope‐Labeled Proteins from Hydrolyzates of the Green AlgaScenedesmus obliquus

Production of Isotope‐Labeled Algal Hydrolyzates

Adaptation of the Protein Overproducer to the Algal Medium

Preparation of Homogenously Isotope‐Labeled Protein by Fermentation on Algal Media

Amino Acid‐Type Specific Labeling

Mass Spectrometric Analysis of the Labeled Amino Acids

Selective Labeling Schemes

Reverse‐Labeling Schemes

Selective Protonation of Methyl Groups in2H‐Labeled Proteins

Structure Determination of Selectively Methyl Protonated Proteins

Introducing1H,12CAromatic Residues into Otherwise13CUniformly Labeled Proteins

Backbone‐Labeled Proteins

Selective13CMethyl Group Labeling

Intein‐Based Protein Engineering forNMRSpectroscopy

Segmental Labeling of Proteins

Intein‐Mediated Protein Ligation (IPL)/Expressed Protein Ligation (EPL) using theIMPACTSystem

Reconstitution of Split Inteins

Stabilizing Proteins by Intein‐Mediated Backbone Cyclization

In vitroCyclization of Proteins

In vivoCyclization

Stability Enhancement by Backbone Cyclization

Alternatives toE. coliExpression Systems

Expression Vectors

Halobacteriumsalinarum

Saccharomycescerevisiae

Schizosaccharomycespombe

Pichiapastoris

Baculovirus

Transient Mammalian Expression

Stable Mammalian Expression

Viral Vectors

Comparison of Expression Systems

Isotope Labeling andNMR

Target Proteins

The Use of Cell‐Free Protein Expression forNMRAnalysis

The Cell‐Free Protein Expression SystemRTS

FromPCRProduct to15N‐Labeled Protein

Conclusion
Monocot Expression Systems for Molecular Farming
Authors: Christou Paul , Stoger Eva , Twyman Richard M.
Published: March 2008

Originally published in: Molecular Farming. Edited by Rainer Fischer and Stefan Schillberg. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30786‐9

The sections in this article are

Introduction

Cereal Production Crops

Technical Aspects of Molecular Farming in Cereals

Cereal Transformation

Expression Construct Design

Production Considerations for Cereals

Examples of Recombinant Proteins Produced in Cereals

ProdiGene and Maize

Recombinant Proteins Expressed in Rice

Recombinant Proteins Produced in Wheat

Recombinant Proteins Produced in Barley

Conclusions
Large‐scale Protein Production in Plants: Host Plants, Systems and Expression
Authors: Twyman Richard M.
Published: March 2008

Originally published in: Molecular Farming. Edited by Rainer Fischer and Stefan Schillberg. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30786‐9

The sections in this article are

Introduction

Host Species for Molecular Farming

Leafy Crops

Tobacco (
Nicotiana tabacum
)

Tobacco (
Nicotiana benthamiana
)

Alfalfa (
Medicago sativa
)

White clover (
Trifolium repens
)

Lettuce (
Lactuca sativa
)

Spinach (
Spinacia oleracea
)

Lupin (
Lupinus spp
.)

Dry Seed Crops

Maize (
Zea mays
)

Rice (
Oryza sativa
)

Wheat (
Triticum aestivium
)

Barley (
Hordeum vulgare
)

Soybean (
Glycine max
)

Pea (
Pisum sativum
)

Pigeon pea (
Cajanus cajan
)

Peanut (
Arachis hypogaea
)

Fruit and vegetable crops

Potato (
Solanum tuberosum
)

Tomato (
Lycopersicon esculentum
)

Carrot (
Daucus carota
)

Banana (
Musa
spp.)

Oilcrops

Rapeseed/Canola (
Brassica napus
)

Falseflax (
Camelina sativa
)

Safflower (
Carthamus tinctorius
)

Unicellular Plants and Aquatic Plants Maintained in Bioreactors

Chlamydomonas reinhardtii

Physcomitrella patens

Duckweed (
Lemna minor
)

Non‐cultivated Model Plants

Arabidopsis thaliana

Expression systems for molecular farming

Transgenic plants

Transplastomic plants

Virus‐infected plants

Transiently transformed leaves

Hydroponic cultures

Hairy roots

Shooty teratomas

Suspension cell cultures

Expression strategies and protein yields

Conclusions
Plant Viral Expression Vectors
Authors: Yusibov Vidadi , Rabindran Shailaja
Published: March 2008

Originally published in: Molecular Farming. Edited by Rainer Fischer and Stefan Schillberg. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30786‐9

The sections in this article are

Introduction

Plant RNA Viruses as Expression Vectors

Tobacco mosaic virus (TMV)

Potato virus X (PVX)

Cowpea mosaic virus (CPMV)

Alfalfa mosaic virus (AlMV)

Biological Activity of Target Molecules

Efficacy of Plant Virus‐produced Antigens

Vaccine Antigens

Particle‐based Vaccine Antigen Delivery

Other Uses of Plant Virus Particles

Plant Viruses as Gene Function Discovery Tools

New Approaches to the Development of Viral Vectors

Conclusion
Foreign Protein Expression Using Plant Cell
Authors: Shadwick Fiona S. , Doran Pauline M.
Published: March 2008

Originally published in: Molecular Farming. Edited by Rainer Fischer and Stefan Schillberg. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30786‐9

The sections in this article are

Foreign Protein Production Systems

Production of Foreign Proteins Using Plant Tissue Culture

Suspended Cell Cultures

Hairy Root Cultures

Shooty Teratoma Cultures

Scale‐up Considerations for Different Forms of Plant Tissue Culture

Strategies for Improving Foreign Protein Accumulation and Product Recovery in Plant Tissue Culture

Expression Systems

Modifications to Existing Expression Constructs

Transient Expression Using Viral Vectors

Secretion of Foreign Proteins

Foreign Protein Stability

Stability Inside the Cells

Stability Outside the Cells

Medium Additives

Medium Properties

Bioprocess Developments

Product Recovery from the Medium

Oxygen Transfer and Dissolved Oxygen Concentration

Conclusions
Functional Expression of Ion Channels in Mammalian Systems
Authors: Clare Jeffrey J.
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

cDNACloning and Manipulation

Choice of Host Cell Background

Post‐translational Processing of Heterologous Expressed Ion Channels

Cytotoxicity

Transient Expression Systems

Standard Transient Expression

Viral Expression Systems

Stable Expression of Ion Channels

Bicistronic Expression Systems

Stable Expression of Multiple Subunits

Inducible Expression

Conclusions

Acknowledgements
Production of Recombinant Proteins by In Vitro Folding
Authors: Lange Christian , Rudolph Rainer
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

The Inclusion Body Problem

Cost and Scale Limitations in Industrial Protein Folding

Treatment of Inclusion Bodies

Isolation of Inclusion Bodies

Solubilization of Inclusion Bodies

Refolding in Solution

Protein Design Considerations

Oxidative Refolding With Disulfide Bond Formation

Transfer of the Unfolded Proteins Into Refolding Buffer

Refolding Additives

Cofactors in Protein Folding

Chaperones and Folding‐helper Proteins

An Artificial Chaperone System

Pressure‐induced Folding

Temperature‐leap Techniques

Recycling of Aggregates

Alternative Refolding Techniques

Matrix‐assisted Refolding

Folding by Gel Filtration

Direct Refolding of Inclusion Body Material

Conclusions

Experimental Protocols

Acknowledgements
Protein Production inEscherichia coli
Authors: Altenbuchner Josef , Mattes Ralf
Published: March 2008

Originally published in: Production of Recombinant Proteins. Edited by Gerd Gellissen. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31036‐4

The sections in this article are

Introduction

Strains, Genome, and Cultivation

Expression Vectors

Replication of pMB1‐derived Vectors

Plasmid Partitioning

Genome Engineering

E. coliPromoters

Regulation of Gene Expression

Negative Control

Positive Control

l‐Arabinose Operon

l‐Rhamnose Operon

Transcription and Translation

Translation Initiation

Codon Usage

Translation Termination

Transcription Termination and mRNA Stability

Protein Production

Inclusion Body Formation

Chaperones as Facilitators of Folding

Fusion Protein Technology

Methionine Processing

Secretion into the Periplasm

Disulfide Bond Formation and Folding

Twin Arginine Translocation (TAT) of Folded Proteins

Disulfide Bond Formation in the Cytoplasm

Cell Surface Display and Secretion across the Outer Membrane

Examples of Products and Processes

Conclusions

Appendix
Protein Production in
Pseudomonas fluorescens
Authors: Chew Lawrence C. , Ramseier Tom M. , Retallack Diane M. , Schneider Jane C. , Squires Charles H. , Talbot Henry W.
Published: March 2008

Originally published in: Production of Recombinant Proteins. Edited by Gerd Gellissen. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31036‐4

The sections in this article are

Introduction

Biology of
Pseudomonas fluorescens

History and Taxonomy of
Pseudomonas fluorescens
Strain Biovar I MB101

Cultivation

Genomics and Functional Genomics of
P. fluorescens
Strain MB101

Core Expression Platform for Heterologous Proteins

Antibiotic‐free Plasmids using
pyrF
and
proC

Gene Deletion Strategy and Re‐usable Markers

Periplasmic Secretion and Use of Transposomes

Alternative Expression Systems: Anthranilate and Benzoate‐inducible Promoters

Production of Heterologous Proteins in
P. fluorescens

Pharmaceutical Proteins

Industrial Enzymes

Agricultural Proteins

Conclusions

Appendix
Protein Production inStaphylococcus carnosusand other Gram‐Positive Bacteria
Authors: Freudl Roland
Published: March 2008

Originally published in: Production of Recombinant Proteins. Edited by Gerd Gellissen. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31036‐4

The sections in this article are

Introduction

Major Protein Export Routes in Gram‐positive Bacteria

The General Secretion (Sec) Pathway

The Twin‐Arginine Translocation (Tat) Pathway

Secretion Signals

Extracytosolic Protein Folding

The Cell Wall as a Barrier for the Secretion of Heterologous Proteins

Degradation of Exported Proteins by Cell‐associated and Secreted Proteases

Staphylococcus carnosus

General Description

Microbiological and Molecular Biological Tools

S. carnosusas Host Organism for the Analysis of Staphylococcal‐related Pathogenicity Aspects

Secretory Production of Heterologous Proteins byS. carnosus

TheStaphylococcus hyicusLipase: Secretory Signals and Heterologous Expression inS. carnosus

Use of the Pre‐pro‐part of theS. hyicusLipase for the Secretion of Heterologous Proteins inS. carnosus

Process Development for the Secretory Production of a Human Calcitonin Precursor Fusion Protein byS. carnosus

Surface Display onS. carnosus

Appendix
Protein Production inHansenulapolymorpha
Authors: Ah Kang Hyun , Gellissen Gerd
Published: March 2008

Originally published in: Production of Recombinant Proteins. Edited by Gerd Gellissen. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31036‐4

The sections in this article are

History, Phylogenetic Position, Basic Genetics and Biochemistry ofH.polymorpha

Characteristics of theH.polymorphaGenome

N‐linked Glycosylation inH.polymorpha

TheH.polymorpha‐based Expression Platform

Transformation

Strains

Plasmids and Available Elements

Product and Process Examples

Conclusion

Limitations of theH.polymorpha‐based Expression Platform

Impact of Functional Genomics on Development of theH.polymorphaRB11‐based Expression Platform

Appendix
Protein Production inPichia pastoris
Authors: Ilgen Christine , Lin‐Cereghino Joan , Cregg James M.
Published: March 2008

Originally published in: Production of Recombinant Proteins. Edited by Gerd Gellissen. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31036‐4

The sections in this article are

Introduction

Construction of Expression Strains

Expression Vector Components

Alternative Promoters

Selectable Markers

Host Strains

Methanol Utilization Phenotype

Protease‐deficient Host Strains

Construction of Expression Strains

Multicopy Strains

Growth in Fermentor Cultures

Post‐translational Modification of Secreted Proteins

Secretion Signals

O‐linked Glycosylation

N‐linked Glycosylation

“Humanization” of N‐linked Carbohydrate

Conclusions

Acknowledgments

Appendix
Protein Production inAspergillus sojae
Authors: Heerikhuisen Margreet , van den Hondel Cees , Punt Peter
Published: March 2008

Originally published in: Production of Recombinant Proteins. Edited by Gerd Gellissen. Copyright © 2005 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31036‐4

The sections in this article are

Introduction

Taxonomy

The Expression Platform

Strain Selection

Transformation

Protoplasting

Dominant Selection Markers

Auxotrophic Selection Markers

Re‐usable Selection Marker

Promoter Elements

Aspergillus sojaeas a Cell Factory for Foreign Proteins

Production of Fungal Proteins

Production of Non‐fungal Proteins

Controlled Fermentation

Strain Development

Protease‐deficient Strains

Ultra‐violet (UV) Mutagenesis

Gene Disruption

Controlled Batch Fermentations

Low‐viscosity Mutants

Gene Disruption

Controlled Fermentations

Conclusion

Acknowledgments

Appendix
Antibiotics and the Ribosome
Authors: Hansen Jeffrey L.
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

The Ribosome

Introduction

Binding of tRNA

Peptidyl Transferase Activity

Structure of the Ribosome

Antibiotics

Introduction

Antibiotics that Bind to the 50S Subunit

MLSBAntibiotics

Macrolides

Macrolides, 15‐ and 16‐Membered

Binding Interactions Between the Lactone Ring and the Ribosome

Sugar Interactions with the Ribosome

A Covalent Bond

Macrolides, 14‐Membered

Rational Drug Design of Macrolides

Lincosamides

Streptogramins

Chloramphenicol

Nucleoside Analogue Antibiotics

Puromycin

Aminoacyl‐4‐aminohexosyl‐cytosine Antibiotics

Other Antibiotics that Bind to the 50S Subunit

Sparsomycin

Anisomycin

Prospects for Rational Drug Design of Antibiotics that Bind to the Ribosome

Acknowledgments
Ribosome‐associated Proteins
Authors: Rospert Sabine , Gautschi Matthias , Rakwalska Magdalena , Raue Uta
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

Signal Recognition Particle, Nascent Polypeptide–associated Complex, and Trigger Factor

Signal Recognition Particle

An Interplay between Eukaryotic SRP and Nascent Polypeptide–associated Complex?

Interplay between Bacterial SRP and Trigger Factor?

Functional Redundancy: TF and the Bacterial Hsp70 Homologue DnaK

Chaperones Bound to the Eukaryotic Ribosome: Hsp70 and Hsp40 Systems

Sis1p and Ssa1p: an Hsp70/Hsp40 System Involved in Translation Initiation?

Ssb1/2p, an Hsp70 Homologue Distributed Between Ribosomes and Cytosol

Function of Ssb1/2p in Degradation and Protein Folding

Zuotin and Ssz1p: a Stable Chaperone Complex Bound to the Yeast Ribosome

A Functional Chaperone Triad Consisting of Ssb1/2p, Ssz1p, and Zuotin

Effects of Ribosome‐bound Chaperones on the Yeast Prion [
PSI
+
]

Enzymes Acting on Nascent Polypeptide Chains

Methionine Aminopeptidases

N
α
‐acetyltransferases

A Complex Arrangement at the Yeast Ribosomal Tunnel Exit
The Mechanism of Recording in Pro‐ and Eukaryotes
Authors: Poole Elizabeth S. , Major Louise L. , Cridge Andrew G. , Tate Warren P.
Published: March 2008

Originally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1

The sections in this article are

Introduction

Maintaining Decoding Accuracy and the Reading Frame

The Use of a Stop Signal for both Elongation and Termination of Protein Synthesis

The Mechanism for Sec Incorporation at UGA Sites in Bacterial mRNAs

The Gene Products

The Mechanism of Sec Incorporation

The Competition between Sec Incorporation and Canonical Decoding of UGA by RF2

Mechanism for Sec Incorporation at UGA Sites in Eukaryotic and Archaeal mRNAs

The Gene Products

The Mechanism of Sec Incorporation at Specific UGA Stop Codons

Why does Recoding Occur at Stop Signals?

The Stop Signal of Prokaryotic Genomes — Engineered for High Efficiency Decoding?

The Stop Signal of Eukaryotic Genomes – Diversity Contributes to Recoding

Readthrough of a Stop Signal: Decoding Stop as Sense

Bypassing of a Stop Codon: ‘Free‐wheeling’ on the mRNA

Frameshifting Around Stop or Sense Codons

Forward Frameshifting: the +1 Event

Programed −1 Frameshifting: A Common Mechanism used by Many Viruses During Gene Expression

Conclusion
Structure of the Ribosome
Authors: Blaha Gregor , Ivanov Pavel
Published: March 2008

Originally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1

The sections in this article are

Introduction

General Features of the Ribosome and Ribosomal Subunits

A Special Feature of the 50S Subunit: The Tunnel

Features of the Ribosomal Subunits at Atomic Resolution

The Domain Structure of the Ribosomal Subunits

Interactions of RNA with RNA or Struts and Bolts in the Three‐dimensional Fold of rRNA: Coaxial Stacking and A‐minor Motifs

Coaxial Stacking

A‐minor Motifs

Ribose Zippers and Patches of A‐minor Motifs

Canonical Ribose Zipper

Single‐base Ribose Zipper

Progress and New Developments in Understanding rRNA Structures

K‐turn

Lonepair Triloop

Classification of Lonepair Triloops

Systemizing Base Pairs

Systemizing RNA Structural Elements

RNA–protein Interactions

Problem of RNA Recognition

Chemistry of RNA–protein Interactions

rRNA–protein Interaction
Assembly of The Prokaryotic Ribosome
Authors: Nierhaus Knud H.
Published: March 2008

Originally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1

The sections in this article are

Introduction

Processing of rRNAs

Precursor Particles and Reconstitution Intermediates

Assembly‐initiator Proteins

Proteins Essential for the Early Assembly: The Assembly Gradient

Late‐assembly Components

Proteins Solely Involved in Assembly

Assembly Maps
Assembly of the Eukaryotic Ribosome
Authors: Lafontaine Denis L.
Published: March 2008

Originally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1

The sections in this article are

Introduction

Why so manyRRPs?

(Pre‐)ribosome Assembly, the Proteomic Era

RibosomalRNAProcessing, Getting there…

RibosomalRNAModification: A Solved Issue?

Ribose Methylation, Pseudouridines Formation and the snoRNAs

The Emergence of the snoRNAs

Non‐ribosomalRNASubstrates for the snoRNAs

Possible Function(s) ofRNAModifications

Base Methylation

U3 snoRNP, the ‘SSUProcessome’, and the Central Pseudoknot

SnoRNASynthesis and Intranuclear Trafficking

SnoRNAs Synthesis

Non‐core snoRNPProteins Required for snoRNAAccumulation

Interactions between Cleavage Factors and Core snoRNPProteins

SnoRNAs Trafficking

CB/NBare Conserved Sites of SmallRNPSynthesis

Ribosome Intranuclear Movements and Ribosome Export

The Cytoplasmic Phase of Ribosome Maturation

Regulatory Mechanisms, all along

Outlook

Conclusions

UsefulWWWlinks

Acknowledgements
Genetic Code Organization and Protein Structure
Authors: Budisa Nediljko
Published: March 2008

Originally published in: Engineering the Genetic Code. By Nediljko Budisa. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31243‐6

The sections in this article are

Basic Features and Adaptive Nature of the Universal Genetic Code

Metabolism and Intracellular Uptake of Canonical Amino Acids

Physicochemical Properties of Canonical Amino Acids

Reasons for the Occurrence of Only 20 Amino Acids in the Genetic Code

What Properties of Amino Acids are Best Preserved by the Genetic Code?

Evolutionary Legacy: Dual Nature of Conserved Code and Finite Number of Protein Folds

Natural Variations in Assignment of Codons of the Universal Genetic Code

Nucleoside Modifications and Codon Reassignments

Codon Reassignment Concepts Possibly Relevant to Code Engineering

Genome Size, Composition, Complexity and Codon Reassignments

Stop Codon Takeover, Codon Capture and Codon Ambiguity
The Cellular Translation Apparatus
Authors: Budisa Nediljko
Published: March 2008

Originally published in: Engineering the Genetic Code. By Nediljko Budisa. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31243‐6

The sections in this article are

Natural Laws, Genetic Information and the “Central Dogma” of Molecular Biology

Cellular Investments in Ribosome‐mediated Protein Synthesis

Molecular Architecture ofAARS

Structure and Function of thetRNAMolecule

Aminoacylation Reaction

AARS:tRNAInteractions – Identity Sets

Translational Proofreading

Ribosomal Decoding – A Brief Overview

Codon Bias and the Fidelity of Protein Synthesis

Preprogrammed Context‐dependent Recoding: fMet, Sec, Pyl, etc

Beyond Basic Coding – Posttranslational Modifications
The Ribosomal Elongation Cycle
Authors: Nierhaus Knud H.
Published: March 2008

Originally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1

The sections in this article are

Introduction

Models of the Elongation Cycle

The Hybrid‐site Model for Elongation

The Allosteric Three‐site Model (α–ɛ Model; Reciprocal Coupling between the A‐ and E‐sites)

Decoding and A‐site Occupation

Some General Remarks about Proofreading

Discrimination against Noncognate aa‐tRNAs

Decoding of an aa‐tRNA (Cognate versus Near‐cognate aa‐tRNAs)

Roles of EF‐Tu

Mimicry at the Ribosomal A‐site

Translational Errors

The PTF Reaction

A Short Intermission: Two Enzymatic Principles of PTF Activity

Chemical Concept: A Transient Covalent Bond between Active Center and Substrate(s)

Physical Concept: The Template Model

Data from the Crystal Structures

Why both the Physical and Chemical Concepts for Peptide‐bond Formation?

The Translocation Reaction

Conservation in the Elongation Factor‐G Binding Site

Dynamics within the Ribosome
Gene Expression: Basic Concepts
Authors: Cullen Paul , Lorkowski Stefan , Kratz Mario , Werner Michel , Marschall Christoph , Klein Hanns‐Georg , Goodlett David , Aebersold Ruedi , Wenner Claudia
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: 3‐527‐30448‐2

The sections in this article are

Introduction

Basics of Transcription and Translation in the cell

Introduction

Transcription

Translation

Regulation of transcription

Introduction

m
RNA
expression profiles – the transcriptome

Protein expression profiles — the proteome

Interaction between genes and proteins – the interactome

The transcription machinery and core promoters

Regulatory promoters

Enhancers

Locus control regions

Matrix attachment regions

Insulators

RIDGEs
– Regions of increased gene expression

Enhanceosomes

Chromatin

Silencer elements

Transcription factors, repressors and co‐repressors

Epigenetics

Conclusions