Proteins Structure and Function Proteins 1 Cellular Overview

Proteins: Structure and Function

Proteins 1. Cellular Overview 1. Functions 2. Key Properties 2. Core Topics 1. Amino Acids: properties, classifications, p. I 2. Primary Structure, Secondary Structure, and Motifs 3. Tertiary Structure 1. Fibrous vs. Globular 4. Quaternary Structure

Amazing Proteins: Function 1. Catalysts (Enzymes) • The largest class of proteins, accelerates of reactions DNA Polymerase CK 2 Kinase Catalase 2. Transport & Storage Hemoglobin Serum albumin Ion channels Ovalbumin Casein

Amazing Proteins: Function 4. Structural Collagen Keratin Silk Fibroin 5. Generate Movement Actin Myosin

Amazing Proteins: Function 5. Regulation of Metabolism and Gene Expression Lac repressor Insulin 6. Protection Immunoglobulin Thrombin and Fibrinogen Venom Proteins Ricin

Amazing Proteins: Function 7. Signaling and response (inter and intracellular) Apoptosis Membrane proteins Signal transduction

Amazing Proteins: Properties • Biopolymers of amino acids • Contains a wide range of functional groups • Can interact with other proteins or other biological macromolecules to form complex assemblies • Some are rigid while others display limited flexibility

a-Amino Acids: Protein Building Blocks R-group or side-chain a-amino group Carboxyl group a-carbon

Synthesis of Proteins + H 2 O

Synthesis of Proteins

Synthesis of Proteins N-Terminal End C-Terminal End

Synthesis of Proteins = ≠

Synthesis of Proteins = ≠

Synthesis of Proteins ≠ ≠

COMMON AMINO ACIDS 20 common amino acids make up the multitude of proteins we know of

Amino Acids With Aliphatic Side Chains

Amino Acids With Aliphatic Side Chains

Amino Acids With Aliphatic Side Chains

Amino Acids With Aromatic Side Chains

Amino Acids With Hydroxyl Side Chains

Amino Acid with a Sulfhydryl Side Chain

Disulfide Bond Formation

Amino Acids With Basic Side Chains

Amino Acids With Acidic Side Chains and Their Amide Derivatives

There are some important uncommon amino acids

p. H and Amino Acids Net charge: +1 Net charge: 0 Net charge: -1

Characteristics of Acidic and Basic Amino Acids • Acidic amino acids ▫ Low p. Ka ▫ Negatively charged at physiological p. H ▫ Side chains with –COOH ▫ Predominantly in unprotonated form • Basic amino acids ▫ High p. Ka ▫ Function as bases at physiological p. H ▫ Side chains with N

Protein Structure We use different “levels” to fully describe the structure of a protein.

Primary Structure • Amino acid sequence • Standard: Left to Right means N to C-terminal • Eg. Insulin (AAA 40590) MAPWMHLLTVLALLALWGPNSVQAYSSQHLCG SNLVEALYMTCGRSGFYRPHDRRELEDLQVEQ AELGLEAGGLQPSALEMILQKRGIVDQCCNNI CTFNQLQNYCNVP • The info needed for further folding is contained in the 1 o structure.

Secondary Structure • The regular local structure based on the hydrogen bonding pattern of the polypeptide backbone ▫ α helices ▫ β strands (β sheets) ▫ Turns and Loops • WHY will there be localized folding and twisting? Are all conformations possible?

α Helix • First proposed by Linus Pauling and Robert Corey in 1951. • 3. 6 residues per turn, 1. 5 Angstroms rise per residue • Residues face outward

α Helix • α-helix is stabilized by H-bonding between CO and NH groups • Except for amino acid residues at the end of the α-helix, all main chain CO and NH are H-bonded

α Helix representation

β strand • Fully extended • β sheets are formed by linking 2 or more strands by H-bonding • Beta-sheet also proposed by Corey and Pauling in 1951.

PARALLEL ANTIPARALLEL

The Beta Turn (aka beta bend, tight turn) • allows the peptide chain to reverse direction • carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away • proline and glycine are prevalent in beta turns

Mixed β Sheets

Twisted β Sheets

Loops

What Determines the Secondary Structure? • The amino acid sequence determines the secondary structure • The α helix can be regarded as the default conformation – Amino acids that favor α helices: Glu, Gln, Met, Ala, Leu – Amino acids that disrupt α helices: Val, Thr, Ile, Ser, Asx, Pro

Can the Secondary Structure Be Predicted? • Predictions of secondary structure of proteins adopted by a sequence of six or fewer residues have proved to be 60 to 70% accurate • Many protein chemists have tried to predict structure based on sequence ▫ Chou-Fasman: each amino acid is assigned a "propensity" forming helices or sheets ▫ Chou-Fasman is only modestly successful and doesn't predict how sheets and helices arrange ▫ George Rose may be much closer to solving the problem. See Proteins 22, 81 -99 (1995)

Tertiary Structure • The overall 3 -D fold of a single polypeptide chain • The amino acid sequence determines the tertiary structure (Christian Anfinsen) • The polypeptide chain folds so that its hydrophobic side chains are buried and its polar charged chains are on the surface ▫ Exception : membrane proteins ▫ Reverse : hydrophobic out, hydrophilic in • Driven by hydrophobic interactions • Stabilized by H-bonding, LDF, noncovalent interactions, dipole interactions, ionic interactions, disulfide bonds

Fibrous and Globular Proteins

Fibrous Proteins • Much or most of the polypeptide chain is organized approximately parallel to a single axis • Fibrous proteins are often mechanically strong • Fibrous proteins are usually insoluble • Usually play a structural role in nature

Examples of Fibrous Proteins • Alpha Keratin: hair, nails, claws, horns, beaks • Beta Keratin: silk fibers (alternating Gly-Ala-Ser)

Examples of Fibrous Proteins • Collagen: connective tissuetendons, cartilage, bones, teeth ▫ Nearly one residue out of three is Gly ▫ Proline content is unusually high ▫ Unusual amino acids found: (4 -hydroxyproline, 3 hydroxyproline , 5 hydroxylysine) ▫ Special uncommon triple helix!

Globular Proteins • Most polar residues face the outside of the protein and interact with solvent • Most hydrophobic residues face the interior of the protein and interact with each other • Packing of residues is close but empty spaces exist in the form of small cavities • Helices and sheets often pack in layers • Hydrophobic residues are sandwiched between the layers • Outside layers are covered with mostly polar residues that interact favorably with solvent

An amphiphilic helix in flavodoxin: A nonpolar helix in citrate synthase: A polar helix in calmodulin:

Quaternary Structures • Spatial arrangement of subunits and the nature of their interactions. Can be hetero and/or homosubunits • Simplest example: dimer (e. g. insulin) ADVANTAGES of 4 o Structures ▫ ▫ Stability: reduction of surface to volume ratio Genetic economy and efficiency Bringing catalytic sites together Cooperativity

Protein Folding • The largest favorable contribution to folding is the entropy term for the interaction of nonpolar residues with the solvent • CHAPERONES assist protein folding ▫ to protect nascent proteins from the concentrated protein matrix in the cell and perhaps to accelerate slow steps