cs790 – bioinformaticsprotein structure and function1 review of fundamental concepts know how...
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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
Protein Structure and Function 2CS790 – Bioinformatics
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
Protein Structure and Function 4CS790 – Bioinformatics
Proteins are chains of amino acidsProteins are chains of amino acids Polymer – a molecule composed of repeating units
Protein Structure and Function 5CS790 – Bioinformatics
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
Protein Structure and Function 6CS790 – Bioinformatics
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
Protein Structure and Function 7CS790 – Bioinformatics
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
Protein Structure and Function 8CS790 – Bioinformatics
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
Protein Structure and Function 9CS790 – Bioinformatics
The Hydrophobic Amino AcidsThe Hydrophobic Amino Acids
Proline severelyProline severelylimits allowablelimits allowableconformations!conformations!
Protein Structure and Function 10CS790 – Bioinformatics
The Charged Amino AcidsThe Charged Amino Acids
Protein Structure and Function 11CS790 – Bioinformatics
The Polar Amino AcidsThe Polar Amino Acids
Protein Structure and Function 12CS790 – Bioinformatics
More Polar Amino AcidsMore Polar Amino Acids
And then there’s…And then there’s…
Protein Structure and Function 13CS790 – Bioinformatics
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.
Protein Structure and Function 14CS790 – Bioinformatics
Phi and psiPhi and psi = = 180° is
extended conformation
: C to N–H : C=O to C
C
C=O
N–H
Protein Structure and Function 15CS790 – Bioinformatics
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
Protein Structure and Function 16CS790 – Bioinformatics
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
Protein Structure and Function 17CS790 – Bioinformatics
The alpha helixThe alpha helix 60°
Protein Structure and Function 18CS790 – Bioinformatics
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
Protein Structure and Function 19CS790 – Bioinformatics
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
Protein Structure and Function 20CS790 – Bioinformatics
The beta strand (& sheet)The beta strand (& sheet) 135° +135°
Protein Structure and Function 21CS790 – Bioinformatics
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
Protein Structure and Function 22CS790 – Bioinformatics
Parallel and anti-parallel Parallel and anti-parallel -sheets-sheets Anti-parallel is slightly energetically favored
Anti-parallelAnti-parallel ParallelParallel
Protein Structure and Function 23CS790 – Bioinformatics
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 and Function 25CS790 – Bioinformatics
Protein Structure ExamplesProtein Structure Examples
Protein Structure and Function 26CS790 – Bioinformatics
Views of a proteinViews of a protein
Wireframe Ball and stick
Protein Structure and Function 27CS790 – Bioinformatics
Views of a proteinViews of a proteinSpacefill Cartoon CPK colors
Carbon = green, black, or grey
Nitrogen = blue
Oxygen = red
Sulfur = yellow
Hydrogen = white