扬州大学：《生物化学 Biochemistry》课程教学课件（讲稿）04 The Three-dimentional Structure of Proteins

The Three-dimentionalStructure of Proteins

The Three-dimentional Structure of Proteins

KeyPrinciplesProtein structures are stabilized by non-covalent interactionsandforces.Protein segmentscanadoptregular secondary structuressuch as the alpha helix and the beta conformation.Tertiary structures is determined by amino acid sequenceThe3Dstructuresofproteinscanbedetermined

Key Principles  Protein structures are stabilized by non-covalent interactions and forces.  Protein segments can adopt regular secondary structures such as the alpha helix and the beta conformation.  Tertiary structures is determined by amino acid sequence.  The 3D structures of proteins can be determined

The RelationshipbetweenProteinStructure and Functioninprinciple,proteinscanassumeanuncountablenumberofspecialarrangements,orconformationschemicalorstructuralfunctionsrelatetouniquethree-dimensionalstructures

OverviewofProtein StructureProtein Conformationslimitednumberofconformationspredominateunderbiologicalconditionsconformations=thermodynamicallythemoststable,thatis,lowestfreeenergy (G)native = proteins in any functional, foldedconformations

Overview of Protein Structure 

A Protein's Conformation Is Stabilized LargelybyWeakInteractionsstability=tendencyofaproteintomaintainanativeconformationunfoldedproteinshavehighconformationalentropychemical interactionsstabilizenativeconformations=strongdisulfide(covalent)bondsareuncommon-weak (noncovalent)interactionsandforcesarenumerous.hydrogenbonds.hydrophobiceffect.ionicinteractions

PackingofHydrophobicAminoAcidsAwayfrom WaterFavors Protein Foldinghydrophobiceffect=predominating weak interactionsolvationlayer=highlystructuredshellofH,Oaroundahydrophobicmolecule-decreaseswhennonpolargroupsclustertogether- decrease causes afavorable increase in net entropyhydrophobicRchainsformahydrophobicproteincore

PolarGroupsContributeHydrogenBondsandlonPairs to ProteinFoldingrepeatingsecondarystructures(αhelicesandβsheets)optimize hydrogen bondinginteractionofoppositelychargedgroups=ionpair=saltbridge-strengthincreasesinanenvironmentoflowerdielectricconstant, -polaraqueoussolvent:~80- nonpolar protein interior: ~ 4

Individual van der Waals InteractionsAreWeak but CombinetoPromote Foldingvan derWaals interactions =dipole-dipole interactions overshortdistancesindividual interactions contribute little tooverall proteinstabilityhighnumberofinteractionscanbesubstantial

Proteins are Linear Polymers of Amino AcidsRPRR2OH,N-CH-HNHN-CHCH-CH-HH,OAminoacid1Aminoacid2DipeptidePeptide formation is the creation of anamide bondbetween the carboxyl group of one amino acid and theaminogroupofanotheraminoacid

Proteins are Linear Polymers of Amino Acids Peptide formation is the creation of an amide bond between the carboxyl group of one amino acid and the amino group of another amino acid

ThepeptidebondisplanarHInapairoflinked aminoacids,sixatoms(Ca,C,ON,H,and Ca)lie inaplane.Side chains are shown as green balls

The peptide bond is planar  In a pair of linked amino acids, six atoms (Cα, C, O, N, H, and Cα) lie in a plane.  Side chains are shown as green balls