Protein Structure and Function

by Gregory A Petsko and Dagmar Ringe


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Chapter 1 From Sequence to Structure
Chapter 2 From Structure to Function
Chapter 3 Control of Protein Function
Chapter 4 From Sequence to Function: Case Studies in Structural and Functional Genomics
Chapter 5 Structure Determination

Chapter 1: From Sequence to Structure [PDF

1-0 Overview: Protein Function and Architecture[Full Text] [PDF]
-Proteins are the most versatile macromolecules of the cell
-There are four levels of protein structure

1-1 Amino Acids[Full Text] [PDF]
-The chemical characters of the amino-acid side chains have important consequences for the way they participate in the folding and functions of proteins

1-2 Genes and Proteins[Full Text] [PDF]
-There is a linear relationship between the DNA base sequence of a gene and the amino-acid sequence of the protein it encodes
-The organization of the genetic code reflects the chemical grouping of the amino-acids

1-3 The Peptide Bond[Full Text] [PDF]
-Proteins are linear polymers of amino acids connected by amide bonds
-The properties of the peptide bond have important effects on the stability and flexibility of polypeptide chains in water

1-4 Bonds that Stabilize Folded Proteins[Full Text] [PDF]
-Folded proteins are stabilized mainly by weak noncovalent interactions
-The hydrogen-bonding properties of water have important effects on protein stability

1-5 Importance and Determinants of Secondary Structure[Full Text] [PDF]
-Folded proteins have segments of regular conformation
-The arrangement of secondary structure elements provides a convenient way of classifying types of folds
-Steric constraints dictate the possible types of secondary structure
-The simplest secondary structure element is the beta turn

1-6 Properties of the Alpha Helix[Full Text] [PDF]
-Alpha helices are versatile cylindrical structures stabilized by a network of backbone hydrogen bonds
-Alpha helices can be amphipathic, with one polar and one nonpolar face
-Collagen and polyproline helices have special properties

1-7 Properties of the Beta Sheet[Full Text] [PDF]
-Beta sheets are extended structures that sometimes form barrels
-Amphipathic beta sheets are found on the surfaces of proteins

1-8 Prediction of Secondary Structure[Full Text] [PDF]
-Certain amino acids are more usually found in alpha helices, others in beta sheets

1-9 Folding[Full Text] [PDF]
-The folded structure of a protein is directly determined by its primary structure
-Competition between self-interactions and interactions with water drives protein folding
-Computational prediction of folding is not yet reliable
-Helical membrane proteins may fold by condensation of preformed secondary structure elements in the bilayer

1-10 Tertiary Structure[Full Text] [PDF]
-The condensing of multiple secondary structural elements leads to tertiary structure
-Bound water molecules on the surface of a folded protein are an important part of the structure
-Tertiary structure is stabilized by efficient packing of atoms in the protein interior

1-11 Membrane Protein Structure[Full Text] [PDF]
-The principles governing the structures of integral membrane proteins are the same as those for water-soluble proteins and lead to formation of the same secondary structure elements

1-12 Protein Stability: Weak Interactions and Flexibility[Full Text] [PDF]
-The folded protein is a thermodynamic compromise
-Protein structure can be disrupted by a variety of agents
-The marginal stability of protein tertiary structure allows proteins to be flexible

1-13 Protein Stability: Post-Translational Modifications[Full Text] [PDF]
-Covalent bonds can add stability to tertiary structure
-Post-translational modification can alter both the tertiary structure and the stability of a protein

1-14 The Protein Domain[Full Text] [PDF]
-Globular proteins are composed of structural domains
-Domains have hydrophobic cores
-Multidomain proteins probably evolved by the fusion of genes that once coded for separate proteins

1-15 The Universe of Protein Structures[Full Text] [PDF]
-The number of protein folds is large but limited
-Protein structures are modular and proteins can be grouped into families on the basis of the domains they contain
-The modular nature of protein structure allows for sequence insertions and deletions

1-16 Protein Motifs[Full Text] [PDF]
-Protein motifs may be defined by their primary sequence or by the arrangement of secondary structure elements
-Identifying motifs from sequence is not straightforward

1-17 Alpha Domains and Beta Domains[Full Text] [PDF]
-Protein domains can be classified according to their secondary structural elements
-Two common motifs for alpha domains are the four-helix bundle and the globin fold
-Beta domains contain strands connected in two distinct ways
-Antiparallel beta sheets can form barrels and sandwiches

1-18 Alpha/Beta, Alpha+Beta and Cross-Linked Domains[Full Text] [PDF]
-In alpha/beta domains each strand of parallel beta sheet is usually connected to the next by an alpha helix
-There are two major families of alpha/beta domains: barrels and twists
-Alpha+beta domains have independent helical motifs packed against a beta sheet
-Metal ions and disulfide bridges form cross-links in irregular domains

1-19 Quaternary Structure: General Principles[Full Text] [PDF]
-Many proteins are composed of more than one polypeptide chain
-All specific intermolecular interactions depend on complementarity

1-20 Quaternary Structure: Intermolecular Interfaces[Full Text] [PDF]
-All types of protein-stabilizing interactions contribute to the formation of intermolecular interfaces
-Inappropriate quaternary interactions can have dramatic functional consequences

1-21 Quaternary Structure: Geometry[Full Text] [PDF]
-Protein assemblies built of identical subunits are usually symmetric

1-22 Protein Flexibility[Full Text] [PDF]
-Proteins are flexible molecules
-Conformational fluctuations in domain structure tend to be local
-Protein motions involve groups of non-bonded as well as covalently bonded atoms
-Triggered conformational changes can cause large movements of side chains, loops, or domains

Chapter 2: From Structure to Function [PDFBack to top

2-0 Overview: The Structural Basis of Protein Function[Full Text] [PDF]
-There are many levels of protein function
-There are four fundamental biochemical functions of proteins

2-1 Recognition, Complementarity and Active Sites[Full Text] [PDF]
-Protein functions such as molecular recognition and catalysis depend on complementarity
-Molecular recognition depends on specialized microenvironments that result from protein tertiary structure
-Specialized microenvironments at binding sites contribute to catalysis

2-2 Flexibility and Protein Function[Full Text] [PDF]
-The flexibility of tertiary structure allows proteins to adapt to their ligands
-Protein flexibility is essential for biochemical function
-The degree of flexibility varies in proteins with different functions

2-3 Location of Binding Sites[Full Text] [PDF]
-Binding sites for macromolecules on a protein's surface can be concave, convex, or flat
-Binding sites for small ligands are clefts, pockets or cavities
-Catalytic sites often occur at domain and subunit interfaces

2-4 Nature of Binding Sites[Full Text] [PDF]
-Binding sites generally have a higher than average amount of exposed hydrophobic surface
-Binding sites for small molecules are usually concave and partly hydrophobic
-Weak interactions can lead to an easy exchange of partners
-Displacement of water also drives binding events
-Contributions to binding affinity can sometimes be distinguished from contributions to binding specificity

2-5 Functional Properties of Structural Proteins[Full Text] [PDF]
-Proteins as frameworks, connectors and scaffolds
-Some structural proteins only form stable assemblies
-Some catalytic proteins can also have a structural role
-Some structural proteins serve as scaffolds

2-6 Catalysis: Overview[Full Text] [PDF]
-Catalysts accelerate the rate of a chemical reaction without changing its overall equilibrium
-Catalysis usually requires more than one factor
-Catalysis is reducing the activation-energy barrier to a reaction

2-7 Active-Site Geometry[Full Text] [PDF]
-Reactive groups in enzyme active sites are optimally positioned to interact with the substrate

2-8 Proximity and Ground-State Destabilization[Full Text] [PDF]
-Some active sites chiefly promote proximity
-Some active sites destabilize ground states

2-9 Stabilization of Transition States and Exclusion of Water[Full Text] [PDF]
-Some active sites primarily stabilize transition states
-Many active sites must protect their substrates from water, but must be accessible at the same time

2-10 Redox Reactions[Full Text] [PDF]
-A relatively small number of chemical reactions account for most biological transformations
-Oxidation/reduction reactions involve the transfer of electrons and often require specific cofactors

2-11 Addition/Elimination, Hydrolysis and Decarboxylation[Full Text] [PDF]
-Addition reactions add atoms or chemical groups to double bonds, while elimination reactions remove them to form double bonds
-Esters, amides and acetals are cleaved by reaction with water; their formation requires removal of water
-Loss of carbon dioxide is a common strategy for removing a single carbon atom from a molecule

2-12 Active-Site Chemistry[Full Text] [PDF]
-Active sites promote acid-base catalysis

2-13 Cofactors[Full Text] [PDF]
-Many active sites use cofactors to assist catalysis

2-14 Multi-Step Reactions[Full Text] [PDF]
-Some active sites employ multi-step mechanisms

2-15 Multifunctional Enzymes[Full Text] [PDF]
-Some enzymes can catalyze more than one reaction
-Some bifunctional enzymes have only one active site
-Some bifunctional enzymes contain two active sites

2-16 Multifunctional Enzymes with Tunnels[Full Text] [PDF]
-Some bifunctional enzymes shuttle unstable intermediates through a tunnel connecting the active sites
-Trifunctional enzymes can shuttle intermediates over huge distances
-Some enzymes also have non-enzymatic functions

Chapter 3: Control of Protein Function [PDFBack to top

3-0 Overview: Mechanisms of Regulation[Full Text] [PDF]
-Protein function in living cells is precisely regulated
-Proteins can be targeted to specific compartments and complexes
-Protein activity can be regulated by binding of an effector and by covalent modification
-Protein activity may be regulated by protein quantity and lifetime
-A single protein may be subject to many regulatory influences

3-1 Protein Interaction Domains[Full Text] [PDF]
-The flow of information within the cell is regulated and integrated by the combinatorial use of small protein domains that recognize specific ligands

3-2 Regulation by Location[Full Text] [PDF]
-Protein function in the cell is context-dependent
-There are several ways of targeting proteins in cells

3-3 Control by pH and the Redox Environment[Full Text] [PDF]
-Protein function is modulated by the environment in which the protein operates
-Changes in redox environment can greatly affect protein structure and function
-Changes in pH can drastically alter protein structure and function

3-4 Effector Ligands: Competitive Binding and Cooperativity[Full Text] [PDF]
-Protein function can be controlled by effector ligands that bind competitively to ligand-binding or active sites
-Cooperative binding by effector ligands amplifies their effects

3-5 Effector Ligands: Conformational Change and Allostery[Full Text] [PDF]
-Effector molecules can cause conformational changes at distant sites
-ATCase is an allosteric enzyme with regulatory and active sites on different subunits
-Disruption of function does not necessarily mean that the active site or ligand-binding site has been disrupted
-Binding of gene regulatory proteins to DNA is often controlled by ligand-induced conformational changes

3-6 Protein Switches Based on Nucleotide Hydrolysis[Full Text] [PDF]
-Conformational changes driven by nucleotide binding and hydrolysis are the basis for switching and motor properties of proteins
-All nucleotide switch proteins have some common structural and functional features

3-7 GTPase Switches: Small Signaling G Proteins[Full Text] [PDF]
-The switching cycle of nucleotide hydrolysis and exchange in G proteins is modulated by the binding of other proteins

3-8 GTPase Switches: Signal Relay by Heterotrimeric GTPases[Full Text] [PDF]
-Heterotrimeric G proteins relay and amplify extracellular signals from a receptor to an intracellular signaling pathway

3-9 GTPase Switches: Protein Synthesis[Full Text] [PDF]
-EF-Tu is activated by binding to the ribosome, which thereby signals it to release its bound tRNA

3-10 Motor Protein Switches[Full Text] [PDF]
-Myosin and kinesin are ATP-dependent nucleotide switches that move along actin filaments and microtubules respectively

3-11 Regulation by Degradation[Full Text] [PDF]
-Protein function can be controlled by protein lifetime
-Proteins are targeted to proteasomes for degradation

3-12 Control of Protein Function by Phosphorylation[Full Text] [PDF]
-Protein function can be controlled by covalent modification
-Phosphorylation is the most important covalent switch mechanism for the control of protein function

3-13 Regulation of Signaling Protein Kinases: Activation Mechanism[Full Text] [PDF]
-Protein kinases are themselves controlled by phosphorylation
-Src kinases both activate and inhibit themselves

3-14 Regulation of Signaling Protein Kinases: Cdk Activation[Full Text] [PDF]
-Cyclin acts as an effector ligand for cyclin-dependent kinases

3-15 Two-Component Signaling Systems in Bacteria[Full Text] [PDF]
-Two-component signal carriers employ a small conformational change that is driven by covalent attachment of a phosphate group

3-16 Control by Proteolysis: Activation of Precursors[Full Text] [PDF]
-Limited proteolysis can activate enzymes
-Polypeptide hormones are produced by limited proteolysis

3-17 Protein Splicing: Autoproteolysis by Inteins[Full Text] [PDF]
-Some proteins contain self-excising inteins
-The mechanism of autocatalysis is similar for inteins from unicellular organisms and metazoan Hedgehog protein

3-18 Glycosylation[Full Text] [PDF]
-Glycosylation can change the properties of a protein and provide recognition sites

3-19 Protein Targeting by Lipid Modifications[Full Text] [PDF]
-Covalent attachment of lipids targets proteins to membranes and other proteins
-The GTPases that direct intracellular membrane traffic are reversibly associated with internal membranes of the cell

3-20 Methylation, N-acetylation, Sumoylation and Nitrosylation[Full Text] [PDF]
-Fundamental biological processes can also be regulated by other post-translational modifications of proteins

Chapter 4: From Sequence to Function [PDFBack to top

4-0 Overview: From Sequence to Function in the Age of Genomics[Full Text] [PDF]
-Genomics is making an increasing contribution to the study of protein structure and function

4-1 Sequence Alignment and Comparison[Full Text] [PDF]
-Sequence comparison provides a measure of the relationship between genes
-Alignment is the first step in determining whether two sequences are similar to each other
-Multiple alignments and phylogenetic trees

4-2 Protein Profiling[Full Text] [PDF]
-Structural data can help sequence comparison find related proteins
-Sequence and structural motifs and patterns can identify proteins with similar biochemical functions
-Protein-family profiles can be generated from multiple alignments of protein families for which representative structures are known

4-3 Deriving Function from Sequence[Full Text] [PDF]
-Sequence information is increasing exponentially
-In some cases function can be inferred from sequence

4-4 Experimental Tools for Probing Protein Function[Full Text] [PDF]
-Gene function can sometimes be established experimentally without information from protein structure or sequence homology

4-5 Divergent and Convergent Evolution[Full Text] [PDF]
-Evolution has produced a relatively limited number of protein folds and catalytic mechanisms
-Proteins that differ in sequence and structure may have converged to similar active sites, catalytic mechanisms and biochemical function
-Proteins with low sequence similarity but very similar overall structure and active sites are likely to be homologous
-Convergent and divergent evolution are sometimes difficult to distinguish
-Divergent evolution can produce proteins with sequence and structural similarity but different functions

4-6 Structure from Sequence: Homology Modeling[Full Text] [PDF]
-Structure can be derived from sequence by reference to known protein folds and protein structures
-Homology modeling is used to deduce the structure of a sequence with reference to the structure of a close homolog

4-7 Structure from Sequence: Profile-Based Threading and "Rosetta"[Full Text] [PDF]
-Profile-based threading tries to predict the structure of a sequence even if no sequence homologs are known
-The Rosetta method attempts to predict protein structure from sequence without the aid of a homologous sequence or structure

4-8 Deducing Function from Structure: Protein Superfamilies[Full Text] [PDF]
-Members of a structural superfamily often have related biochemical functions
-The four superfamilies of serine proteases are examples of convergent evolution
-Very closely related protein families can have completely different biochemical and biological functions

4-9 Strategies for Identifying Binding Sites[Full Text] [PDF]
-Binding sites can sometimes be located in three-dimensional structures by purely computational means
-Experimental means of locating binding sites are at present more accurate than computational methods

4-10 Strategies for Identifying Catalytic Residues[Full Text] [PDF]
-Site-directed mutagenesis can identify residues involved in binding or catalysis
-Active-site residues in a structure can sometimes be recognized computationally by their geometry
-Docking programs model the binding of ligands

4-11 TIM Barrels: One Structure with Diverse Functions[Full Text] [PDF]
-Knowledge of a protein's structure does not necessarily make it possible to predict its biochemical or cellular functions

4-12 PLP Enzymes: Diverse Structures with One Function[Full Text] [PDF]
-A protein's biochemical function and catalytic mechanism do not necessarily predict its three-dimensional structure

4-13 Moonlighting: Proteins with More than One Function[Full Text] [PDF]
-In multicellular organisms, multifunctional proteins help expand the number of protein functions that can be derived from relatively small genomes

4-14 Chameleon Sequences: One Sequence with More than One Fold[Full Text] [PDF]
-Some amino-acid sequences can assume different secondary structures in different structural contexts

4-15 Prions, Amyloids and Serpins: Metastable Protein Folds[Full Text] [PDF]
-A single sequence can adopt more than one stable structure

4-16 Functions for Uncharacterized Genes: Galactonate Dehydratase[Full Text] [PDF]
-Determining biochemical function from sequence and structure becomes more accurate as more family members are identified
-Alignments based on conservation of residues that carry out the same active-site chemistry can identify more family members than sequence comparisons alone
-In well studied model organisms, information from genetics and cell biology can help identify the substrate of an "unknown" enzyme and the actual reaction catalyzed

4-17 Starting from Scratch: A Gene Product of Unknown Function[Full Text] [PDF]
-Function cannot always be determined from sequence, even with the aid of structural information and chemical intuition

Chapter 5: Structure Determination [PDFBack to top

5-1 The Interpretation of Structural Information[Full Text] [PDF]
-Experimentally determined protein structures are the result of the interpretation of different types of data
-Both the accuracy and the precision of a structure can vary
-The information content of a structure is determined by its resolution

5-2 Structure Determination by X-Ray Crystallography and NMR[Full Text] [PDF]
-Protein crystallography involves summing the scattered X-ray waves from a macromolecular crystal
-NMR spectroscopy involves determining internuclear distances by measuring perturbations between assigned resonances from atoms in the protein in solution

5-3 Quality and Representation of Crystal and NMR Structures[Full Text] [PDF]
-The quality of a finished structure depends largely on the amount of data collected
-Different conventions for representing the structures of proteins are useful for different purposes


Glossary [PDF]