amino acids and protein structure
DESCRIPTION
Amino Acids and Protein Structure. Protein structure. Four levels of protein structure Linear Sub-Structure 3D Structure Complex Structure. polarity. Hydrogen Bonding Intermolecular Forces Dipole- Dipole Ion-Dipole Van der Waals. Hydrophobic Effect. - PowerPoint PPT PresentationTRANSCRIPT
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AMINO ACIDS AND PROTEIN STRUCTURE
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PROTEIN STRUCTURE Four levels of
protein structure Linear Sub-Structure 3D Structure Complex Structure
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POLARITY Hydrogen Bonding Intermolecular
Forces Dipole-Dipole Ion-Dipole Van der Waals
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HYDROPHOBIC EFFECT Nonpolar molecules
disrupt dynamic hydrogen bonds
Hydrophobic amino acids include alanine, valine,
leucine, isoleucine, phenylalanine, tryptophan and methionine
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HYDROPHOBICITY IN PROTEIN FOLDING Hydrophobic amino
acids face the interior of the protein
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HYDROPHOBICITY NUMBER Hydrophobicity
Scale Physical scales
based on surface tension or energy solvation
Wimley-White Scale Peptide bonds and
side chains Experimentally
determined values
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CHARGE Refers to the total
external charge, while polarity refers to the difference in charge
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CHARGE IN PROTEIN INTERACTIONS Opposites attract,
so charge can influence protein binding activity
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AMINO ACID SIZE
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SUMMARY
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PROTEIN FOLDING Physical structures
resulting from amino acid sequences
Predictive techniques FoldIt
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INTERACTION Binding sites
Chemical bonds from with ligands Specific molecules and ions
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CASP Critical Assessment of Protein Structure
Prediction Competition structure Advancing predictive science Based on structure, complex, domain, function
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SCOP Structural Classification
of Proteins Collaborative
classification effort Based on amino acid
sequence, domain structure, and function
Classified into families and superfamilies
Sourced from Protein Data Bank (PDB)
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PROTEIN STRUCTURE ALIGNMENT Protein data bank – PDB Useful for low sequence similarity Computational methods X-Ray Crystallography NMR Spectroscopy
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DALI Distance alignment
matrix based on hexapeptide contact patterns
FSSP (Families of Structurally Similar Proteins) Database
Server-based DaliLite standalone
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COMBINATORIAL EXTENSION Breaks structures into
aligned fragment pairs Originally only structural
superpositions and inter-residue distances
Now includes secondary structure, solvent exposure, hydrogen-bonding patterns, and dihedral angles
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SSAP Sequential Structure
Alignment Program Vectors between
non-contiguous residues
Optimal local alignments compiled into summary matrix
Dynamic programming
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X-RAY CRYSTALLOGRAPHY Crystal X-ray diffraction Angles and
intensities Electron density Atom positions and
chemical bonds Good resolution
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NUCLEAR MAGNETIC RESONANCE (NMR) Water solution Solid methods in
development Sample is placed in
magnet Different nuclei
absorb different radio frequencies
Interaction Determine orientation
and structure