cs790 – bioinformaticsprotein structure and function1 review of fundamental concepts know how...

Protein Structure and Function 1CS790 – Bioinformatics

Review of fundamental conceptsReview of fundamental concepts Know how electron orbitals and subshells are

filled• Know why atoms “prefer” a specific number of

covalent bonds:O 2 N 3 H 1C 4 S 2

O and N tend to form hydrogen bonds, C does not.• Symmetry and electronegativity


Fundamental concepts, cont’dFundamental concepts, cont’d Types of molecular interactions

• Covalent polar ionic

• Hydrogen bonds

• Van der Waals interactions

Concentraction: moles/liter Acids and bases

• pH = log[H+]

• pH = pKa : protonated/unprotonated species at equilibrium

• pH < pKa : more protonated

• pH > pKa : less protonated

CS790 – Bioinformatics

The Structure andThe Structure andFunctions of ProteinsFunctions of Proteins

CS 790 – BioinformaticsCS 790 – Bioinformatics


Proteins are chains of amino acidsProteins are chains of amino acids Polymer – a molecule composed of repeating units


Amino acid compositionAmino acid composition Basic Amino Acid

Structure:• The side chain, R,

varies for each ofthe 20 amino acids

C

RR

C

H

NO

OHH

H

Aminogroup

Carboxylgroup

Side chain


The Peptide BondThe Peptide Bond

Dehydration synthesis Repeating backbone: N–C –C –N–C –C

• Convention – start at amino terminus and proceed to carboxy terminus

O O


Peptidyl polymersPeptidyl polymers A few amino acids in a chain are called a

polypeptide. A protein is usually composed of 50 to 400+ amino acids.

Since part of the amino acid is lost during dehydration synthesis, we call the units of a protein amino acid residues.carbonylcarbonylcarboncarbon

amideamidenitrogennitrogen


Side chain propertiesSide chain properties Recall that the electronegativity of carbon is at

about the middle of the scale for light elements• Carbon does not make hydrogen bonds with water

easily – hydrophobic• O and N are generally more likely than C to h-bond

to water – hydrophilic We group the amino acids into three general

groups:• Hydrophobic• Charged (positive/basic & negative/acidic)• Polar


The Hydrophobic Amino AcidsThe Hydrophobic Amino Acids

Proline severelyProline severelylimits allowablelimits allowableconformations!conformations!


The Charged Amino AcidsThe Charged Amino Acids


The Polar Amino AcidsThe Polar Amino Acids


More Polar Amino AcidsMore Polar Amino Acids

And then there’s…And then there’s…


Planarity of the peptide bondPlanarity of the peptide bond

Phi () – the angle of rotation about the N-C bond.

Psi () – the angle of rotation about the C-C bond.

The planar bond angles and bond lengths are fixed.


Phi and psiPhi and psi = = 180° is

extended conformation

: C to N–H : C=O to C

C

C=O

N–H


The Ramachandran PlotThe Ramachandran Plot

G. N. Ramachandran – first calculations of sterically allowed regions of phi and psi

Note the structural importance of glycine

Observed(non-glycine)

Observed(glycine)Calculated


Primary & Secondary StructurePrimary & Secondary Structure Primary structurePrimary structure = the linear sequence of

amino acids comprising a protein:AGVGTVPMTAYGNDIQYYGQVT…

Secondary structureSecondary structure• Regular patterns of hydrogen bonding in proteins

result in two patterns that emerge in nearly every protein structure known: the -helix and the-sheet

• The location of direction of these periodic, repeating structures is known as the secondary secondary structurestructure of the protein


The alpha helixThe alpha helix 60°


Properties of the alpha helixProperties of the alpha helix 60° Hydrogen bondsHydrogen bonds

between C=O ofresidue n, andNH of residuen+4

3.6 residues/turn 1.5 Å/residue rise 100°/residue turn


Properties of Properties of -helices-helices 4 – 40+ residues in length Often amphipathic or “dual-natured”

• Half hydrophobic and half hydrophilic• Mostly when surface-exposed

If we examine many -helices,we find trends…• Helix formers: Ala, Glu, Leu,

Met• Helix breakers: Pro, Gly, Tyr,

Ser


The beta strand (& sheet)The beta strand (& sheet) 135° +135°


Properties of beta sheetsProperties of beta sheets Formed of stretches of 5-10 residues in

extended conformation Pleated – each C a bit

above or below the previous Parallel/aniparallelParallel/aniparallel,

contiguous/non-contiguous


Parallel and anti-parallel Parallel and anti-parallel -sheets-sheets Anti-parallel is slightly energetically favored

Anti-parallelAnti-parallel ParallelParallel


Turns and LoopsTurns and Loops Secondary structure elements are connected by

regions of turns and loops Turns – short regions

of non-, non-conformation

Loops – larger stretches with no secondary structure. Often disordered.• “Random coil”• Sequences vary much more than secondary

structure regions

Levels of Protein Levels of Protein StructureStructure

Secondary structure elements combine to form tertiary structure

Quaternary structure occurs in multienzyme complexes• Many proteins are

active only as homodimers, homotetramers, etc.


Protein Structure ExamplesProtein Structure Examples


Views of a proteinViews of a protein

Wireframe Ball and stick


Views of a proteinViews of a proteinSpacefill Cartoon CPK colors

Carbon = green, black, or grey

Nitrogen = blue

Oxygen = red

Sulfur = yellow

Hydrogen = white

cs790 – bioinformaticsprotein structure and function1 review of fundamental concepts know how...

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