Protein Structure Protein Structure BasicsBasics

Presented byPresented byAlison Fraser, Christine Lee, Alison Fraser, Christine Lee,

Pradhuman Jhala, Corban Pradhuman Jhala, Corban RiveraRivera

Importance of ProteinsImportance of Proteins Muscle structure depends on Muscle structure depends on

protein-protein interactionsprotein-protein interactions Transport across membranes Transport across membranes

involves protein-solute interactionsinvolves protein-solute interactions Nerve activity requires transmitter Nerve activity requires transmitter

substance-protein interactionssubstance-protein interactions Immune protection requires Immune protection requires

antibody-antigen interactionsantibody-antigen interactions

OverviewOverview Primary StructurePrimary Structure Secondary StructureSecondary Structure Tertiary StructureTertiary Structure Quaternary StructureQuaternary Structure

Primary StructurePrimary Structure Polypeptide chains Polypeptide chains

Amino AcidsAmino Acids Largest polypeptide Largest polypeptide

chain approx has chain approx has 5000AA but most have 5000AA but most have less than 2000AAless than 2000AA

Amino Acid Basic Amino Acid Basic Structure HStructure H22N-CH-N-CH-COOHCOOH

Arrangement of the 20 Arrangement of the 20 amino acids in the amino acids in the polypeptide is the amino polypeptide is the amino acid sequence which acid sequence which composes the primary composes the primary structure of the proteinstructure of the protein

National Genome Research Institutegenome.gov

http://www.people.virginia.edu/~rjh9u/aminacid.html

20 Amino Acids

Nonpolar,hydrophobic

Polar, uncharged

Polar, charged

Amino Acid ClassificationAmino Acid Classification

A Venn diagram showing the relationship of the 20 naturally occurring amino acids to a selection of physio-chemical properties thought to be important in the determination of protein structure.

StereochemistryStereochemistry Configuration of amino acids in proteinsConfiguration of amino acids in proteins The CORN LawThe CORN Law

Bond FormationBond Formation

Linking two amino Linking two amino acids togetheracids together

Definitions (N-Definitions (N-terminal, C-terminal, terminal, C-terminal, polypeptide polypeptide backbone, amino backbone, amino acid residue, side acid residue, side chains)chains)

http://web.mit.edu/esgbio/www/lm/proteins/peptidebond.html

Primary StructurePrimary Structure What is a native protein?What is a native protein? Protein conformation & problem of Protein conformation & problem of

protein foldingprotein folding Hydrophobic, hydrophilicHydrophobic, hydrophilic ChargeCharge ChaperonesChaperones

Special Purpose Amino Special Purpose Amino AcidsAcids

ProlineProline

CysteineCysteine

IntroductionIntroduction Peptide bond geometryPeptide bond geometry Ramachandran plotRamachandran plot StructuresStructures

Protein Secondary Protein Secondary StructureStructure

Regular local structures formed by Regular local structures formed by single strands of peptide chain due single strands of peptide chain due to constraints on backbone to constraints on backbone conformationconformation

Peptide BondPeptide Bond

http://cmgm.stanford.edu/biochem/biochem201/Slides/

Peptide Bond Peptide Bond Resonance Resonance C-N bond length of the peptide is C-N bond length of the peptide is

10% shorter than that found in usual 10% shorter than that found in usual C-N amine bondsC-N amine bonds

Peptide bond planer Peptide bond planer ωω, angle around peptide bond, , angle around peptide bond,

0000 for cis, 180 for cis, 18000 for trans for trans

Ramachandran PlotRamachandran Plot

http://hykim.chungbuk.ac.kr/lectures/biochem/4-5/fig6-9(L).jpg

Alpha HelixAlpha Helix

http://cmgm.stanford.edu/biochem/biochem201/Slides/

Alpha HelixAlpha Helix

Left-handedLeft-handed Right-handedRight-handed

http://www.rtc.riken.go.jp

Alpha Structure FeaturesAlpha Structure Features 3.6 residues per turn3.6 residues per turn 5.4 angstroms in length per turn5.4 angstroms in length per turn carboxyl group of residue i hydrogen carboxyl group of residue i hydrogen

bonds to amino group of residue i+4bonds to amino group of residue i+4

Helix StructuresHelix Structures Φ ψ H Bond R/t Φ ψ H Bond R/t

A/tA/tAlpha Alpha -57.8 -47 i, i + 4 3.6 -57.8 -47 i, i + 4 3.6 1313

3-10 Helix -49 -26 i, i + 3 3.0 3-10 Helix -49 -26 i, i + 3 3.0 10 10

Pi Helix Pi Helix -57 -80 i , i + -57 -80 i , i + 5 4.4 165 4.4 16

http://broccoli.mfn.ki.se

More Helix StructuresMore Helix Structures

TypeType ΦΦ ψψ commentscomments

CollagenCollagen -51-51 153153 Fibrous proteinsFibrous proteinsThree left Three left

handed helicieshanded helicies(GlyXY)n, X Y = Pro / (GlyXY)n, X Y = Pro /

LysLys

Type II helicesType II helices -79-79 150150 left-handed helicies left-handed helicies formed formed by by polyglycinepolyglycine

Beta Sheet Beta Sheet

http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/images/sheet.gif

Beta Sheet FeaturesBeta Sheet Features Sheets can be made up of any Sheets can be made up of any

number of strandsnumber of strands Orientation and hydrogen bonding Orientation and hydrogen bonding

pattern of strands gives rise to flat pattern of strands gives rise to flat or twisted sheetsor twisted sheets

Parallel sheets buried inside, while Parallel sheets buried inside, while Antiparallel sheets occurs on the Antiparallel sheets occurs on the surfacesurface

More Beta StructuresMore Beta Structures

Beta Bulge chymotrypsin (1CHG.PDB) involving residues 33 and 41-42

Anti parallel

Beta Twist pancreatic trypsin inhibitor (5PTI)0 to 30 degrees per residue

Distortion of tetrahedral N atom

http://broccoli.mfn.ki.se

Beta turnsBeta turns

i + 1 Pro

i + 2 Pro or Gly

i + 3 Gly

http://rayl0.bio.uci.edu/~mjhsieh/sstour/image/betaturn.png

Interactions Interactions Covalent bondsCovalent bonds Disulphide bond (2.2 Disulphide bond (2.2 00A) between two Cys A) between two Cys

residuesresidues Non-covalent bondsNon-covalent bonds

Long range electrostatic interactionLong range electrostatic interactionShort range (4 Short range (4 00A) van der Waals interactionA) van der Waals interactionHydrogen bond (3 Hydrogen bond (3 00A)A)

Tertiary Protein Tertiary Protein StructureStructure

Defines the three dimensional Defines the three dimensional conformation of an entire peptide conformation of an entire peptide chain in spacechain in space

Determined by the primary structureDetermined by the primary structure Modular in natureModular in nature

Aspects which determine Aspects which determine tertiary structuretertiary structure

Covalent disulfide bonds from Covalent disulfide bonds from between closely aligned cysteine between closely aligned cysteine residues form the unique Amino Acid residues form the unique Amino Acid cystine.cystine.

Nearly all of the polar, hydrophilic R Nearly all of the polar, hydrophilic R groups are located in the surface, groups are located in the surface, where they may interact with waterwhere they may interact with water

The nonpolar, hydropobic R groups The nonpolar, hydropobic R groups are usually located inside the are usually located inside the moleculemolecule

Motifs and DomainsMotifs and Domains Motif – a small structural domain Motif – a small structural domain

that can be recognized in a variety that can be recognized in a variety of proteinsof proteins

Domain – Portion of a protein that Domain – Portion of a protein that has a tertiary structure of its own. has a tertiary structure of its own. In larger proteins each domain is In larger proteins each domain is connected to other domains by short connected to other domains by short flexible regions of polypeptide. flexible regions of polypeptide.

Modular Nature of Modular Nature of ProtiensProtiens

Epidermal Growth Epidermal Growth Factor (EGF) domain Factor (EGF) domain is a module present is a module present in several different in several different proteins illustrated proteins illustrated here in orange.here in orange.

Each color Each color represents a represents a different domaindifferent domain

Domain ShufflingDomain Shuffling Occurs in evolutionOccurs in evolution New proteins arise by joining of New proteins arise by joining of

preexisting protein domain or preexisting protein domain or modules.modules.

Quaternary StructureQuaternary Structure Not all proteins have Not all proteins have

a quaternary a quaternary structurestructure

A composite of A composite of multiple poly-peptide multiple poly-peptide chains is called an chains is called an oligomer or oligomer or multimericmultimeric

Hemoglobin is an Hemoglobin is an example of a tetramerexample of a tetramer

Globular vs. FibrousGlobular vs. Fibrous

Protein FoldingProtein Folding Protein folding constitutes the Protein folding constitutes the

process by which a poly-peptide process by which a poly-peptide chain reduces its free energy by chain reduces its free energy by taking a secondary, tertiary, and taking a secondary, tertiary, and possibly a quaternary structurepossibly a quaternary structure

ThermodynamicsThermodynamics Proteins follow Proteins follow

spontaneous spontaneous reactions to reach reactions to reach the conformation the conformation of lowest free of lowest free energyenergy

Reaction Reaction spontaneity is spontaneity is modeled by the modeled by the equation equation ΔΔG= G= ΔΔH-H-TTΔΔS S

Molecular VisualizationMolecular Visualization Goal: Clear Goal: Clear

visualization of visualization of molecular structuremolecular structure

Different visualization Different visualization modes elucidate modes elucidate different molecular different molecular propertiesproperties

Some representations Some representations include Ribbons, include Ribbons, SpaceFill and SpaceFill and BackboneBackbone