- Written by two outstanding names in the field, Gregory Petsko and Dagmar Ringe. - Considers the principles of protein structure and folding, functional properties of proteins and regulation of protein function, and introduces the basic principles whereby structure and function are deduced from sequence. - Fully up-to-date with emphasis on what sequence can tell you about structure and function. - Ideal for undergraduates and graduates studying the fundamental principles of protein structure and function in departments of biochemistry and molecular biology, and working scientists needing an up-to-date introduction to the field.
Overview: Protein Function and Architecture.
Genes and Proteins.
The Peptide Bond.
Bonds that Stablize Folded Proteins.
Importance and Determinants of Secondary Structure.
Properties of the Alpha Helix.
Properties of the Beta Sheet.
Prediction of Secondary Structure.
Membrane Protein Structure.
Protein Stability 1: Weak Interactions and Flexibility.
Protein Stability 2: Post-Translational Modifications.
The Protein Domain.
The Universe of Protein Structures.
Alpha Domains and Beta Domains.
Alpha/Beta, Alpha+Beta and Cross-Linked Domains.
Quaternary Structure: General Principles.
Quaternary Structure: Intermolecular Interfaces.
Quaternary Structure: Geometry.
2. From Structure to Function:.
Overview: The Structural Basis of Protein Function.
Recognition, Complementarity and Active Sites.
Flexibility and Protein Function.
Location of Binding Sites.
Nature of Binding Sites.
Functional Properties of Structural Proteins.
Proximity and Ground-State Destabilization.
Stabilization of Transition States and Exclusion of Water.
Addition/Elimination, Hydrolysis and Decarboxylation.
Multifunctional Enzymes with Tunnels.
3. Control of Protein Function:.
Overview: Mechanisms of Regulation.
Protein Interaction Domains.
Regulation by Location.
Control by pH and Redox Environment.
Effector Ligands: Competitive Binding and Cooperativity.
Effector Ligands: Conformational Change and Allostery.
Protein Switches Based on Nucleotide Hydrolysis.
GTPase Switches: Small Signaling G proteins.
GTPase Switches: Signal Relay by Heterotrimeric GTPases.
Gtpase Switches: Protein Synthesis.
Motor Protein Switches.
Regulation by Degradation.
Control of Protein Function by Phosphorylation.
Regulation of Signaling Protein Kinases: Activation Mechnism.
Regulation of Signaling Protein Kinases: Cdk Activation.
Two-Component Signaling Systems in Bacteria.
Control by Proteolysis: Activation of Precursors.
Protein Splicing: Autoproteolysis by Inteins.
Protein Targeting by Lipid Modification.
Methylation, N-acetylation, Sumoylation and Nitrosylation.
4. From Sequence to Function:.
Overview: From Sequence to Function in the Age of Genomics.
Sequence Alignment and Comparison.
Deriving Function from Sequence.
Experimental Tools for Probing Protein Function.
Divergent and Convergent Evolution.
Structure from Sequence: Homology Modeling.
Structure from Sequence: Profile-Based Threading and “Rosetta”.
Deducing Function from Structure: Protein Superfamilies.
Strategies for Identifying Binding Sites.
Strategies for Identifying Catalytic Residues.
TIM Barrels: One Structure with Diverse Functions.
PLP Enzymes: Diverse Structures with One Function.
Moonlighting: Proteins with More Than One Function.
Chameleon Sequences: One Sequence with More than One Fold.
Prions, Amyloids and Serpins: Metastable Protein Folds.
Functions for Uncharacterized Genes: Galactonate Dehydratase.
Starting from Scratch: A Gene Product of Unknown Function.
5. Structure Determination:.
The Interpretation of Structural Information.
Structure Determination by X-Ray Crystallography and NWR.
Quality and Representation of Crystal and NMR Structures