Phospholipid bilayer “Mosaic” of proteins

The fluid-mosaic model

Carry out a cell’s functions: Cell division Energy generation Protein synthesis Synthesis of hormones Response to hormone signals Structure Motility Recycling of cell materials DNA replication RNA synthesis Transport across membrane Transport within cell Response to infection etc., etc., etc….

Proteins

“What is the secret of life?” I asked.

“I forget,” said Sandra.

“Protein,” the bartender declared. “They found out something about protein.“

“Yeah,” said Sandra, “that's it.”

--Kurt Vonnegut in Cat’s Cradle

Polymers of amino acids

Proteins

Side chain gives distinctive chemical properties

Amino acids

Protein = any of 20 amino acids arranged in any order

Amino acids

Amino acids joined by peptide bonds

Protein structure

Primary (1°) structure = amino-acid sequenceProtein structure

C CNH3+

CH2

H

N

O

CH2

S

CH3

C C

CH2

H

N

OH

C

O

OH

C C

H

H

N

OH

C C

CH2

H

N

OH

C C

CH

H

N

OH

CH3 CH3

C C

CH2

H

OH

OH

CH2

CH2

CH2

NH2

methionine aspartate glycine phenylalanine valine lysine

N-Met-Asp-Gly-Phe-Val-Lys-C

MDGFVK

Primary (1°) structure = amino-acid sequenceProtein structure

Lysozyme, 211 amino acids:

MetLeuGlyLysAsnAspProMetCysLeuValLeuValLeuLeuGlyLeuThrAlaLeuLeuGlyIleCysGlnGlyGlyThrGlyCysTyrGlySerValSerArgIleAspThrThrGlyAlaSerCysArgThrAlaLysProGluGlyLeuSerTyrCysGlyValArgAlaSerArgThrIleAlaGluArgAspLeuGlySerMetAsnLysTyrLysValLeuIleLysArgValGlyGluAlaLeuCysIleGluProAlaValIleAlaGlyIleIleSerArgGluSerHisAlaGlyLysIleLeuLysAsnGlyTrpGlyAspArgGlyAsnGlyPheGlyLeuMetGlnValAspLysArgTyrHisLysIleGluGlyThrTrpAsnGlyGluAlaHisIleArgGlnGlyThrArgIleLeuIleAspMetValLysLysIleGlnArgLysPheProArgTrpThrArgAspGlnGlnLeuLysGlyGlyIleSerAlaTyrAsnAlaGlyValGlyAsnValArgSerTyrGluArgMetAspIleGlyThrLeuHisAspAspTyrSerAsnAspValValAlaArgAlaGlnTyrPheLysGlnHisGlyTyr

Shape is critical to function! Enzyme binds substrate Antibody binds invading virus Transport protein binds specific molecule

Protein structure

HIV Protease

Folding determines 3D shape Amino-acid sequence determines folding

Protein structure

Lysozyme, 211 amino acids:

MetLeuGlyLysAsnAspProMetCysLeuValLeuValLeuLeuGlyLeuThrAlaLeuLeuGlyIleCysGlnGlyGlyThrGlyCysTyrGlySerValSerArgIleAspThrThrGlyAlaSerCysArgThrAlaLysProGluGlyLeuSerTyrCysGlyValArgAlaSerArgThrIleAlaGluArgAspLeuGlySerMetAsnLysTyrLysValLeuIleLysArgValGlyGluAlaLeuCysIleGluProAlaValIleAlaGlyIleIleSerArgGluSerHisAlaGlyLysIleLeuLysAsnGlyTrpGlyAspArgGlyAsnGlyPheGlyLeuMetGlnValAspLysArgTyrHisLysIleGluGlyThrTrpAsnGlyGluAlaHisIleArgGlnGlyThrArgIleLeuIleAspMetValLysLysIleGlnArgLysPheProArgTrpThrArgAspGlnGlnLeuLysGlyGlyIleSerAlaTyrAsnAlaGlyValGlyAsnValArgSerTyrGluArgMetAspIleGlyThrLeuHisAspAspTyrSerAsnAspValValAlaArgAlaGlnTyrPheLysGlnHisGlyTyr

Secondary (2°) structure = local foldingProtein structure

-helix -sheet

Held together by non-covalent interactionsProtein structure

Tertiary (3°) structure = overall 3D structureProtein structure

Tertiary (3°) structure = overall 3D structureProtein structure

myoglobinfatty acid

binding protein

CheY

Protein may fold into distinct domainsProtein structure

pyruvate kinase

PEP + ADP →Pyruvate + ATP

regulatory domain

PEP binding domain

ADP binding domain

Quaternary (4°) structure = intermolecular interactionProtein structure

Quaternary (4°) structure = intermolecular interactionProtein structure

Unfolding: disruption of non-covalent interactionsDenaturation

Proteins can be denatured by heatingDenaturation

Proteins have optimum temperature and pH for activityDenaturation

temperature →

pro

tein

funct

ion →

pH →pro

tein

funct

ion →

enzyme fromListeria bacteria

enzyme fromhuman cells

enzyme fromhot spring bacteria

pepsin

yeastenzyme human

hemoglobin

737

What happens when a protein denatures, or misfolds?Denaturation

Prions: Pathogens without genesNormal form of Prion Protein is found in nerve cells but exact function is unknown.

Abnormal form is folded in “sheets” rather than helices

Loss of dopaminergic neurons of the substantia nigra in the midbrain.

Loss of motor skills

Parkinson’s Disease

alpha synuclein

Causes Parkinson’s Disease. Can be passed from cell to cell.

Alpha-Synuclein

JA Steiner et al. 2011

Trans-membrane (integral) proteins Peripheral membrane proteins

Fluid-mosaic model

Rhodopsin structure

retinal

trans-membrane domain (hydrophobic)

RPE65 structure